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1. Biocontrol in built environments to reduce pathogen exposure and infection risk.

Author

Gottel, Neil, Hill, Megan, Neal, Maxwell, Zengler, Karsten, Gilbert, Jack, and Allard, Sarah

Subjects
AMR, antibiotic resistance, bacillus, biocontrol, built environment, indoor microbiome, metabolic modelling, probiotic cleaning, Humans, Microbiota, Bacteria, Bacillus, Anti-Bacterial Agents, Built Environment
Abstract

The microbiome of the built environment comprises bacterial, archaeal, fungal, and viral communities associated with human-made structures. Even though most of these microbes are benign, antibiotic-resistant pathogens can colonize and emerge indoors, creating infection risk through surface transmission or inhalation. Several studies have catalogued the microbial composition and ecology in different built environment types. These have informed in vitro studies that seek to replicate the physicochemical features that promote pathogenic survival and transmission, ultimately facilitating the development and validation of intervention techniques used to reduce pathogen accumulation. Such interventions include using Bacillus-based cleaning products on surfaces or integrating bacilli into printable materials. Though this work is in its infancy, early research suggests the potential to use microbial biocontrol to reduce hospital- and home-acquired multidrug-resistant infections. Although these techniques hold promise, there is an urgent need to better understand the microbial ecology of built environments and to determine how these biocontrol solutions alter species interactions. This review covers our current understanding of microbial ecology of the built environment and proposes strategies to translate that knowledge into effective biocontrol of antibiotic-resistant pathogens.

Published
2024

2. Mass Testing and Characterization of 20-inch PMTs for JUNO

Author

Abusleme, Angel, Adam, Thomas, Ahmad, Shakeel, Ahmed, Rizwan, Aiello, Sebastiano, Akram, Muhammad, Aleem, Abid, Alexandros, Tsagkarakis, An, Fengpeng, An, Qi, Andronico, Giuseppe, Anfimov, Nikolay, Antonelli, Vito, Antoshkina, Tatiana, Asavapibhop, Burin, de Andre, Joao Pedro Athayde Marcondes, Auguste, Didier, Bai, Weidong, Balashov, Nikita, Baldini, Wander, Barresi, Andrea, Basilico, Davide, Baussan, Eric, Bellato, Marco, Bergnoli, Antonio, Birkenfeld, Thilo, Blin, Sylvie, Blum, David, Blyth, Simon, Bolshakova, Anastasia, Bongrand, Mathieu, Bordereau, Clement, Breton, Dominique, Brigatti, Augusto, Brugnera, Riccardo, Bruno, Riccardo, Budano, Antonio, Busto, Jose, Butorov, Ilya, Cabrera, Anatael, Caccianiga, Barbara, Cai, Hao, Cai, Xiao, Cai, Yanke, Cai, Zhiyan, Callegari, Riccardo, Cammi, Antonio, Campeny, Agustin, Cao, Chuanya, Cao, Guofu, Cao, Jun, Caruso, Rossella, Cerna, Cedric, Chan, Chi, Chang, Jinfan, Chang, Yun, Chen, Guoming, Chen, Pingping, Chen, Po-An, Chen, Shaomin, Chen, Xurong, Chen, Yixue, Chen, Yu, Chen, Zhiyuan, Chen, Zikang, Cheng, Jie, Cheng, Yaping, Cheng, Yu Chin, Chetverikov, Alexey, Chiesa, Davide, Chimenti, Pietro, Chukanov, Artem, Claverie, Gerard, Clementi, Catia, Clerbaux, Barbara, Molla, Marta Colomer, Di Lorenzo, Selma Conforti, Corti, Daniele, Corso, Flavio Dal, Dalager, Olivia, De La Taille, Christophe, Deng, Zhi, Deng, Ziyan, Depnering, Wilfried, Diaz, Marco, Ding, Xuefeng, Ding, Yayun, Dirgantara, Bayu, Dmitrievsky, Sergey, Dohnal, Tadeas, Dolzhikov, Dmitry, Donchenko, Georgy, Dong, Jianmeng, Doroshkevich, Evgeny, Dracos, Marcos, Druillole, Frederic, Du, Ran, Du, Shuxian, Dusini, Stefano, Dvorak, Martin, Enqvist, Timo, Enzmann, Heike, Fabbri, Andrea, Fan, Donghua, Fan, Lei, Fang, Jian, Fang, Wenxing, Fargetta, Marco, Fedoseev, Dmitry, Fei, Zhengyong, Feng, Li-Cheng, Feng, Qichun, Ford, Richard, Fournier, Amelie, Gan, Haonan, Gao, Feng, Garfagnini, Alberto, Gavrikov, Arsenii, Giammarchi, Marco, Giudice, Nunzio, Gonchar, Maxim, Gong, Guanghua, Gong, Hui, Gornushkin, Yuri, Gottel, Alexandre, Grassi, Marco, Gromov, Vasily, Gu, Minghao, Gu, Xiaofei, Gu, Yu, Guan, Mengyun, Guan, Yuduo, Guardone, Nunzio, Guo, Cong, Guo, Jingyuan, Guo, Wanlei, Guo, Xinheng, Guo, Yuhang, Hackspacher, Paul, Hagner, Caren, Han, Ran, Han, Yang, He, Miao, He, Wei, Heinz, Tobias, Hellmuth, Patrick, Heng, Yuekun, Herrera, Rafael, Hor, YuenKeung, Hou, Shaojing, Hsiung, Yee, Hu, Bei-Zhen, Hu, Hang, Hu, Jianrun, Hu, Jun, Hu, Shouyang, Hu, Tao, Hu, Yuxiang, Hu, Zhuojun, Huang, Guihong, Huang, Hanxiong, Huang, Kaixuan, Huang, Wenhao, Huang, Xin, Huang, Xingtao, Huang, Yongbo, Hui, Jiaqi, Huo, Lei, Huo, Wenju, Huss, Cedric, Hussain, Safeer, Ioannisian, Ara, Isocrate, Roberto, Jelmini, Beatrice, Jeria, Ignacio, Ji, Xiaolu, Jia, Huihui, Jia, Junji, Jian, Siyu, Jiang, Di, Jiang, Wei, Jiang, Xiaoshan, Jing, Xiaoping, Jollet, Cecile, Joutsenvaara, Jari, Kalousis, Leonidas, Kampmann, Philipp, Kang, Li, Karaparambil, Rebin, Kazarian, Narine, Khatun, Amina, Khosonthongkee, Khanchai, Korablev, Denis, Kouzakov, Konstantin, Krasnoperov, Alexey, Kutovskiy, Nikolay, Kuusiniemi, Pasi, Lachenmaier, Tobias, Landini, Cecilia, Leblanc, Sebastien, Lebrin, Victor, Lefevre, Frederic, Lei, Ruiting, Leitner, Rupert, Leung, Jason, Li, Daozheng, Li, Demin, Li, Fei, Li, Fule, Li, Gaosong, Li, Huiling, Li, Mengzhao, Li, Min, Li, Nan, Li, Qingjiang, Li, Ruhui, Li, Rui, Li, Shanfeng, Li, Tao, Li, Teng, Li, Weidong, Li, Weiguo, Li, Xiaomei, Li, Xiaonan, Li, Xinglong, Li, Yi, Li, Yichen, Li, Yufeng, Li, Zepeng, Li, Zhaohan, Li, Zhibing, Li, Ziyuan, Li, Zonghai, Liang, Hao, Liao, Jiajun, Limphirat, Ayut, Lin, Guey-Lin, Lin, Shengxin, Lin, Tao, Ling, Jiajie, Lippi, Ivano, Liu, Fang, Liu, Haidong, Liu, Haotian, Liu, Hongbang, Liu, Hongjuan, Liu, Hongtao, Liu, Hui, Liu, Jianglai, Liu, Jinchang, Liu, Min, Liu, Qian, Liu, Qin, Liu, Runxuan, Liu, Shubin, Liu, Shulin, Liu, Xiaowei, Liu, Xiwen, Liu, Yan, Liu, Yunzhe, Lokhov, Alexey, Lombardi, Paolo, Lombardo, Claudio, Loo, Kai, Lu, Chuan, Lu, Haoqi, Lu, Jingbin, Lu, Junguang, Lu, Shuxiang, Lubsandorzhiev, Bayarto, Lubsandorzhiev, Sultim, Ludhova, Livia, Lukanov, Arslan, Luo, Daibin, Luo, Fengjiao, Luo, Guang, Luo, Shu, Luo, Wuming, Luo, Xiaojie, Lyashuk, Vladimir, Ma, Bangzheng, Ma, Bing, Ma, Qiumei, Ma, Si, Ma, Xiaoyan, Ma, Xubo, Maalmi, Jihane, Mai, Jingyu, Malyshkin, Yury, Mandujano, Roberto Carlos, Mantovani, Fabio, Manzali, Francesco, Mao, Xin, Mao, Yajun, Mari, Stefano M., Marini, Filippo, Martellini, Cristina, Chassard, Gisele Martin, Martini, Agnese, Mayer, Matthias, Mayilyan, Davit, Mednieks, Ints, Meng, Yue, Meregaglia, Anselmo, Meroni, Emanuela, Meyhofer, David, Mezzetto, Mauro, Miller, Jonathan, Miramonti, Lino, Montini, Paolo, Montuschi, Michele, Muller, Axel, Nastasi, Massimiliano, Naumov, Dmitry V., Naumova, Elena, Navas-Nicolas, Diana, Nemchenok, Igor, Thi, Minh Thuan Nguyen, Ning, Feipeng, Ning, Zhe, Nunokawa, Hiroshi, Oberauer, Lothar, Ochoa-Ricoux, Juan Pedro, Olshevskiy, Alexander, Orestano, Domizia, Ortica, Fausto, Othegraven, Rainer, Paoloni, Alessandro, Parmeggiano, Sergio, Pei, Yatian, Pelicci, Luca, Pelliccia, Nicomede, Peng, Anguo, Peng, Haiping, Peng, Yu, Peng, Zhaoyuan, Perrot, Frederic, Petitjean, Pierre-Alexandre, Petrucci, Fabrizio, Pilarczyk, Oliver, Rico, Luis Felipe Pineres, Popov, Artyom, Poussot, Pascal, Previtali, Ezio, Qi, Fazhi, Qi, Ming, Qian, Sen, Qian, Xiaohui, Qian, Zhen, Qiao, Hao, Qin, Zhonghua, Qiu, Shoukang, Ranucci, Gioacchino, Raper, Neill, Re, Alessandra, Rebber, Henning, Rebii, Abdel, Redchuk, Mariia, Ren, Bin, Ren, Jie, Ricci, Barbara, Rifai, Mariam, Roche, Mathieu, Rodphai, Narongkiat, Romani, Aldo, Roskovec, Bedrich, Ruan, Xichao, Rybnikov, Arseniy, Sadovsky, Andrey, Saggese, Paolo, Sanfilippo, Simone, Sangka, Anut, Sawangwit, Utane, Sawatzki, Julia, Schever, Michaela, Schwab, Cedric, Schweizer, Konstantin, Selyunin, Alexandr, Serafini, Andrea, Settanta, Giulio, Settimo, Mariangela, Shao, Zhuang, Sharov, Vladislav, Shaydurova, Arina, Shi, Jingyan, Shi, Yanan, Shutov, Vitaly, Sidorenkov, Andrey, Simkovic, Fedor, Sirignano, Chiara, Siripak, Jaruchit, Sisti, Monica, Slupecki, Maciej, Smirnov, Mikhail, Smirnov, Oleg, Sogo-Bezerra, Thiago, Sokolov, Sergey, Songwadhana, Julanan, Soonthornthum, Boonrucksar, Sotnikov, Albert, Sramek, Ondrej, Sreethawong, Warintorn, Stahl, Achim, Stanco, Luca, Stankevich, Konstantin, Stefanik, Dusan, Steiger, Hans, Steinmann, Jochen, Sterr, Tobias, Stock, Matthias Raphael, Strati, Virginia, Studenikin, Alexander, Su, Jun, Sun, Shifeng, Sun, Xilei, Sun, Yongjie, Sun, Yongzhao, Sun, Zhengyang, Suwonjandee, Narumon, Szelezniak, Michal, Tang, Jian, Tang, Qiang, Tang, Quan, Tang, Xiao, Theisen, Eric, Tietzsch, Alexander, Tkachev, Igor, Tmej, Tomas, Torri, Marco Danilo Claudio, Treskov, Konstantin, Triossi, Andrea, Troni, Giancarlo, Trzaska, Wladyslaw, Tuve, Cristina, Ushakov, Nikita, Vedin, Vadim, Verde, Giuseppe, Vialkov, Maxim, Viaud, Benoit, Vollbrecht, Cornelius Moritz, Volpe, Cristina, von Sturm, Katharina, Vorobel, Vit, Voronin, Dmitriy, Votano, Lucia, Walker, Pablo, Wang, Caishen, Wang, Chung-Hsiang, Wang, En, Wang, Guoli, Wang, Jian, Wang, Jun, Wang, Lu, Wang, Meifen, Wang, Meng, Wang, Ruiguang, Wang, Siguang, Wang, Wei, Wang, Wenshuai, Wang, Xi, Wang, Xiangyue, Wang, Yangfu, Wang, Yaoguang, Wang, Yi, Wang, Yifang, Wang, Yuanqing, Wang, Yuman, Wang, Zhe, Wang, Zheng, Wang, Zhimin, Wang, Zongyi, Watcharangkool, Apimook, Wei, Wei, Wei, Wenlu, Wei, Yadong, Wen, Kaile, Wen, Liangjian, Wiebusch, Christopher, Wong, Steven Chan-Fai, Wonsak, Bjoern, Wu, Diru, Wu, Qun, Wu, Zhi, Wurm, Michael, Wurtz, Jacques, Wysotzki, Christian, Xi, Yufei, Xia, Dongmei, Xiao, Xiang, Xie, Xiaochuan, Xie, Yuguang, Xie, Zhangquan, Xin, Zhao, Xing, Zhizhong, Xu, Benda, Xu, Cheng, Xu, Donglian, Xu, Fanrong, Xu, Hangkun, Xu, Jilei, Xu, Jing, Xu, Meihang, Xu, Yin, Xu, Yu, Yan, Baojun, Yan, Taylor, Yan, Wenqi, Yan, Xiongbo, Yan, Yupeng, Yang, Changgen, Yang, Chengfeng, Yang, Huan, Yang, Jie, Yang, Lei, Yang, Xiaoyu, Yang, Yifan, Yao, Haifeng, Ye, Jiaxuan, Ye, Mei, Ye, Ziping, Yermia, Frederic, Yin, Na, You, Zhengyun, Yu, Boxiang, Yu, Chiye, Yu, Chunxu, Yu, Hongzhao, Yu, Miao, Yu, Xianghui, Yu, Zeyuan, Yu, Zezhong, Yuan, Cenxi, Yuan, Chengzhuo, Yuan, Ying, Yuan, Zhenxiong, Yue, Baobiao, Zafar, Noman, Zavadskyi, Vitalii, Zeng, Shan, Zeng, Tingxuan, Zeng, Yuda, Zhan, Liang, Zhang, Aiqiang, Zhang, Bin, Zhang, Binting, Zhang, Feiyang, Zhang, Guoqing, Zhang, Honghao, Zhang, Jialiang, Zhang, Jiawen, Zhang, Jie, Zhang, Jin, Zhang, Jingbo, Zhang, Jinnan, Zhang, Mohan, Zhang, Peng, Zhang, Qingmin, Zhang, Shiqi, and Zha, Shu

Subjects
Physics - Instrumentation and Detectors, High Energy Physics - Experiment
Abstract

Main goal of the JUNO experiment is to determine the neutrino mass ordering using a 20kt liquid-scintillator detector. Its key feature is an excellent energy resolution of at least 3 % at 1 MeV, for which its instruments need to meet a certain quality and thus have to be fully characterized. More than 20,000 20-inch PMTs have been received and assessed by JUNO after a detailed testing program which began in 2017 and elapsed for about four years. Based on this mass characterization and a set of specific requirements, a good quality of all accepted PMTs could be ascertained. This paper presents the performed testing procedure with the designed testing systems as well as the statistical characteristics of all 20-inch PMTs intended to be used in the JUNO experiment, covering more than fifteen performance parameters including the photocathode uniformity. This constitutes the largest sample of 20-inch PMTs ever produced and studied in detail to date, i.e. 15,000 of the newly developed 20-inch MCP-PMTs from Northern Night Vision Technology Co. (NNVT) and 5,000 of dynode PMTs from Hamamatsu Photonics K. K.(HPK).

Published
2022
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3. Search for Low-Energy Signals from Fast Radio Bursts with the Borexino Detector

Author

Appel, S., Bagdasarian, Z., Basilico, D., Bellini, G., Benziger, J., Biondi, R., Caccianiga, B., Calaprice, F., Caminata, A., Chepurnov, A., D'Angelo, D., Derbin, A., Di Giacinto, A., Di Marcello, V., Ding, X. F., Di Ludovico, A., Di Noto, L., Drachnev, I., Franco, D., Galbiati, C., Ghiano, C., Giammarchi, M., Goretti, A., Gottel, A. S., Gromov, M., Guffantic, D., Ianni, Aldo, Ianni, Andrea, Jany, A., Kobychev, V., Korga, G., Kumaran, S., Laubenstein, M., Litvinovich, E., Lombardi, P., Lomskaya, I., Ludhova, L., Lukyanchenko, G., Machulin, I., Martyn, J., Meroni, E., Miramonti, L., Misiaszek, M., Muratova, V., Nugmanov, R., Oberauer, L., Orekhov, V., Ortica, F., Pallavicini, M., Pelicci, L., Penek, O., Pietrofaccia, L., Pilipenko, N., Pocar, A., Raikov, G., Ranalli, M. T., Ranucci, G., Razeto, A., Re, A., Redchuk, M., Rossi, N., Schonert, S., Semenov, D., Settanta, G., Skorokhvatov, M., Singhal, A., Smirnov, O., Sotnikov, A., Tartaglia, R., Testera, G., Unzhakov, E., Vishneva, A., Vogelaar, R. B., von Feilitzsch, F., Wojcik, M., Wurm, M., Zavatarelli, S., Zhutikov, I., Zuber, K., and Zuzel, G.

Subjects
High Energy Physics - Experiment, Astrophysics - Instrumentation and Methods for Astrophysics, High Energy Physics - Phenomenology
Abstract

The search for neutrino events in correlation with several of the most intense fast radio bursts (FRBs) has been performed using the Borexino data. We have searched for signals with visible energies above $250$~keV within a time window of $\pm$1000~s corresponding to the detection time of a particular FRB. We also applied an alternative approach based on searching for specific shapes of neutrino-electron scattering spectra in the full exposure spectrum of the Borexino detector. In particular, two incoming neutrino spectra were considered: the monoenergetic line and the spectrum expected from supernovae. The same spectra were considered for electron antineutrinos detected through the inverse beta-decay reaction. No statistically significant excess over the background was observed. As a result, the strongest upper limits on FRB-associated neutrino fluences of all flavors have been obtained in the $0.5 - 50$~MeV neutrino energy range., Comment: 14 pages, 10 figures

Published
2021
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4. SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment

Author

Marotz, Clarisse, Belda-Ferre, Pedro, Ali, Farhana, Das, Promi, Huang, Shi, Cantrell, Kalen, Jiang, Lingjing, Martino, Cameron, Diner, Rachel E, Rahman, Gibraan, McDonald, Daniel, Armstrong, George, Kodera, Sho, Donato, Sonya, Ecklu-Mensah, Gertrude, Gottel, Neil, Salas Garcia, Mariana C, Chiang, Leslie Y, Salido, Rodolfo A, Shaffer, Justin P, Bryant, Mac Kenzie, Sanders, Karenina, Humphrey, Greg, Ackermann, Gail, Haiminen, Niina, Beck, Kristen L, Kim, Ho-Cheol, Carrieri, Anna Paola, Parida, Laxmi, Vázquez-Baeza, Yoshiki, Torriani, Francesca J, Knight, Rob, Gilbert, Jack, Sweeney, Daniel A, and Allard, Sarah M

Subjects
Microbiology, Biological Sciences, Clinical Research, Lung, Genetics, Emerging Infectious Diseases, Pneumonia & Influenza, Prevention, Pneumonia, Infectious Diseases, 2.2 Factors relating to the physical environment, Aetiology, Infection, Good Health and Well Being, COVID-19, Hospitals, Humans, Pandemics, Phylogeny, RNA, Ribosomal, 16S, RNA, Viral, SARS-CoV-2, Built environment, 16S rRNA, Microbiome, Ecology, Medical Microbiology, Evolutionary biology
Abstract

BackgroundSARS-CoV-2 is an RNA virus responsible for the coronavirus disease 2019 (COVID-19) pandemic. Viruses exist in complex microbial environments, and recent studies have revealed both synergistic and antagonistic effects of specific bacterial taxa on viral prevalence and infectivity. We set out to test whether specific bacterial communities predict SARS-CoV-2 occurrence in a hospital setting.MethodsWe collected 972 samples from hospitalized patients with COVID-19, their health care providers, and hospital surfaces before, during, and after admission. We screened for SARS-CoV-2 using RT-qPCR, characterized microbial communities using 16S rRNA gene amplicon sequencing, and used these bacterial profiles to classify SARS-CoV-2 RNA detection with a random forest model.ResultsSixteen percent of surfaces from COVID-19 patient rooms had detectable SARS-CoV-2 RNA, although infectivity was not assessed. The highest prevalence was in floor samples next to patient beds (39%) and directly outside their rooms (29%). Although bed rail samples more closely resembled the patient microbiome compared to floor samples, SARS-CoV-2 RNA was detected less often in bed rail samples (11%). SARS-CoV-2 positive samples had higher bacterial phylogenetic diversity in both human and surface samples and higher biomass in floor samples. 16S microbial community profiles enabled high classifier accuracy for SARS-CoV-2 status in not only nares, but also forehead, stool, and floor samples. Across these distinct microbial profiles, a single amplicon sequence variant from the genus Rothia strongly predicted SARS-CoV-2 presence across sample types, with greater prevalence in positive surface and human samples, even when compared to samples from patients in other intensive care units prior to the COVID-19 pandemic.ConclusionsThese results contextualize the vast diversity of microbial niches where SARS-CoV-2 RNA is detected and identify specific bacterial taxa that associate with the viral RNA prevalence both in the host and hospital environment. Video Abstract.

Published
2021

5. LEGaTO: Low-Energy, Secure, and Resilient Toolset for Heterogeneous Computing

Author

Salami, B., Parasyris, K., Cristal, A., Unsal, O., Martorell, X., Carpenter, P., De La Cruz, R., Bautista, L., Jimenez, D., Alvarez, C., Nabavi, S., Madonar, S., Pericas, M., Trancoso, P., Abduljabbar, M., Chen, J., Soomro, P. N., Manivannan, M, Berge, M., Krupop, S., Klawonn, F., Mekhlafi, Al, May, S., Becker, T., Gaydadjiev, G., Odman, D., Salomonsson, H., Dubhashi, D., Port, O., Etsion, Y., Do, Le Quoc, Fetzer, Christof, Kaiser, M., Kucza, N., Hagemeyer, J., Griessl, R., Tigges, L., Mika, K., Huffmeier, A., Jungeblu, Th., Pasin, M., Schiavoni, V., Rocha, I., Gottel, C., and Felber, P.

Subjects
Computer Science - Distributed, Parallel, and Cluster Computing
Abstract

The LEGaTO project leverages task-based programming models to provide a software ecosystem for Made in-Europe heterogeneous hardware composed of CPUs, GPUs, FPGAs and dataflow engines. The aim is to attain one order of magnitude energy savings from the edge to the converged cloud/HPC, balanced with the security and resilience challenges. LEGaTO is an ongoing three-year EU H2020 project started in December 2017., Comment: 6 pages, 9 figures

Published
2019

6. Germination and Inhibitory Activity of Spore-Forming Microbes on Surface Materials Used in Healthcare Settings

Author

Gottel, Neil Robert

Subjects
Microbiology, AMR, bacillus, built environment, germination, MRSA, spore
Abstract

Surfaces in healthcare settings are colonized by pathogens, where they persist and are transmitted to other locations. Cleaning solutions that contain bacterial spores are an alternative to current methods for cleaning healthcare surfaces. My dissertation investigates how effectively these spores germinate on surfaces used in healthcare settings, whether they inhibit the survival of methicillin-resistant Staphylococcus aureus (MRSA), and if incorporated into a 3D printed structure, how effectively they germinate and inhibit MRSA. The first chapter investigates the germination efficiency of bacterial spores on surfaces from healthcare settings. Droplets of media containing a mixture of 5 Bacillus spp. and Priestia spp. were placed on laminate or vinyl, at either ambient or elevated relative humidity, then collected over a three-day timeseries via swabbing, followed by heat shocking and plating to determine the ratio of germinated spores to the total number of spores and cells. I found that there was a low, baseline level of germination, and that only very nutrient rich media would achieve high germination rates. The type of surface and the humidity also had a significant influence, but only at later timepoints in the experiments. The second chapter focuses on the inhibition of MRSA using the spore mix from chapter 1. Droplets containing MRSA by itself or in co-culture with the spore mix were placed on laminate or vinyl and incubated at over a three-day timeseries. CFU enumeration was used to determine whether the survival of MRSA was influenced by the spore mix. Surface, humidity, and competition medium significantly influenced the survival of MRSA, but the presence of the spore mix did not inhibit MRSA survival. The third chapter uses 3D printed structures that contain a strain of B. subtilis shown to have potent anti-MRSA inhibitory activity. Using optical density readings and CFU enumeration, the germination and growth of B. subtilis out of the structure and its inhibition of MRSA was investigated. Approximately 20% of the spores in the structures germinate and move out of the structure in liquid culture to inhibit MRSA, but the structures do not completely eliminate MRSA in either liquid culture or on solid agar surfaces.

Published
2024

7. Children with Autism and Their Typically Developing Siblings Differ in Amplicon Sequence Variants and Predicted Functions of Stool-Associated Microbes

Author

David, Maude M, Tataru, Christine, Daniels, Jena, Schwartz, Jessey, Keating, Jessica, Hampton-Marcell, Jarrad, Gottel, Neil, Gilbert, Jack A, and Wall, Dennis P

Subjects
Intellectual and Developmental Disabilities (IDD), Behavioral and Social Science, Genetics, Clinical Research, Autism, Brain Disorders, Mental Health, Pediatric, Aetiology, 2.3 Psychological, social and economic factors, 2.1 Biological and endogenous factors, Mental health, autism spectrum disorder, microbiome, crowdsource, 16S rRNA gene sequencing, Clostridiales, Lachnospiraceae, butyrate, 16S V4 sequencing
Abstract

The existence of a link between the gut microbiome and autism spectrum disorder (ASD) is well established in mice, but in human populations, efforts to identify microbial biomarkers have been limited due to a lack of appropriately matched controls, stratification of participants within the autism spectrum, and sample size. To overcome these limitations, we crowdsourced the recruitment of families with age-matched sibling pairs between 2 and 7 years old (within 2 years of each other), where one child had a diagnosis of ASD and the other did not. Parents collected stool samples, provided a home video of their ASD child's natural social behavior, and responded online to diet and behavioral questionnaires. 16S rRNA V4 amplicon sequencing of 117 samples (60 ASD and 57 controls) identified 21 amplicon sequence variants (ASVs) that differed significantly between the two cohorts: 11 were found to be enriched in neurotypical children (six ASVs belonging to the Lachnospiraceae family), while 10 were enriched in children with ASD (including Ruminococcaceae and Bacteroidaceae families). Summarizing the expected KEGG orthologs of each predicted genome, the taxonomic biomarkers associated with children with ASD can use amino acids as precursors for butyragenic pathways, potentially altering the availability of neurotransmitters like glutamate and gamma aminobutyric acid (GABA).IMPORTANCE Autism spectrum disorder (ASD), which now affects 1 in 54 children in the United States, is known to have comorbidity with gut disorders of a variety of types; however, the link to the microbiome remains poorly characterized. Recent work has provided compelling evidence to link the gut microbiome to the autism phenotype in mouse models, but identification of specific taxa associated with autism has suffered replicability issues in humans. This has been due in part to sample size that sufficiently covers the spectrum of phenotypes known to autism (which range from subtle to severe) and a lack of appropriately matched controls. Our original study proposes to overcome these limitations by collecting stool-associated microbiome on 60 sibling pairs of children, one with autism and one neurotypically developing, both 2 to 7 years old and no more than 2 years apart in age. We use exact sequence variant analysis and both permutation and differential abundance procedures to identify 21 taxa with significant enrichment or depletion in the autism cohort compared to their matched sibling controls. Several of these 21 biomarkers have been identified in previous smaller studies; however, some are new to autism and known to be important in gut-brain interactions and/or are associated with specific fatty acid biosynthesis pathways.

Published
2021

8. Draft Genome Sequence of Pseudarthrobacter sp. Strain ATCC 49442 (Formerly Micrococcus luteus), a Pyridine-Degrading Bacterium

Author

Gupta, Nidhi, Skinner, Kelly A, Summers, Zarath M, Edirisinghe, Janaka N, Weisenhorn, Pamela B, Faria, José P, Marshall, Christopher W, Sharma, Anukriti, Gottel, Neil R, Gilbert, Jack A, Henry, Christopher S, and O’Loughlin, Edward J

Abstract

We present here the draft genome sequence of a pyridine-degrading bacterium, Micrococcus luteus ATCC 49442, which was reclassified as Pseudarthrobacter sp. strain ATCC 49442 based on its draft genome sequence. Its genome length is 4.98 Mbp, with 64.81% GC content.

Published
2020

9. Chemical composition of material extractives influences microbial growth and dynamics on wetted wood materials.

Author

Zhao, Dan, Cardona, Cesar, Gottel, Neil, Winton, Valerie J, Thomas, Paul M, Raba, Daniel A, Kelley, Scott T, Henry, Christopher, Gilbert, Jack A, and Stephens, Brent

Abstract

The impact of material chemical composition on microbial growth on building materials remains relatively poorly understood. We investigate the influence of the chemical composition of material extractives on microbial growth and community dynamics on 30 different wood species that were naturally inoculated, wetted, and held at high humidity for several weeks. Microbial growth was assessed by visual assessment and molecular sequencing. Unwetted material powders and microbial swab samples were analyzed using reverse phase liquid chromatography with tandem mass spectrometry. Different wood species demonstrated varying susceptibility to microbial growth after 3 weeks and visible coverage and fungal qPCR concentrations were correlated (R2 = 0.55). Aspergillaceae was most abundant across all samples; Meruliaceae was more prevalent on 8 materials with the highest visible microbial growth. A larger and more diverse set of compounds was detected from the wood shavings compared to the microbial swabs, indicating a complex and heterogeneous chemical composition within wood types. Several individual compounds putatively identified in wood samples showed statistically significant, near-monotonic associations with microbial growth, including C11H16O4, C18H34O4, and C6H15NO. A pilot experiment confirmed the inhibitory effects of dosing a sample of wood materials with varying concentrations of liquid C6H15NO (assuming it presented as Diethylethanolamine).

Published
2020

10. Draft Genome Sequence of 2-Methylpyridine-, 2-Ethylpyridine-, and 2-Hydroxypyridine-Degrading Arthrobacter sp. Strain ATCC 49987.

Author

Gupta, Nidhi, Skinner, Kelly A, Summers, Zarath M, Edirisinghe, Janaka N, Faria, José P, Marshall, Christopher W, Sharma, Anukriti, Gottel, Neil R, Gilbert, Jack A, Henry, Christopher S, and O'Loughlin, Edward J

Subjects
Human Genome, Genetics
Abstract

Here, we report the draft genome sequence of Arthrobacter sp. strain ATCC 49987, consisting of three contigs with a total length of 4.4 Mbp. Based on the genome sequence, we suggest reclassification of Arthrobacter sp. strain ATCC 49987 as Pseudarthrobacter sp. strain ATCC 49987.

Published
2020

11. Spatial Compartmentalization of the Microbiome between the Lumen and Crypts Is Lost in the Murine Cecum following the Process of Surgery, Including Overnight Fasting and Exposure to Antibiotics

Author

Zaborin, Alexander, Bernabe, Beatriz Penalver, Keskey, Robert, Sangwan, Naseer, Hyoju, Sanjiv, Gottel, Neil, Gilbert, Jack A, Zaborina, Olga, and Alverdy, John C

Subjects
Digestive Diseases, 1.1 Normal biological development and functioning, Underpinning research, 16S rRNA, butyrate, cecal crypts, hypoxia gradient, Mucispirillum schaedleri, murine cecum microbiome, shotgun sequencing, spatial compartmentalization, surgery, Mucispirillum schaedleri
Abstract

The cecum is a unique region in the mammalian intestinal tract in which the microbiome is localized to two compartments, the lumen and the crypts. The microbiome within crypts is particularly important as it is in direct contact with lining epithelial cells including stem cells. Here, we analyzed the microbiome in cecum of mice using multiple techniques including metagenomics. The lumen microbiome comprised Firmicutes and Bacteroidetes whereas the crypts were dominated by Proteobacteria and Deferribacteres, and the mucus comprised a mixture of these 4 phyla. The lumen microbial functional potential comprised mainly carbon metabolism, while the crypt microbiome was enriched for genes encoding stress resistance. In order to determine how this structure, assembly, and function are altered under provocative conditions, we exposed mice to overnight starvation (S), antibiotics (A), and a major surgical injury (partial hepatectomy [H]), as occurs with major surgery in humans. We have previously demonstrated that the combined effect of this "SAH" treatment leads to a major disturbance of the cecal microbiota at the bottom of crypts in a manner that disrupts crypt cell homeostasis. Here, we applied the SAH conditions and observed a loss of compartmentalization in both composition and function of the cecal microbiome associated with major shifts in local physicochemical cues including decrease of hypoxia, increase of pH, and loss of butyrate production. Taken together, these studies demonstrated a defined order, structure, and function of the cecal microbiome that can be disrupted under provocative conditions such as major surgery and its attendant exposures.IMPORTANCE The proximal colon and cecum are two intestinal regions in which the microbiome localizes to two spatially distinct compartments, the lumen and crypts. The differences in composition and function of luminal and crypt microbiome in the cecum and the effect of physiological stress on their compartmentalization remain poorly characterized. Here, we characterized the composition and function of the lumen-, mucus-, and crypt-associated microbiome in the cecum of mice. We observed a highly ordered microbial architecture within the cecum whose assembly and function become markedly disrupted when provoked by physiological stress such as surgery and its attendant preoperative treatments (i.e., overnight fasting and antibiotics). Major shifts in local physicochemical cues including a decrease in hypoxia levels, an increase in pH, and a loss of butyrate production were associated with the loss of compositional and functional compartmentalization of the cecal microbiome.

Published
2020

12. Effects of Extended Postmortem Interval on Microbial Communities in Organs of the Human Cadaver

Author

Lutz, Holly, Vangelatos, Alexandria, Gottel, Neil, Osculati, Antonio, Visona, Silvia, Finley, Sheree J, Gilbert, Jack A, and Javan, Gulnaz T

Subjects
thanatomicrobiome, cadaver, 16S rRNA, internal organs, manner of death, Environmental Science and Management, Soil Sciences, Microbiology
Abstract

Human thanatomicrobiota studies have shown that microorganisms inhabit and proliferate externally and internally throughout the body and are the primary mediators of putrefaction after death. Yet little is known about the source and diversity of the thanatomicrobiome or the underlying factors leading to delayed decomposition exhibited by reproductive organs. The use of the V4 hypervariable region of bacterial 16S rRNA gene sequences for taxonomic classification ("barcoding") and phylogenetic analyses of human postmortem microbiota has recently emerged as a possible tool in forensic microbiology. The goal of this study was to apply a 16S rRNA barcoding approach to investigate variation among different organs, as well as the extent to which microbial associations among different body organs in human cadavers can be used to predict forensically important determinations, such as cause and time of death. We assessed microbiota of organ tissues including brain, heart, liver, spleen, prostate, and uterus collected at autopsy from criminal casework of 40 Italian cadavers with times of death ranging from 24 to 432 h. Both the uterus and prostate had a significantly higher alpha diversity compared to other anatomical sites, and exhibited a significantly different microbial community composition from non-reproductive organs, which we found to be dominated by the bacterial orders MLE1-12, Saprospirales, and Burkholderiales. In contrast, reproductive organs were dominated by Clostridiales, Lactobacillales, and showed a marked decrease in relative abundance of MLE1-12. These results provide insight into the observation that the uterus and prostate are the last internal organs to decay during human decomposition. We conclude that distinct community profiles of reproductive versus non-reproductive organs may help guide the application of forensic microbiology tools to investigations of human cadavers.

Published
2020

13. Microbiome profile associated with malignant pleural effusion.

Author

Shojaee, Samira, Sharma, Anukriti, Gottel, Neil, Sanchez, Trinidad, Gilbert, Jack A, and Rahman, Najib M

Subjects
General Science & Technology
Abstract

INTRODUCTION:There is ongoing research into the development of novel molecular markers that may complement fluid cytology malignant pleural effusion (MPE) diagnosis. In this exploratory pilot study, we hypothesized that there are distinct differences in the pleural fluid microbiome profile of malignant and non-malignant pleural diseases. METHOD:From a prospectively enrolled pleural fluid biorepository, samples of MPE were included. Non-MPE effusion were included as comparators. 16S rRNA gene V4 region amplicon sequencing was performed. Exact Sequence Variants (ESVs) were used for diversity analyses. The Shannon and Richness indices of alpha diversity and UniFrac beta diversity measures were tested for significance using permutational multivariate analysis of variance. Analyses of Composition of Microbiome was used to identify differentially abundant bacterial ESVs between the groups controlled for multiple hypothesis testing. RESULTS:38 patients with MPE and 9 with non-MPE were included. A subgroup of patients with metastatic adenocarcinoma histology were identified among MPE group (adenocarcinoma of lung origin (LA-MPE) = 11, breast origin (BA-MPE) = 11). MPE presented with significantly greater alpha diversity compared to non-MPE group. Within the MPE group, BA-MPE was more diverse compared to LA-MPE group. In multivariable analysis, ESVs belonging to family S24-7 and genera Allobaculum, Stenotrophomonas, and Epulopiscium were significantly enriched in the malignant group compared to the non-malignant group. CONCLUSION:Our results are the first to demonstrate a microbiome signature according to MPE and non-MPE. The role of microbiome in pleural effusion pathogenesis needs further exploration.

Published
2020

14. Concurrent measurement of microbiome and allergens in the air of bedrooms of allergy disease patients in the Chicago area

Author

Richardson, Miles, Gottel, Neil, Gilbert, Jack A, Gordon, Julian, Gandhi, Prasanthi, Reboulet, Rachel, and Hampton-Marcell, Jarrad T

Subjects
Microbiology, Biological Sciences, Health Effects of Indoor Air Pollution, 2.2 Factors relating to the physical environment, Aetiology, Air Microbiology, Air Pollution, Indoor, Allergens, Animals, Asthma, Bacteria, Cats, Chicago, Dogs, Dust, Environmental Monitoring, Fungi, Housing, Humans, Microbiota, Pets, RNA, Ribosomal, 16S, Respiratory Hypersensitivity, Ecology, Medical Microbiology, Evolutionary biology
Abstract

The particulate and biological components of indoor air have a substantial impact on human health, especially immune respiratory conditions such as asthma. To better explore the relationship between allergens, the microbial community, and the indoor living environment, we sampled the bedrooms of 65 homes in the Chicago area using 23the patient-friendly Inspirotec electrokinetic air sampling device, which collects airborne particles for characterization of both allergens and microbial DNA. The sampling device captured sufficient microbial material to enable 16S rRNA amplicon sequencing data to be generated for every sample in the study. Neither the presence of HEPA filters nor the height at which the air sampling device was placed had any influence on the microbial community profile. A core microbiota of 31 OTUs was present in more than three quarters of the samples, comprising around 45% of the relative sequence counts in each bedroom. The most abundant single organisms were Staphylococcus, with other core taxa both human and outdoor-associated. Bacterial alpha diversity was significantly increased in bedrooms that reported having open windows, those with flowering plants in the vicinity, and those in homes occupied by dogs. Porphyromonas, Moraxella, Sutterella, and Clostridium, along with family Neisseraceae, were significantly enriched in homes with dogs; interestingly, cats did not show a significant impact on microbial diversity or relative abundance. While dog allergen load was significantly correlated with bacterial alpha diversity, the taxa that significantly correlated with allergen burden did not exclusively overlap with those enriched in homes with dogs. Alternaria allergen load was positively correlated with bacterial alpha diversity, while Aspergillus allergen load was negatively correlated. The Alternaria allergen load was also significantly correlated with open windows. Microbial communities were significantly differentiated between rural, suburban, and urban homes and houses that were physically closer to each other maintained significantly more similar microbiota. We have demonstrated that it is possible to determine significant associations between allergen burden and the microbiota in air from the same sample and that these associations relate to the characteristics of the home and neighborhoods.

Published
2019

15. Synchrony and idiosyncrasy in the gut microbiome of wild baboons

Author

Björk, Johannes R., Dasari, Mauna R., Roche, Kim, Grieneisen, Laura, Gould, Trevor J., Grenier, Jean-Christophe, Yotova, Vania, Gottel, Neil, Jansen, David, Gesquiere, Laurence R., Gordon, Jacob B., Learn, Niki H., Wango, Tim L., Mututua, Raphael S., Kinyua Warutere, J., Siodi, Long’ida, Mukherjee, Sayan, Barreiro, Luis B., Alberts, Susan C., Gilbert, Jack A., Tung, Jenny, Blekhman, Ran, and Archie, Elizabeth A.

Published
2022
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16. Microbial Similarity between Students in a Common Dormitory Environment Reveals the Forensic Potential of Individual Microbial Signatures

Author

Richardson, Miles, Gottel, Neil, Gilbert, Jack A, and Lax, Simon

Subjects
Genetics, Human Genome, Entropy, Genetic Markers, Humans, Microbiota, Phylogeny, Students, built environments, microbial ecology, microbial transmission, Microbiology
Abstract

The microbiota of the built environment is an amalgamation of both human and environmental sources. While human sources have been examined within single-family households or in public environments, it is unclear what effect a large number of cohabitating people have on the microbial communities of their shared environment. We sampled the public and private spaces of a college dormitory, disentangling individual microbial signatures and their impact on the microbiota of common spaces. We compared multiple methods for marker gene sequence clustering and found that minimum entropy decomposition (MED) was best able to distinguish between the microbial signatures of different individuals and was able to uncover more discriminative taxa across all taxonomic groups. Further, weighted UniFrac- and random forest-based graph analyses uncovered two distinct spheres of hand- or shoe-associated samples. Using graph-based clustering, we identified spheres of interaction and found that connection between these clusters was enriched for hands, implicating them as a primary means of transmission. In contrast, shoe-associated samples were found to be freely interacting, with individual shoes more connected to each other than to the floors they interact with. Individual interactions were highly dynamic, with groups of samples originating from individuals clustering freely with samples from other individuals, while all floor and shoe samples consistently clustered together.IMPORTANCE Humans leave behind a microbial trail, regardless of intention. This may allow for the identification of individuals based on the "microbial signatures" they shed in built environments. In a shared living environment, these trails intersect, and through interaction with common surfaces may become homogenized, potentially confounding our ability to link individuals to their associated microbiota. We sought to understand the factors that influence the mixing of individual signatures and how best to process sequencing data to best tease apart these signatures.

Published
2019

17. Mice Fed an Obesogenic Western Diet, Administered Antibiotics, and Subjected to a Sterile Surgical Procedure Develop Lethal Septicemia with Multidrug-Resistant Pathobionts

Author

Hyoju, Sanjiv K, Zaborin, Alexander, Keskey, Robert, Sharma, Anukriti, Arnold, Wyatt, van den Berg, Fons, Kim, Sangman M, Gottel, Neil, Bethel, Cindy, Charnot-Katsikas, Angella, Jianxin, Peng, Adriaansens, Carleen, Papazian, Emily, Gilbert, Jack A, Zaborina, Olga, and Alverdy, John C

Subjects
Digestive Diseases, Nutrition, Infectious Diseases, Hematology, Vaccine Related, Prevention, Biodefense, Emerging Infectious Diseases, Antimicrobial Resistance, Sepsis, Aetiology, 2.1 Biological and endogenous factors, Infection, Animals, Anti-Bacterial Agents, C-Reactive Protein, Diet, Western, Drug Resistance, Bacterial, Gastrointestinal Microbiome, In Situ Nick-End Labeling, Interleukin-6, Male, Mice, Mice, Inbred C57BL, RNA, Ribosomal, 16S, Western diet, gut microbiome, gut-derived sepsis, pathobionts, surgery, Microbiology
Abstract

Despite antibiotics and sterile technique, postoperative infections remain a real and present danger to patients. Recent estimates suggest that 50% of the pathogens associated with postoperative infections have become resistant to the standard antibiotics used for prophylaxis. Risk factors identified in such cases include obesity and antibiotic exposure. To study the combined effect of obesity and antibiotic exposure on postoperative infection, mice were allowed to gain weight on an obesogenic Western-type diet (WD), administered antibiotics and then subjected to an otherwise recoverable sterile surgical injury (30% hepatectomy). The feeding of a WD alone resulted in a major imbalance of the cecal microbiota characterized by a decrease in diversity, loss of Bacteroidetes, a bloom in Proteobacteria, and the emergence of antibiotic-resistant organisms among the cecal microbiota. When WD-fed mice were administered antibiotics and subjected to 30% liver resection, lethal sepsis, characterized by multiple-organ damage, developed. Notable was the emergence and systemic dissemination of multidrug-resistant (MDR) pathobionts, including carbapenem-resistant, extended-spectrum β-lactamase-producing Serratia marcescens, which expressed a virulent and immunosuppressive phenotype. Analysis of the distribution of exact sequence variants belonging to the genus Serratia suggested that these strains originated from the cecal mucosa. No mortality or MDR pathogens were observed in identically treated mice fed a standard chow diet. Taken together, these results suggest that consumption of a Western diet and exposure to certain antibiotics may predispose to life-threating postoperative infection associated with MDR organisms present among the gut microbiota.IMPORTANCE Obesity remains a prevalent and independent risk factor for life-threatening infection following major surgery. Here, we demonstrate that when mice are fed an obesogenic Western diet (WD), they become susceptible to lethal sepsis with multiple organ damage after exposure to antibiotics and an otherwise-recoverable surgical injury. Analysis of the gut microbiota in this model demonstrates that WD alone leads to loss of Bacteroidetes, a bloom of Proteobacteria, and evidence of antibiotic resistance development even before antibiotics are administered. After antibiotics and surgery, lethal sepsis with organ damage developed in in mice fed a WD with the appearance of multidrug-resistant pathogens in the liver, spleen, and blood. The importance of these findings lies in exposing how the selective pressures of diet, antibiotic exposure, and surgical injury can converge on the microbiome, resulting in lethal sepsis and organ damage without the introduction of an exogenous pathogen.

Published
2019

18. A Simple Microbiome in the European Common Cuttlefish, Sepia officinalis

Author

Lutz, Holly L, Ramírez-Puebla, S Tabita, Abbo, Lisa, Durand, Amber, Schlundt, Cathleen, Gottel, Neil R, Sjaarda, Alexandra K, Hanlon, Roger T, Gilbert, Jack A, and Welch, Jessica L Mark

Subjects
Digestive Diseases, Genetics, Vaccine Related, Cephalopoda, Piscirickettsiaceae, Vibrionaceae, enrofloxacin, fluorescence assays, microbiome, Piscirickettsiaceae, Vibrionaceae
Abstract

The European common cuttlefish, Sepia officinalis, is used extensively in biological and biomedical research, yet its microbiome remains poorly characterized. We analyzed the microbiota of the digestive tract, gills, and skin in mariculture-raised S. officinalis using a combination of 16S rRNA amplicon sequencing, quantitative PCR (qPCR), and fluorescence spectral imaging. Sequencing revealed a highly simplified microbiota consisting largely of two single bacterial amplicon sequence variants (ASVs) of Vibrionaceae and Piscirickettsiaceae The esophagus was dominated by a single ASV of the genus Vibrio Imaging revealed bacteria in the family Vibrionaceae distributed in a discrete layer that lines the esophagus. This Vibrio was also the primary ASV found in the microbiota of the stomach, cecum, and intestine, but occurred at lower abundance, as determined by qPCR, and was found only scattered in the lumen rather than in a discrete layer via imaging analysis. Treatment of animals with the commonly used antibiotic enrofloxacin led to a nearly 80% reduction of the dominant Vibrio ASV in the esophagus but did not significantly alter the relative abundance of bacteria overall between treated versus control animals. Data from the gills were dominated by a single ASV in the family Piscirickettsiaceae, which imaging visualized as small clusters of cells. We conclude that bacteria belonging to the Gammaproteobacteria are the major symbionts of the cuttlefish Sepia officinalis cultured from eggs in captivity and that the esophagus and gills are major colonization sites.IMPORTANCE Microbes can play critical roles in the physiology of their animal hosts, as evidenced in cephalopods by the role of Vibrio (Aliivibrio) fischeri in the light organ of the bobtail squid and the role of Alpha- and Gammaproteobacteria in the reproductive system and egg defense in a variety of cephalopods. We sampled the cuttlefish microbiome throughout the digestive tract, gills, and skin and found dense colonization of an unexpected site, the esophagus, by a microbe of the genus Vibrio, as well as colonization of gills by Piscirickettsiaceae This finding expands the range of organisms and body sites known to be associated with Vibrio and is of potential significance for understanding host-symbiont associations, as well as for understanding and maintaining the health of cephalopods in mariculture.

Published
2019

19. Impacts of indoor surface finishes on bacterial viability

Author

Hu, Jinglin, Maamar, Sarah Ben, Glawe, Adam J, Gottel, Neil, Gilbert, Jack A, and Hartmann, Erica M

Subjects
Prevention, Emerging Infectious Diseases, Infectious Diseases, Aetiology, 2.2 Factors relating to the physical environment, Infection, Actinobacteria, Air Pollution, Indoor, Anti-Infective Agents, Bacillus, Enterococcus hirae, Environmental Microbiology, Microbacterium, Microbial Viability, Microbiota, Micrococcaceae, Northwestern United States, Paint, Pantoea, Surface Properties, antimicrobial resistance, antimicrobial surface paint, bacterial viability, efficacy of antimicrobial products, indoor microbiome, sporulation, Earth Sciences, Engineering, Medical and Health Sciences, Building & Construction
Abstract

Microbes in indoor environments are constantly being exposed to antimicrobial surface finishes. Many are rendered non-viable after spending extended periods of time under low-moisture, low-nutrient surface conditions, regardless of whether those surfaces have been amended with antimicrobial chemicals. However, some microorganisms remain viable even after prolonged exposure to these hostile conditions. Work with specific model pathogens makes it difficult to draw general conclusions about how chemical and physical properties of surfaces affect microbes. Here, we explore the survival of a synthetic community of non-model microorganisms isolated from built environments following exposure to three chemically and physically distinct surface finishes. Our findings demonstrated the differences in bacterial survival associated with three chemically and physically distinct materials. Alkaline clay surfaces select for an alkaliphilic bacterium, Kocuria rosea, whereas acidic mold-resistant paint favors Bacillus timonensis, a Gram-negative spore-forming bacterium that also survives on antimicrobial surfaces after 24 hours of exposure. Additionally, antibiotic-resistant Pantoea allii did not exhibit prolonged retention on antimicrobial surfaces. Our controlled microcosm experiment integrates measurement of indoor chemistry and microbiology to elucidate the complex biochemical interactions that influence the indoor microbiome.

Published
2019

20. Sex-specific effects of microbiome perturbations on cerebral Aβ amyloidosis and microglia phenotypes

Author

Dodiya, Hemraj B, Kuntz, Thomas, Shaik, Shabana M, Baufeld, Caroline, Leibowitz, Jeffrey, Zhang, Xulun, Gottel, Neil, Zhang, Xiaoqiong, Butovsky, Oleg, Gilbert, Jack A, and Sisodia, Sangram S

Subjects
Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Aging, Alzheimer's Disease, Genetics, Brain Disorders, Acquired Cognitive Impairment, Neurodegenerative, Dementia, Neurosciences, 2.1 Biological and endogenous factors, Aetiology, Amyloid Neuropathies, Amyloid beta-Protein Precursor, Animals, Anti-Bacterial Agents, Brain Diseases, Disease Models, Animal, Fecal Microbiota Transplantation, Female, Gastrointestinal Microbiome, Male, Mice, Microglia, Plaque, Amyloid, Sex Factors, Medical and Health Sciences, Immunology
Abstract

We demonstrated that an antibiotic cocktail (ABX)-perturbed gut microbiome is associated with reduced amyloid-β (Aβ) plaque pathology and astrogliosis in the male amyloid precursor protein (APP)SWE /presenilin 1 (PS1)ΔE9 transgenic model of Aβ amyloidosis. We now show that in an independent, aggressive APPSWE/PS1L166P (APPPS1-21) mouse model of Aβ amyloidosis, an ABX-perturbed gut microbiome is associated with a reduction in Aβ pathology and alterations in microglial morphology, thus establishing the generality of the phenomenon. Most importantly, these latter alterations occur only in brains of male mice, not in the brains of female mice. Furthermore, ABX treatment lead to alterations in levels of selected microglial expressed transcripts indicative of the "M0" homeostatic state in male but not in female mice. Finally, we found that transplants of fecal microbiota from age-matched APPPS1-21 male mice into ABX-treated APPPS1-21 male restores the gut microbiome and partially restores Aβ pathology and microglial morphology, thus demonstrating a causal role of the microbiome in the modulation of Aβ amyloidosis and microglial physiology in mouse models of Aβ amyloidosis.

Published
2019

21. Triplicate PCR reactions for 16S rRNA gene amplicon sequencing are unnecessary

Author

Marotz, Clarisse, Sharma, Anukriti, Humphrey, Greg, Gottel, Neil, Daum, Christopher, Gilbert, Jack A, Eloe-Fadrosh, Emiley, and Knight, Rob

Subjects
Biotechnology, Genetics, Bacteria, DNA, Bacterial, Polymerase Chain Reaction, RNA, Ribosomal, 16S, Sequence Analysis, DNA, 16S rRNA gene amplicon sequencing, microbiome, PCR, replicate PCR reactions, Biological Sciences, Technology, Bioinformatics
Abstract

Conventional wisdom holds that PCR amplification for sequencing should employ pooled replicate reactions to reduce bias due to jackpot effects and chimera formation. However, modern amplicon data analysis employs methods that may be less sensitive to such artifacts. Here we directly compare results from single versus triplicate reactions for 16S amplicon sequencing and find no significant impact of adopting a less labor-intensive single-reaction protocol.

Published
2019

22. Draft Genome Sequence of Rhodococcus sp. Strain ATCC 49988, a Quinoline-Degrading Bacterium

Author

Gupta, Nidhi, Skinner, Kelly A, Summers, Zarath M, Edirisinghe, Janaka N, Faria, José P, Marshall, Christopher W, Sharma, Anukriti, Gottel, Neil R, Gilbert, Jack A, Henry, Christopher S, and O’Loughlin, Edward J

Subjects
Genetics, Human Genome
Abstract

We report here the 4.9-Mb genome sequence of a quinoline-degrading bacterium, Rhodococcus sp. strain ATCC 49988. The draft genome data will enable the identification of genes and future genetic modification to enhance traits relevant to heteroaromatic compound degradation.

Published
2019

23. Microbial and metabolic succession on common building materials under high humidity conditions.

Author

Lax, Simon, Cardona, Cesar, Zhao, Dan, Winton, Valerie J, Goodney, Gabriel, Gao, Peng, Gottel, Neil, Hartmann, Erica M, Henry, Chris, Thomas, Paul M, Kelley, Scott T, Stephens, Brent, and Gilbert, Jack A

Subjects
Bacteria, Viruses, Fungi, RNA, Ribosomal, 16S, Humidity, Environmental Monitoring, Phylogeny, Construction Materials, RNA, Ribosomal, 16S
Abstract

Despite considerable efforts to characterize the microbial ecology of the built environment, the metabolic mechanisms underpinning microbial colonization and successional dynamics remain unclear, particularly at high moisture conditions. Here, we applied bacterial/viral particle counting, qPCR, amplicon sequencing of the genes encoding 16S and ITS rRNA, and metabolomics to longitudinally characterize the ecological dynamics of four common building materials maintained at high humidity. We varied the natural inoculum provided to each material and wet half of the samples to simulate a potable water leak. Wetted materials had higher growth rates and lower alpha diversity compared to non-wetted materials, and wetting described the majority of the variance in bacterial, fungal, and metabolite structure. Inoculation location was weakly associated with bacterial and fungal beta diversity. Material type influenced bacterial and viral particle abundance and bacterial and metabolic (but not fungal) diversity. Metabolites indicative of microbial activity were identified, and they too differed by material.

Published
2019

24. The human microbiota is associated with cardiometabolic risk across the epidemiologic transition.

Author

Fei, Na, Bernabé, Beatriz Peñalver, Lie, Louise, Baghdan, Danny, Bedu-Addo, Kweku, Plange-Rhule, Jacob, Forrester, Terrence E, Lambert, Estelle V, Bovet, Pascal, Gottel, Neil, Riesen, Walter, Korte, Wolfgang, Luke, Amy, Kliethermes, Stephanie A, Layden, Brian T, Gilbert, Jack A, and Dugas, Lara R

Subjects
Mouth, Humans, Cardiovascular Diseases, Metabolic Diseases, Risk Factors, Adult, Middle Aged, South Africa, Ghana, Jamaica, United States, Female, Male, Waist Circumference, Gastrointestinal Microbiome, General Science & Technology
Abstract

Oral and fecal microbial biomarkers have previously been associated with cardiometabolic (CM) risk, however, no comprehensive attempt has been made to explore this association in minority populations or across different geographic regions. We characterized gut- and oral-associated microbiota and CM risk in 655 participants of African-origin, aged 25-45, from Ghana, South Africa, Jamaica, and the United States (US). CM risk was classified using the CM risk cut-points for elevated waist circumference, elevated blood pressure and elevated fasted blood glucose, low high-density lipoprotein (HDL), and elevated triglycerides. Gut-associated bacterial alpha diversity negatively correlated with elevated blood pressure and elevated fasted blood glucose. Similarly, gut bacterial beta diversity was also significantly differentiated by waist circumference, blood pressure, triglyceridemia and HDL-cholesterolemia. Notably, differences in inter- and intra-personal gut microbial diversity were geographic-region specific. Participants meeting the cut-points for 3 out of the 5 CM risk factors were significantly more enriched with Lachnospiraceae, and were significantly depleted of Clostridiaceae, Peptostreptococcaceae, and Prevotella. The predicted relative proportions of the genes involved in the pathways for lipopolysaccharides (LPS) and butyrate synthesis were also significantly differentiated by the CM risk phenotype, whereby genes involved in the butyrate synthesis via lysine, glutarate and 4-aminobutyrate/succinate pathways and LPS synthesis pathway were enriched in participants with greater CM risk. Furthermore, inter-individual oral microbiota diversity was also significantly associated with the CM risk factors, and oral-associated Streptococcus, Prevotella, and Veillonella were enriched in participants with 3 out of the 5 CM risk factors. We demonstrate that in a diverse cohort of African-origin adults, CM risk is significantly associated with reduced microbial diversity, and the enrichment of specific bacterial taxa and predicted functional traits in both gut and oral environments. As well as providing new insights into the associations between the gut and oral microbiota and CM risk, this study also highlights the potential for novel therapeutic discoveries which target the oral and gut microbiota in CM risk.

Published
2019

25. Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women.

Author

Dugas, Lara R, Bernabé, Beatriz Peñalver, Priyadarshini, Medha, Fei, Na, Park, Seo Jin, Brown, Laquita, Plange-Rhule, Jacob, Nelson, David, Toh, Evelyn C, Gao, Xiang, Dong, Qunfeng, Sun, Jun, Kliethermes, Stephanie, Gottel, Neil, Luke, Amy, Gilbert, Jack A, and Layden, Brian T

Subjects
Humans, Obesity, Fatty Acids, Volatile, Receptors, Cell Surface, Receptors, G-Protein-Coupled, Body Mass Index, Feeding Behavior, Adult, African Americans, South Africa, Ghana, Female, Adiposity, Diet, High-Fat, Gastrointestinal Microbiome, Fecal Microbiota Transplantation, Diet, High-Fat, Fatty Acids, Volatile, Receptors, Cell Surface, G-Protein-Coupled
Abstract

We compared the gut microbial populations in 100 women, from rural Ghana and urban US [50% lean (BMI

Published
2018

26. Geoneutrino Detection and Other Non-Solar Neutrino Physics Achievements of Borexino

Author

Zavatarelli, Sandra, Agostini, M., Altenmuller, K., Appel, S., Atroshchenko, V., Bagdasarian, Z., Basilico, D., Bellini, G., Benziger, J., Biondi, R., Bravo, D., Caccianiga, B., Caminata, A., Calaprice, F., Cavalcante, P., Chepurnov, A., D’Angelo, D., Davini, S., Derbin, A., Di Giacinto, A., Di Marcello, V., Ding, X. F., Di Ludovico, A., Di Noto, L., Drachnev, I., Fiorentini, F., Formozov, A., Franco, D., Galbiati, C., Ghiano, C., Giammarchi, M., Goretti, A., Gottel, A. S., Gromov, M., Guffanti, D., Ianni, Aldo, Ianni, Andrea, Jany, A., Jeschke, D., Kobychev, V., Korga, G., Kumaran, S., Laubenstein, M., Litvinovich, E., Lombardi, P., Lomskaya, I., Ludhova, L., Lukyanchenko, G., Lukyanchenko, L., Machulin, I., Mantovani, F., Martyn, J., Meroni, E., Meyer, M., Miramonti, L., Misiaszek, M., Montuschi, M., Muratova, V., Neumair, B., Nieslony, M., Nugmanov, R., Oberauer, L., Orekhov, V., Ortica, F., Pallavicini, M., Papp, L., Pelicci, L., Penek, O., Pietrofaccia, L., Pilipenko, N., Pocar, A., Raikov, G., Ranalli, M. T., Ranucci, G., Razeto, A., Re, A., Redchuk, M., Ricci, B., Romani, A., Rossi, N., Schonert, S., Semenov, D., Settanta, G., Skorokhvatov, M., Singhal, A., Smirnov, O., Sotnikov, A., Strati, V., Suvorov, Y., Tartaglia, R., Testera, G., Thurn, J., Unzhakov, E., Villante, F., Vishneva, A., Vogelaar, R. B., von Feilitzsch, F., Wojcik, M., Wurm, M., Zavatarelli, S., Zuber, K., and Zuzel, G.

Published
2022
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27. SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment

Author

Clarisse Marotz, Pedro Belda-Ferre, Farhana Ali, Promi Das, Shi Huang, Kalen Cantrell, Lingjing Jiang, Cameron Martino, Rachel E. Diner, Gibraan Rahman, Daniel McDonald, George Armstrong, Sho Kodera, Sonya Donato, Gertrude Ecklu-Mensah, Neil Gottel, Mariana C. Salas Garcia, Leslie Y. Chiang, Rodolfo A. Salido, Justin P. Shaffer, Mac Kenzie Bryant, Karenina Sanders, Greg Humphrey, Gail Ackermann, Niina Haiminen, Kristen L. Beck, Ho-Cheol Kim, Anna Paola Carrieri, Laxmi Parida, Yoshiki Vázquez-Baeza, Francesca J. Torriani, Rob Knight, Jack Gilbert, Daniel A. Sweeney, and Sarah M. Allard

Subjects
Built environment, SARS-CoV-2, 16S rRNA, Microbiome, COVID-19, Microbial ecology, QR100-130
Abstract

Abstract Background SARS-CoV-2 is an RNA virus responsible for the coronavirus disease 2019 (COVID-19) pandemic. Viruses exist in complex microbial environments, and recent studies have revealed both synergistic and antagonistic effects of specific bacterial taxa on viral prevalence and infectivity. We set out to test whether specific bacterial communities predict SARS-CoV-2 occurrence in a hospital setting. Methods We collected 972 samples from hospitalized patients with COVID-19, their health care providers, and hospital surfaces before, during, and after admission. We screened for SARS-CoV-2 using RT-qPCR, characterized microbial communities using 16S rRNA gene amplicon sequencing, and used these bacterial profiles to classify SARS-CoV-2 RNA detection with a random forest model. Results Sixteen percent of surfaces from COVID-19 patient rooms had detectable SARS-CoV-2 RNA, although infectivity was not assessed. The highest prevalence was in floor samples next to patient beds (39%) and directly outside their rooms (29%). Although bed rail samples more closely resembled the patient microbiome compared to floor samples, SARS-CoV-2 RNA was detected less often in bed rail samples (11%). SARS-CoV-2 positive samples had higher bacterial phylogenetic diversity in both human and surface samples and higher biomass in floor samples. 16S microbial community profiles enabled high classifier accuracy for SARS-CoV-2 status in not only nares, but also forehead, stool, and floor samples. Across these distinct microbial profiles, a single amplicon sequence variant from the genus Rothia strongly predicted SARS-CoV-2 presence across sample types, with greater prevalence in positive surface and human samples, even when compared to samples from patients in other intensive care units prior to the COVID-19 pandemic. Conclusions These results contextualize the vast diversity of microbial niches where SARS-CoV-2 RNA is detected and identify specific bacterial taxa that associate with the viral RNA prevalence both in the host and hospital environment. Video Abstract

Published
2021
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31. JUNO sensitivity to the annihilation of MeV dark matter in the galactic halo

Author

Abusleme, A, Adam, T, Ahmad, S, Ahmed, R, Aiello, S, Akram, M, Aleem, A, Alexandros, T, An, F, An, Q, Andronico, G, Anfimov, N, Antonelli, V, Antoshkina, T, Asavapibhop, B, de Andre, J, Auguste, D, Bai, W, Balashov, N, Baldini, W, Barresi, A, Basilico, D, Baussan, E, Bellato, M, Bergnoli, A, Birkenfeld, T, Blin, S, Blum, D, Blyth, S, Bolshakova, A, Bongrand, M, Bordereau, C, Breton, D, Brigatti, A, Brugnera, R, Bruno, R, Budano, A, Busto, J, Cabrera, A, Caccianiga, B, Cai, H, Cai, X, Cai, Y, Cai, Z, Callegari, R, Cammi, A, Campeny, A, Cao, C, Cao, G, Cao, J, Caruso, R, Cerna, C, Chan, C, Chang, J, Chang, Y, Chen, G, Chen, P, Chen, S, Chen, X, Chen, Y, Chen, Z, Cheng, J, Cheng, Y, Chetverikov, A, Chiesa, D, Chimenti, P, Chu, Z, Chukanov, A, Claverie, G, Clementi, C, Clerbaux, B, Di Lorenzo, S, Corti, D, Corso, F, Dalager, O, De La Taille, C, Deng, Z, Depnering, W, Diaz, M, Ding, X, Ding, Y, Dirgantara, B, Dmitrievsky, S, Dohnal, T, Dolzhikov, D, Donchenko, G, Dong, J, Doroshkevich, E, Dou, W, Dracos, M, Druillole, F, Du, R, Du, S, Dusini, S, Dvorak, M, Eck, J, Enqvist, T, Fabbri, A, Fahrendholz, U, Fan, D, Fan, L, Fang, J, Fang, W, Fargetta, M, Fedoseev, D, Fei, Z, Feng, L, Feng, Q, Ferraro, F, Ford, R, Fournier, A, Gan, H, Gao, F, Garfagnini, A, Gavrikov, A, Giammarchi, M, Giudice, N, Gonchar, M, Gong, G, Gong, H, Gornushkin, Y, Gottel, A, Grassi, M, Gromov, V, Gu, M, Gu, X, Gu, Y, Guan, M, Guan, Y, Guardone, N, Guo, C, Guo, J, Guo, W, Guo, X, Guo, Y, Hagner, C, Han, R, Han, Y, He, M, He, W, Heinz, T, Hellmuth, P, Heng, Y, Herrera, R, Hor, Y, Hou, S, Hsiung, Y, Hu, B, Hu, H, Hu, J, Hu, S, Hu, T, Hu, Y, Hu, Z, Huang, G, Huang, H, Huang, K, Huang, W, Huang, X, Huang, Y, Hui, J, Huo, L, Huo, W, Huss, C, Hussain, S, Ioannisian, A, Isocrate, R, Jelmini, B, Jeria, I, Ji, X, Jia, H, Jia, J, Jian, S, Jiang, D, Jiang, W, Jiang, X, Jing, X, Jollet, C, Joutsenvaara, J, Kalousis, L, Kampmann, P, Kang, L, Karaparambil, R, Kazarian, N, Khatun, A, Khosonthongkee, K, Korablev, D, Kouzakov, K, Krasnoperov, A, Kutovskiy, N, Kuusiniemi, P, Lachenmaier, T, Landini, C, Leblanc, S, Lebrin, V, Lefevre, F, Lei, R, Leitner, R, Leung, J, Li, D, Li, F, Li, G, Li, H, Li, M, Li, N, Li, Q, Li, R, Li, S, Li, T, Li, W, Li, X, Li, Y, Li, Z, Liang, H, Liao, J, Limphirat, A, Lin, G, Lin, S, Lin, T, Ling, J, Lippi, I, Liu, F, Liu, H, Liu, J, Liu, M, Liu, Q, Liu, R, Liu, S, Liu, X, Liu, Y, Lokhov, A, Lombardi, P, Lombardo, C, Loo, K, Lu, C, Lu, H, Lu, J, Lu, P, Lu, S, Lubsandorzhiev, B, Lubsandorzhiev, S, Ludhova, L, Lukanov, A, Luo, D, Luo, F, Luo, G, Luo, S, Luo, W, Luo, X, Lyashuk, V, Ma, B, Ma, Q, Ma, S, Ma, X, Maalmi, J, Magoni, M, Mai, J, Malyshkin, Y, Mandujano, R, Mantovani, F, Mao, X, Mao, Y, Mari, S, Marini, F, Martellini, C, Martin-Chassard, G, Martini, A, Mayer, M, Mayilyan, D, Mednieks, I, Meinusch, A, Meng, Y, Meregaglia, A, Meroni, E, Meyhofer, D, Mezzetto, M, Miller, J, Miramonti, L, Molla, M, Montini, P, Montuschi, M, Muller, A, Nastasi, M, Naumov, D, Naumova, E, Navas-Nicolas, D, Nemchenok, I, Thi, M, Ning, F, Ning, Z, Nunokawa, H, Oberauer, L, Ochoa-Ricoux, J, Olshevskiy, A, Orestano, D, Ortica, F, Othegraven, R, Paoloni, A, Parmeggiano, S, Pei, Y, Pelicci, L, Pelliccia, N, Peng, A, Peng, H, Peng, Y, Peng, Z, Perrot, F, Petitjean, P, Petrucci, F, Pilarczyk, O, Rico, L, Popov, A, Poussot, P, Previtali, E, Qi, F, Qi, M, Qian, S, Qian, X, Qian, Z, Qiao, H, Qin, Z, Qiu, S, Ranucci, G, Raper, N, Rasheed, R, Re, A, Rebber, H, Rebii, A, Redchuk, M, Ren, B, Ren, J, Ricci, B, Rifai, M, Roche, M, Rodphai, N, Romani, A, Roskovec, B, Ruan, X, Rybnikov, A, Sadovsky, A, Saggese, P, Sanfilippo, S, Sangka, A, Sawangwit, U, Sawatzki, J, Schever, M, Schwab, C, Schweizer, K, Selyunin, A, Serafini, A, Settanta, G, Settimo, M, Shao, Z, Sharov, V, Shaydurova, A, Shi, J, Shi, Y, Shutov, V, Sidorenkov, A, Simkovic, F, Sirignano, C, Siripak, J, Sisti, M, Slupecki, M, Smirnov, M, Smirnov, O, Sogo-Bezerra, T, Sokolov, S, Songwadhana, J, Soonthornthum, B, Sotnikov, A, Sramek, O, Sreethawong, W, Stahl, A, Stanco, L, Stankevich, K, Stefanik, D, Steiger, H, Steinmann, J, Sterr, T, Stock, M, Strati, V, Studenikin, A, Su, J, Sun, S, Sun, X, Sun, Y, Sun, Z, Suwonjandee, N, Szelezniak, M, Tang, J, Tang, Q, Tang, X, Hariharan, V, Theisen, E, Tietzsch, A, Tkachev, I, Tmej, T, Torri, M, Treskov, K, Triossi, A, Troni, G, Trzaska, W, Tuve, C, Ushakov, N, Vedin, V, Verde, G, Vialkov, M, Viaud, B, Vollbrecht, C, Volpe, C, Sturm, K, Vorobel, V, Voronin, D, Votano, L, Walker, P, Wang, C, Wang, E, Wang, G, Wang, J, Wang, L, Wang, M, Wang, R, Wang, S, Wang, W, Wang, X, Wang, Y, Weng, Y, Wang, Z, Watcharangkool, A, Wei, W, Wei, Y, Wen, K, Wen, L, Weng, J, Wiebusch, C, Wong, S, Wonsak, B, Wu, D, Wu, Q, Wu, Z, Wurm, M, Wurtz, J, Wysotzki, C, Xi, Y, Xia, D, Xiao, X, Xie, X, Xie, Y, Xie, Z, Xin, Z, Xing, Z, Xu, B, Xu, C, Xu, D, Xu, F, Xu, H, Xu, J, Xu, M, Xu, Y, Yan, B, Yan, Q, Yan, T, Yan, W, Yan, X, Yan, Y, Yang, C, Yang, H, Yang, J, Yang, L, Yang, X, Yang, Y, Yeng, Y, 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P. A. M., Auguste D., Bai W., Balashov N., Baldini W., Barresi A., Basilico D., Baussan E., Bellato M., Bergnoli A., Birkenfeld T., Blin S., Blum D., Blyth S., Bolshakova A., Bongrand M., Bordereau C., Breton D., Brigatti A., Brugnera R., Bruno R., Budano A., Busto J., Cabrera A., Caccianiga B., Cai H., Cai X., Cai Y., Cai Z., Callegari R., Cammi A., Campeny A., Cao C., Cao G., Cao J., Caruso R., Cerna C., Chan C., Chang J., Chang Y., Chen G., Chen P., Chen P. -A., Chen S., Chen X., Chen Y., Chen Z., Cheng J., Cheng Y., Cheng Y. C., Chetverikov A., Chiesa D., Chimenti P., Chu Z., Chukanov A., Claverie G., Clementi C., Clerbaux B., Di Lorenzo S. C., Corti D., Corso F. D., Dalager O., De La Taille C., Deng Z., Depnering W., Diaz M., Ding X., Ding Y., Dirgantara B., Dmitrievsky S., Dohnal T., Dolzhikov D., Donchenko G., Dong J., Doroshkevich E., Dou W., Dracos M., Druillole F., Du R., Du S., Dusini S., Dvorak M., Eck J., Enqvist T., Fabbri A., Fahrendholz U., Fan D., Fan L., Fang J., Fang W., Fargetta M., Fedoseev D., Fei Z., Feng L. -C., Feng Q., Ferraro F., Ford R., Fournier A., Gan H., Gao F., Garfagnini A., Gavrikov A., Giammarchi M., Giudice N., Gonchar M., Gong G., Gong H., Gornushkin Y., Gottel A., Grassi M., Gromov V., Gu M., Gu X., Gu Y., Guan M., Guan Y., Guardone N., Guo C., Guo J., Guo W., Guo X., Guo Y., Hagner C., Han R., Han Y., He M., He W., Heinz T., Hellmuth P., Heng Y., Herrera R., Hor Y., Hou S., Hsiung Y., Hu B. -Z., Hu H., Hu J., Hu S., Hu T., Hu Y., Hu Z., Huang G., Huang H., Huang K., Huang W., Huang X., Huang Y., Hui J., Huo L., Huo W., Huss C., Hussain S., Ioannisian A., Isocrate R., Jelmini B., Jeria I., Ji X., Jia H., Jia J., Jian S., Jiang D., Jiang W., Jiang X., Jing X., Jollet C., Joutsenvaara J., Kalousis L., Kampmann P., Kang L., Karaparambil R., Kazarian N., Khatun A., Khosonthongkee K., Korablev D., Kouzakov K., Krasnoperov A., Kutovskiy N., Kuusiniemi P., Lachenmaier T., Landini C., Leblanc S., Lebrin V., Lefevre F., Lei R., Leitner R., Leung J., Li D., Li F., Li G., Li H., Li M., Li N., Li Q., Li R., Li S., Li T., Li W., Li X., Li Y., Li Z., Liang H., Liao J., Limphirat A., Lin G. -L., Lin S., Lin T., Ling J., Lippi I., Liu F., Liu H., Liu J., Liu M., Liu Q., Liu R., Liu S., Liu X., Liu Y., Lokhov A., Lombardi P., Lombardo C., Loo K., Lu C., Lu H., Lu J., Lu P., Lu S., Lubsandorzhiev B., Lubsandorzhiev S., Ludhova L., Lukanov A., Luo D., Luo F., Luo G., Luo S., Luo W., Luo X., Lyashuk V., Ma B., Ma Q., Ma S., Ma X., Maalmi J., Magoni M., Mai J., Malyshkin Y., Mandujano R. C., Mantovani F., Mao X., Mao Y., Mari S. M., Marini F., Martellini C., Martin-Chassard G., Martini A., Mayer M., Mayilyan D., Mednieks I., Meinusch A., Meng Y., Meregaglia A., Meroni E., Meyhofer D., Mezzetto M., Miller J., Miramonti L., Molla M. C., Montini P., Montuschi M., Muller A., Nastasi M., Naumov D. V., Naumova E., Navas-Nicolas D., Nemchenok I., Thi M. T. N., Ning F., Ning Z., Nunokawa H., Oberauer L., Ochoa-Ricoux J. P., Olshevskiy A., Orestano D., Ortica F., Othegraven R., Paoloni A., Parmeggiano S., Pei Y., Pelicci L., Pelliccia N., Peng A., Peng H., Peng Y., Peng Z., Perrot F., Petitjean P. -A., Petrucci F., Pilarczyk O., Rico L. F. P., Popov A., Poussot P., Previtali E., Qi F., Qi M., Qian S., Qian X., Qian Z., Qiao H., Qin Z., Qiu S., Ranucci G., Raper N., Rasheed R., Re A., Rebber H., Rebii A., Redchuk M., Ren B., Ren J., Ricci B., Rifai M., Roche M., Rodphai N., Romani A., Roskovec B., Ruan X., Rybnikov A., Sadovsky A., Saggese P., Sanfilippo S., Sangka A., Sawangwit U., Sawatzki J., Schever M., Schwab C., Schweizer K., Selyunin A., Serafini A., Settanta G., Settimo M., Shao Z., Sharov V., Shaydurova A., Shi J., Shi Y., Shutov V., Sidorenkov A., Simkovic F., Sirignano C., Siripak J., Sisti M., Slupecki M., Smirnov M., Smirnov O., Sogo-Bezerra T., Sokolov S., Songwadhana J., Soonthornthum B., Sotnikov A., Sramek O., Sreethawong W., Stahl A., Stanco L., Stankevich K., Stefanik D., Steiger H., Steinmann J., Sterr T., Stock M. R., Strati V., Studenikin A., Su J., Sun S., Sun X., Sun Y., Sun Z., Suwonjandee N., Szelezniak M., Tang J., Tang Q., Tang X., Hariharan V. T., Theisen E., Tietzsch A., Tkachev I., Tmej T., Torri M. D. C., Treskov K., Triossi A., Troni G., Trzaska W., Tuve C., Ushakov N., Vedin V., Verde G., Vialkov M., Viaud B., Vollbrecht C. M., Volpe C., Sturm K. V., Vorobel V., Voronin D., Votano L., Walker P., Wang C., Wang C. -H., Wang E., Wang G., Wang J., Wang L., Wang M., Wang R., Wang S., Wang W., Wang X., Wang Y., Weng Y., Wang Z., Watcharangkool A., Wei W., Wei Y., Wen K., Wen L., Weng J., Wiebusch C., Wong S. C. -F., Wonsak B., Wu D., Wu Q., Wu Z., Wurm M., Wurtz J., Wysotzki C., Xi Y., Xia D., Xiao X., Xie X., Xie Y., Xie Z., Xin Z., Xing Z., Xu B., Xu C., Xu D., Xu F., Xu H., Xu J., Xu M., Xu Y., Yan B., Yan Q., Yan T., Yan W., Yan X., Yan Y., Yang C., Yang H., Yang J., Yang L., Yang X., Yang Y., Yeng Y., Yao H., Ye J., Ye M., Ye Z., Yermia F., You Z., Yu B., Yu C., Yu H., Yu M., Yu X., Yu Z., Yuan C., Yuan Y., Yuan Z., Yue B., Zafar N., Zavadskyi V., Zeng S., Zeng T., Zeng Y., Zhan L., Zhang A., Zhang B., Zhang F., Zhang G., Zhang H., Zhang J., Zhang M., Zhang P., Zhang Q., Zhang S., Zhang T., Zhang X., Zhang Y., Zhang Z., Zhao F., Zhao J., Zhao R., Zhao S., Zheng D., Zheng H., Zheng Y., Zhong W., Zhou J., Zhou L., Zhou N., Zhou S., Zhou T., Zhou X., Zhu J., Zhu K., Zhu Z., Zhuang B., Zhuang H., Zong L., Zou J., Zwickel S., Abusleme, A, Adam, T, Ahmad, S, Ahmed, R, Aiello, S, Akram, M, Aleem, A, Alexandros, T, An, F, An, Q, Andronico, G, Anfimov, N, Antonelli, V, Antoshkina, T, 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R, Paoloni, A, Parmeggiano, S, Pei, Y, Pelicci, L, Pelliccia, N, Peng, A, Peng, H, Peng, Y, Peng, Z, Perrot, F, Petitjean, P, Petrucci, F, Pilarczyk, O, Rico, L, Popov, A, Poussot, P, Previtali, E, Qi, F, Qi, M, Qian, S, Qian, X, Qian, Z, Qiao, H, Qin, Z, Qiu, S, Ranucci, G, Raper, N, Rasheed, R, Re, A, Rebber, H, Rebii, A, Redchuk, M, Ren, B, Ren, J, Ricci, B, Rifai, M, Roche, M, Rodphai, N, Romani, A, Roskovec, B, Ruan, X, Rybnikov, A, Sadovsky, A, Saggese, P, Sanfilippo, S, Sangka, A, Sawangwit, U, Sawatzki, J, Schever, M, Schwab, C, Schweizer, K, Selyunin, A, Serafini, A, Settanta, G, Settimo, M, Shao, Z, Sharov, V, Shaydurova, A, Shi, J, Shi, Y, Shutov, V, Sidorenkov, A, Simkovic, F, Sirignano, C, Siripak, J, Sisti, M, Slupecki, M, Smirnov, M, Smirnov, O, Sogo-Bezerra, T, Sokolov, S, Songwadhana, J, Soonthornthum, B, Sotnikov, A, Sramek, O, Sreethawong, W, Stahl, A, Stanco, L, Stankevich, K, Stefanik, D, Steiger, H, Steinmann, J, Sterr, T, Stock, M, Strati, V, Studenikin, A, Su, J, Sun, S, Sun, X, Sun, Y, Sun, Z, Suwonjandee, N, Szelezniak, M, Tang, J, Tang, Q, Tang, X, Hariharan, V, Theisen, E, Tietzsch, A, Tkachev, I, Tmej, T, Torri, M, Treskov, K, Triossi, A, Troni, G, Trzaska, W, Tuve, C, Ushakov, N, Vedin, V, Verde, G, Vialkov, M, Viaud, B, Vollbrecht, C, Volpe, C, Sturm, K, Vorobel, V, Voronin, D, Votano, L, Walker, P, Wang, C, Wang, E, Wang, G, Wang, J, Wang, L, Wang, M, Wang, R, Wang, S, Wang, W, Wang, X, Wang, Y, Weng, Y, Wang, Z, Watcharangkool, A, Wei, W, Wei, Y, Wen, K, Wen, L, Weng, J, Wiebusch, C, Wong, S, Wonsak, B, Wu, D, Wu, Q, Wu, Z, Wurm, M, Wurtz, J, Wysotzki, C, Xi, Y, Xia, D, Xiao, X, Xie, X, Xie, Y, Xie, Z, Xin, Z, Xing, Z, Xu, B, Xu, C, Xu, D, Xu, F, Xu, H, Xu, J, Xu, M, Xu, Y, Yan, B, Yan, Q, Yan, T, Yan, W, Yan, X, Yan, Y, Yang, C, Yang, H, Yang, J, Yang, L, Yang, X, Yang, Y, Yeng, Y, Yao, H, Ye, J, Ye, M, Ye, Z, Yermia, F, You, Z, Yu, B, Yu, C, Yu, H, Yu, M, Yu, X, Yu, Z, Yuan, C, Yuan, Y, Yuan, Z, Yue, B, Zafar, N, Zavadskyi, V, Zeng, S, Zeng, T, Zeng, Y, Zhan, L, Zhang, A, Zhang, B, Zhang, F, Zhang, G, Zhang, H, Zhang, J, Zhang, M, Zhang, P, Zhang, Q, Zhang, S, Zhang, T, Zhang, X, Zhang, Y, Zhang, Z, Zhao, F, Zhao, J, Zhao, R, Zhao, S, Zheng, D, Zheng, H, Zheng, Y, Zhong, W, Zhou, J, Zhou, L, Zhou, N, Zhou, S, Zhou, T, Zhou, X, Zhu, J, Zhu, K, Zhu, Z, Zhuang, B, Zhuang, H, Zong, L, Zou, J, Zwickel, S, Abusleme A., Adam T., Ahmad S., Ahmed R., Aiello S., Akram M., Aleem A., Alexandros T., An F., An Q., Andronico G., Anfimov N., Antonelli V., Antoshkina T., Asavapibhop B., de Andre J. P. A. M., Auguste D., Bai W., Balashov N., Baldini W., Barresi A., Basilico D., Baussan E., Bellato M., Bergnoli A., Birkenfeld T., Blin S., Blum D., Blyth S., Bolshakova A., Bongrand M., Bordereau C., Breton D., Brigatti A., Brugnera R., Bruno R., Budano A., Busto J., Cabrera A., Caccianiga B., Cai H., Cai X., Cai Y., Cai Z., Callegari R., Cammi A., Campeny A., Cao C., Cao G., Cao J., Caruso R., Cerna C., Chan C., Chang J., Chang Y., Chen G., Chen P., Chen P. -A., Chen S., Chen X., Chen Y., Chen Z., Cheng J., Cheng Y., Cheng Y. C., Chetverikov A., Chiesa D., Chimenti P., Chu Z., Chukanov A., Claverie G., Clementi C., Clerbaux B., Di Lorenzo S. C., Corti D., Corso F. D., Dalager O., De La Taille C., Deng Z., Depnering W., Diaz M., Ding X., Ding Y., Dirgantara B., Dmitrievsky S., Dohnal T., Dolzhikov D., Donchenko G., Dong J., Doroshkevich E., Dou W., Dracos M., Druillole F., Du R., Du S., Dusini S., Dvorak M., Eck J., Enqvist T., Fabbri A., Fahrendholz U., Fan D., Fan L., Fang J., Fang W., Fargetta M., Fedoseev D., Fei Z., Feng L. -C., Feng Q., Ferraro F., Ford R., Fournier A., Gan H., Gao F., Garfagnini A., Gavrikov A., Giammarchi M., Giudice N., Gonchar M., Gong G., Gong H., Gornushkin Y., Gottel A., Grassi M., Gromov V., Gu M., Gu X., Gu Y., Guan M., Guan Y., Guardone N., Guo C., Guo J., Guo W., Guo X., Guo Y., Hagner C., Han R., Han Y., He M., He W., Heinz T., Hellmuth P., Heng Y., Herrera R., Hor Y., Hou S., Hsiung Y., Hu B. -Z., Hu H., Hu J., Hu S., Hu T., Hu Y., Hu Z., Huang G., Huang H., Huang K., Huang W., Huang X., Huang Y., Hui J., Huo L., Huo W., Huss C., Hussain S., Ioannisian A., Isocrate R., Jelmini B., Jeria I., Ji X., Jia H., Jia J., Jian S., Jiang D., Jiang W., Jiang X., Jing X., Jollet C., Joutsenvaara J., Kalousis L., Kampmann P., Kang L., Karaparambil R., Kazarian N., Khatun A., Khosonthongkee K., Korablev D., Kouzakov K., Krasnoperov A., Kutovskiy N., Kuusiniemi P., Lachenmaier T., Landini C., Leblanc S., Lebrin V., Lefevre F., Lei R., Leitner R., Leung J., Li D., Li F., Li G., Li H., Li M., Li N., Li Q., Li R., Li S., Li T., Li W., Li X., Li Y., Li Z., Liang H., Liao J., Limphirat A., Lin G. -L., Lin S., Lin T., Ling J., Lippi I., Liu F., Liu H., Liu J., Liu M., Liu Q., Liu R., Liu S., Liu X., Liu Y., Lokhov A., Lombardi P., Lombardo C., Loo K., Lu C., Lu H., Lu J., Lu P., Lu S., Lubsandorzhiev B., Lubsandorzhiev S., Ludhova L., Lukanov A., Luo D., Luo F., Luo G., Luo S., Luo W., Luo X., Lyashuk V., Ma B., Ma Q., Ma S., Ma X., Maalmi J., Magoni M., Mai J., Malyshkin Y., Mandujano R. C., Mantovani F., Mao X., Mao Y., Mari S. M., Marini F., Martellini C., Martin-Chassard G., Martini A., Mayer M., Mayilyan D., Mednieks I., Meinusch A., Meng Y., Meregaglia A., Meroni E., Meyhofer D., Mezzetto M., Miller J., Miramonti L., Molla M. C., Montini P., Montuschi M., Muller A., Nastasi M., Naumov D. V., Naumova E., Navas-Nicolas D., Nemchenok I., Thi M. T. N., Ning F., Ning Z., Nunokawa H., Oberauer L., Ochoa-Ricoux J. P., Olshevskiy A., Orestano D., Ortica F., Othegraven R., Paoloni A., Parmeggiano S., Pei Y., Pelicci L., Pelliccia N., Peng A., Peng H., Peng Y., Peng Z., Perrot F., Petitjean P. -A., Petrucci F., Pilarczyk O., Rico L. F. P., Popov A., Poussot P., Previtali E., Qi F., Qi M., Qian S., Qian X., Qian Z., Qiao H., Qin Z., Qiu S., Ranucci G., Raper N., Rasheed R., Re A., Rebber H., Rebii A., Redchuk M., Ren B., Ren J., Ricci B., Rifai M., Roche M., Rodphai N., Romani A., Roskovec B., Ruan X., Rybnikov A., Sadovsky A., Saggese P., Sanfilippo S., Sangka A., Sawangwit U., Sawatzki J., Schever M., Schwab C., Schweizer K., Selyunin A., Serafini A., Settanta G., Settimo M., Shao Z., Sharov V., Shaydurova A., Shi J., Shi Y., Shutov V., Sidorenkov A., Simkovic F., Sirignano C., Siripak J., Sisti M., Slupecki M., Smirnov M., Smirnov O., Sogo-Bezerra T., Sokolov S., Songwadhana J., Soonthornthum B., Sotnikov A., Sramek O., Sreethawong W., Stahl A., Stanco L., Stankevich K., Stefanik D., Steiger H., Steinmann J., Sterr T., Stock M. R., Strati V., Studenikin A., Su J., Sun S., Sun X., Sun Y., Sun Z., Suwonjandee N., Szelezniak M., Tang J., Tang Q., Tang X., Hariharan V. T., Theisen E., Tietzsch A., Tkachev I., Tmej T., Torri M. D. C., Treskov K., Triossi A., Troni G., Trzaska W., Tuve C., Ushakov N., Vedin V., Verde G., Vialkov M., Viaud B., Vollbrecht C. M., Volpe C., Sturm K. V., Vorobel V., Voronin D., Votano L., Walker P., Wang C., Wang C. -H., Wang E., Wang G., Wang J., Wang L., Wang M., Wang R., Wang S., Wang W., Wang X., Wang Y., Weng Y., Wang Z., Watcharangkool A., Wei W., Wei Y., Wen K., Wen L., Weng J., Wiebusch C., Wong S. C. -F., Wonsak B., Wu D., Wu Q., Wu Z., Wurm M., Wurtz J., Wysotzki C., Xi Y., Xia D., Xiao X., Xie X., Xie Y., Xie Z., Xin Z., Xing Z., Xu B., Xu C., Xu D., Xu F., Xu H., Xu J., Xu M., Xu Y., Yan B., Yan Q., Yan T., Yan W., Yan X., Yan Y., Yang C., Yang H., Yang J., Yang L., Yang X., Yang Y., Yeng Y., Yao H., Ye J., Ye M., Ye Z., Yermia F., You Z., Yu B., Yu C., Yu H., Yu M., Yu X., Yu Z., Yuan C., Yuan Y., Yuan Z., Yue B., Zafar N., Zavadskyi V., Zeng S., Zeng T., Zeng Y., Zhan L., Zhang A., Zhang B., Zhang F., Zhang G., Zhang H., Zhang J., Zhang M., Zhang P., Zhang Q., Zhang S., Zhang T., Zhang X., Zhang Y., Zhang Z., Zhao F., Zhao J., Zhao R., Zhao S., Zheng D., Zheng H., Zheng Y., Zhong W., Zhou J., Zhou L., Zhou N., Zhou S., Zhou T., Zhou X., Zhu J., Zhu K., Zhu Z., Zhuang B., Zhuang H., Zong L., Zou J., and Zwickel S.

Abstract

We discuss JUNO sensitivity to the annihilation of MeV dark matter in the galactic halo via detecting inverse beta decay reactions of electron anti-neutrinos resulting from the annihilation. We study possible backgrounds to the signature, including the reactor neutrinos, diffuse supernova neutrino background, charged- and neutral-current interactions of atmospheric neutrinos, backgrounds from muon-induced fast neutrons and cosmogenic isotopes. A fiducial volume cut, as well as the pulse shape discrimination and the muon veto are applied to suppress the above backgrounds. It is shown that JUNO sensitivity to the thermally averaged dark matter annihilation rate in 10 years of exposure would be significantly better than the present-day best limit set by Super-Kamiokande and would be comparable to that expected by Hyper-Kamiokande.

Published
2023

32. JUNO sensitivity to 7Be, pep, and CNO solar neutrinos

Author

Abusleme, A, Adam, T, Ahmad, S, Ahmed, R, Aiello, S, Akram, M, Aleem, A, Alexandros, T, An, F, An, Q, Andronico, G, Anfimov, N, Antonelli, V, Antoshkina, T, Asavapibhop, B, de Andre, J, Auguste, D, Bai, W, Balashov, N, Baldini, W, Barresi, A, Basilico, D, Baussan, E, Bellato, M, Beretta, M, Bergnoli, A, Bick, D, Bieger, L, Biktemerova, S, Birkenfeld, T, Blum, D, Blyth, S, Bolshakova, A, Bongrand, M, Bordereau, C, Breton, D, Brigatti, A, Brugnera, R, Bruno, R, Budano, A, Busto, J, Cabrera, A, Caccianiga, B, Cai, H, Cai, X, Cai, Y, Cai, Z, Callier, S, Cammi, A, Campeny, A, Cao, C, Cao, G, Cao, J, Caruso, R, Cerna, C, Cerrone, V, Chan, C, Chang, J, Chang, Y, Chen, C, Chen, G, Chen, P, Chen, S, Chen, Y, Chen, Z, Cheng, J, Cheng, Y, Chepurnov, A, Chetverikov, A, Chiesa, D, Chimenti, P, Chu, Z, Chukanov, A, Claverie, G, Clementi, C, Clerbaux, B, Molla, M, Di Lorenzo, S, Coppi, A, Corti, D, Csakli, S, Dal Corso, F, Dalager, O, Datta, J, De La Taille, C, Deng, Z, Depnering, W, Ding, X, Ding, Y, Dirgantara, B, Dittrich, C, Dmitrievsky, S, Dohnal, T, Dolzhikov, D, Donchenko, G, Dong, J, Doroshkevich, E, Dou, W, Dracos, M, Druillole, F, Du, R, Du, S, Dugas, K, Dusini, S, Duyang, H, Eck, J, Enqvist, T, Fabbri, A, Fahrendholz, U, Fan, L, Fang, J, Fang, W, Fargetta, M, Fedoseev, D, Fei, Z, Feng, L, Feng, Q, Ferraro, F, Fournier, A, Gan, H, Gao, F, Garfagnini, A, Gavrikov, A, Giammarchi, M, Giudice, N, Gonchar, M, Gong, G, Gong, H, Gornushkin, Y, Gottel, A, Grassi, M, Gromov, M, Gromov, V, Gu, M, Gu, X, Gu, Y, Guan, M, Guan, Y, Guardone, N, Guo, C, Guo, W, Guo, X, Hagner, C, Han, R, Han, Y, He, M, He, W, Heinz, T, Hellmuth, P, Heng, Y, Herrera, R, Hor, Y, Hou, S, Hsiung, Y, Hu, B, Hu, H, Hu, J, Hu, S, Hu, T, Hu, Y, Hu, Z, Huang, G, Huang, H, Huang, J, Huang, K, Huang, W, Huang, X, Huang, Y, Hui, J, Huo, L, Huo, W, Huss, C, Hussain, S, Imbert, L, Ioannisian, A, Isocrate, R, Jelmini, B, Jeria, I, Ji, X, Jia, H, Jia, J, Jian, S, Jiang, C, Jiang, D, Jiang, W, Jiang, X, Jing, X, Jollet, C, Kampmann, P, Kang, L, Karaparambil, R, Kazarian, N, Khan, A, Khatun, A, Khosonthongkee, K, Korablev, D, Kouzakov, K, Krasnoperov, A, Kuleshov, S, Kutovskiy, N, Lachenmaier, T, Landini, C, Leblanc, S, Lebrin, V, Lefevre, F, Lei, R, Leitner, R, Leung, J, Li, D, Li, F, Li, G, Li, H, Li, J, Li, M, Li, N, Li, Q, Li, R, Li, S, Li, T, Li, W, Li, X, Li, Y, Li, Z, Liang, H, Liao, J, Limphirat, A, Lin, G, Lin, S, Lin, T, Ling, J, Ling, X, Lippi, I, Liu, C, Liu, F, Liu, H, Liu, J, Liu, M, Liu, Q, Liu, R, Liu, S, Liu, X, Liu, Y, Liu, Z, Lokhov, A, Lombardi, P, Lombardo, C, Loo, K, Lu, C, Lu, H, Lu, J, Lu, P, Lu, S, Lubsandorzhiev, B, Lubsandorzhiev, S, Ludhova, L, Lukanov, A, Luo, D, Luo, F, Luo, G, Luo, J, Luo, S, Luo, W, Luo, X, Lyashuk, V, Ma, B, Ma, Q, Ma, S, Ma, X, Maalmi, J, Magoni, M, Mai, J, Malyshkin, Y, Mandujano, R, Mantovani, F, Mao, X, Mao, Y, Mari, S, Marini, F, Martini, A, Mayer, M, Mayilyan, D, Mednieks, I, Meng, Y, Meraviglia, A, Meregaglia, A, Meroni, E, Meyhofer, D, Miramonti, L, Mohan, N, Montini, P, Montuschi, M, Muller, A, Nastasi, M, Naumov, D, Naumova, E, Navas-Nicolas, D, Nemchenok, I, Thi, M, Nikolaev, A, Ning, F, Ning, Z, Nunokawa, H, Oberauer, L, Ochoa-Ricoux, J, Olshevskiy, A, Orestano, D, Ortica, F, Othegraven, R, Paoloni, A, Parmeggiano, S, Pei, Y, Pelicci, L, Peng, A, Peng, H, Peng, Y, Peng, Z, Perrot, F, Petitjean, P, Petrucci, F, Pilarczyk, O, Rico, L, Popov, A, Poussot, P, Previtali, E, Qi, F, Qi, M, Qi, X, Qian, S, Qian, X, Qian, Z, Qiao, H, Qin, Z, Qiu, S, Ranucci, G, Rasheed, R, Re, A, Rebii, A, Redchuk, M, Ren, B, Ren, J, Ricci, B, Rifai, M, Roche, M, Rodphai, N, Romani, A, Roskovec, B, Ruan, X, Rybnikov, A, Sadovsky, A, Saggese, P, Sandanayake, D, Sanfilippo, S, Sangka, A, Sawangwit, U, Schever, M, Schwab, C, Schweizer, K, Selyunin, A, Serafini, A, Settimo, M, Sharov, V, Shaydurova, A, Shi, J, Shi, Y, Shutov, V, Sidorenkov, A, Simkovic, F, Singhal, A, Sirignano, C, Siripak, J, Sisti, M, Smirnov, M, Smirnov, O, Sogo-Bezerra, T, Sokolov, S, Songwadhana, J, Soonthornthum, B, Sotnikov, A, Sramek, O, Sreethawong, W, Stahl, A, Stanco, L, Stankevich, K, Steiger, H, Steinmann, J, Sterr, T, Stock, M, Strati, V, Studenikin, A, Su, J, Sun, S, Sun, X, Sun, Y, Sun, Z, Suwonjandee, N, Szelezniak, M, Takenaka, A, Tang, J, Tang, Q, Tang, X, Hariharan, V, Theisen, E, Tietzsch, A, Tkachev, I, Tmej, T, Torri, M, Tortorici, F, Treskov, K, Triossi, A, Triozzi, R, Trzaska, W, Tung, Y, Tuve, C, Ushakov, N, Vedin, V, Verde, G, Vialkov, M, Viaud, B, Vollbrecht, C, von Sturm, K, Vorobel, V, Voronin, D, Votano, L, Walker, P, Wang, C, Wang, E, Wang, G, Wang, J, Wang, L, Wang, M, Wang, R, Wang, S, Wang, W, Wang, X, Wang, Y, Wang, Z, Watcharangkool, A, Wei, W, Wei, Y, Wen, K, Wen, L, Weng, J, Wiebusch, C, Wirth, R, Wonsak, B, Wu, D, Wu, Q, Wu, Y, Wu, Z, Wurm, M, Wurtz, J, Wysotzki, C, Xi, Y, Xia, D, Xiao, X, Xie, X, Xie, Y, Xie, Z, Xin, Z, Xing, Z, Xu, B, Xu, C, Xu, D, Xu, F, Xu, H, Xu, J, Xu, M, Xu, Y, Yan, B, Yan, Q, Yan, T, Yan, X, Yan, Y, Yang, C, Yang, J, Yang, L, Yang, X, Yang, Y, Yao, H, Ye, J, Ye, M, Ye, Z, Yermia, F, You, Z, Yu, B, Yu, C, Yu, G, Yu, H, Yu, M, Yu, X, Yu, Z, Yuan, C, Yuan, Y, Yuan, Z, Yue, B, Zafar, N, Zavadskyi, V, Zeng, S, Zeng, T, Zeng, Y, Zhan, L, Zhang, A, Zhang, B, Zhang, F, Zhang, H, Zhang, J, Zhang, M, Zhang, P, Zhang, Q, Zhang, S, Zhang, T, Zhang, X, Zhang, Y, Zhang, Z, Zhao, J, Zhao, R, Zhao, S, Zheng, D, Zheng, H, Zheng, Y, Zhong, W, Zhou, J, Zhou, L, Zhou, N, Zhou, S, Zhou, T, Zhou, X, Zhu, J, Zhu, K, Zhu, Z, Zhuang, B, Zhuang, H, Zong, L, Zou, J, Zufle, J, Zwickel, S, Abusleme A., Adam T., Ahmad S., Ahmed R., Aiello S., Akram M., Aleem A., Alexandros T., An F., An Q., Andronico G., Anfimov N., Antonelli V., Antoshkina T., Asavapibhop B., de Andre J. P. A. M., Auguste D., Bai W., Balashov N., Baldini W., Barresi A., Basilico D., Baussan E., Bellato M., Beretta M., Bergnoli A., Bick D., Bieger L., Biktemerova S., Birkenfeld T., Blum D., Blyth S., Bolshakova A., Bongrand M., Bordereau C., Breton D., Brigatti A., Brugnera R., Bruno R., Budano A., Busto J., Cabrera A., Caccianiga B., Cai H., Cai X., Cai Y., Cai Z., Callier S., Cammi A., Campeny A., Cao C., Cao G., Cao J., Caruso R., Cerna C., Cerrone V., Chan C., Chang J., Chang Y., Chen C., Chen G., Chen P., Chen S., Chen Y., Chen Z., Cheng J., Cheng Y., Cheng Y. C., Chepurnov A., Chetverikov A., Chiesa D., Chimenti P., Chu Z., Chukanov A., Claverie G., Clementi C., Clerbaux B., Molla M. C., Di Lorenzo S. C., Coppi A., Corti D., Csakli S., Dal Corso F., Dalager O., Datta J., De La Taille C., Deng Z., Depnering W., Ding X., Ding Y., Dirgantara B., Dittrich C., Dmitrievsky S., Dohnal T., Dolzhikov D., Donchenko G., Dong J., Doroshkevich E., Dou W., Dracos M., Druillole F., Du R., Du S., Dugas K., Dusini S., Duyang H., Eck J., Enqvist T., Fabbri A., Fahrendholz U., Fan L., Fang J., Fang W., Fargetta M., Fedoseev D., Fei Z., Feng L. -C., Feng Q., Ferraro F., Fournier A., Gan H., Gao F., Garfagnini A., Gavrikov A., Giammarchi M., Giudice N., Gonchar M., Gong G., Gong H., Gornushkin Y., Gottel A., Grassi M., Gromov M., Gromov V., Gu M., Gu X., Gu Y., Guan M., Guan Y., Guardone N., Guo C., Guo W., Guo X., Hagner C., Han R., Han Y., He M., He W., Heinz T., Hellmuth P., Heng Y., Herrera R., Hor Y., Hou S., Hsiung Y., Hu B. -Z., Hu H., Hu J., Hu S., Hu T., Hu Y., Hu Z., Huang G., Huang H., Huang J., Huang K., Huang W., Huang X., Huang Y., Hui J., Huo L., Huo W., Huss C., Hussain S., Imbert L., Ioannisian A., Isocrate R., Jelmini B., Jeria I., Ji X., Jia H., Jia J., Jian S., Jiang C., Jiang D., Jiang W., Jiang X., Jing X., Jollet C., Kampmann P., Kang L., Karaparambil R., Kazarian N., Khan A., Khatun A., Khosonthongkee K., Korablev D., Kouzakov K., Krasnoperov A., Kuleshov S., Kutovskiy N., Lachenmaier T., Landini C., Leblanc S., Lebrin V., Lefevre F., Lei R., Leitner R., Leung J., Li D., Li F., Li G., Li H., Li J., Li M., Li N., Li Q., Li R., Li S., Li T., Li W., Li X., Li Y., Li Z., Liang H., Liao J., Limphirat A., Lin G. -L., Lin S., Lin T., Ling J., Ling X., Lippi I., Liu C., Liu F., Liu H., Liu J., Liu M., Liu Q., Liu R., Liu S., Liu X., Liu Y., Liu Z., Lokhov A., Lombardi P., Lombardo C., Loo K., Lu C., Lu H., Lu J., Lu P., Lu S., Lubsandorzhiev B., Lubsandorzhiev S., Ludhova L., Lukanov A., Luo D., Luo F., Luo G., Luo J., Luo S., Luo W., Luo X., Lyashuk V., Ma B., Ma Q., Ma S., Ma X., Maalmi J., Magoni M., Mai J., Malyshkin Y., Mandujano R. C., Mantovani F., Mao X., Mao Y., Mari S. M., Marini F., Martini A., Mayer M., Mayilyan D., Mednieks I., Meng Y., Meraviglia A., Meregaglia A., Meroni E., Meyhofer D., Miramonti L., Mohan N., Montini P., Montuschi M., Muller A., Nastasi M., Naumov D. V., Naumova E., Navas-Nicolas D., Nemchenok I., Thi M. T. N., Nikolaev A., Ning F., Ning Z., Nunokawa H., Oberauer L., Ochoa-Ricoux J. P., Olshevskiy A., Orestano D., Ortica F., Othegraven R., Paoloni A., Parmeggiano S., Pei Y., Pelicci L., Peng A., Peng H., Peng Y., Peng Z., Perrot F., Petitjean P. -A., Petrucci F., Pilarczyk O., Rico L. F. P., Popov A., Poussot P., Previtali E., Qi F., Qi M., Qi X., Qian S., Qian X., Qian Z., Qiao H., Qin Z., Qiu S., Ranucci G., Rasheed R., Re A., Rebii A., Redchuk M., Ren B., Ren J., Ricci B., Rifai M., Roche M., Rodphai N., Romani A., Roskovec B., Ruan X., Rybnikov A., Sadovsky A., Saggese P., Sandanayake D., Sanfilippo S., Sangka A., Sawangwit U., Schever M., Schwab C., Schweizer K., Selyunin A., Serafini A., Settimo M., Sharov V., Shaydurova A., Shi J., Shi Y., Shutov V., Sidorenkov A., Simkovic F., Singhal A., Sirignano C., Siripak J., Sisti M., Smirnov M., Smirnov O., Sogo-Bezerra T., Sokolov S., Songwadhana J., Soonthornthum B., Sotnikov A., Sramek O., Sreethawong W., Stahl A., Stanco L., Stankevich K., Steiger H., Steinmann J., Sterr T., Stock M. R., Strati V., Studenikin A., Su J., Sun S., Sun X., Sun Y., Sun Z., Suwonjandee N., Szelezniak M., Takenaka A., Tang J., Tang Q., Tang X., Hariharan V. T., Theisen E., Tietzsch A., Tkachev I., Tmej T., Torri M. D. C., Tortorici F., Treskov K., Triossi A., Triozzi R., Trzaska W., Tung Y. -C., Tuve C., Ushakov N., Vedin V., Verde G., Vialkov M., Viaud B., Vollbrecht C. M., von Sturm K., Vorobel V., Voronin D., Votano L., Walker P., Wang C., Wang C. -H., Wang E., Wang G., Wang J., Wang L., Wang M., Wang R., Wang S., Wang W., Wang X., Wang Y., Wang Z., Watcharangkool A., Wei W., Wei Y., Wen K., Wen L., Weng J., Wiebusch C., Wirth R., Wonsak B., Wu D., Wu Q., Wu Y., Wu Z., Wurm M., Wurtz J., Wysotzki C., Xi Y., Xia D., Xiao X., Xie X., Xie Y., Xie Z., Xin Z., Xing Z., Xu B., Xu C., Xu D., Xu F., Xu H., Xu J., Xu M., Xu Y., Yan B., Yan Q., Yan T., Yan X., Yan Y., Yang C., Yang J., Yang L., Yang X., Yang Y., Yao H., Ye J., Ye M., Ye Z., Yermia F., You Z., Yu B., Yu C., Yu G., Yu H., Yu M., Yu X., Yu Z., Yuan C., Yuan Y., Yuan Z., Yue B., Zafar N., Zavadskyi V., Zeng S., Zeng T., Zeng Y., Zhan L., Zhang A., Zhang B., Zhang F., Zhang H., Zhang J., Zhang M., Zhang P., Zhang Q., Zhang S., Zhang T., Zhang X., Zhang Y., Zhang Z., Zhao J., Zhao R., Zhao S., Zheng D., Zheng H., Zheng Y., Zhong W., Zhou J., Zhou L., Zhou N., Zhou S., Zhou T., Zhou X., Zhu J., Zhu 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P. A. M., Auguste D., Bai W., Balashov N., Baldini W., Barresi A., Basilico D., Baussan E., Bellato M., Beretta M., Bergnoli A., Bick D., Bieger L., Biktemerova S., Birkenfeld T., Blum D., Blyth S., Bolshakova A., Bongrand M., Bordereau C., Breton D., Brigatti A., Brugnera R., Bruno R., Budano A., Busto J., Cabrera A., Caccianiga B., Cai H., Cai X., Cai Y., Cai Z., Callier S., Cammi A., Campeny A., Cao C., Cao G., Cao J., Caruso R., Cerna C., Cerrone V., Chan C., Chang J., Chang Y., Chen C., Chen G., Chen P., Chen S., Chen Y., Chen Z., Cheng J., Cheng Y., Cheng Y. C., Chepurnov A., Chetverikov A., Chiesa D., Chimenti P., Chu Z., Chukanov A., Claverie G., Clementi C., Clerbaux B., Molla M. C., Di Lorenzo S. 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C., Mantovani F., Mao X., Mao Y., Mari S. M., Marini F., Martini A., Mayer M., Mayilyan D., Mednieks I., Meng Y., Meraviglia A., Meregaglia A., Meroni E., Meyhofer D., Miramonti L., Mohan N., Montini P., Montuschi M., Muller A., Nastasi M., Naumov D. V., Naumova E., Navas-Nicolas D., Nemchenok I., Thi M. T. N., Nikolaev A., Ning F., Ning Z., Nunokawa H., Oberauer L., Ochoa-Ricoux J. P., Olshevskiy A., Orestano D., Ortica F., Othegraven R., Paoloni A., Parmeggiano S., Pei Y., Pelicci L., Peng A., Peng H., Peng Y., Peng Z., Perrot F., Petitjean P. -A., Petrucci F., Pilarczyk O., Rico L. F. 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Abstract

The Jiangmen Underground Neutrino Observatory (JUNO), the first multi-kton liquid scintillator detector, which is under construction in China, will have a unique potential to perform a real-time measurement of solar neutrinos well below the few MeV threshold typical of Water Cherenkov detectors. JUNO’s large target mass and excellent energy resolution are prerequisites for reaching unprecedented levels of precision. In this paper, we provide estimation of the JUNO sensitivity to 7Be, pep, and CNO solar neutrinos that can be obtained via a spectral analysis above the 0.45 MeV threshold. This study is performed assuming different scenarios of the liquid scintillator radiopurity, ranging from the most optimistic one corresponding to the radiopurity levels obtained by the Borexino experiment, up to the minimum requirements needed to perform the neutrino mass ordering determination with reactor antineutrinos — the main goal of JUNO. Our study shows that in most scenarios, JUNO will be able to improve the current best measurements on 7Be, pep, and CNO solar neutrino fluxes. We also perform a study on the JUNO capability to detect periodical time variations in the solar neutrino flux, such as the day-night modulation induced by neutrino flavor regeneration in Earth, and the modulations induced by temperature changes driven by helioseismic waves.

Published
2023

33. Triplicate PCR reactions for 16S rRNA gene amplicon sequencing are unnecessary

Author

Clarisse Marotz, Anukriti Sharma, Greg Humphrey, Neil Gottel, Christopher Daum, Jack A Gilbert, Emiley Eloe-Fadrosh, and Rob Knight

Subjects
16S rRNA gene amplicon sequencing, microbiome, PCR, replicate PCR reactions, Biology (General), QH301-705.5
Abstract

Conventional wisdom holds that PCR amplification for sequencing should employ pooled replicate reactions to reduce bias due to jackpot effects and chimera formation. However, modern amplicon data analysis employs methods that may be less sensitive to such artifacts. Here we directly compare results from single versus triplicate reactions for 16S amplicon sequencing and find no significant impact of adopting a less labor-intensive single-reaction protocol.

Published
2019
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34. Concurrent measurement of microbiome and allergens in the air of bedrooms of allergy disease patients in the Chicago area

Author

Miles Richardson, Neil Gottel, Jack A. Gilbert, Julian Gordon, Prasanthi Gandhi, Rachel Reboulet, and Jarrad T. Hampton-Marcell

Subjects
Microbial ecology, QR100-130
Abstract

Abstract The particulate and biological components of indoor air have a substantial impact on human health, especially immune respiratory conditions such as asthma. To better explore the relationship between allergens, the microbial community, and the indoor living environment, we sampled the bedrooms of 65 homes in the Chicago area using 23the patient-friendly Inspirotec electrokinetic air sampling device, which collects airborne particles for characterization of both allergens and microbial DNA. The sampling device captured sufficient microbial material to enable 16S rRNA amplicon sequencing data to be generated for every sample in the study. Neither the presence of HEPA filters nor the height at which the air sampling device was placed had any influence on the microbial community profile. A core microbiota of 31 OTUs was present in more than three quarters of the samples, comprising around 45% of the relative sequence counts in each bedroom. The most abundant single organisms were Staphylococcus, with other core taxa both human and outdoor-associated. Bacterial alpha diversity was significantly increased in bedrooms that reported having open windows, those with flowering plants in the vicinity, and those in homes occupied by dogs. Porphyromonas, Moraxella, Sutterella, and Clostridium, along with family Neisseraceae, were significantly enriched in homes with dogs; interestingly, cats did not show a significant impact on microbial diversity or relative abundance. While dog allergen load was significantly correlated with bacterial alpha diversity, the taxa that significantly correlated with allergen burden did not exclusively overlap with those enriched in homes with dogs. Alternaria allergen load was positively correlated with bacterial alpha diversity, while Aspergillus allergen load was negatively correlated. The Alternaria allergen load was also significantly correlated with open windows. Microbial communities were significantly differentiated between rural, suburban, and urban homes and houses that were physically closer to each other maintained significantly more similar microbiota. We have demonstrated that it is possible to determine significant associations between allergen burden and the microbiota in air from the same sample and that these associations relate to the characteristics of the home and neighborhoods.

Published
2019
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35. Microbial and metabolic succession on common building materials under high humidity conditions

Author

Simon Lax, Cesar Cardona, Dan Zhao, Valerie J. Winton, Gabriel Goodney, Peng Gao, Neil Gottel, Erica M. Hartmann, Chris Henry, Paul M. Thomas, Scott T. Kelley, Brent Stephens, and Jack A. Gilbert

Subjects
Science
Abstract

Microbes inhabit built environments and could contribute to degradation of surfaces especially in damp conditions. Here the authors explore how communities of microbes and their metabolites affect four types of built surfaces under varying environmental conditions.

Published
2019
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36. Children with Autism and Their Typically Developing Siblings Differ in Amplicon Sequence Variants and Predicted Functions of Stool-Associated Microbes

Author

Maude M. David, Christine Tataru, Jena Daniels, Jessey Schwartz, Jessica Keating, Jarrad Hampton-Marcell, Neil Gottel, Jack A. Gilbert, and Dennis P. Wall

Subjects
autism spectrum disorder, microbiome, crowdsource, 16S rRNA gene sequencing, Clostridiales, Lachnospiraceae, Microbiology, QR1-502
Abstract

ABSTRACT The existence of a link between the gut microbiome and autism spectrum disorder (ASD) is well established in mice, but in human populations, efforts to identify microbial biomarkers have been limited due to a lack of appropriately matched controls, stratification of participants within the autism spectrum, and sample size. To overcome these limitations, we crowdsourced the recruitment of families with age-matched sibling pairs between 2 and 7 years old (within 2 years of each other), where one child had a diagnosis of ASD and the other did not. Parents collected stool samples, provided a home video of their ASD child’s natural social behavior, and responded online to diet and behavioral questionnaires. 16S rRNA V4 amplicon sequencing of 117 samples (60 ASD and 57 controls) identified 21 amplicon sequence variants (ASVs) that differed significantly between the two cohorts: 11 were found to be enriched in neurotypical children (six ASVs belonging to the Lachnospiraceae family), while 10 were enriched in children with ASD (including Ruminococcaceae and Bacteroidaceae families). Summarizing the expected KEGG orthologs of each predicted genome, the taxonomic biomarkers associated with children with ASD can use amino acids as precursors for butyragenic pathways, potentially altering the availability of neurotransmitters like glutamate and gamma aminobutyric acid (GABA). IMPORTANCE Autism spectrum disorder (ASD), which now affects 1 in 54 children in the United States, is known to have comorbidity with gut disorders of a variety of types; however, the link to the microbiome remains poorly characterized. Recent work has provided compelling evidence to link the gut microbiome to the autism phenotype in mouse models, but identification of specific taxa associated with autism has suffered replicability issues in humans. This has been due in part to sample size that sufficiently covers the spectrum of phenotypes known to autism (which range from subtle to severe) and a lack of appropriately matched controls. Our original study proposes to overcome these limitations by collecting stool-associated microbiome on 60 sibling pairs of children, one with autism and one neurotypically developing, both 2 to 7 years old and no more than 2 years apart in age. We use exact sequence variant analysis and both permutation and differential abundance procedures to identify 21 taxa with significant enrichment or depletion in the autism cohort compared to their matched sibling controls. Several of these 21 biomarkers have been identified in previous smaller studies; however, some are new to autism and known to be important in gut-brain interactions and/or are associated with specific fatty acid biosynthesis pathways.

Published
2021
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37. Effects of Extended Postmortem Interval on Microbial Communities in Organs of the Human Cadaver

Author

Holly Lutz, Alexandria Vangelatos, Neil Gottel, Antonio Osculati, Silvia Visona, Sheree J. Finley, Jack A. Gilbert, and Gulnaz T. Javan

Subjects
thanatomicrobiome, cadaver, 16S rRNA, internal organs, manner of death, Microbiology, QR1-502
Abstract

Human thanatomicrobiota studies have shown that microorganisms inhabit and proliferate externally and internally throughout the body and are the primary mediators of putrefaction after death. Yet little is known about the source and diversity of the thanatomicrobiome or the underlying factors leading to delayed decomposition exhibited by reproductive organs. The use of the V4 hypervariable region of bacterial 16S rRNA gene sequences for taxonomic classification (“barcoding”) and phylogenetic analyses of human postmortem microbiota has recently emerged as a possible tool in forensic microbiology. The goal of this study was to apply a 16S rRNA barcoding approach to investigate variation among different organs, as well as the extent to which microbial associations among different body organs in human cadavers can be used to predict forensically important determinations, such as cause and time of death. We assessed microbiota of organ tissues including brain, heart, liver, spleen, prostate, and uterus collected at autopsy from criminal casework of 40 Italian cadavers with times of death ranging from 24 to 432 h. Both the uterus and prostate had a significantly higher alpha diversity compared to other anatomical sites, and exhibited a significantly different microbial community composition from non-reproductive organs, which we found to be dominated by the bacterial orders MLE1-12, Saprospirales, and Burkholderiales. In contrast, reproductive organs were dominated by Clostridiales, Lactobacillales, and showed a marked decrease in relative abundance of MLE1-12. These results provide insight into the observation that the uterus and prostate are the last internal organs to decay during human decomposition. We conclude that distinct community profiles of reproductive versus non-reproductive organs may help guide the application of forensic microbiology tools to investigations of human cadavers.

Published
2020
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38. Spatial Compartmentalization of the Microbiome between the Lumen and Crypts Is Lost in the Murine Cecum following the Process of Surgery, Including Overnight Fasting and Exposure to Antibiotics

Author

Alexander Zaborin, Beatriz Penalver Bernabe, Robert Keskey, Naseer Sangwan, Sanjiv Hyoju, Neil Gottel, Jack A. Gilbert, Olga Zaborina, and John C. Alverdy

Subjects
16S rRNA, butyrate, cecal crypts, hypoxia gradient, Mucispirillum schaedleri, murine cecum microbiome, Microbiology, QR1-502
Abstract

ABSTRACT The cecum is a unique region in the mammalian intestinal tract in which the microbiome is localized to two compartments, the lumen and the crypts. The microbiome within crypts is particularly important as it is in direct contact with lining epithelial cells including stem cells. Here, we analyzed the microbiome in cecum of mice using multiple techniques including metagenomics. The lumen microbiome comprised Firmicutes and Bacteroidetes whereas the crypts were dominated by Proteobacteria and Deferribacteres, and the mucus comprised a mixture of these 4 phyla. The lumen microbial functional potential comprised mainly carbon metabolism, while the crypt microbiome was enriched for genes encoding stress resistance. In order to determine how this structure, assembly, and function are altered under provocative conditions, we exposed mice to overnight starvation (S), antibiotics (A), and a major surgical injury (partial hepatectomy [H]), as occurs with major surgery in humans. We have previously demonstrated that the combined effect of this “SAH” treatment leads to a major disturbance of the cecal microbiota at the bottom of crypts in a manner that disrupts crypt cell homeostasis. Here, we applied the SAH conditions and observed a loss of compartmentalization in both composition and function of the cecal microbiome associated with major shifts in local physicochemical cues including decrease of hypoxia, increase of pH, and loss of butyrate production. Taken together, these studies demonstrated a defined order, structure, and function of the cecal microbiome that can be disrupted under provocative conditions such as major surgery and its attendant exposures. IMPORTANCE The proximal colon and cecum are two intestinal regions in which the microbiome localizes to two spatially distinct compartments, the lumen and crypts. The differences in composition and function of luminal and crypt microbiome in the cecum and the effect of physiological stress on their compartmentalization remain poorly characterized. Here, we characterized the composition and function of the lumen-, mucus-, and crypt-associated microbiome in the cecum of mice. We observed a highly ordered microbial architecture within the cecum whose assembly and function become markedly disrupted when provoked by physiological stress such as surgery and its attendant preoperative treatments (i.e., overnight fasting and antibiotics). Major shifts in local physicochemical cues including a decrease in hypoxia levels, an increase in pH, and a loss of butyrate production were associated with the loss of compositional and functional compartmentalization of the cecal microbiome.

Published
2020
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39. Microbiome profile associated with malignant pleural effusion.

Author

Samira Shojaee, Anukriti Sharma, Neil Gottel, Trinidad Sanchez, Jack A Gilbert, and Najib M Rahman

Subjects
Medicine, Science
Abstract

IntroductionThere is ongoing research into the development of novel molecular markers that may complement fluid cytology malignant pleural effusion (MPE) diagnosis. In this exploratory pilot study, we hypothesized that there are distinct differences in the pleural fluid microbiome profile of malignant and non-malignant pleural diseases.MethodFrom a prospectively enrolled pleural fluid biorepository, samples of MPE were included. Non-MPE effusion were included as comparators. 16S rRNA gene V4 region amplicon sequencing was performed. Exact Sequence Variants (ESVs) were used for diversity analyses. The Shannon and Richness indices of alpha diversity and UniFrac beta diversity measures were tested for significance using permutational multivariate analysis of variance. Analyses of Composition of Microbiome was used to identify differentially abundant bacterial ESVs between the groups controlled for multiple hypothesis testing.Results38 patients with MPE and 9 with non-MPE were included. A subgroup of patients with metastatic adenocarcinoma histology were identified among MPE group (adenocarcinoma of lung origin (LA-MPE) = 11, breast origin (BA-MPE) = 11). MPE presented with significantly greater alpha diversity compared to non-MPE group. Within the MPE group, BA-MPE was more diverse compared to LA-MPE group. In multivariable analysis, ESVs belonging to family S24-7 and genera Allobaculum, Stenotrophomonas, and Epulopiscium were significantly enriched in the malignant group compared to the non-malignant group.ConclusionOur results are the first to demonstrate a microbiome signature according to MPE and non-MPE. The role of microbiome in pleural effusion pathogenesis needs further exploration.

Published
2020
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40. Sub-percent precision measurement of neutrino oscillation parameters with JUNO

Author

Abusleme, A, Adam, T, Ahmad, S, Ahmed, R, Aiello, S, Akram, M, Aleem, A, An, F, An, Q, Andronico, G, Anfimov, N, Antonelli, V, Antoshkina, T, Asavapibhop, B, de Andre, J, Auguste, D, Bai, W, Balashov, N, Baldini, W, Barresi, A, Basilico, D, Baussan, E, Bellato, M, Bergnoli, A, Birkenfeld, T, Blin, S, Blum, D, Blyth, S, Bolshakova, A, Bongrand, M, Bordereau, C, Breton, D, Brigatti, A, Brugnera, R, Bruno, R, Budano, A, Busto, J, Butorov, I, Cabrera, A, Caccianiga, B, Cai, H, Cai, X, Cai, Y, Cai, Z, Callegari, R, Cammi, A, Campeny, A, Cao, C, Cao, G, Cao, J, Caruso, R, Cerna, C, Chan, C, Chang, J, Chang, Y, Chen, G, Chen, P, Chen, S, Chen, X, Chen, Y, Chen, Z, Cheng, J, Cheng, Y, Chin Cheng, Y, Chetverikov, A, Chiesa, D, Chimenti, P, Chukanov, A, Claverie, G, Clementi, C, Clerbaux, B, Conforti Di Lorenzo, S, Corti, D, Dal Corso, F, Dalager, O, De La Taille, C, Deng, Z, Depnering, W, Diaz, M, Ding, X, Ding, Y, Dirgantara, B, Dmitrievsky, S, Dohnal, T, Dolzhikov, D, Donchenko, G, Dong, J, Doroshkevich, E, Dracos, M, Druillole, F, Du, R, Du, S, Dusini, S, Dvorak, M, Enqvist, T, Enzmann, H, Fabbri, A, Fan, D, Fan, L, Fang, J, Fang, W, Fargetta, M, Fedoseev, D, Fei, Z, Feng, L, Feng, Q, Ford, R, Fournier, A, Gan, H, Gao, F, Garfagnini, A, Gavrikov, A, Giammarchi, M, Giudice, N, Gonchar, M, Gong, G, Gong, H, Gornushkin, Y, Gottel, A, Grassi, M, Gromov, V, Gu, M, Gu, X, Gu, Y, Guan, M, Guan, Y, Guardone, N, Guo, C, Guo, J, Guo, W, Guo, X, Guo, Y, Hackspacher, P, Hagner, C, Han, R, Han, Y, He, M, He, W, Heinz, T, Hellmuth, P, Heng, Y, Herrera, R, Hor, Y, Hou, S, Hsiung, Y, Hu, B, Hu, H, Hu, J, Hu, S, Hu, T, Hu, Y, Hu, Z, Huang, G, Huang, H, Huang, K, Huang, W, Huang, X, Huang, Y, Hui, J, Huo, L, Huo, W, Huss, C, Hussain, S, Ioannisian, A, Isocrate, R, Jelmini, B, Jeria, I, Ji, X, Jia, H, Jia, J, Jian, S, Jiang, D, Jiang, W, Jiang, X, Jing, X, Jollet, C, Joutsenvaara, J, Kalousis, L, Kampmann, P, Kang, L, Karaparambil, R, Kazarian, N, Khatun, A, Khosonthongkee, K, Korablev, D, Kouzakov, K, Krasnoperov, A, Kutovskiy, N, Kuusiniemi, P, Lachenmaier, T, Landini, C, Leblanc, S, Lebrin, V, Lefevre, F, Lei, R, Leitner, R, Leung, J, Li, D, Li, F, Li, G, Li, H, Li, M, Li, N, Li, Q, Li, R, Li, S, Li, T, Li, W, Li, X, Li, Y, Li, Z, Liang, H, Liao, J, Limphirat, A, Lin, G, Lin, S, Lin, T, Ling, J, Lippi, I, Liu, F, Liu, H, Liu, J, Liu, M, Liu, Q, Liu, R, Liu, S, Liu, X, Liu, Y, Lokhov, A, Lombardi, P, Lombardo, C, Loo, K, Lu, C, Lu, H, Lu, J, Lu, S, Lubsandorzhiev, B, Lubsandorzhiev, S, Ludhova, L, Lukanov, A, Luo, D, Luo, F, Luo, G, Luo, S, Luo, W, Luo, X, Lyashuk, V, Ma, B, Ma, Q, Ma, S, Ma, X, Maalmi, J, Mai, J, Malyshkin, Y, Carlos Mandujano, R, Mantovani, F, Manzali, F, Mao, X, Mao, Y, Mari, S, Marini, F, Martellini, C, Martin-Chassard, G, Martini, A, Mayer, M, Mayilyan, D, Mednieks, I, Meinusch, A, Meng, Y, Meregaglia, A, Meroni, E, Meyho, D, Mezzetto, M, Miller, J, Miramonti, L, Colomer Molla, M, Montini, P, Montuschi, M, Muller, A, Nastasi, M, Naumov, D, Naumova, E, Navas-Nicolas, D, Nemchenok, I, Thuan Nguyen Thi, M, Ning, F, Ning, Z, Nunokawa, H, Oberauer, L, Pedro Ochoa-Ricoux, J, Olshevskiy, A, Orestano, D, Ortica, F, Othegraven, R, Paoloni, A, Parmeggiano, S, Pei, Y, Pelicci, L, Pelliccia, N, Peng, A, Peng, H, Peng, Y, Peng, Z, Perrot, F, Petitjean, P, Petrucci, F, Pilarczyk, O, Felipe Pineres, L, Popov, A, Poussot, P, Previtali, E, Qi, F, Qi, M, Qian, S, Qian, X, Qian, Z, Qiao, H, Qin, Z, Qiu, S, Ranucci, G, Raper, N, Rasheed, R, Re, A, Rebber, H, Rebii, A, Redchuk, M, Ren, B, Ren, J, Ricci, B, Rifai, M, Roche, M, Rodphai, N, Romani, A, Roskovec, B, Ruan, X, Rybnikov, A, Sadovsky, A, Saggese, P, Sanfilippo, S, Sangka, A, Sawangwit, U, Sawatzki, J, Schever, M, Schwab, C, Schweizer, K, Selyunin, A, Serafini, A, Settanta, G, Settimo, M, Shao, Z, Sharov, V, Shaydurova, A, Shi, J, Shi, Y, Shutov, V, Sidorenkov, A, Simkovic, F, Sirignano, C, Siripak, J, Sisti, M, Slupecki, M, Smirnov, M, Smirnov, O, Sogo-Bezerra, T, Sokolov, S, Songwadhana, J, Soonthornthum, B, Sotnikov, A, Sramek, O, Sreethawong, W, Stahl, A, Stanco, L, Stankevich, K, Stefanik, D, Steiger, H, Steinmann, J, Sterr, T, Raphael Stock, M, Strati, V, Studenikin, A, Su, J, Sun, S, Sun, X, Sun, Y, Sun, Z, Suwonjandee, N, Szelezniak, M, Tang, J, Tang, Q, Tang, X, Thara Hariharan, V, Theisen, E, Tietzsch, A, Tkachev, I, Tmej, T, Danilo Claudio Torri, M, Treskov, K, Triossi, A, Troni, G, Trzaska, W, Tsagkarakis, A, Tuve, C, Ushakov, N, Vedin, V, Verde, G, Vialkov, M, Viaud, B, Moritz Vollbrecht, C, Volpe, C, Von Sturm, K, Vorobel, V, Voronin, D, Votano, L, Walker, P, Wang, C, Wang, E, Wang, G, Wang, J, Wang, L, Wang, M, Wang, R, Wang, S, Wang, W, Wang, X, Wang, Y, Wang, Z, Watcharangkool, A, Wei, W, Wei, Y, Wen, K, Wen, L, Wiebusch, C, Chan-Fai Wong, S, Wonsak, B, Wu, D, Wu, Q, Wu, Z, Wurm, M, Wurtz, J, Wysotzki, C, Xi, Y, Xia, D, Xiao, X, Xie, X, Xie, Y, Xie, Z, Xin, Z, Xing, Z, Xu, B, Xu, C, Xu, D, Xu, F, Xu, H, Xu, J, Xu, M, Xu, Y, Yan, B, Yan, T, Yan, W, Yan, X, Yan, Y, Yang, C, Yang, H, Yang, J, Yang, L, Yang, X, Yang, Y, Yao, H, Ye, J, Ye, M, Ye, Z, Yermia, F, Yin, N, You, Z, Yu, B, Yu, C, Yu, H, Yu, M, Yu, X, Yu, Z, Yuan, C, Yuan, Y, Yuan, Z, Yue, B, Zafar, N, Zavadskyi, V, Zeng, S, Zeng, T, Zeng, Y, Zhan, L, Zhang, A, Zhang, B, Zhang, F, Zhang, G, Zhang, H, Zhang, J, Zhang, M, Zhang, P, Zhang, Q, Zhang, S, Zhang, T, Zhang, X, Zhang, Y, Zhang, Z, Zhao, F, Zhao, J, Zhao, R, Zhao, S, Zheng, D, Zheng, H, Zheng, Y, Zhong, W, Zhou, J, Zhou, L, Zhou, N, Zhou, S, Zhou, T, Zhou, X, Zhu, J, Zhu, K, Zhu, Z, Zhuang, B, Zhuang, H, Zong, L, Zou, J, Abusleme A., Adam T., Ahmad S., Ahmed R., Aiello S., Akram M., Aleem A., An F., An Q., Andronico G., Anfimov N., Antonelli V., Antoshkina T., Asavapibhop B., de Andre J. P. A. M., Auguste D., Bai W., Balashov N., Baldini W., Barresi A., Basilico D., Baussan E., Bellato M., Bergnoli A., Birkenfeld T., Blin S., Blum D., Blyth S., Bolshakova A., Bongrand M., Bordereau C., Breton D., Brigatti A., Brugnera R., Bruno R., Budano A., Busto J., Butorov I., Cabrera A., Caccianiga B., Cai H., Cai X., Cai Y., Cai Z., Callegari R., Cammi A., Campeny A., Cao C., Cao G., Cao J., Caruso R., Cerna C., Chan C., Chang J., Chang Y., Chen G., Chen P., Chen P. -A., Chen S., Chen X., Chen Y., Chen Z., Cheng J., Cheng Y., Chin Cheng Y., Chetverikov A., Chiesa D., Chimenti P., Chukanov A., Claverie G., Clementi C., Clerbaux B., Conforti Di Lorenzo S., Corti D., Dal Corso F., Dalager O., De La Taille C., Deng Z., Depnering W., Diaz M., Ding X., Ding Y., Dirgantara B., Dmitrievsky S., Dohnal T., Dolzhikov D., Donchenko G., Dong J., Doroshkevich E., Dracos M., Druillole F., Du R., Du S., Dusini S., Dvorak M., Enqvist T., Enzmann H., Fabbri A., Fan D., Fan L., Fang J., Fang W., Fargetta M., Fedoseev D., Fei Z., Feng L. -C., Feng Q., Ford R., Fournier A., Gan H., Gao F., Garfagnini A., Gavrikov A., Giammarchi M., Giudice N., Gonchar M., Gong G., Gong H., Gornushkin Y., Gottel A., Grassi M., Gromov V., Gu M., Gu X., Gu Y., Guan M., Guan Y., Guardone N., Guo C., Guo J., Guo W., Guo X., Guo Y., Hackspacher P., Hagner C., Han R., Han Y., He M., He W., Heinz T., Hellmuth P., Heng Y., Herrera R., Hor Y., Hou S., Hsiung Y., Hu B. -Z., Hu H., Hu J., Hu S., Hu T., Hu Y., Hu Z., Huang G., Huang H., Huang K., Huang W., Huang X., Huang Y., Hui J., Huo L., Huo W., Huss C., Hussain S., Ioannisian A., Isocrate R., Jelmini B., Jeria I., Ji X., Jia H., Jia J., Jian S., Jiang D., Jiang W., Jiang X., Jing X., Jollet C., Joutsenvaara J., Kalousis L., Kampmann P., Kang L., Karaparambil R., Kazarian N., Khatun A., Khosonthongkee K., Korablev D., Kouzakov K., Krasnoperov A., Kutovskiy N., Kuusiniemi P., Lachenmaier T., Landini C., Leblanc S., Lebrin V., Lefevre F., Lei R., Leitner R., Leung J., Li D., Li F., Li G., Li H., Li M., Li N., Li Q., Li R., Li S., Li T., Li W., Li X., Li Y., Li Z., Liang H., Liao J., Limphirat A., Lin G. -L., Lin S., Lin T., Ling J., Lippi I., Liu F., Liu H., Liu J., Liu M., Liu Q., Liu R., Liu S., Liu X., Liu Y., Lokhov A., Lombardi P., Lombardo C., Loo K., Lu C., Lu H., Lu J., Lu S., Lubsandorzhiev B., Lubsandorzhiev S., Ludhova L., Lukanov A., Luo D., Luo F., Luo G., Luo S., Luo W., Luo X., Lyashuk V., Ma B., Ma Q., Ma S., Ma X., Maalmi J., Mai J., Malyshkin Y., Carlos Mandujano R., Mantovani F., Manzali F., Mao X., Mao Y., Mari S. M., Marini F., Martellini C., Martin-Chassard G., Martini A., Mayer M., Mayilyan D., Mednieks I., Meinusch A., Meng Y., Meregaglia A., Meroni E., Meyho D., Mezzetto M., Miller J., Miramonti L., Colomer Molla M., Montini P., Montuschi M., Muller A., Nastasi M., Naumov D. V., Naumova E., Navas-Nicolas D., Nemchenok I., Thuan Nguyen Thi M., Ning F., Ning Z., Nunokawa H., Oberauer L., Pedro Ochoa-Ricoux J., Olshevskiy A., Orestano D., Ortica F., Othegraven R., Paoloni A., Parmeggiano S., Pei Y., Pelicci L., Pelliccia N., Peng A., Peng H., Peng Y., Peng Z., Perrot F., Petitjean P. -A., Petrucci F., Pilarczyk O., Felipe Pineres L., Popov A., Poussot P., Previtali E., Qi F., Qi M., Qian S., Qian X., Qian Z., Qiao H., Qin Z., Qiu S., Ranucci G., Raper N., Rasheed R., Re A., Rebber H., Rebii A., Redchuk M., Ren B., Ren J., Ricci B., Rifai M., Roche M., Rodphai N., Romani A., Roskovec B., Ruan X., Rybnikov A., Sadovsky A., Saggese P., Sanfilippo S., Sangka A., Sawangwit U., Sawatzki J., Schever M., Schwab C., Schweizer K., Selyunin A., Serafini A., Settanta G., Settimo M., Shao Z., Sharov V., Shaydurova A., Shi J., Shi Y., Shutov V., Sidorenkov A., Simkovic F., Sirignano C., Siripak J., Sisti M., Slupecki M., Smirnov M., Smirnov O., Sogo-Bezerra T., Sokolov S., Songwadhana J., Soonthornthum B., Sotnikov A., Sramek O., Sreethawong W., Stahl A., Stanco L., Stankevich K., Stefanik D., Steiger H., Steinmann J., Sterr T., Raphael Stock M., Strati V., Studenikin A., Su J., Sun S., Sun X., Sun Y., Sun Z., Suwonjandee N., Szelezniak M., Tang J., Tang Q., Tang X., Thara Hariharan V., Theisen E., Tietzsch A., Tkachev I., Tmej T., Danilo Claudio Torri M., Treskov K., Triossi A., Troni G., Trzaska W., Tsagkarakis A., Tuve C., Ushakov N., Vedin V., Verde G., Vialkov M., Viaud B., Moritz Vollbrecht C., Volpe C., Von Sturm K., Vorobel V., Voronin D., Votano L., Walker P., Wang C., Wang C. -H., Wang E., Wang G., Wang J., Wang L., Wang M., Wang R., Wang S., Wang W., Wang X., Wang Y., Wang Z., Watcharangkool A., Wei W., Wei Y., Wen K., Wen L., Wiebusch C., Chan-Fai Wong S., Wonsak B., Wu D., Wu Q., Wu Z., Wurm M., Wurtz J., Wysotzki C., Xi Y., Xia D., Xiao X., Xie X., Xie Y., Xie Z., Xin Z., Xing Z., Xu B., Xu C., Xu D., Xu F., Xu H., Xu J., Xu M., Xu Y., Yan B., Yan T., Yan W., Yan X., Yan Y., Yang C., Yang H., Yang J., Yang L., Yang X., Yang Y., Yao H., Ye J., Ye M., Ye Z., Yermia F., Yin N., You Z., Yu B., Yu C., Yu H., Yu M., Yu X., Yu Z., Yuan C., Yuan Y., Yuan Z., Yue B., Zafar N., Zavadskyi V., Zeng S., Zeng T., Zeng Y., Zhan L., Zhang A., Zhang B., Zhang F., Zhang G., Zhang H., Zhang J., Zhang M., Zhang P., Zhang Q., Zhang S., Zhang T., Zhang X., Zhang Y., Zhang Z., Zhao F., Zhao J., Zhao R., Zhao S., Zheng D., Zheng H., Zheng Y., Zhong W., Zhou J., Zhou L., Zhou N., Zhou S., Zhou T., Zhou X., Zhu J., Zhu K., Zhu Z., Zhuang B., Zhuang H., Zong L., Zou J., Abusleme, A, Adam, T, Ahmad, S, Ahmed, R, Aiello, S, Akram, M, Aleem, A, An, F, An, Q, Andronico, G, Anfimov, N, Antonelli, V, Antoshkina, T, Asavapibhop, B, de Andre, J, Auguste, D, Bai, W, Balashov, N, Baldini, W, Barresi, A, Basilico, D, Baussan, E, Bellato, M, Bergnoli, A, Birkenfeld, T, Blin, S, Blum, D, Blyth, S, Bolshakova, A, Bongrand, M, Bordereau, C, Breton, D, Brigatti, A, Brugnera, R, Bruno, R, Budano, A, Busto, J, Butorov, I, Cabrera, A, Caccianiga, B, Cai, H, Cai, X, Cai, Y, Cai, Z, Callegari, R, Cammi, A, Campeny, A, Cao, C, Cao, G, Cao, J, Caruso, R, Cerna, C, Chan, C, Chang, J, Chang, Y, Chen, G, Chen, P, Chen, S, Chen, X, Chen, Y, Chen, Z, Cheng, J, Cheng, Y, Chin Cheng, Y, Chetverikov, A, Chiesa, D, Chimenti, P, Chukanov, A, Claverie, G, Clementi, C, Clerbaux, B, Conforti Di Lorenzo, S, Corti, D, Dal Corso, F, Dalager, O, De La Taille, C, Deng, Z, Depnering, W, Diaz, M, Ding, X, Ding, Y, Dirgantara, B, Dmitrievsky, S, Dohnal, T, Dolzhikov, D, Donchenko, G, Dong, J, Doroshkevich, E, Dracos, M, Druillole, F, Du, R, Du, S, Dusini, S, Dvorak, M, Enqvist, T, Enzmann, H, Fabbri, A, Fan, D, Fan, L, Fang, J, Fang, W, Fargetta, M, Fedoseev, D, Fei, Z, Feng, L, Feng, Q, Ford, R, Fournier, A, Gan, H, Gao, F, Garfagnini, A, Gavrikov, A, Giammarchi, M, Giudice, N, Gonchar, M, Gong, G, Gong, H, Gornushkin, Y, Gottel, A, Grassi, M, Gromov, V, Gu, M, Gu, X, Gu, Y, Guan, M, Guan, Y, Guardone, N, Guo, C, Guo, J, Guo, W, Guo, X, Guo, Y, Hackspacher, P, Hagner, C, Han, R, Han, Y, He, M, He, W, Heinz, T, Hellmuth, P, Heng, Y, Herrera, R, Hor, Y, Hou, S, Hsiung, Y, Hu, B, Hu, H, Hu, J, Hu, S, Hu, T, Hu, Y, Hu, Z, Huang, G, Huang, H, Huang, K, Huang, W, Huang, X, Huang, Y, Hui, J, Huo, L, Huo, W, Huss, C, Hussain, S, Ioannisian, A, Isocrate, R, Jelmini, B, Jeria, I, Ji, X, Jia, H, Jia, J, Jian, S, Jiang, D, Jiang, W, Jiang, X, Jing, X, Jollet, C, Joutsenvaara, J, Kalousis, L, Kampmann, P, Kang, L, Karaparambil, R, Kazarian, N, Khatun, A, Khosonthongkee, K, Korablev, D, Kouzakov, K, Krasnoperov, A, Kutovskiy, N, Kuusiniemi, P, Lachenmaier, T, Landini, C, Leblanc, S, Lebrin, V, Lefevre, F, Lei, R, Leitner, R, Leung, J, Li, D, Li, F, Li, G, Li, H, Li, M, Li, N, Li, Q, Li, R, Li, S, Li, T, Li, W, Li, X, Li, Y, Li, Z, Liang, H, Liao, J, Limphirat, A, Lin, G, Lin, S, Lin, T, Ling, J, Lippi, I, Liu, F, Liu, H, Liu, J, Liu, M, Liu, Q, Liu, R, Liu, S, Liu, X, Liu, Y, Lokhov, A, Lombardi, P, Lombardo, C, Loo, K, Lu, C, Lu, H, Lu, J, Lu, S, Lubsandorzhiev, B, Lubsandorzhiev, S, Ludhova, L, Lukanov, A, Luo, D, Luo, F, Luo, G, Luo, S, Luo, W, Luo, X, Lyashuk, V, Ma, B, Ma, Q, Ma, S, Ma, X, Maalmi, J, Mai, J, Malyshkin, Y, Carlos Mandujano, R, Mantovani, F, Manzali, F, Mao, X, Mao, Y, Mari, S, Marini, F, Martellini, C, Martin-Chassard, G, Martini, A, Mayer, M, Mayilyan, D, Mednieks, I, Meinusch, A, Meng, Y, Meregaglia, A, Meroni, E, Meyho, D, Mezzetto, M, Miller, J, Miramonti, L, Colomer Molla, M, Montini, P, Montuschi, M, Muller, A, Nastasi, M, Naumov, D, Naumova, E, Navas-Nicolas, D, Nemchenok, I, Thuan Nguyen Thi, M, Ning, F, Ning, Z, Nunokawa, H, Oberauer, L, Pedro Ochoa-Ricoux, J, Olshevskiy, A, Orestano, D, Ortica, F, Othegraven, R, Paoloni, A, Parmeggiano, S, Pei, Y, Pelicci, L, Pelliccia, N, Peng, A, Peng, H, Peng, Y, Peng, Z, Perrot, F, Petitjean, P, Petrucci, F, Pilarczyk, O, Felipe Pineres, L, Popov, A, Poussot, P, Previtali, E, Qi, F, Qi, M, Qian, S, Qian, X, Qian, Z, Qiao, H, Qin, Z, Qiu, S, Ranucci, G, Raper, N, Rasheed, R, Re, A, Rebber, H, Rebii, A, Redchuk, M, Ren, B, Ren, J, Ricci, B, Rifai, M, Roche, M, Rodphai, N, Romani, A, Roskovec, B, Ruan, X, Rybnikov, A, Sadovsky, A, Saggese, P, Sanfilippo, S, Sangka, A, Sawangwit, U, Sawatzki, J, Schever, M, Schwab, C, Schweizer, K, Selyunin, A, Serafini, A, Settanta, G, Settimo, M, Shao, Z, Sharov, V, Shaydurova, A, Shi, J, Shi, Y, Shutov, V, Sidorenkov, A, Simkovic, F, Sirignano, C, Siripak, J, Sisti, M, Slupecki, M, Smirnov, M, Smirnov, O, Sogo-Bezerra, T, Sokolov, S, Songwadhana, J, Soonthornthum, B, Sotnikov, A, Sramek, O, Sreethawong, W, Stahl, A, Stanco, L, Stankevich, K, Stefanik, D, Steiger, H, Steinmann, J, Sterr, T, Raphael Stock, M, Strati, V, Studenikin, A, Su, J, Sun, S, Sun, X, Sun, Y, Sun, Z, Suwonjandee, N, Szelezniak, M, Tang, J, Tang, Q, Tang, X, Thara Hariharan, V, Theisen, E, Tietzsch, A, Tkachev, I, Tmej, T, Danilo Claudio Torri, M, Treskov, K, Triossi, A, Troni, G, Trzaska, W, Tsagkarakis, A, Tuve, C, Ushakov, N, Vedin, V, Verde, G, Vialkov, M, Viaud, B, Moritz Vollbrecht, C, Volpe, C, Von Sturm, K, Vorobel, V, Voronin, D, Votano, L, Walker, P, Wang, C, Wang, E, Wang, G, Wang, J, Wang, L, Wang, M, Wang, R, Wang, S, Wang, W, Wang, X, Wang, Y, Wang, Z, Watcharangkool, A, Wei, W, Wei, Y, Wen, K, Wen, L, Wiebusch, C, Chan-Fai Wong, S, Wonsak, B, Wu, D, Wu, Q, Wu, Z, Wurm, M, Wurtz, J, Wysotzki, C, Xi, Y, Xia, D, Xiao, X, Xie, X, Xie, Y, Xie, Z, Xin, Z, Xing, Z, Xu, B, Xu, C, Xu, D, Xu, F, Xu, H, Xu, J, Xu, M, Xu, Y, Yan, B, Yan, T, Yan, W, Yan, X, Yan, Y, Yang, C, Yang, H, Yang, J, Yang, L, Yang, X, Yang, Y, Yao, H, Ye, J, Ye, M, Ye, Z, Yermia, F, Yin, N, You, Z, Yu, B, Yu, C, Yu, H, Yu, M, Yu, X, Yu, Z, Yuan, C, Yuan, Y, Yuan, Z, Yue, B, Zafar, N, Zavadskyi, V, Zeng, S, Zeng, T, Zeng, Y, Zhan, L, Zhang, A, Zhang, B, Zhang, F, Zhang, G, Zhang, H, Zhang, J, Zhang, M, Zhang, P, Zhang, Q, Zhang, S, Zhang, T, Zhang, X, Zhang, Y, Zhang, Z, Zhao, F, Zhao, J, Zhao, R, Zhao, S, Zheng, D, Zheng, H, Zheng, Y, Zhong, W, Zhou, J, Zhou, L, Zhou, N, Zhou, S, Zhou, T, Zhou, X, Zhu, J, Zhu, K, Zhu, Z, Zhuang, B, Zhuang, H, Zong, L, Zou, J, Abusleme A., Adam T., Ahmad S., Ahmed R., Aiello S., Akram M., Aleem A., An F., An Q., Andronico G., Anfimov N., Antonelli V., Antoshkina T., Asavapibhop B., de Andre J. P. A. M., Auguste D., Bai W., Balashov N., Baldini W., Barresi A., Basilico D., Baussan E., Bellato M., Bergnoli A., Birkenfeld T., Blin S., Blum D., Blyth S., Bolshakova A., Bongrand M., Bordereau C., Breton D., Brigatti A., Brugnera R., Bruno R., Budano A., Busto J., Butorov I., Cabrera A., Caccianiga B., Cai H., Cai X., Cai Y., Cai Z., Callegari R., Cammi A., Campeny A., Cao C., Cao G., Cao J., Caruso R., Cerna C., Chan C., Chang J., Chang Y., Chen G., Chen P., Chen P. -A., Chen S., Chen X., Chen Y., Chen Z., Cheng J., Cheng Y., Chin Cheng Y., Chetverikov A., Chiesa D., Chimenti P., Chukanov A., Claverie G., Clementi C., Clerbaux B., Conforti Di Lorenzo S., Corti D., Dal Corso F., Dalager O., De La Taille C., Deng Z., Depnering W., Diaz M., Ding X., Ding Y., Dirgantara B., Dmitrievsky S., Dohnal T., Dolzhikov D., Donchenko G., Dong J., Doroshkevich E., Dracos M., Druillole F., Du R., Du S., Dusini S., Dvorak M., Enqvist T., Enzmann H., Fabbri A., Fan D., Fan L., Fang J., Fang W., Fargetta M., Fedoseev D., Fei Z., Feng L. -C., Feng Q., Ford R., Fournier A., Gan H., Gao F., Garfagnini A., Gavrikov A., Giammarchi M., Giudice N., Gonchar M., Gong G., Gong H., Gornushkin Y., Gottel A., Grassi M., Gromov V., Gu M., Gu X., Gu Y., Guan M., Guan Y., Guardone N., Guo C., Guo J., Guo W., Guo X., Guo Y., Hackspacher P., Hagner C., Han R., Han Y., He M., He W., Heinz T., Hellmuth P., Heng Y., Herrera R., Hor Y., Hou S., Hsiung Y., Hu B. -Z., Hu H., Hu J., Hu S., Hu T., Hu Y., Hu Z., Huang G., Huang H., Huang K., Huang W., Huang X., Huang Y., Hui J., Huo L., Huo W., Huss C., Hussain S., Ioannisian A., Isocrate R., Jelmini B., Jeria I., Ji X., Jia H., Jia J., Jian S., Jiang D., Jiang W., Jiang X., Jing X., Jollet C., Joutsenvaara J., Kalousis L., Kampmann P., Kang L., Karaparambil R., Kazarian N., Khatun A., Khosonthongkee K., Korablev D., Kouzakov K., Krasnoperov A., Kutovskiy N., Kuusiniemi P., Lachenmaier T., Landini C., Leblanc S., Lebrin V., Lefevre F., Lei R., Leitner R., Leung J., Li D., Li F., Li G., Li H., Li M., Li N., Li Q., Li R., Li S., Li T., Li W., Li X., Li Y., Li Z., Liang H., Liao J., Limphirat A., Lin G. -L., Lin S., Lin T., Ling J., Lippi I., Liu F., Liu H., Liu J., Liu M., Liu Q., Liu R., Liu S., Liu X., Liu Y., Lokhov A., Lombardi P., Lombardo C., Loo K., Lu C., Lu H., Lu J., Lu S., Lubsandorzhiev B., Lubsandorzhiev S., Ludhova L., Lukanov A., Luo D., Luo F., Luo G., Luo S., Luo W., Luo X., Lyashuk V., Ma B., Ma Q., Ma S., Ma X., Maalmi J., Mai J., Malyshkin Y., Carlos Mandujano R., Mantovani F., Manzali F., Mao X., Mao Y., Mari S. M., Marini F., Martellini C., Martin-Chassard G., Martini A., Mayer M., Mayilyan D., Mednieks I., Meinusch A., Meng Y., Meregaglia A., Meroni E., Meyho D., Mezzetto M., Miller J., Miramonti L., Colomer Molla M., Montini P., Montuschi M., Muller A., Nastasi M., Naumov D. V., Naumova E., Navas-Nicolas D., Nemchenok I., Thuan Nguyen Thi M., Ning F., Ning Z., Nunokawa H., Oberauer L., Pedro Ochoa-Ricoux J., Olshevskiy A., Orestano D., Ortica F., Othegraven R., Paoloni A., Parmeggiano S., Pei Y., Pelicci L., Pelliccia N., Peng A., Peng H., Peng Y., Peng Z., Perrot F., Petitjean P. -A., Petrucci F., Pilarczyk O., Felipe Pineres L., Popov A., Poussot P., Previtali E., Qi F., Qi M., Qian S., Qian X., Qian Z., Qiao H., Qin Z., Qiu S., Ranucci G., Raper N., Rasheed R., Re A., Rebber H., Rebii A., Redchuk M., Ren B., Ren J., Ricci B., Rifai M., Roche M., Rodphai N., Romani A., Roskovec B., Ruan X., Rybnikov A., Sadovsky A., Saggese P., Sanfilippo S., Sangka A., Sawangwit U., Sawatzki J., Schever M., Schwab C., Schweizer K., Selyunin A., Serafini A., Settanta G., Settimo M., Shao Z., Sharov V., Shaydurova A., Shi J., Shi Y., Shutov V., Sidorenkov A., Simkovic F., Sirignano C., Siripak J., Sisti M., Slupecki M., Smirnov M., Smirnov O., Sogo-Bezerra T., Sokolov S., Songwadhana J., Soonthornthum B., Sotnikov A., Sramek O., Sreethawong W., Stahl A., Stanco L., Stankevich K., Stefanik D., Steiger H., Steinmann J., Sterr T., Raphael Stock M., Strati V., Studenikin A., Su J., Sun S., Sun X., Sun Y., Sun Z., Suwonjandee N., Szelezniak M., Tang J., Tang Q., Tang X., Thara Hariharan V., Theisen E., Tietzsch A., Tkachev I., Tmej T., Danilo Claudio Torri M., Treskov K., Triossi A., Troni G., Trzaska W., Tsagkarakis A., Tuve C., Ushakov N., Vedin V., Verde G., Vialkov M., Viaud B., Moritz Vollbrecht C., Volpe C., Von Sturm K., Vorobel V., Voronin D., Votano L., Walker P., Wang C., Wang C. -H., Wang E., Wang G., Wang J., Wang L., Wang M., Wang R., Wang S., Wang W., Wang X., Wang Y., Wang Z., Watcharangkool A., Wei W., Wei Y., Wen K., Wen L., Wiebusch C., Chan-Fai Wong S., Wonsak B., Wu D., Wu Q., Wu Z., Wurm M., Wurtz J., Wysotzki C., Xi Y., Xia D., Xiao X., Xie X., Xie Y., Xie Z., Xin Z., Xing Z., Xu B., Xu C., Xu D., Xu F., Xu H., Xu J., Xu M., Xu Y., Yan B., Yan T., Yan W., Yan X., Yan Y., Yang C., Yang H., Yang J., Yang L., Yang X., Yang Y., Yao H., Ye J., Ye M., Ye Z., Yermia F., Yin N., You Z., Yu B., Yu C., Yu H., Yu M., Yu X., Yu Z., Yuan C., Yuan Y., Yuan Z., Yue B., Zafar N., Zavadskyi V., Zeng S., Zeng T., Zeng Y., Zhan L., Zhang A., Zhang B., Zhang F., Zhang G., Zhang H., Zhang J., Zhang M., Zhang P., Zhang Q., Zhang S., Zhang T., Zhang X., Zhang Y., Zhang Z., Zhao F., Zhao J., Zhao R., Zhao S., Zheng D., Zheng H., Zheng Y., Zhong W., Zhou J., Zhou L., Zhou N., Zhou S., Zhou T., Zhou X., Zhu J., Zhu K., Zhu Z., Zhuang B., Zhuang H., Zong L., and Zou J.

Abstract

JUNO is a multi-purpose neutrino observatory under construction in the south of China. This publication presents new sensitivity estimates for the measurement of the , , , and oscillation parameters using reactor antineutrinos, which is one of the primary physics goals of the experiment. The sensitivities are obtained using the best knowledge available to date on the location and overburden of the experimental site, the nuclear reactors in the surrounding area and beyond, the detector response uncertainties, and the reactor antineutrino spectral shape constraints expected from the TAO satellite detector. It is found that the and oscillation parameters will be determined to 0.5% precision or better in six years of data collection. In the same period, the parameter will be determined to about % precision for each mass ordering hypothesis. The new precision represents approximately an order of magnitude improvement over existing constraints for these three parameters.

Published
2022

41. Mass testing and characterization of 20-inch PMTs for JUNO

Author

Abusleme, A, Adam, T, Ahmad, S, Ahmed, R, Aiello, S, Akram, M, Aleem, A, Alexandros, T, An, F, An, Q, Andronico, G, Anfimov, N, Antonelli, V, Antoshkina, T, Asavapibhop, B, de Andre, J, Auguste, D, Bai, W, Balashov, N, Baldini, W, Barresi, A, Basilico, D, Baussan, E, Bellato, M, Bergnoli, A, Birkenfeld, T, Blin, S, Blum, D, Blyth, S, Bolshakova, A, Bongrand, M, Bordereau, C, Breton, D, Brigatti, A, Brugnera, R, Bruno, R, Budano, A, Busto, J, Butorov, I, Cabrera, A, Caccianiga, B, Cai, H, Cai, X, Cai, Y, Cai, Z, Callegari, R, Cammi, A, Campeny, A, Cao, C, Cao, G, Cao, J, Caruso, R, Cerna, C, Chan, C, Chang, J, Chang, Y, Chen, G, Chen, P, Chen, S, Chen, X, Chen, Y, Chen, Z, Cheng, J, Cheng, Y, Chetverikov, A, Chiesa, D, Chimenti, P, Chukanov, A, Claverie, G, Clementi, C, Clerbaux, B, Colomer Molla, M, Conforti Di Lorenzo, S, Corti, D, Corso, F, Dalager, O, De La Taille, C, Deng, Z, Depnering, W, Diaz, M, Ding, X, Ding, Y, Dirgantara, B, Dmitrievsky, S, Dohnal, T, Dolzhikov, D, Donchenko, G, Dong, J, Doroshkevich, E, Dracos, M, Druillole, F, Du, R, Du, S, Dusini, S, Dvorak, M, Enqvist, T, Enzmann, H, Fabbri, A, Fan, D, Fan, L, Fang, J, Fang, W, Fargetta, M, Fedoseev, D, Fei, Z, Feng, L, Feng, Q, Ford, R, Fournier, A, Gan, H, Gao, F, Garfagnini, A, Gavrikov, A, Giammarchi, M, Giudice, N, Gonchar, M, Gong, G, Gong, H, Gornushkin, Y, Gottel, A, Grassi, M, Gromov, V, Gu, M, Gu, X, Gu, Y, Guan, M, Guan, Y, Guardone, N, Guo, C, Guo, J, Guo, W, Guo, X, Guo, Y, Hackspacher, P, Hagner, C, Han, R, Han, Y, He, M, He, W, Heinz, T, Hellmuth, P, Heng, Y, Herrera, R, Hor, Y, Hou, S, Hsiung, Y, Hu, B, Hu, H, Hu, J, Hu, S, Hu, T, Hu, Y, Hu, Z, Huang, G, Huang, H, Huang, K, Huang, W, Huang, X, Huang, Y, Hui, J, Huo, L, Huo, W, Huss, C, Hussain, S, Ioannisian, A, Isocrate, R, Jelmini, B, Jeria, I, Ji, X, Jia, H, Jia, J, Jian, S, Jiang, D, Jiang, W, Jiang, X, Jing, X, Jollet, C, Joutsenvaara, J, Kalousis, L, Kampmann, P, Kang, L, Karaparambil, R, Kazarian, N, Khatun, A, Khosonthongkee, K, Korablev, D, Kouzakov, K, Krasnoperov, A, Kutovskiy, N, Kuusiniemi, P, Lachenmaier, T, Landini, C, Leblanc, S, Lebrin, V, Lefevre, F, Lei, R, Leitner, R, Leung, J, Li, D, Li, F, Li, G, Li, H, Li, M, Li, N, Li, Q, Li, R, Li, S, Li, T, Li, W, Li, X, Li, Y, Li, Z, Liang, H, Liao, J, Limphirat, A, Lin, G, Lin, S, Lin, T, Ling, J, Lippi, I, Liu, F, Liu, H, Liu, J, Liu, M, Liu, Q, Liu, R, Liu, S, Liu, X, Liu, Y, Lokhov, A, Lombardi, P, Lombardo, C, Loo, K, Lu, C, Lu, H, Lu, J, Lu, S, Lubsandorzhiev, B, Lubsandorzhiev, S, Ludhova, L, Lukanov, A, Luo, D, Luo, F, Luo, G, Luo, S, Luo, W, Luo, X, Lyashuk, V, Ma, B, Ma, Q, Ma, S, Ma, X, Maalmi, J, Mai, J, Malyshkin, Y, Mandujano, R, Mantovani, F, Manzali, F, Mao, X, Mao, Y, Mari, S, Marini, F, Martellini, C, Martin-Chassard, G, Martini, A, Mayer, M, Mayilyan, D, Mednieks, I, Meng, Y, Meregaglia, A, Meroni, E, Meyhofer, D, Mezzetto, M, Miller, J, Miramonti, L, Montini, P, Montuschi, M, Muller, A, Nastasi, M, Naumov, D, Naumova, E, Navas-Nicolas, D, Nemchenok, I, Nguyen Thi, M, Ning, F, Ning, Z, Nunokawa, H, Oberauer, L, Ochoa-Ricoux, J, Olshevskiy, A, Orestano, D, Ortica, F, Othegraven, R, Paoloni, A, Parmeggiano, S, Pei, Y, Pelicci, L, Pelliccia, N, Peng, A, Peng, H, Peng, Y, Peng, Z, Perrot, F, Petitjean, P, Petrucci, F, Pilarczyk, O, Pineres Rico, L, Popov, A, Poussot, P, Previtali, E, Qi, F, Qi, M, Qian, S, Qian, X, Qian, Z, Qiao, H, Qin, Z, Qiu, S, Ranucci, G, Raper, N, Re, A, Rebber, H, Rebii, A, Redchuk, M, Ren, B, Ren, J, Ricci, B, Rifai, M, Roche, M, Rodphai, N, Romani, A, Roskovec, B, Ruan, X, Rybnikov, A, Sadovsky, A, Saggese, P, Sanfilippo, S, Sangka, A, Sawangwit, U, Sawatzki, J, Schever, M, Schwab, C, Schweizer, K, Selyunin, A, Serafini, A, Settanta, G, Settimo, M, Shao, Z, Sharov, V, Shaydurova, A, Shi, J, Shi, Y, Shutov, V, Sidorenkov, A, Simkovic, F, Sirignano, C, Siripak, J, Sisti, M, Slupecki, M, Smirnov, M, Smirnov, O, Sogo-Bezerra, T, Sokolov, S, Songwadhana, J, Soonthornthum, B, Sotnikov, A, Sramek, O, Sreethawong, W, Stahl, A, Stanco, L, Stankevich, K, Stefanik, D, Steiger, H, Steinmann, J, Sterr, T, Stock, M, Strati, V, Studenikin, A, Su, J, Sun, S, Sun, X, Sun, Y, Sun, Z, Suwonjandee, N, Szelezniak, M, Tang, J, Tang, Q, Tang, X, Theisen, E, Tietzsch, A, Tkachev, I, Tmej, T, Torri, M, Treskov, K, Triossi, A, Troni, G, Trzaska, W, Tuve, C, Ushakov, N, Vedin, V, Verde, G, Vialkov, M, Viaud, B, Vollbrecht, C, Volpe, C, von Sturm, K, Vorobel, V, Voronin, D, Votano, L, Walker, P, Wang, C, Wang, E, Wang, G, Wang, J, Wang, L, Wang, M, Wang, R, Wang, S, Wang, W, Wang, X, Wang, Y, Wang, Z, Watcharangkool, A, Wei, W, Wei, Y, Wen, K, Wen, L, Wiebusch, C, Wong, S, Wonsak, B, Wu, D, Wu, Q, Wu, Z, Wurm, M, Wurtz, J, Wysotzki, C, Xi, Y, Xia, D, Xiao, X, Xie, X, Xie, Y, Xie, Z, Xin, Z, Xing, Z, Xu, B, Xu, C, Xu, D, Xu, F, Xu, H, Xu, J, Xu, M, Xu, Y, Yan, B, Yan, T, Yan, W, Yan, X, Yan, Y, Yang, C, Yang, H, Yang, J, Yang, L, Yang, X, Yang, Y, Yao, H, Ye, J, Ye, M, Ye, Z, Yermia, F, Yin, N, You, Z, Yu, B, Yu, C, Yu, H, Yu, M, Yu, X, Yu, Z, Yuan, C, Yuan, Y, Yuan, Z, Yue, B, Zafar, N, Zavadskyi, V, Zeng, S, Zeng, T, Zeng, Y, Zhan, L, Zhang, A, Zhang, B, Zhang, F, Zhang, G, Zhang, H, Zhang, J, Zhang, M, Zhang, P, Zhang, Q, Zhang, S, Zhang, T, Zhang, X, Zhang, Y, Zhang, Z, Zhao, F, Zhao, J, Zhao, R, Zhao, S, Zheng, D, Zheng, H, Zheng, Y, Zhong, W, Zhou, J, Zhou, L, Zhou, N, Zhou, S, Zhou, T, Zhou, X, Zhu, J, Zhu, K, Zhu, Z, Zhuang, B, Zhuang, H, Zong, L, Zou, J, Abusleme A., Adam T., Ahmad S., Ahmed R., Aiello S., Akram M., Aleem A., Alexandros T., An F., An Q., Andronico G., Anfimov N., Antonelli V., Antoshkina T., Asavapibhop B., de Andre J. P. A. M., Auguste D., Bai W., Balashov N., Baldini W., Barresi A., Basilico D., Baussan E., Bellato M., Bergnoli A., Birkenfeld T., Blin S., Blum D., Blyth S., Bolshakova A., Bongrand M., Bordereau C., Breton D., Brigatti A., Brugnera R., Bruno R., Budano A., Busto J., Butorov I., Cabrera A., Caccianiga B., Cai H., Cai X., Cai Y., Cai Z., Callegari R., Cammi A., Campeny A., Cao C., Cao G., Cao J., Caruso R., Cerna C., Chan C., Chang J., Chang Y., Chen G., Chen P., Chen P. -A., Chen S., Chen X., Chen Y., Chen Z., Cheng J., Cheng Y., Cheng Y. C., Chetverikov A., Chiesa D., Chimenti P., Chukanov A., Claverie G., Clementi C., Clerbaux B., Colomer Molla M., Conforti Di Lorenzo S., Corti D., Corso F. D., Dalager O., De La Taille C., Deng Z., Depnering W., Diaz M., Ding X., Ding Y., Dirgantara B., Dmitrievsky S., Dohnal T., Dolzhikov D., Donchenko G., Dong J., Doroshkevich E., Dracos M., Druillole F., Du R., Du S., Dusini S., Dvorak M., Enqvist T., Enzmann H., Fabbri A., Fan D., Fan L., Fang J., Fang W., Fargetta M., Fedoseev D., Fei Z., Feng L. -C., Feng Q., Ford R., Fournier A., Gan H., Gao F., Garfagnini A., Gavrikov A., Giammarchi M., Giudice N., Gonchar M., Gong G., Gong H., Gornushkin Y., Gottel A., Grassi M., Gromov V., Gu M., Gu X., Gu Y., Guan M., Guan Y., Guardone N., Guo C., Guo J., Guo W., Guo X., Guo Y., Hackspacher P., Hagner C., Han R., Han Y., He M., He W., Heinz T., Hellmuth P., Heng Y., Herrera R., Hor Y. K., Hou S., Hsiung Y., Hu B. -Z., Hu H., Hu J., Hu S., Hu T., Hu Y., Hu Z., Huang G., Huang H., Huang K., Huang W., Huang X., Huang Y., Hui J., Huo L., Huo W., Huss C., Hussain S., Ioannisian A., Isocrate R., Jelmini B., Jeria I., Ji X., Jia H., Jia J., Jian S., Jiang D., Jiang W., Jiang X., Jing X., Jollet C., Joutsenvaara J., Kalousis L., Kampmann P., Kang L., Karaparambil R., Kazarian N., Khatun A., Khosonthongkee K., Korablev D., Kouzakov K., Krasnoperov A., Kutovskiy N., Kuusiniemi P., Lachenmaier T., Landini C., Leblanc S., Lebrin V., Lefevre F., Lei R., Leitner R., Leung J., Li D., Li F., Li G., Li H., Li M., Li N., Li Q., Li R., Li S., Li T., Li W., Li X., Li Y., Li Z., Liang H., Liao J., Limphirat A., Lin G. -L., Lin S., Lin T., Ling J., Lippi I., Liu F., Liu H., Liu J., Liu M., Liu Q., Liu R., Liu S., Liu X., Liu Y., Lokhov A., Lombardi P., Lombardo C., Loo K., Lu C., Lu H., Lu J., Lu S., Lubsandorzhiev B., Lubsandorzhiev S., Ludhova L., Lukanov A., Luo D., Luo F., Luo G., Luo S., Luo W., Luo X., Lyashuk V., Ma B., Ma Q., Ma S., Ma X., Maalmi J., Mai J., Malyshkin Y., Mandujano R. C., Mantovani F., Manzali F., Mao X., Mao Y., Mari S. M., Marini F., Martellini C., Martin-Chassard G., Martini A., Mayer M., Mayilyan D., Mednieks I., Meng Y., Meregaglia A., Meroni E., Meyhofer D., Mezzetto M., Miller J., Miramonti L., Montini P., Montuschi M., Muller A., Nastasi M., Naumov D. V., Naumova E., Navas-Nicolas D., Nemchenok I., Nguyen Thi M. T., Ning F., Ning Z., Nunokawa H., Oberauer L., Ochoa-Ricoux J. P., Olshevskiy A., Orestano D., Ortica F., Othegraven R., Paoloni A., Parmeggiano S., Pei Y., Pelicci L., Pelliccia N., Peng A., Peng H., Peng Y., Peng Z., Perrot F., Petitjean P. -A., Petrucci F., Pilarczyk O., Pineres Rico L. F., Popov A., Poussot P., Previtali E., Qi F., Qi M., Qian S., Qian X., Qian Z., Qiao H., Qin Z., Qiu S., Ranucci G., Raper N., Re A., Rebber H., Rebii A., Redchuk M., Ren B., Ren J., Ricci B., Rifai M., Roche M., Rodphai N., Romani A., Roskovec B., Ruan X., Rybnikov A., Sadovsky A., Saggese P., Sanfilippo S., Sangka A., Sawangwit U., Sawatzki J., Schever M., Schwab C., Schweizer K., Selyunin A., Serafini A., Settanta G., Settimo M., Shao Z., Sharov V., Shaydurova A., Shi J., Shi Y., Shutov V., Sidorenkov A., Simkovic F., Sirignano C., Siripak J., Sisti M., Slupecki M., Smirnov M., Smirnov O., Sogo-Bezerra T., Sokolov S., Songwadhana J., Soonthornthum B., Sotnikov A., Sramek O., Sreethawong W., Stahl A., Stanco L., Stankevich K., Stefanik D., Steiger H., Steinmann J., Sterr T., Stock M. R., Strati V., Studenikin A., Su J., Sun S., Sun X., Sun Y., Sun Z., Suwonjandee N., Szelezniak M., Tang J., Tang Q., Tang X., Theisen E., Tietzsch A., Tkachev I., Tmej T., Torri M. D. C., Treskov K., Triossi A., Troni G., Trzaska W., Tuve C., Ushakov N., Vedin V., Verde G., Vialkov M., Viaud B., Vollbrecht C. M., Volpe C., von Sturm K., Vorobel V., Voronin D., Votano L., Walker P., Wang C., Wang C. -H., Wang E., Wang G., Wang J., Wang L., Wang M., Wang R., Wang S., Wang W., Wang X., Wang Y., Wang Z., Watcharangkool A., Wei W., Wei Y., Wen K., Wen L., Wiebusch C., Wong S. C. -F., Wonsak B., Wu D., Wu Q., Wu Z., Wurm M., Wurtz J., Wysotzki C., Xi Y., Xia D., Xiao X., Xie X., Xie Y., Xie Z., Xin Z., Xing Z., Xu B., Xu C., Xu D., Xu F., Xu H., Xu J., Xu M., Xu Y., Yan B., Yan T., Yan W., Yan X., Yan Y., Yang C., Yang H., Yang J., Yang L., Yang X., Yang Y., Yao H., Ye J., Ye M., Ye Z., Yermia F., Yin N., You Z., Yu B., Yu C., Yu H., Yu M., Yu X., Yu Z., Yuan C., Yuan Y., Yuan Z., Yue B., Zafar N., Zavadskyi V., Zeng S., Zeng T., Zeng Y., Zhan L., Zhang A., Zhang B., Zhang F., Zhang G., Zhang H., Zhang J., Zhang M., Zhang P., Zhang Q., Zhang S., Zhang T., Zhang X., Zhang Y., Zhang Z., Zhao F., Zhao J., Zhao R., Zhao S., Zheng D., Zheng H., Zheng Y., Zhong W., Zhou J., Zhou L., Zhou N., Zhou S., Zhou T., Zhou X., Zhu J., Zhu K., Zhu Z., Zhuang B., Zhuang H., Zong L., Zou J., Abusleme, A, Adam, T, Ahmad, S, Ahmed, R, Aiello, S, Akram, M, Aleem, A, Alexandros, T, An, F, An, Q, Andronico, G, Anfimov, N, Antonelli, V, Antoshkina, T, Asavapibhop, B, de Andre, J, Auguste, D, Bai, W, Balashov, N, Baldini, W, Barresi, A, Basilico, D, Baussan, E, Bellato, M, Bergnoli, A, Birkenfeld, T, Blin, S, Blum, D, Blyth, S, Bolshakova, A, Bongrand, M, Bordereau, C, Breton, D, Brigatti, A, Brugnera, R, Bruno, R, Budano, A, Busto, J, Butorov, I, Cabrera, A, Caccianiga, B, Cai, H, Cai, X, Cai, Y, Cai, Z, Callegari, R, Cammi, A, Campeny, A, Cao, C, Cao, G, Cao, J, Caruso, R, Cerna, C, Chan, C, Chang, J, Chang, Y, Chen, G, Chen, P, Chen, S, Chen, X, Chen, Y, Chen, Z, Cheng, J, Cheng, Y, Chetverikov, A, Chiesa, D, Chimenti, P, Chukanov, A, Claverie, G, Clementi, C, Clerbaux, B, Colomer Molla, M, Conforti Di Lorenzo, S, Corti, D, Corso, F, Dalager, O, De La Taille, C, Deng, Z, Depnering, W, Diaz, M, Ding, X, Ding, Y, Dirgantara, B, Dmitrievsky, S, Dohnal, T, Dolzhikov, D, Donchenko, G, Dong, J, Doroshkevich, E, Dracos, M, Druillole, F, Du, R, Du, S, Dusini, S, Dvorak, M, Enqvist, T, Enzmann, H, Fabbri, A, Fan, D, Fan, L, Fang, J, Fang, W, Fargetta, M, Fedoseev, D, Fei, Z, Feng, L, Feng, Q, Ford, R, Fournier, A, Gan, H, Gao, F, Garfagnini, A, Gavrikov, A, Giammarchi, M, Giudice, N, Gonchar, M, Gong, G, Gong, H, Gornushkin, Y, Gottel, A, Grassi, M, Gromov, V, Gu, M, Gu, X, Gu, Y, Guan, M, Guan, Y, Guardone, N, Guo, C, Guo, J, Guo, W, Guo, X, Guo, Y, Hackspacher, P, Hagner, C, Han, R, Han, Y, He, M, He, W, Heinz, T, Hellmuth, P, Heng, Y, Herrera, R, Hor, Y, Hou, S, Hsiung, Y, Hu, B, Hu, H, Hu, J, Hu, S, Hu, T, Hu, Y, Hu, Z, Huang, G, Huang, H, Huang, K, Huang, W, Huang, X, Huang, Y, Hui, J, Huo, L, Huo, W, Huss, C, Hussain, S, Ioannisian, A, Isocrate, R, Jelmini, B, Jeria, I, Ji, X, Jia, H, Jia, J, Jian, S, Jiang, D, Jiang, W, Jiang, X, Jing, X, Jollet, C, Joutsenvaara, J, Kalousis, L, Kampmann, P, Kang, L, Karaparambil, R, Kazarian, N, Khatun, A, Khosonthongkee, K, Korablev, D, Kouzakov, K, Krasnoperov, A, Kutovskiy, N, Kuusiniemi, P, Lachenmaier, T, Landini, C, Leblanc, S, Lebrin, V, Lefevre, F, Lei, R, Leitner, R, Leung, J, Li, D, Li, F, Li, G, Li, H, Li, M, Li, N, Li, Q, Li, R, Li, S, Li, T, Li, W, Li, X, Li, Y, Li, Z, Liang, H, Liao, J, Limphirat, A, Lin, G, Lin, S, Lin, T, Ling, J, Lippi, I, Liu, F, Liu, H, Liu, J, Liu, M, Liu, Q, Liu, R, Liu, S, Liu, X, Liu, Y, Lokhov, A, Lombardi, P, Lombardo, C, Loo, K, Lu, C, Lu, H, Lu, J, Lu, S, Lubsandorzhiev, B, Lubsandorzhiev, S, Ludhova, L, Lukanov, A, Luo, D, Luo, F, Luo, G, Luo, S, Luo, W, Luo, X, Lyashuk, V, Ma, B, Ma, Q, Ma, S, Ma, X, Maalmi, J, Mai, J, Malyshkin, Y, Mandujano, R, Mantovani, F, Manzali, F, Mao, X, Mao, Y, Mari, S, Marini, F, Martellini, C, Martin-Chassard, G, Martini, A, Mayer, M, Mayilyan, D, Mednieks, I, Meng, Y, Meregaglia, A, Meroni, E, Meyhofer, D, Mezzetto, M, Miller, J, Miramonti, L, Montini, P, Montuschi, M, Muller, A, Nastasi, M, Naumov, D, Naumova, E, Navas-Nicolas, D, Nemchenok, I, Nguyen Thi, M, Ning, F, Ning, Z, Nunokawa, H, Oberauer, L, Ochoa-Ricoux, J, Olshevskiy, A, Orestano, D, Ortica, F, Othegraven, R, Paoloni, A, Parmeggiano, S, Pei, Y, Pelicci, L, Pelliccia, N, Peng, A, Peng, H, Peng, Y, Peng, Z, Perrot, F, Petitjean, P, Petrucci, F, Pilarczyk, O, Pineres Rico, L, Popov, A, Poussot, P, Previtali, E, Qi, F, Qi, M, Qian, S, Qian, X, Qian, Z, Qiao, H, Qin, Z, Qiu, S, Ranucci, G, Raper, N, Re, A, Rebber, H, Rebii, A, Redchuk, M, Ren, B, Ren, J, Ricci, B, Rifai, M, Roche, M, Rodphai, N, Romani, A, Roskovec, B, Ruan, X, Rybnikov, A, Sadovsky, A, Saggese, P, Sanfilippo, S, Sangka, A, Sawangwit, U, Sawatzki, J, Schever, M, Schwab, C, Schweizer, K, Selyunin, A, Serafini, A, Settanta, G, Settimo, M, Shao, Z, Sharov, V, Shaydurova, A, Shi, J, Shi, Y, Shutov, V, Sidorenkov, A, Simkovic, F, Sirignano, C, Siripak, J, Sisti, M, Slupecki, M, Smirnov, M, Smirnov, O, Sogo-Bezerra, T, Sokolov, S, Songwadhana, J, Soonthornthum, B, Sotnikov, A, Sramek, O, Sreethawong, W, Stahl, A, Stanco, L, Stankevich, K, Stefanik, D, Steiger, H, Steinmann, J, Sterr, T, Stock, M, Strati, V, Studenikin, A, Su, J, Sun, S, Sun, X, Sun, Y, Sun, Z, Suwonjandee, N, Szelezniak, M, Tang, J, Tang, Q, Tang, X, Theisen, E, Tietzsch, A, Tkachev, I, Tmej, T, Torri, M, Treskov, K, Triossi, A, Troni, G, Trzaska, W, Tuve, C, Ushakov, N, Vedin, V, Verde, G, Vialkov, M, Viaud, B, Vollbrecht, C, Volpe, C, von Sturm, K, Vorobel, V, Voronin, D, Votano, L, Walker, P, Wang, C, Wang, E, Wang, G, Wang, J, Wang, L, Wang, M, Wang, R, Wang, S, Wang, W, Wang, X, Wang, Y, Wang, Z, Watcharangkool, A, Wei, W, Wei, Y, Wen, K, Wen, L, Wiebusch, C, Wong, S, Wonsak, B, Wu, D, Wu, Q, Wu, Z, Wurm, M, Wurtz, J, Wysotzki, C, Xi, Y, Xia, D, Xiao, X, Xie, X, Xie, Y, Xie, Z, Xin, Z, Xing, Z, Xu, B, Xu, C, Xu, D, Xu, F, Xu, H, Xu, J, Xu, M, Xu, Y, Yan, B, Yan, T, Yan, W, Yan, X, Yan, Y, Yang, C, Yang, H, Yang, J, Yang, L, Yang, X, Yang, Y, Yao, H, Ye, J, Ye, M, Ye, Z, Yermia, F, Yin, N, You, Z, Yu, B, Yu, C, Yu, H, Yu, M, Yu, X, Yu, Z, Yuan, C, Yuan, Y, Yuan, Z, Yue, B, Zafar, N, Zavadskyi, V, Zeng, S, Zeng, T, Zeng, Y, Zhan, L, Zhang, A, Zhang, B, Zhang, F, Zhang, G, Zhang, H, Zhang, J, Zhang, M, Zhang, P, Zhang, Q, Zhang, S, Zhang, T, Zhang, X, Zhang, Y, Zhang, Z, Zhao, F, Zhao, J, Zhao, R, Zhao, S, Zheng, D, Zheng, H, Zheng, Y, Zhong, W, Zhou, J, Zhou, L, Zhou, N, Zhou, S, Zhou, T, Zhou, X, Zhu, J, Zhu, K, Zhu, Z, Zhuang, B, Zhuang, H, Zong, L, Zou, J, Abusleme A., Adam T., Ahmad S., Ahmed R., Aiello S., Akram M., Aleem A., Alexandros T., An F., An Q., Andronico G., Anfimov N., Antonelli V., Antoshkina T., Asavapibhop B., de Andre J. P. A. M., Auguste D., Bai W., Balashov N., Baldini W., Barresi A., Basilico D., Baussan E., Bellato M., Bergnoli A., Birkenfeld T., Blin S., Blum D., Blyth S., Bolshakova A., Bongrand M., Bordereau C., Breton D., Brigatti A., Brugnera R., Bruno R., Budano A., Busto J., Butorov I., Cabrera A., Caccianiga B., Cai H., Cai X., Cai Y., Cai Z., Callegari R., Cammi A., Campeny A., Cao C., Cao G., Cao J., Caruso R., Cerna C., Chan C., Chang J., Chang Y., Chen G., Chen P., Chen P. -A., Chen S., Chen X., Chen Y., Chen Z., Cheng J., Cheng Y., Cheng Y. C., Chetverikov A., Chiesa D., Chimenti P., Chukanov A., Claverie G., Clementi C., Clerbaux B., Colomer Molla M., Conforti Di Lorenzo S., Corti D., Corso F. D., Dalager O., De La Taille C., Deng Z., Depnering W., Diaz M., Ding X., Ding Y., Dirgantara B., Dmitrievsky S., Dohnal T., Dolzhikov D., Donchenko G., Dong J., Doroshkevich E., Dracos M., Druillole F., Du R., Du S., Dusini S., Dvorak M., Enqvist T., Enzmann H., Fabbri A., Fan D., Fan L., Fang J., Fang W., Fargetta M., Fedoseev D., Fei Z., Feng L. -C., Feng Q., Ford R., Fournier A., Gan H., Gao F., Garfagnini A., Gavrikov A., Giammarchi M., Giudice N., Gonchar M., Gong G., Gong H., Gornushkin Y., Gottel A., Grassi M., Gromov V., Gu M., Gu X., Gu Y., Guan M., Guan Y., Guardone N., Guo C., Guo J., Guo W., Guo X., Guo Y., Hackspacher P., Hagner C., Han R., Han Y., He M., He W., Heinz T., Hellmuth P., Heng Y., Herrera R., Hor Y. K., Hou S., Hsiung Y., Hu B. -Z., Hu H., Hu J., Hu S., Hu T., Hu Y., Hu Z., Huang G., Huang H., Huang K., Huang W., Huang X., Huang Y., Hui J., Huo L., Huo W., Huss C., Hussain S., Ioannisian A., Isocrate R., Jelmini B., Jeria I., Ji X., Jia H., Jia J., Jian S., Jiang D., Jiang W., Jiang X., Jing X., Jollet C., Joutsenvaara J., Kalousis L., Kampmann P., Kang L., Karaparambil R., Kazarian N., Khatun A., Khosonthongkee K., Korablev D., Kouzakov K., Krasnoperov A., Kutovskiy N., Kuusiniemi P., Lachenmaier T., Landini C., Leblanc S., Lebrin V., Lefevre F., Lei R., Leitner R., Leung J., Li D., Li F., Li G., Li H., Li M., Li N., Li Q., Li R., Li S., Li T., Li W., Li X., Li Y., Li Z., Liang H., Liao J., Limphirat A., Lin G. -L., Lin S., Lin T., Ling J., Lippi I., Liu F., Liu H., Liu J., Liu M., Liu Q., Liu R., Liu S., Liu X., Liu Y., Lokhov A., Lombardi P., Lombardo C., Loo K., Lu C., Lu H., Lu J., Lu S., Lubsandorzhiev B., Lubsandorzhiev S., Ludhova L., Lukanov A., Luo D., Luo F., Luo G., Luo S., Luo W., Luo X., Lyashuk V., Ma B., Ma Q., Ma S., Ma X., Maalmi J., Mai J., Malyshkin Y., Mandujano R. C., Mantovani F., Manzali F., Mao X., Mao Y., Mari S. M., Marini F., Martellini C., Martin-Chassard G., Martini A., Mayer M., Mayilyan D., Mednieks I., Meng Y., Meregaglia A., Meroni E., Meyhofer D., Mezzetto M., Miller J., Miramonti L., Montini P., Montuschi M., Muller A., Nastasi M., Naumov D. V., Naumova E., Navas-Nicolas D., Nemchenok I., Nguyen Thi M. T., Ning F., Ning Z., Nunokawa H., Oberauer L., Ochoa-Ricoux J. P., Olshevskiy A., Orestano D., Ortica F., Othegraven R., Paoloni A., Parmeggiano S., Pei Y., Pelicci L., Pelliccia N., Peng A., Peng H., Peng Y., Peng Z., Perrot F., Petitjean P. -A., Petrucci F., Pilarczyk O., Pineres Rico L. F., Popov A., Poussot P., Previtali E., Qi F., Qi M., Qian S., Qian X., Qian Z., Qiao H., Qin Z., Qiu S., Ranucci G., Raper N., Re A., Rebber H., Rebii A., Redchuk M., Ren B., Ren J., Ricci B., Rifai M., Roche M., Rodphai N., Romani A., Roskovec B., Ruan X., Rybnikov A., Sadovsky A., Saggese P., Sanfilippo S., Sangka A., Sawangwit U., Sawatzki J., Schever M., Schwab C., Schweizer K., Selyunin A., Serafini A., Settanta G., Settimo M., Shao Z., Sharov V., Shaydurova A., Shi J., Shi Y., Shutov V., Sidorenkov A., Simkovic F., Sirignano C., Siripak J., Sisti M., Slupecki M., Smirnov M., Smirnov O., Sogo-Bezerra T., Sokolov S., Songwadhana J., Soonthornthum B., Sotnikov A., Sramek O., Sreethawong W., Stahl A., Stanco L., Stankevich K., Stefanik D., Steiger H., Steinmann J., Sterr T., Stock M. R., Strati V., Studenikin A., Su J., Sun S., Sun X., Sun Y., Sun Z., Suwonjandee N., Szelezniak M., Tang J., Tang Q., Tang X., Theisen E., Tietzsch A., Tkachev I., Tmej T., Torri M. D. C., Treskov K., Triossi A., Troni G., Trzaska W., Tuve C., Ushakov N., Vedin V., Verde G., Vialkov M., Viaud B., Vollbrecht C. M., Volpe C., von Sturm K., Vorobel V., Voronin D., Votano L., Walker P., Wang C., Wang C. -H., Wang E., Wang G., Wang J., Wang L., Wang M., Wang R., Wang S., Wang W., Wang X., Wang Y., Wang Z., Watcharangkool A., Wei W., Wei Y., Wen K., Wen L., Wiebusch C., Wong S. C. -F., Wonsak B., Wu D., Wu Q., Wu Z., Wurm M., Wurtz J., Wysotzki C., Xi Y., Xia D., Xiao X., Xie X., Xie Y., Xie Z., Xin Z., Xing Z., Xu B., Xu C., Xu D., Xu F., Xu H., Xu J., Xu M., Xu Y., Yan B., Yan T., Yan W., Yan X., Yan Y., Yang C., Yang H., Yang J., Yang L., Yang X., Yang Y., Yao H., Ye J., Ye M., Ye Z., Yermia F., Yin N., You Z., Yu B., Yu C., Yu H., Yu M., Yu X., Yu Z., Yuan C., Yuan Y., Yuan Z., Yue B., Zafar N., Zavadskyi V., Zeng S., Zeng T., Zeng Y., Zhan L., Zhang A., Zhang B., Zhang F., Zhang G., Zhang H., Zhang J., Zhang M., Zhang P., Zhang Q., Zhang S., Zhang T., Zhang X., Zhang Y., Zhang Z., Zhao F., Zhao J., Zhao R., Zhao S., Zheng D., Zheng H., Zheng Y., Zhong W., Zhou J., Zhou L., Zhou N., Zhou S., Zhou T., Zhou X., Zhu J., Zhu K., Zhu Z., Zhuang B., Zhuang H., Zong L., and Zou J.

Abstract

Main goal of the JUNO experiment is to determine the neutrino mass ordering using a 20 kt liquid-scintillator detector. Its key feature is an excellent energy resolution of at least 3% at 1 MeV, for which its instruments need to meet a certain quality and thus have to be fully characterized. More than 20,000 20-inch PMTs have been received and assessed by JUNO after a detailed testing program which began in 2017 and elapsed for about four years. Based on this mass characterization and a set of specific requirements, a good quality of all accepted PMTs could be ascertained. This paper presents the performed testing procedure with the designed testing systems as well as the statistical characteristics of all 20-inch PMTs intended to be used in the JUNO experiment, covering more than fifteen performance parameters including the photocathode uniformity. This constitutes the largest sample of 20-inch PMTs ever produced and studied in detail to date, i.e. 15,000 of the newly developed 20-inch MCP-PMTs from Northern Night Vision Technology Co. (NNVT) and 5000 of dynode PMTs from Hamamatsu Photonics K. K.(HPK).

Published
2022

42. Search for low-energy signals from fast radio bursts with the Borexino detector

Author

Appel, S, Bagdasarian, Z, Basilico, D, Bellini, G, Benziger, J, Biondi, R, Caccianiga, B, Calaprice, F, Caminata, A, Chepurnov, A, D'Angelo, D, Derbin, A, Giacinto, A, Marcello, V, Ding, X, Ludovico, A, Noto, L, Drachnev, I, Franco, D, Galbiati, C, Ghiano, C, Giammarchi, M, Goretti, A, Gottel, A, Gromov, M, Guffanti, D, Ianni, A, Jany, A, Kobychev, V, Korga, G, Kumaran, S, Laubenstein, M, Litvinovich, E, Lombardi, P, Lomskaya, I, Ludhova, L, Lukyanchenko, G, Machulin, I, Martyn, J, Meroni, E, Miramonti, L, Misiaszek, M, Muratova, V, Nugmanov, R, Oberauer, L, Orekhov, V, Ortica, F, Pallavicini, M, Pelicci, L, Penek, O, Pietrofaccia, L, Pilipenko, N, Pocar, A, Raikov, G, Ranalli, M, Ranucci, G, Razeto, A, Re, A, Redchuk, M, Rossi, N, Schonert, S, Semenov, D, Settanta, G, Skorokhvatov, M, Singhal, A, Smirnov, O, Sotnikov, A, Tartaglia, R, Testera, G, Unzhakov, E, Vishneva, A, Vogelaar, R, Feilitzsch, F, Wojcik, M, Wurm, M, Zavatarelli, S, Zhutikov, I, Zuber, K, Zuzel, G, Appel S., Bagdasarian Z., Basilico D., Bellini G., Benziger J., Biondi R., Caccianiga B., Calaprice F., Caminata A., Chepurnov A., D'Angelo D., Derbin A., Giacinto A. D., Marcello V. D., Ding X. F., Ludovico A. D., Noto L. D., Drachnev I., Franco D., Galbiati C., Ghiano C., Giammarchi M., Goretti A., Gottel A. S., Gromov M., Guffanti D., Ianni A., Jany A., Kobychev V., Korga G., Kumaran S., Laubenstein M., Litvinovich E., Lombardi P., Lomskaya I., Ludhova L., Lukyanchenko G., Machulin I., Martyn J., Meroni E., Miramonti L., Misiaszek M., Muratova V., Nugmanov R., Oberauer L., Orekhov V., Ortica F., Pallavicini M., Pelicci L., Penek O., Pietrofaccia L., Pilipenko N., Pocar A., Raikov G., Ranalli M. T., Ranucci G., Razeto A., Re A., Redchuk M., Rossi N., Schonert S., Semenov D., Settanta G., Skorokhvatov M., Singhal A., Smirnov O., Sotnikov A., Tartaglia R., Testera G., Unzhakov E., Vishneva A., Vogelaar R. B., Feilitzsch F., Wojcik M., Wurm M., Zavatarelli S., Zhutikov I., Zuber K., Zuzel G., Appel, S, Bagdasarian, Z, Basilico, D, Bellini, G, Benziger, J, Biondi, R, Caccianiga, B, Calaprice, F, Caminata, A, Chepurnov, A, D'Angelo, D, Derbin, A, Giacinto, A, Marcello, V, Ding, X, Ludovico, A, Noto, L, Drachnev, I, Franco, D, Galbiati, C, Ghiano, C, Giammarchi, M, Goretti, A, Gottel, A, Gromov, M, Guffanti, D, Ianni, A, Jany, A, Kobychev, V, Korga, G, Kumaran, S, Laubenstein, M, Litvinovich, E, Lombardi, P, Lomskaya, I, Ludhova, L, Lukyanchenko, G, Machulin, I, Martyn, J, Meroni, E, Miramonti, L, Misiaszek, M, Muratova, V, Nugmanov, R, Oberauer, L, Orekhov, V, Ortica, F, Pallavicini, M, Pelicci, L, Penek, O, Pietrofaccia, L, Pilipenko, N, Pocar, A, Raikov, G, Ranalli, M, Ranucci, G, Razeto, A, Re, A, Redchuk, M, Rossi, N, Schonert, S, Semenov, D, Settanta, G, Skorokhvatov, M, Singhal, A, Smirnov, O, Sotnikov, A, Tartaglia, R, Testera, G, Unzhakov, E, Vishneva, A, Vogelaar, R, Feilitzsch, F, Wojcik, M, Wurm, M, Zavatarelli, S, Zhutikov, I, Zuber, K, Zuzel, G, Appel S., Bagdasarian Z., Basilico D., Bellini G., Benziger J., Biondi R., Caccianiga B., Calaprice F., Caminata A., Chepurnov A., D'Angelo D., Derbin A., Giacinto A. D., Marcello V. D., Ding X. F., Ludovico A. D., Noto L. D., Drachnev I., Franco D., Galbiati C., Ghiano C., Giammarchi M., Goretti A., Gottel A. S., Gromov M., Guffanti D., Ianni A., Jany A., Kobychev V., Korga G., Kumaran S., Laubenstein M., Litvinovich E., Lombardi P., Lomskaya I., Ludhova L., Lukyanchenko G., Machulin I., Martyn J., Meroni E., Miramonti L., Misiaszek M., Muratova V., Nugmanov R., Oberauer L., Orekhov V., Ortica F., Pallavicini M., Pelicci L., Penek O., Pietrofaccia L., Pilipenko N., Pocar A., Raikov G., Ranalli M. T., Ranucci G., Razeto A., Re A., Redchuk M., Rossi N., Schonert S., Semenov D., Settanta G., Skorokhvatov M., Singhal A., Smirnov O., Sotnikov A., Tartaglia R., Testera G., Unzhakov E., Vishneva A., Vogelaar R. B., Feilitzsch F., Wojcik M., Wurm M., Zavatarelli S., Zhutikov I., Zuber K., and Zuzel G.

Abstract

The search for neutrino events in correlation with 42 most intense fast radio bursts (FRBs) has been performed using the Borexino dataset from 05/2007 to 06/2021. We have searched for signals with visible energies above 250 keV within a time window of ±1000 s corresponding to detection time of a particular FRB. We also applied an alternative approach based on searching for specific shapes of neutrino-electron scattering spectra in the full exposure data of the Borexino detector. In particular, two incoming neutrino spectra were considered: the monoenergetic line and the spectrum expected from supernovae. The same spectra were considered for electron antineutrinos detected through inverse beta-decay reaction. No statistically significant excess over the background was observed. As a result, the strongest upper limits on FRB-associated neutrino fluences of all flavors have been obtained in the 0.5–50 MeV neutrino energy range.

Published
2022

43. Mediastinal Lymph Node and Airway Microbiome Associations in Lung Cancer and Sarcoidosis

Author

Shojaee, S., primary, Sharma, A., additional, Tareen, M.K., additional, Sanchez, T.M., additional, Gottel, N., additional, James, W.E., additional, Lee, P.M., additional, Yermakhanova, G., additional, Syed, A.A., additional, Iden, T., additional, Grogan, E., additional, Deppen, S., additional, Kammer, M.N., additional, Maldonado, F., additional, Fowler, A.A., additional, Drake, W.P., additional, White, S.R., additional, and Gilbert, J.A., additional

Published
2023
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44. Microbial Similarity between Students in a Common Dormitory Environment Reveals the Forensic Potential of Individual Microbial Signatures

Author

Miles Richardson, Neil Gottel, Jack A. Gilbert, and Simon Lax

Subjects
built environments, microbial ecology, microbial transmission, Microbiology, QR1-502
Abstract

ABSTRACT The microbiota of the built environment is an amalgamation of both human and environmental sources. While human sources have been examined within single-family households or in public environments, it is unclear what effect a large number of cohabitating people have on the microbial communities of their shared environment. We sampled the public and private spaces of a college dormitory, disentangling individual microbial signatures and their impact on the microbiota of common spaces. We compared multiple methods for marker gene sequence clustering and found that minimum entropy decomposition (MED) was best able to distinguish between the microbial signatures of different individuals and was able to uncover more discriminative taxa across all taxonomic groups. Further, weighted UniFrac- and random forest-based graph analyses uncovered two distinct spheres of hand- or shoe-associated samples. Using graph-based clustering, we identified spheres of interaction and found that connection between these clusters was enriched for hands, implicating them as a primary means of transmission. In contrast, shoe-associated samples were found to be freely interacting, with individual shoes more connected to each other than to the floors they interact with. Individual interactions were highly dynamic, with groups of samples originating from individuals clustering freely with samples from other individuals, while all floor and shoe samples consistently clustered together. IMPORTANCE Humans leave behind a microbial trail, regardless of intention. This may allow for the identification of individuals based on the “microbial signatures” they shed in built environments. In a shared living environment, these trails intersect, and through interaction with common surfaces may become homogenized, potentially confounding our ability to link individuals to their associated microbiota. We sought to understand the factors that influence the mixing of individual signatures and how best to process sequencing data to best tease apart these signatures.

Published
2019
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45. Mice Fed an Obesogenic Western Diet, Administered Antibiotics, and Subjected to a Sterile Surgical Procedure Develop Lethal Septicemia with Multidrug-Resistant Pathobionts

Author

Sanjiv K. Hyoju, Alexander Zaborin, Robert Keskey, Anukriti Sharma, Wyatt Arnold, Fons van den Berg, Sangman M. Kim, Neil Gottel, Cindy Bethel, Angella Charnot-Katsikas, Peng Jianxin, Carleen Adriaansens, Emily Papazian, Jack A. Gilbert, Olga Zaborina, and John C. Alverdy

Subjects
Western diet, gut microbiome, gut-derived sepsis, pathobionts, surgery, Microbiology, QR1-502
Abstract

ABSTRACT Despite antibiotics and sterile technique, postoperative infections remain a real and present danger to patients. Recent estimates suggest that 50% of the pathogens associated with postoperative infections have become resistant to the standard antibiotics used for prophylaxis. Risk factors identified in such cases include obesity and antibiotic exposure. To study the combined effect of obesity and antibiotic exposure on postoperative infection, mice were allowed to gain weight on an obesogenic Western-type diet (WD), administered antibiotics and then subjected to an otherwise recoverable sterile surgical injury (30% hepatectomy). The feeding of a WD alone resulted in a major imbalance of the cecal microbiota characterized by a decrease in diversity, loss of Bacteroidetes, a bloom in Proteobacteria, and the emergence of antibiotic-resistant organisms among the cecal microbiota. When WD-fed mice were administered antibiotics and subjected to 30% liver resection, lethal sepsis, characterized by multiple-organ damage, developed. Notable was the emergence and systemic dissemination of multidrug-resistant (MDR) pathobionts, including carbapenem-resistant, extended-spectrum β-lactamase-producing Serratia marcescens, which expressed a virulent and immunosuppressive phenotype. Analysis of the distribution of exact sequence variants belonging to the genus Serratia suggested that these strains originated from the cecal mucosa. No mortality or MDR pathogens were observed in identically treated mice fed a standard chow diet. Taken together, these results suggest that consumption of a Western diet and exposure to certain antibiotics may predispose to life-threating postoperative infection associated with MDR organisms present among the gut microbiota. IMPORTANCE Obesity remains a prevalent and independent risk factor for life-threatening infection following major surgery. Here, we demonstrate that when mice are fed an obesogenic Western diet (WD), they become susceptible to lethal sepsis with multiple organ damage after exposure to antibiotics and an otherwise-recoverable surgical injury. Analysis of the gut microbiota in this model demonstrates that WD alone leads to loss of Bacteroidetes, a bloom of Proteobacteria, and evidence of antibiotic resistance development even before antibiotics are administered. After antibiotics and surgery, lethal sepsis with organ damage developed in in mice fed a WD with the appearance of multidrug-resistant pathogens in the liver, spleen, and blood. The importance of these findings lies in exposing how the selective pressures of diet, antibiotic exposure, and surgical injury can converge on the microbiome, resulting in lethal sepsis and organ damage without the introduction of an exogenous pathogen.

Published
2019
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46. A Simple Microbiome in the European Common Cuttlefish, Sepia officinalis

Author

Holly L. Lutz, S. Tabita Ramírez-Puebla, Lisa Abbo, Amber Durand, Cathleen Schlundt, Neil R. Gottel, Alexandra K. Sjaarda, Roger T. Hanlon, Jack A. Gilbert, and Jessica L. Mark Welch

Subjects
Cephalopoda, Piscirickettsiaceae, Vibrionaceae, enrofloxacin, fluorescence assays, microbiome, Microbiology, QR1-502
Abstract

ABSTRACT The European common cuttlefish, Sepia officinalis, is used extensively in biological and biomedical research, yet its microbiome remains poorly characterized. We analyzed the microbiota of the digestive tract, gills, and skin in mariculture-raised S. officinalis using a combination of 16S rRNA amplicon sequencing, quantitative PCR (qPCR), and fluorescence spectral imaging. Sequencing revealed a highly simplified microbiota consisting largely of two single bacterial amplicon sequence variants (ASVs) of Vibrionaceae and Piscirickettsiaceae. The esophagus was dominated by a single ASV of the genus Vibrio. Imaging revealed bacteria in the family Vibrionaceae distributed in a discrete layer that lines the esophagus. This Vibrio was also the primary ASV found in the microbiota of the stomach, cecum, and intestine, but occurred at lower abundance, as determined by qPCR, and was found only scattered in the lumen rather than in a discrete layer via imaging analysis. Treatment of animals with the commonly used antibiotic enrofloxacin led to a nearly 80% reduction of the dominant Vibrio ASV in the esophagus but did not significantly alter the relative abundance of bacteria overall between treated versus control animals. Data from the gills were dominated by a single ASV in the family Piscirickettsiaceae, which imaging visualized as small clusters of cells. We conclude that bacteria belonging to the Gammaproteobacteria are the major symbionts of the cuttlefish Sepia officinalis cultured from eggs in captivity and that the esophagus and gills are major colonization sites. IMPORTANCE Microbes can play critical roles in the physiology of their animal hosts, as evidenced in cephalopods by the role of Vibrio (Aliivibrio) fischeri in the light organ of the bobtail squid and the role of Alpha- and Gammaproteobacteria in the reproductive system and egg defense in a variety of cephalopods. We sampled the cuttlefish microbiome throughout the digestive tract, gills, and skin and found dense colonization of an unexpected site, the esophagus, by a microbe of the genus Vibrio, as well as colonization of gills by Piscirickettsiaceae. This finding expands the range of organisms and body sites known to be associated with Vibrio and is of potential significance for understanding host-symbiont associations, as well as for understanding and maintaining the health of cephalopods in mariculture.

Published
2019
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47. The human microbiota is associated with cardiometabolic risk across the epidemiologic transition.

Author

Na Fei, Beatriz Peñalver Bernabé, Louise Lie, Danny Baghdan, Kweku Bedu-Addo, Jacob Plange-Rhule, Terrence E Forrester, Estelle V Lambert, Pascal Bovet, Neil Gottel, Walter Riesen, Wolfgang Korte, Amy Luke, Stephanie A Kliethermes, Brian T Layden, Jack A Gilbert, and Lara R Dugas

Subjects
Medicine, Science
Abstract

Oral and fecal microbial biomarkers have previously been associated with cardiometabolic (CM) risk, however, no comprehensive attempt has been made to explore this association in minority populations or across different geographic regions. We characterized gut- and oral-associated microbiota and CM risk in 655 participants of African-origin, aged 25-45, from Ghana, South Africa, Jamaica, and the United States (US). CM risk was classified using the CM risk cut-points for elevated waist circumference, elevated blood pressure and elevated fasted blood glucose, low high-density lipoprotein (HDL), and elevated triglycerides. Gut-associated bacterial alpha diversity negatively correlated with elevated blood pressure and elevated fasted blood glucose. Similarly, gut bacterial beta diversity was also significantly differentiated by waist circumference, blood pressure, triglyceridemia and HDL-cholesterolemia. Notably, differences in inter- and intra-personal gut microbial diversity were geographic-region specific. Participants meeting the cut-points for 3 out of the 5 CM risk factors were significantly more enriched with Lachnospiraceae, and were significantly depleted of Clostridiaceae, Peptostreptococcaceae, and Prevotella. The predicted relative proportions of the genes involved in the pathways for lipopolysaccharides (LPS) and butyrate synthesis were also significantly differentiated by the CM risk phenotype, whereby genes involved in the butyrate synthesis via lysine, glutarate and 4-aminobutyrate/succinate pathways and LPS synthesis pathway were enriched in participants with greater CM risk. Furthermore, inter-individual oral microbiota diversity was also significantly associated with the CM risk factors, and oral-associated Streptococcus, Prevotella, and Veillonella were enriched in participants with 3 out of the 5 CM risk factors. We demonstrate that in a diverse cohort of African-origin adults, CM risk is significantly associated with reduced microbial diversity, and the enrichment of specific bacterial taxa and predicted functional traits in both gut and oral environments. As well as providing new insights into the associations between the gut and oral microbiota and CM risk, this study also highlights the potential for novel therapeutic discoveries which target the oral and gut microbiota in CM risk.

Published
2019
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49. Study of antineutrinos from the Earth and the Cosmos with the Borexino detector

Author

Zavatarelli, Sandra, primary, Agostini, M., additional, Altenmuller, K., additional, Appel, S., additional, Atroshchenko, V., additional, Bagdasarian, Z., additional, Basilico, D., additional, Bellini, G., additional, Benziger, J., additional, Biondi, R., additional, Bravo, D., additional, Caccianiga, B., additional, Caminata, A., additional, Calaprice, F., additional, Cavalcante, P., additional, Chepurnov, A., additional, D’Angelo, D., additional, Davini, S., additional, Derbin, A., additional, Di Giacinto, A., additional, Di Marcello, V., additional, Ding, X.F., additional, Di Ludovico, A., additional, Di Noto, L., additional, Drachnev, I., additional, Formozov, A., additional, Franco, D., additional, Galbiati, C., additional, Ghiano, C., additional, Giammarchi, M., additional, Goretti, A., additional, Gottel, A.S., additional, Gromov, M., additional, Guffanti, D., additional, Ianni, Aldo, additional, Ianni, Andrea, additional, Jany, A., additional, Jeschke, D., additional, Kobychev, V., additional, Korga, G., additional, Kumaran, S., additional, Laubenstein, M., additional, Litvinovich, E., additional, Lombardi, P., additional, Lomskaya, I., additional, Ludhova, L., additional, Lukyanchenko, G., additional, Lukyanchenko, L., additional, Machulin, I., additional, Martyn, J., additional, Meroni, E., additional, Meyer, M., additional, Miramonti, L., additional, Misiaszek, M., additional, Muratova, V., additional, Neumair, B., additional, Nieslony, M., additional, Nugmanov, R., additional, Oberauer, L., additional, Orekhov, V., additional, Ortica, F., additional, Pallavicini, M., additional, Papp, L., additional, Pelicci, L., additional, Penek, O, additional, Pietrofaccia, L., additional, Pilipenko, N., additional, Pocar, A., additional, Raikov, G., additional, Ranalli, M.T., additional, Ranucci, G., additional, Razeto, A., additional, Re, A., additional, Redchuk, M., additional, Romani, A., additional, Rossi, N., additional, Schonert, S., additional, Semenov, D., additional, Settanta, G., additional, Skorokhvatov, M., additional, Singhal, A., additional, Smirnov, O., additional, Sotnikov, A., additional, Suvorov, Y., additional, Tartaglia, R., additional, Testera, G., additional, Thurn, J., additional, Unzhakov, E., additional, Villante, F., additional, Vishneva, A., additional, Vogelaar, R.B., additional, von Feilitzsch, F., additional, Wojcik, M., additional, Wurm, M., additional, Zavatarelli, S., additional, Zuber, K., additional, and Zuzel, G., additional

Published
2023
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50. Study of antineutrinos from the Earth and the Cosmos with the Borexino detector

Author

Sandra Zavatarelli, M. Agostini, K. Altenmuller, S. Appel, V. Atroshchenko, Z. Bagdasarian, D. Basilico, G. Bellini, J. Benziger, R. Biondi, D. Bravo, B. Caccianiga, A. Caminata, F. Calaprice, P. Cavalcante, A. Chepurnov, D. D’Angelo, S. Davini, A. Derbin, A. Di Giacinto, V. Di Marcello, X.F. Ding, A. Di Ludovico, L. Di Noto, I. Drachnev, A. Formozov, D. Franco, C. Galbiati, C. Ghiano, M. Giammarchi, A. Goretti, A.S. Gottel, M. Gromov, D. Guffanti, Aldo Ianni, Andrea Ianni, A. Jany, D. Jeschke, V. Kobychev, G. Korga, S. Kumaran, M. Laubenstein, E. Litvinovich, P. Lombardi, I. Lomskaya, L. Ludhova, G. Lukyanchenko, L. Lukyanchenko, I. Machulin, J. Martyn, E. Meroni, M. Meyer, L. Miramonti, M. Misiaszek, V. Muratova, B. Neumair, M. Nieslony, R. Nugmanov, L. Oberauer, V. Orekhov, F. Ortica, M. Pallavicini, L. Papp, L. Pelicci, O Penek, L. Pietrofaccia, N. Pilipenko, A. Pocar, G. Raikov, M.T. Ranalli, G. Ranucci, A. Razeto, A. Re, M. Redchuk, A. Romani, N. Rossi, S. Schonert, D. Semenov, G. Settanta, M. Skorokhvatov, A. Singhal, O. Smirnov, A. Sotnikov, Y. Suvorov, R. Tartaglia, G. Testera, J. Thurn, E. Unzhakov, F. Villante, A. Vishneva, R.B. Vogelaar, F. von Feilitzsch, M. Wojcik, M. Wurm, S. Zavatarelli, K. Zuber, and G. Zuzel

Published
2023

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