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1. Valorization of volatile fatty acids from the dark fermentation waste Streams-A promising pathway for a biorefinery concept

Author

Sekoai, Patrick T, Ghimire, Anish, Ezeokoli, Obinna T, Rao, Subramanya, Ngan, Y, Habimana, Olivier, Yao, Yuan, Yang, Pu, Fung, Aster Hei Yiu, Yoro, Kelvin O, Daramola, Michael O, and Hung, Chun-Hsiung

Subjects
Affordable and Clean Energy, Engineering, Energy
Abstract

In recent years, much attention has been directed towards the integration of dark fermentation process into a biorefinery concept to enhance the energetic gains, thereby improving the competitiveness of this process. The volatile fatty acids (VFAs) from dark fermentative H2-producing processes serve as precursors for the microbial synthesis of a broad spectrum of biotechnologically-important products such as biofuels and biocommodities. These products are desirable substrates for secondary bioprocesses due to their biodegradable nature and affordability. This short review discusses the use of acidogenic-derived VFAs in the production of value-added compounds such as polyhydroxyalkanoates (PHAs) alongside the microbial-based fuels (hydrogen, biogas, and electricity), and other valuable compounds (succinic acid, citric acid, and butanol). The review also highlights the strategies that have been used to enhance the extraction of VFAs from acidogenic effluents and other related waste streams. The application of novel enhancement techniques such as nanoparticles during VFAs recovery is also discussed in this work. Furthermore, the work highlights some of the recent advances in dark fermentation-based biorefinery, particularly the development of pilot-scale processes. Finally, the review provides some suggestions on the advancement of dark fermentation-based biorefineries using VFAs that are derived from acidogenic processes.

Published
2021

2. Zanubrutinib in patients with previously treated B-cell malignancies intolerant of previous Bruton tyrosine kinase inhibitors in the USA: a phase 2, open-label, single-arm study

Author

Shadman, Mazyar, Flinn, Ian W, Levy, Moshe Y, Porter, Ryan F, Burke, John M, Zafar, Syed F, Misleh, Jamal, Kingsley, Edwin C, Yimer, Habte A, Freeman, Benjamin, Rao, Subramanya S, Chaudhry, Arvind, Tumula, Praveen K, Gandhi, Mitul D, Manda, Sudhir, Chen, Dih-Yih, By, Kunthel, Xu, Linlin, Liu, Ye, Crescenzo, Rocco, Idoine, Adam, Zhang, Xiaoping, Cohen, Aileen, Huang, Jane, and Sharman, Jeff P

Published
2023
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5. Taxonomic and Functional Diversity of Soil and Hypolithic Microbial Communities in Miers Valley, McMurdo Dry Valleys, Antarctica

Author

Wei, Sean TS, Lacap-Bugler, Donnabella C, Lau, Maggie CY, Caruso, Tancredi, Rao, Subramanya, de los Rios, Asunción, Archer, Stephen K, Chiu, Jill MY, Higgins, Colleen, Van Nostrand, Joy D, Zhou, Jizhong, Hopkins, David W, and Pointing, Stephen B

Subjects
Microbiology, Biological Sciences, Ecology, Antarctica, cyanobacteria, Dry Valleys, Geochip, hypolith, soil, Environmental Science and Management, Soil Sciences, Medical microbiology
Abstract

The McMurdo Dry Valleys of Antarctica are an extreme polar desert. Mineral soils support subsurface microbial communities and translucent rocks support development of hypolithic communities on ventral surfaces in soil contact. Despite significant research attention, relatively little is known about taxonomic and functional diversity or their inter-relationships. Here we report a combined diversity and functional interrogation for soil and hypoliths of the Miers Valley in the McMurdo Dry Valleys of Antarctica. The study employed 16S rRNA fingerprinting and high throughput sequencing combined with the GeoChip functional microarray. The soil community was revealed as a highly diverse reservoir of bacterial diversity dominated by actinobacteria. Hypolithic communities were less diverse and dominated by cyanobacteria. Major differences in putative functionality were that soil communities displayed greater diversity in stress tolerance and recalcitrant substrate utilization pathways, whilst hypolithic communities supported greater diversity of nutrient limitation adaptation pathways. A relatively high level of functional redundancy in both soil and hypoliths may indicate adaptation of these communities to fluctuating environmental conditions.

Published
2016

9. An Improved EllipticNet Algorithm for Tate Pairing on Weierstrass’ Curves, Faster Point Arithmetic and Pairing on Selmer Curves and a Note on Double Scalar Multiplication

Author

Rao, Srinivasa Rao Subramanya, Diniz Junqueira Barbosa, Simone, Series editor, Chen, Phoebe, Series editor, Du, Xiaoyong, Series editor, Filipe, Joaquim, Series editor, Kara, Orhun, Series editor, Kotenko, Igor, Series editor, Liu, Ting, Series editor, Sivalingam, Krishna M., Series editor, Washio, Takashi, Series editor, Batten, Lynn, editor, and Li, Gang, editor

Published
2016
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12. Characterization of Mucosa-Associated Microbiota in Matched Cancer and Non-neoplastic Mucosa From Patients With Colorectal Cancer

Author

Polly H. M. Leung, Rao Subramanya, Qianqian Mou, Katherine Ting-wei Lee, Farhadul Islam, Vinod Gopalan, Cu-tai Lu, and Alfred King-yin Lam

Subjects
colorectal cancer, mucosa-associated microbiota, dysbiosis, Fusobacterium, Brevundimonas, 16S rRNA amplicon sequencing, Microbiology, QR1-502
Abstract

Colonic microbiota play important roles in the development of colorectal cancer. We aim to characterise the mucosa-associated microbiota in the tumour as well as the matched non-neoplastic mucosa from patients with colorectal cancer. Microbiota profiling in these samples was done using high-throughput 16S rRNA amplicon sequencing. Our results showed that the microbiota richness and diversity were similar between the tumour and non-neoplastic mucosae. Linear discriminant analysis effect size (LEfSe) analysis identified Fusobacterium and Campylobacter as the key genera of the tumour while Brevundimonas as the key genus of the non-neoplastic mucosa. In patients with shorter survival period, the relative abundance of Fusobacterium and Campylobacter was significantly higher in the tumour. Besides, regardless of the sites, tumour showed higher abundance of Fusobacterium. On the other hand, the relative abundance of Brevundimonas was significantly lower in the tumour. When validated with quantitative ddPCR, we found the absolute numbers of both Fusobacterium and F. nucleatum were significantly higher in the carcinoma from patients with shorter survival period, conventional type of adenocarcinoma in the distal portion of the large intestine (descending colon, sigmoidal colon, and rectum). In conclusion, our study showed a compositional alteration in the mucosa-associated microbiota in the tumour, which may contribute to the progression of colorectal cancer.

Published
2019
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13. A communal catalogue reveals Earths multiscale microbial diversity

Author

Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vzquez-Baeza, Yoshiki, Gonzlez, Antonio, Morton, James T., Mirarab, Siavash, Zech Xu, Zhenjiang, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Jin Song, Se, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Barta, Jiri, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric, Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Monica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frederic, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chris, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Garcia-Amado, Maria Alexandra, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibanez-Alamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan, Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martin-Platero, Antonio M., Martin-Vivaldi, Manuel, Martinez, L. Margarita, Martinez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Monica, Mendelson, Joseph R., Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, OBrien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sanchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Miles, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjoling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, and Zhao, Hongxia

Subjects
Biological diversity -- Observations -- Environmental aspects, Microbial colonies -- Environmental aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Our growing awareness of the microbial worlds importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earths microbial diversity., Author(s): Luke R. Thompson [1, 2, 3]; Jon G. Sanders [1]; Daniel McDonald [1]; Amnon Amir [1]; Joshua Ladau [4]; Kenneth J. Locey [5]; Robert J. Prill [6]; Anupriya Tripathi [...]

Published
2017
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15. Epidemiology, clinical profile, management, and outcome of COVID-19-associated rhino-orbital-cerebral mucormycosis in 2826 patients in India - Collaborative OPAI-IJO Study on Mucormycosis in COVID-19 (COSMIC), Report 1

Author

Sen, Mrittika, Honavar, Santosh, Sengupta, Sabyasachi, Rao, Raksha, Kim, Usha, Sharma, Mukesh, Sachdev, Mahipal, Grover, Ashok, Surve, Abhidnya, Budharapu, Abhishek, Ramadhin, Abhishek, Tripathi, Abhishek, Gupta, Adit, Bhargava, Aditya, Sahu, Animesh, Khairnar, Anjali, Kochar, Anju, Madhavani, Ankita, Shrivastava, Ankur, Desai, Anuja, Paul, Anujeet, Ayyar, Anuradha, Bhatnagar, Aparna, Singhal, Aparna, Nikose, Archana, Bhargava, Arun, Tenagi, Arvind, Kamble, Ashish, Nariani, Ashiyana, Patel, Bhavin, Kashyap, Bibbhuti, Dhawan, Bodhraj, Vohra, Busaraben, Mandke, Charuta, Thrishulamurthy, Chinmayee, Sambare, Chitra, Sarkar, Deepayan, Mankad, Devanshi, Maheshwari, Dhwani, Lalwani, Dilip, Kanani, Dipti, Patel, Diti, Manjandavida, Fairooz, Godhani, Frenali, Agarwal, Garima, Ravulaparthi, Gayatri, Shilpa, Gondhi, Deshpande, Gunjan, Thakkar, Hansa, Shah, Hardik, Ojha, Hare, Jani, Harsha, Gontia, Jyoti, Mishrikotkar, Jyotika, Likhari, Kamalpreet, Prajapati, Kamini, Porwal, Kavita, Koka, Kirthi, Dharawat, Kulveer, Ramamurthy, Lakshmi, Bhattacharyya, Mainak, Saini, Manorama, Christy, Marem, Das, Mausumi, Hada, Maya, Panchal, Mehul, Pandharpurkar, Modini, Ali, Mohammad, Porwal, Mukesh, Gangashetappa, Nagaraju, Mehrotra, Neelima, Bijlani, Neha, Gajendragadkar, Nidhi, Nagarkar, Nitin, Modi, Palak, Rewri, Parveen, Sao, Piyushi, Patil, Prajakta, Giri, Pramod, Kapadia, Priti, Yadav, Priti, Bhagat, Purvi, Parekh, Ragini, Dyaberi, Rajashekhar, Chauhan, Rajender, Kaur, Rajwinder, Duvesh, Ram, Murthy, Ramesh, Dandu, Ravi, Kathiara, Ravija, Beri, Renu, Pandit, Rinal, Rani, Rita, Gupta, Roshmi, Pherwani, Ruchi, Sapkal, Rujuta, Mehta, Rupa, Tadepalli, Sameeksha, Fatima, Samra, Karmarkar, Sandeep, Patil, Sandeep, Shah, Sanjana, Shah, Sankit, Shah, Sapan, Dubey, Sarika, Gandhi, Saurin, Kanakpur, Savitha, Mohan, Shalini, Bhomaj, Sharad, Kerkar, Sheela, Jariwala, Shivani, Sahu, Shivati, Tara, Shruthi, Maru, Shruti, Sharma, Shubhda, Gupta, Shweta, Kumari, Shwetha, Das, Sima, Menon, Smita, Burkule, Snehal, Nisar, Sonam, Kaliaperumal, Subashini, Rao, Subramanya, Pakrasi, Sudipto, Rathod, Sujatha, Biradar, Sunil, Kumar, Suresh, Dutt, Susheen, Bansal, Svati, Ravani, Swati, Lohiya, Sweta, Rizvi, Syed Ali, Gokhale, Tanmay, Lahane, Tatyarao, Vukkadala, Tejaswini, Grover, Triveni, Bhesaniya, Trupti, Chawla, Urmil, Singh, Usha, Une, Vaishali, Nandedkar, Varsha, Subramaniam, Venkata, Eswaran, Vidya, Chaudhry, Vidya, Rangarajan, Viji, Dehane, Vipin, Sahasrabudhe, Vivek, Sowjanya, Yarra, Tupkary, Yashaswini, and Phadke, Yogita

Subjects
Epidemics -- Forecasts and trends -- India, Corticosteroids -- Testing, Mucormycosis -- Diagnosis -- Care and treatment -- Distribution, Market trend/market analysis, Company distribution practices, Health
Abstract

Byline: Mrittika. Sen, Santosh. Honavar, Sabyasachi. Sengupta, Raksha. Rao, Usha. Kim, Mukesh. Sharma, Mahipal. Sachdev, Ashok. Grover, Abhidnya. Surve, Abhishek. Budharapu, Abhishek. Ramadhin, Abhishek. Tripathi, Adit. Gupta, Aditya. Bhargava, Animesh. [...]

Published
2021

20. Phase 2 Study of Zanubrutinib in BTK Inhibitor-Intolerant Patients (Pts) with Relapsed/Refractory B-Cell Malignancies

Author

Shadman, Mazyar, primary, Flinn, Ian W., additional, Levy, Moshe Y., additional, Porter, Ryan, additional, Burke, John M., additional, Cultrera, Jennifer L., additional, Misleh, Jamal, additional, Zafar, Syed F., additional, Freeman, Benjamin, additional, Rao, Subramanya S., additional, Yimer, Habte, additional, Chaudhry, Arvind, additional, Gandhi, Mitul D., additional, Guthrie, Troy H., additional, Kingsley, Edwin, additional, Tumula, Praveen K., additional, Manda, Sudhir, additional, Chen, Dih-Yih, additional, Cohen, Aileen, additional, By, Kunthel, additional, Xu, Linlin, additional, Liu, Ye, additional, and Sharman, Jeff P., additional

Published
2021
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23. Preliminary results of the phase 2 study of zanubrutinib in patients with previously treated B-cell malignancies intolerant to ibrutinib and/or acalabrutinib.

Author

Shadman, Mazyar, primary, Sharman, Jeff Porter, additional, Levy, Moshe Y., additional, Porter, Ryan, additional, Zafar, Syed Farhan, additional, Burke, John M., additional, Chaudhry, Arvind, additional, Freeman, Benjamin Bruce, additional, Misleh, Jamal Ghazi, additional, Yimer, Habte Aragaw, additional, Cultrera, Jennifer L., additional, Guthrie, Troy H., additional, Kingsley, Ed, additional, Rao, Subramanya S., additional, Chen, Dih-Yih, additional, Cohen, Aileen, additional, Feng, Shibao, additional, Huang, Jane, additional, and Flinn, Ian, additional

Published
2021
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25. EpImpact of the use of digital devices on e of COVID-19-associated rhino-orbital-cerebral mucormycosis in 2826 patients in India – Collaborative OPAI-IJO Study on Mucormycosis in COVID-19 (COSMIC), Report 1

Author

Honavar, SantoshG, primary, Sen, Mrittika, additional, Sengupta, Sabyasachi, additional, Rao, Raksha, additional, Kim, Usha, additional, Sharma, Mukesh, additional, Sachdev, Mahipal, additional, Grover, AshokK, additional, Surve, Abhidnya, additional, Budharapu, Abhishek, additional, Ramadhin, AbhishekK, additional, Tripathi, AbhishekKumar, additional, Gupta, Adit, additional, Bhargava, Aditya, additional, Sahu, Animesh, additional, Khairnar, Anjali, additional, Kochar, Anju, additional, Madhavani, Ankita, additional, Shrivastava, AnkurK, additional, Desai, AnujaK, additional, Paul, Anujeet, additional, Ayyar, Anuradha, additional, Bhatnagar, Aparna, additional, Singhal, Aparna, additional, Nikose, ArchanaSunil, additional, Bhargava, Arun, additional, Tenagi, ArvindL, additional, Kamble, Ashish, additional, Nariani, Ashiyana, additional, Patel, Bhavin, additional, Kashyap, Bibbhuti, additional, Dhawan, Bodhraj, additional, Vohra, Busaraben, additional, Mandke, Charuta, additional, Thrishulamurthy, Chinmayee, additional, Sambare, Chitra, additional, Sarkar, Deepayan, additional, Mankad, DevanshiShirishbhai, additional, Maheshwari, Dhwani, additional, Lalwani, Dilip, additional, Kanani, Dipti, additional, Patel, Diti, additional, Manjandavida, FairoozP, additional, Godhani, Frenali, additional, Agarwal, GarimaAmol, additional, Ravulaparthi, Gayatri, additional, Shilpa, GondhiVijay, additional, Deshpande, Gunjan, additional, Thakkar, Hansa, additional, Shah, Hardik, additional, Ojha, HareRam, additional, Jani, Harsha, additional, Gontia, Jyoti, additional, Mishrikotkar, JyotikaP, additional, Likhari, Kamalpreet, additional, Prajapati, Kamini, additional, Porwal, Kavita, additional, Koka, Kirthi, additional, Dharawat, KulveerSingh, additional, Ramamurthy, LakshmiB, additional, Bhattacharyya, Mainak, additional, Saini, Manorama, additional, Christy, MaremC, additional, Das, Mausumi, additional, Hada, Maya, additional, Panchal, Mehul, additional, Pandharpurkar, Modini, additional, Ali, MohammadOsman, additional, Porwal, Mukesh, additional, Gangashetappa, Nagaraju, additional, Mehrotra, Neelima, additional, Bijlani, Neha, additional, Gajendragadkar, Nidhi, additional, Nagarkar, NitinM, additional, Modi, Palak, additional, Rewri, Parveen, additional, Sao, Piyushi, additional, Patil, PrajaktaSalunkhe, additional, Giri, Pramod, additional, Kapadia, Priti, additional, Yadav, Priti, additional, Bhagat, Purvi, additional, Parekh, Ragini, additional, Dyaberi, Rajashekhar, additional, Chauhan, RajenderSingh, additional, Kaur, Rajwinder, additional, Duvesh, RamKishan, additional, Murthy, Ramesh, additional, Dandu, RaviVarma, additional, Kathiara, Ravija, additional, Beri, Renu, additional, Pandit, Rinal, additional, Rani, RitaHepsi, additional, Gupta, Roshmi, additional, Pherwani, Ruchi, additional, Sapkal, Rujuta, additional, Mehta, Rupa, additional, Tadepalli, Sameeksha, additional, Fatima, Samra, additional, Karmarkar, Sandeep, additional, Patil, SandeepSuresh, additional, Shah, Sanjana, additional, Shah, Sankit, additional, Shah, Sapan, additional, Dubey, Sarika, additional, Gandhi, Saurin, additional, Kanakpur, Savitha, additional, Mohan, Shalini, additional, Bhomaj, Sharad, additional, Kerkar, Sheela, additional, Jariwala, Shivani, additional, Sahu, Shivati, additional, Tara, Shruthi, additional, Maru, ShrutiKochar, additional, Sharma, Shubhda, additional, Gupta, Shweta, additional, Kumari, Shwetha, additional, Das, Sima, additional, Menon, Smita, additional, Burkule, Snehal, additional, Nisar, SonamPoonam, additional, Kaliaperumal, Subashini, additional, Rao, Subramanya, additional, Pakrasi, Sudipto, additional, Rathod, Sujatha, additional, Biradar, SunilG, additional, Kumar, Suresh, additional, Dutt, Susheen, additional, Bansal, Svati, additional, Ravani, SwatiAmulbhai, additional, Lohiya, Sweta, additional, Ali Rizvi, SyedWajahat, additional, Gokhale, Tanmay, additional, Lahane, TatyaraoP, additional, Vukkadala, Tejaswini, additional, Grover, Triveni, additional, Bhesaniya, Trupti, additional, Chawla, Urmil, additional, Singh, Usha, additional, Une, VaishaliL, additional, Nandedkar, Varsha, additional, Subramaniam, Venkata, additional, Eswaran, Vidya, additional, Chaudhry, VidyaNair, additional, Rangarajan, Viji, additional, Dehane, Vipin, additional, Sahasrabudhe, VivekM, additional, Sowjanya, Yarra, additional, Tupkary, Yashaswini, additional, and Phadke, Yogita, additional

Published
2021
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27. Characterization of Mucosa-Associated Microbiota in Matched Cancer and Non-neoplastic Mucosa From Patients With Colorectal Cancer

Author

Katherine Ting-Wei Lee, Alfred King-Yin Lam, Cu Tai Lu, Qianqian Mou, Rao Subramanya, Farhadul Islam, Vinod Gopalan, and Polly H.M. Leung

Subjects
Microbiology (medical), medicine.medical_specialty, Colorectal cancer, lcsh:QR1-502, Rectum, colorectal cancer, Gastroenterology, 16S rRNA amplicon sequencing, Microbiology, lcsh:Microbiology, Descending colon, 03 medical and health sciences, Internal medicine, Carcinoma, medicine, mucosa-associated microbiota, Large intestine, 030304 developmental biology, Original Research, 0303 health sciences, biology, 030306 microbiology, dysbiosis, Fusobacterium, medicine.disease, biology.organism_classification, stomatognathic diseases, medicine.anatomical_structure, Adenocarcinoma, Brevundimonas, Dysbiosis
Abstract

Colonic microbiota play important roles in the development of colorectal cancer. We aim to characterise the mucosa-associated microbiota in the tumour as well as the matched non-neoplastic mucosa from patients with colorectal cancer. Microbiota profiling in these samples was done using high-throughput 16S rRNA amplicon sequencing. Our results showed that the microbiota richness and diversity were similar between the tumour and non-neoplastic mucosae. Linear discriminant analysis effect size (LEfSe) analysis identified Fusobacterium and Campylobacter as the key genera of the tumour while Brevundimonas as the key genus of the non-neoplastic mucosa. In patients with shorter survival period, the relative abundance of Fusobacterium and Campylobacter was significantly higher in the tumour. Besides, regardless of the sites, tumour showed higher abundance of Fusobacterium. On the other hand, the relative abundance of Brevundimonas was significantly lower in the tumour. When validated with quantitative ddPCR, we found the absolute numbers of both Fusobacterium and F. nucleatum were significantly higher in the carcinoma from patients with shorter survival period, conventional type of adenocarcinoma in the distal portion of the large intestine (descending colon, sigmoidal colon, and rectum). In conclusion, our study showed a compositional alteration in the mucosa-associated microbiota in the tumour, which may contribute to the progression of colorectal cancer.

Published
2019
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28. A communal catalogue reveals Earth's multiscale microbial diversity

Author

Biological Sciences, Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vazquez-Baeza, Yoshiki, Gonzalez, Antonio, Morton, James T., Mirarab, Siavash, Xu, Zhenjiang Zech, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Song, Se Jin, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Barta, Jiri, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric M., Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Monica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frederic, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chris, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Alexandra Garcia-Amado, Maria, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibanez-Alamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan G., Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martin-Platero, Antonio M., Martin-Vivaldi, Manuel, Margarita Martinez, L., Martinez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Monica, Mendelson, Joseph R., III, Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, O'Brien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sanchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Miles, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjoling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, Zhao, Hongxia, Biological Sciences, Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vazquez-Baeza, Yoshiki, Gonzalez, Antonio, Morton, James T., Mirarab, Siavash, Xu, Zhenjiang Zech, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Song, Se Jin, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Barta, Jiri, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric M., Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Monica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frederic, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chris, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Alexandra Garcia-Amado, Maria, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibanez-Alamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan G., Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martin-Platero, Antonio M., Martin-Vivaldi, Manuel, Margarita Martinez, L., Martinez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Monica, Mendelson, Joseph R., III, Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, O'Brien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sanchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Miles, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjoling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, and Zhao, Hongxia

Abstract

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.

Published
2017

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