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2. Metagenomic Methods for Addressing NASA's Planetary Protection Policy Requirements on Future Missions: A Workshop Report.

Author

Green, Stefan J, Torok, Tamas, Allen, Jonathan E, Eloe-Fadrosh, Emiley, Jackson, Scott A, Jiang, Sunny C, Levine, Stuart S, Levy, Shawn, Schriml, Lynn M, Thomas, W Kelley, Wood, Jason M, and Tighe, Scott W

Subjects
Contamination, DNA, Metagenomics, Planetary protection, Spacecraft Assembly Facility, Astronomical and Space Sciences, Geochemistry, Geology, Astronomy & Astrophysics
Abstract

Molecular biology methods and technologies have advanced substantially over the past decade. These new molecular methods should be incorporated among the standard tools of planetary protection (PP) and could be validated for incorporation by 2026. To address the feasibility of applying modern molecular techniques to such an application, NASA conducted a technology workshop with private industry partners, academics, and government agency stakeholders, along with NASA staff and contractors. The technical discussions and presentations of the Multi-Mission Metagenomics Technology Development Workshop focused on modernizing and supplementing the current PP assays. The goals of the workshop were to assess the state of metagenomics and other advanced molecular techniques in the context of providing a validated framework to supplement the bacterial endospore-based NASA Standard Assay and to identify knowledge and technology gaps. In particular, workshop participants were tasked with discussing metagenomics as a stand-alone technology to provide rapid and comprehensive analysis of total nucleic acids and viable microorganisms on spacecraft surfaces, thereby allowing for the development of tailored and cost-effective microbial reduction plans for each hardware item on a spacecraft. Workshop participants recommended metagenomics approaches as the only data source that can adequately feed into quantitative microbial risk assessment models for evaluating the risk of forward (exploring extraterrestrial planet) and back (Earth harmful biological) contamination. Participants were unanimous that a metagenomics workflow, in tandem with rapid targeted quantitative (digital) PCR, represents a revolutionary advance over existing methods for the assessment of microbial bioburden on spacecraft surfaces. The workshop highlighted low biomass sampling, reagent contamination, and inconsistent bioinformatics data analysis as key areas for technology development. Finally, it was concluded that implementing metagenomics as an additional workflow for addressing concerns of NASA's robotic mission will represent a dramatic improvement in technology advancement for PP and will benefit future missions where mission success is affected by backward and forward contamination.

Published
2023

3. A global metagenomic map of urban microbiomes and antimicrobial resistance.

Author

Danko, David, Bezdan, Daniela, Afshin, Evan E, Ahsanuddin, Sofia, Bhattacharya, Chandrima, Butler, Daniel J, Chng, Kern Rei, Donnellan, Daisy, Hecht, Jochen, Jackson, Katelyn, Kuchin, Katerina, Karasikov, Mikhail, Lyons, Abigail, Mak, Lauren, Meleshko, Dmitry, Mustafa, Harun, Mutai, Beth, Neches, Russell Y, Ng, Amanda, Nikolayeva, Olga, Nikolayeva, Tatyana, Png, Eileen, Ryon, Krista A, Sanchez, Jorge L, Shaaban, Heba, Sierra, Maria A, Thomas, Dominique, Young, Ben, Abudayyeh, Omar O, Alicea, Josue, Bhattacharyya, Malay, Blekhman, Ran, Castro-Nallar, Eduardo, Cañas, Ana M, Chatziefthimiou, Aspassia D, Crawford, Robert W, De Filippis, Francesca, Deng, Youping, Desnues, Christelle, Dias-Neto, Emmanuel, Dybwad, Marius, Elhaik, Eran, Ercolini, Danilo, Frolova, Alina, Gankin, Dennis, Gootenberg, Jonathan S, Graf, Alexandra B, Green, David C, Hajirasouliha, Iman, Hastings, Jaden JA, Hernandez, Mark, Iraola, Gregorio, Jang, Soojin, Kahles, Andre, Kelly, Frank J, Knights, Kaymisha, Kyrpides, Nikos C, Łabaj, Paweł P, Lee, Patrick KH, Leung, Marcus HY, Ljungdahl, Per O, Mason-Buck, Gabriella, McGrath, Ken, Meydan, Cem, Mongodin, Emmanuel F, Moraes, Milton Ozorio, Nagarajan, Niranjan, Nieto-Caballero, Marina, Noushmehr, Houtan, Oliveira, Manuela, Ossowski, Stephan, Osuolale, Olayinka O, Özcan, Orhan, Paez-Espino, David, Rascovan, Nicolás, Richard, Hugues, Rätsch, Gunnar, Schriml, Lynn M, Semmler, Torsten, Sezerman, Osman U, Shi, Leming, Shi, Tieliu, Siam, Rania, Song, Le Huu, Suzuki, Haruo, Court, Denise Syndercombe, Tighe, Scott W, Tong, Xinzhao, Udekwu, Klas I, Ugalde, Juan A, Valentine, Brandon, Vassilev, Dimitar I, Vayndorf, Elena M, Velavan, Thirumalaisamy P, Wu, Jun, Zambrano, María M, Zhu, Jifeng, Zhu, Sibo, Mason, Christopher E, and International MetaSUB Consortium

Subjects
International MetaSUB Consortium, AMR, BGC, NGS, antimicrobial resistance, built Environment, de novo assembly, global health, metagenome, microbiome, shotgun sequencing, Antimicrobial Resistance, Biotechnology, Human Genome, Genetics, Infection, Developmental Biology, Biological Sciences, Medical and Health Sciences
Abstract

We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.

Published
2021

5. COVID-19 pandemic reveals the peril of ignoring metadata standards.

Author

Schriml, Lynn M, Chuvochina, Maria, Davies, Neil, Eloe-Fadrosh, Emiley A, Finn, Robert D, Hugenholtz, Philip, Hunter, Christopher I, Hurwitz, Bonnie L, Kyrpides, Nikos C, Meyer, Folker, Mizrachi, Ilene Karsch, Sansone, Susanna-Assunta, Sutton, Granger, Tighe, Scott, and Walls, Ramona

Published
2020

6. Correction to: Comprehensive benchmarking and ensemble approaches for metagenomic classifiers

Author

McIntyre, Alexa BR, Ounit, Rachid, Afshinnekoo, Ebrahim, Prill, Robert J, Hénaff, Elizabeth, Alexander, Noah, Minot, Samuel S, Danko, David, Foox, Jonathan, Ahsanuddin, Sofia, Tighe, Scott, Hasan, Nur A, Subramanian, Poorani, Moffat, Kelly, Levy, Shawn, Lonardi, Stefano, Greenfield, Nick, Colwell, Rita R, Rosen, Gail L, and Mason, Christopher E

Subjects
Communication and Media Studies, Language, Communication and Culture, Creative Arts and Writing, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Abstract

Following publication of the original article [1], the authors would like to highlight the following two corrections.

Published
2019

7. Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Author

Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, TBK, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susannah G, Ivanova, Natalia N, Copeland, Alex, Clum, Alicia, Becraft, Eric D, Malmstrom, Rex R, Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M, Garrity, George M, Dodsworth, Jeremy A, Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O, Gilbert, Jack A, Nelson, William C, Hallam, Steven J, Jungbluth, Sean P, Ettema, Thijs JG, Tighe, Scott, Konstantinidis, Konstantinos T, Liu, Wen-Tso, Baker, Brett J, Rattei, Thomas, Eisen, Jonathan A, Hedlund, Brian, McMahon, Katherine D, Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Genome Standards Consortium, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H, Eren, AM, Schriml, Lynn, Banfield, Jillian F, Hugenholtz, Philip, and Woyke, Tanja

Subjects
Genome Standards Consortium
Abstract

In the version of this article initially published, the author A. Murat Eren was listed as A.M. Eren. The corresponding affiliation was given as the Knapp Center for Biomedical Discovery, rather than Department of Medicine, University of Chicago, Chicago, Illinois, USA, and Marine Biological Laboratory, Woods Hole, Massachusetts, USA. The errors have been corrected in the HTML and PDF versions of the article as of 29 November 2017. In the version of this article initially published, the following acknowledgment was omitted: A.L. was supported by the Russian Science Foundation (grant number 14-50-00069). The error has been corrected in the HTML and PDF versions of the article as of 7 December 2017.

Published
2018

8. Correction: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Author

Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, TBK, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susannah G, Ivanova, Natalia N, Copeland, Alex, Clum, Alicia, Becraft, Eric D, Malmstrom, Rex R, Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M, Garrity, George M, Dodsworth, Jeremy A, Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O, Gilbert, Jack A, Nelson, William C, Hallam, Steven J, Jungbluth, Sean P, Ettema, Thijs JG, Tighe, Scott, Konstantinidis, Konstantinos T, Liu, Wen-Tso, Baker, Brett J, Rattei, Thomas, Eisen, Jonathan A, Hedlund, Brian, McMahon, Katherine D, Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H, Eren, A Murat, Schriml, Lynn, Banfield, Jillian F, Hugenholtz, Philip, and Woyke, Tanja

Subjects
Biological Sciences, Genetics, Genome Standards Consortium
Published
2018

10. A global metagenomic map of urban microbiomes and antimicrobial resistance

Author

Abdullah, Natasha, Abraao, Marcos, Adel, Ait-hamlat, Afaq, Muhammad, Al-Quaddoomi, Faisal S., Alam, Ireen, Albuquerque, Gabriela E., Alexiev, Alex, Ali, Kalyn, Alvarado-Arnez, Lucia E., Aly, Sarh, Amachee, Jennifer, Amorim, Maria G., Ampadu, Majelia, Amran, Muhammad Al-Fath, An, Nala, Andrew, Watson, Andrianjakarivony, Harilanto, Angelov, Michael, Antelo, Verónica, Aquino, Catharine, Aranguren, Álvaro, Araujo, Luiza F., Vasquez Arevalo, Hitler Francois, Arevalo, Jenny, Arnan, Carme, Alvarado Arnez, Lucia Elena, Arredondo, Fernanda, Arthur, Matthew, Asenjo, Freddy, Aung, Thomas Saw, Auvinet, Juliette, Aventin, Nuria, Ayaz, Sadaf, Baburyan, Silva, Bakere, Abd-Manaaf, Bakhl, Katrin, Bartelli, Thais F., Batdelger, Erdenetsetseg, Baudon, François, Becher, Kevin, Bello, Carla, Benchouaia, Médine, Benisty, Hannah, Benoiston, Anne-Sophie, Benson, Joseph, Benítez, Diego, Bernardes, Juliana, Bertrand, Denis, Beurmann, Silvia, Bitard-Feildel, Tristan, Bittner, Lucie, Black, Christina, Blanc, Guillaume, Blyther, Brittany, Bode, Toni, Boeri, Julia, Boldgiv, Bazartseren, Bolzli, Kevin, Bordigoni, Alexia, Borrelli, Ciro, Bouchard, Sonia, Bouly, Jean-Pierre, Boyd, Alicia, Branco, Gabriela P., Breschi, Alessandra, Brindefalk, Björn, Brion, Christian, Briones, Alan, Buczansla, Paulina, Burke, Catherine M., Burrell, Aszia, Butova, Alina, Buttar, Irvind, Bynoe, Jalia, Bönigk, Sven, Bøifot, Kari O., Caballero, Hiram, Cai, Xiao Wen, Calderon, Dayana, Cantillo, Angela, Carbajo, Miguel, Carbone, Alessandra, Cardenas, Anais, Carrillo, Katerine, Casalot, Laurie, Castro, Sofia, Castro, Ana V., Castro, Astred, Castro, Ana Valeria B., Cawthorne, Simone, Cedillo, Jonathan, Chaker, Salama, Chalangal, Jasna, Chan, Allison, Chasapi, Anastasia I., Chatziefthimiou, Starr, Chaudhuri, Sreya Ray, Chavan, Akash Keluth, Chavez, Francisco, Chem, Gregory, Chen, Xiaoqing, Chen, Michelle, Chen, Jenn-Wei, Chernomoretz, Ariel, Chettouh, Allaeddine, Cheung, Daisy, Chicas, Diana, Chiu, Shirley, Choudhry, Hira, Chrispin, Carl, Ciaramella, Kianna, Cifuentes, Erika, Cohen, Jake, Coil, David A., Collin, Sylvie, Conger, Colleen, Conte, Romain, Corsi, Flavia, Cossio, Cecilia N., Costa, Ana F., Cuebas, Delisia, D’Alessandro, Bruno, Dahlhausen, Katherine E., Darling, Aaron E., Das, Pujita, Davenport, Lucinda B., David, Laurent, Davidson, Natalie R., Dayama, Gargi, Delmas, Stéphane, Deng, Chris K., Dequeker, Chloé, Desert, Alexandre, Devi, Monika, Dezem, Felipe S., Dias, Clara N., Donahoe, Timothy Ryan, Dorado, Sonia, Dorsey, LaShonda, Dotsenko, Valeriia, Du, Steven, Dutan, Alexandra, Eady, Naya, Eisen, Jonathan A., Elaskandrany, Miar, Epping, Lennard, Escalera-Antezana, Juan P., Ettinger, Cassie L., Faiz, Iqra, Fan, Luice, Farhat, Nadine, Faure, Emile, Fauzi, Fazlina, Feigin, Charlie, Felice, Skye, Ferreira, Laís Pereira, Figueroa, Gabriel, Fleiss, Aubin, Flores, Denisse, Velasco Flores, Jhovana L., Fonseca, Marcos A.S., Foox, Jonathan, Forero, Juan Carlos, Francis, Aaishah, French, Kelly, Fresia, Pablo, Friedman, Jacob, Fuentes, Jaime J., Galipon, Josephine, Garcia, Mathilde, Garcia, Laura, García, Catalina, Geiger, Annie, Gerner, Samuel M., Ghose, Sonia L., Giang, Dao Phuong, Giménez, Matías, Giovannelli, Donato, Githae, Dedan, Gkotzis, Spyridon, Godoy, Liliana, Goldman, Samantha, Gonnet, Gaston H., Gonzalez, Juana, Gonzalez, Andrea, Gonzalez-Poblete, Camila, Gray, Andrew, Gregory, Tranette, Greselle, Charlotte, Guasco, Sophie, Guerra, Juan, Gurianova, Nika, Haehr, Wolfgang, Halary, Sebastien, Hartkopf, Felix, Hastings, Jaden J.A., Hawkins-Zafarnia, Arya, Hazrin-Chong, Nur Hazlin, Helfrich, Eric, Hell, Eva, Henry, Tamera, Hernandez, Samuel, Hernandez, Pilar Lopez, Hess-Homeier, David, Hittle, Lauren E., Hoan, Nghiem Xuan, Holik, Aliaksei, Homma, Chiaki, Hoxie, Irene, Huber, Michael, Humphries, Elizabeth, Hyland, Stephanie, Hässig, Andrea, Häusler, Roland, Hüsser, Nathalie, Petit, Robert A., III, Iderzorig, Badamnyambuu, Igarashi, Mizuki, Iqbal, Shaikh B., Ishikawa, Shino, Ishizuka, Sakura, Islam, Sharah, Islam, Riham, Ito, Kohei, Ito, Sota, Ito, Takayuki, Ivankovic, Tomislav, Iwashiro, Tomoki, Jackson, Sarah, Jacobs, JoAnn, James, Marisano, Jaubert, Marianne, Jerier, Marie-Laure, Jiminez, Esmeralda, Jinfessa, Ayantu, De Jong, Ymke, Joo, Hyun Woo, Jospin, Guilllaume, Kajita, Takema, Ahmad Kassim, Affifah Saadah, Kato, Nao, Kaur, Amrit, Kaur, Inderjit, de Souza Gomes Kehdy, Fernanda, Khadka, Vedbar S., Khan, Shaira, Khavari, Mahshid, Ki, Michelle, Kim, Gina, Kim, Hyung Jun, Kim, Sangwan, King, Ryan J., Knights, Kaymisha, KoLoMonaco, Giuseppe, Koag, Ellen, Kobko-Litskevitch, Nadezhda, Korshevniuk, Maryna, Kozhar, Michael, Krebs, Jonas, Kubota, Nanami, Kuklin, Andrii, Kumar, Sheelta S., Kwong, Rachel, Kwong, Lawrence, Lafontaine, Ingrid, Lago, Juliana, Lai, Tsoi Ying, Laine, Elodie, Laiola, Manolo, Lakhneko, Olha, Lamba, Isha, de Lamotte, Gerardo, Lannes, Romain, De Lazzari, Eleonora, Leahy, Madeline, Lee, Hyunjung, Lee, Yunmi, Lee, Lucy, Lemaire, Vincent, Leong, Emily, Leung, Marcus H.Y., Lewandowska, Dagmara, Li, Chenhao, Liang, Weijun, Lin, Moses, Lisboa, Priscilla, Litskevitch, Anna, Liu, Eric Minwei, Liu, Tracy, Livia, Mayra Arauco, Lo, Yui Him, Losim, Sonia, Loubens, Manon, Lu, Jennifer, Lykhenko, Olexandr, Lysakova, Simona, Mahmoud, Salah, Majid, Sara Abdul, Makogon, Natalka, Maldonado, Denisse, Mallari, Krizzy, Malta, Tathiane M., Mamun, Maliha, Manoir, Dimitri, Marchandon, German, Marciniak, Natalia, Marinovic, Sonia, Marques, Brunna, Mathews, Nicole, Matsuzaki, Yuri, Matthys, Vincent, May, Madelyn, McComb, Elias, Meagher, Annabelle, Melamed, Adiell, Menary, Wayne, Mendez, Katterinne N., Mendez, Ambar, Mendy, Irène Mauricette, Meng, Irene, Menon, Ajay, Menor, Mark, Meoded, Roy, Merino, Nancy, Meydan, Cem, Miah, Karishma, Mignotte, Mathilde, Miketic, Tanja, Miranda, Wilson, Mitsios, Athena, Miura, Ryusei, Miyake, Kunihiko, Moccia, Maria D., Mohan, Natasha, Mohsin, Mohammed, Moitra, Karobi, Moldes, Mauricio, Molina, Laura, Molinet, Jennifer, Molomjamts, Orgil-Erdene, Moniruzzaman, Eftar, Moon, Sookwon, de Oliveira Moraes, Isabelle, Moreno, Mario, Mosella, Maritza S., Moser, Josef W., Mozsary, Christopher, Muehlbauer, Amanda L., Muner, Oasima, Munia, Muntaha, Munim, Naimah, Muscat, Maureen, Mustac, Tatjana, Muñoz, Cristina, Nadalin, Francesca, Naeem, Areeg, Nagy-Szakal, Dorottya, Nakagawa, Mayuko, Narce, Ashanti, Nasu, Masaki, Navarrete, Irene González, Naveed, Hiba, Nazario, Bryan, Nedunuri, Narasimha Rao, Neff, Thomas, Nesimi, Aida, Ng, Wan Chiew, Ng, Synti, Nguyen, Gloria, Ngwa, Elsy, Nicolas, Agier, Nicolas, Pierre, Nika, Abdollahi, Noorzi, Hosna, Nosrati, Avigdor, Noushmehr, Houtan, Nunes, Diana N., O’Brien, Kathryn, O’Hara, Niamh B., Oken, Gabriella, Olawoyin, Rantimi A., Oliete, Javier Quilez, Olmeda, Kiara, Oluwadare, Tolulope, Oluwadare, Itunu A., Ordioni, Nils, Orpilla, Jenessa, Orrego, Jacqueline, Ortega, Melissa, Osma, Princess, Osuolale, Israel O., Osuolale, Oluwatosin M., Ota, Mitsuki, Oteri, Francesco, Oto, Yuya, Ounit, Rachid, Ouzounis, Christos A., Pakrashi, Subhamitra, Paras, Rachel, Pardo-Este, Coral, Park, Young-Ja, Pastuszek, Paulina, Patel, Suraj, Pathmanathan, Jananan, Patrignani, Andrea, Perez, Manuel, Peros, Ante, Persaud, Sabrina, Peters, Anisia, Phillips, Adam, Pineda, Lisbeth, Pizzi, Melissa P., Plaku, Alma, Plaku, Alketa, Pompa-Hogan, Brianna, Portilla, María Gabriela, Posada, Leonardo, Priestman, Max, Prithiviraj, Bharath, Priya, Sambhawa, Pugdeethosal, Phanthira, Pugh, Catherine E., Pulatov, Benjamin, Pupiec, Angelika, Pyrshev, Kyrylo, Qing, Tao, Rahiel, Saher, Rahmatulloev, Savlatjon, Rajendran, Kannan, Ramcharan, Aneisa, Ramirez-Rojas, Adan, Rana, Shahryar, Ratnanandan, Prashanthi, Read, Timothy D., Rehrauer, Hubert, Richer, Renee, Rivera, Alexis, Rivera, Michelle, Robertiello, Alessandro, Robinson, Courtney, Rodríguez, Paula, Rojas, Nayra Aguilar, Roldán, Paul, Rosario, Anyelic, Roth, Sandra, Ruiz, Maria, Boja Ruiz, Stephen Eduard, Russell, Kaitlan, Rybak, Mariia, Sabedot, Thais S., Sabina, Mahfuza, Saito, Ikuto, Saito, Yoshitaka, Malca Salas, Gustavo Adolfo, Salazar, Cecilia, San, Kaung Myat, Sanchez, Jorge, Sanchir, Khaliun, Sankar, Ryan, de Souza Santos, Paulo Thiago, Saravi, Zulena, Sasaki, Kai, Sato, Yuma, Sato, Masaki, Sato, Seisuke, Sato, Ryo, Sato, Kaisei, Sayara, Nowshin, Schaaf, Steffen, Schacher, Oli, Schinke, Anna-Lena M., Schlapbach, Ralph, Schori, Christian, Schriml, Jason R., Segato, Felipe, Sepulveda, Felipe, Serpa, Marianna S., De Sessions, Paola F., Severyn, Juan C., Shaaban, Heba, Shakil, Maheen, Shalaby, Sarah, Shari, Aliyah, Shim, Hyenah, Shirahata, Hikaru, Shiwa, Yuh, Siam, Rania, Da Silva, Ophélie, Silva, Jordana M., Simon, Gwenola, Singh, Shaleni K., Sluzek, Kasia, Smith, Rebecca, So, Eunice, Andreu Somavilla, Núria, Sonohara, Yuya, Rufino de Sousa, Nuno, Souza, Camila, Sperry, Jason, Sprinsky, Nicolas, Stark, Stefan G., La Storia, Antonietta, Suganuma, Kiyoshi, Suliman, Hamood, Sullivan, Jill, Supie, Arif Asyraf Md, Suzuki, Chisato, Takagi, Sora, Takahara, Fumie, Takahashi, Naoya, Takahashi, Kou, Takeda, Tomoki, Takenaka, Isabella K., Tanaka, Soma, Tang, Anyi, Man Tang, Yuk, Tarcitano, Emilio, Tassinari, Andrea, Taye, Mahdi, Terrero, Alexis, Thambiraja, Eunice, Thiébaut, Antonin, Thomas, Sade, Thomas, Andrew M., Togashi, Yuto, Togashi, Takumi, Tomaselli, Anna, Tomita, Masaru, Tomita, Itsuki, Tong, Xinzhao, Toth, Oliver, Toussaint, Nora C., Tran, Jennifer M., Truong, Catalina, Tsonev, Stefan I., Tsuda, Kazutoshi, Tsurumaki, Takafumi, Tuz, Michelle, Tymoshenko, Yelyzaveta, Urgiles, Carmen, Usui, Mariko, Vacant, Sophie, Valentine, Brandon, Vann, Laura E., Velter, Fabienne, Ventorino, Valeria, Vera-Wolf, Patricia, Vicedomini, Riccardo, Suarez-Villamil, Michael A., Vincent, Sierra, Vivancos-Koopman, Renee, Wan, Andrew, Wang, Cindy, Warashina, Tomoro, Watanabe, Ayuki, Weekes, Samuel, Werner, Johannes, Westfall, David, Wieler, Lothar H., Williams, Michelle, Wolf, Silver A., Wong, Brian, Wong, Yan Ling, Wong, Tyler, Wright, Rasheena, Wunderlin, Tina, Yamanaka, Ryota, Yang, Jingcheng, Yano, Hirokazu, Yeh, George C., Yemets, Olena, Yeskova, Tetiana, Yoshikawa, Shusei, Zafar, Laraib, Zhang, Yang, Zhang, Shu, Zhang, Amy, Zheng, Yuanting, Zubenko, Stas, Danko, David, Bezdan, Daniela, Afshin, Evan E., Ahsanuddin, Sofia, Bhattacharya, Chandrima, Butler, Daniel J., Chng, Kern Rei, Donnellan, Daisy, Hecht, Jochen, Jackson, Katelyn, Kuchin, Katerina, Karasikov, Mikhail, Lyons, Abigail, Mak, Lauren, Meleshko, Dmitry, Mustafa, Harun, Mutai, Beth, Neches, Russell Y., Ng, Amanda, Nikolayeva, Olga, Nikolayeva, Tatyana, Png, Eileen, Ryon, Krista A., Sanchez, Jorge L., Sierra, Maria A., Thomas, Dominique, Young, Ben, Abudayyeh, Omar O., Alicea, Josue, Bhattacharyya, Malay, Blekhman, Ran, Castro-Nallar, Eduardo, Cañas, Ana M., Chatziefthimiou, Aspassia D., Crawford, Robert W., De Filippis, Francesca, Deng, Youping, Desnues, Christelle, Dias-Neto, Emmanuel, Dybwad, Marius, Elhaik, Eran, Ercolini, Danilo, Frolova, Alina, Gankin, Dennis, Gootenberg, Jonathan S., Graf, Alexandra B., Green, David C., Hajirasouliha, Iman, Hernandez, Mark, Iraola, Gregorio, Jang, Soojin, Kahles, Andre, Kelly, Frank J., Kyrpides, Nikos C., Łabaj, Paweł P., Lee, Patrick K.H., Ljungdahl, Per O., Mason-Buck, Gabriella, McGrath, Ken, Mongodin, Emmanuel F., Moraes, Milton Ozorio, Nagarajan, Niranjan, Nieto-Caballero, Marina, Oliveira, Manuela, Ossowski, Stephan, Osuolale, Olayinka O., Özcan, Orhan, Paez-Espino, David, Rascovan, Nicolás, Richard, Hugues, Rätsch, Gunnar, Schriml, Lynn M., Semmler, Torsten, Sezerman, Osman U., Shi, Leming, Shi, Tieliu, Song, Le Huu, Suzuki, Haruo, Court, Denise Syndercombe, Tighe, Scott W., Udekwu, Klas I., Ugalde, Juan A., Vassilev, Dimitar I., Vayndorf, Elena M., Velavan, Thirumalaisamy P., Wu, Jun, Zambrano, María M., Zhu, Jifeng, Zhu, Sibo, and Mason, Christopher E.

Published
2021
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11. Comprehensive benchmarking and ensemble approaches for metagenomic classifiers

Author

McIntyre, Alexa BR, Ounit, Rachid, Afshinnekoo, Ebrahim, Prill, Robert J, Hénaff, Elizabeth, Alexander, Noah, Minot, Samuel S, Danko, David, Foox, Jonathan, Ahsanuddin, Sofia, Tighe, Scott, Hasan, Nur A, Subramanian, Poorani, Moffat, Kelly, Levy, Shawn, Lonardi, Stefano, Greenfield, Nick, Colwell, Rita R, Rosen, Gail L, and Mason, Christopher E

Subjects
Genetics, Networking and Information Technology R&D (NITRD), Human Genome, Biotechnology, Benchmarking, Contig Mapping, DNA Barcoding, Taxonomic, Humans, Metagenome, Microbiota, Phylogeny, Sequence Analysis, DNA, Software, Metagenomics, Shotgun sequencing, Taxonomy, Classification, Comparison, Ensemble methods, Metaclassification, Pathogen detection, Meta-classification, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundOne of the main challenges in metagenomics is the identification of microorganisms in clinical and environmental samples. While an extensive and heterogeneous set of computational tools is available to classify microorganisms using whole-genome shotgun sequencing data, comprehensive comparisons of these methods are limited.ResultsIn this study, we use the largest-to-date set of laboratory-generated and simulated controls across 846 species to evaluate the performance of 11 metagenomic classifiers. Tools were characterized on the basis of their ability to identify taxa at the genus, species, and strain levels, quantify relative abundances of taxa, and classify individual reads to the species level. Strikingly, the number of species identified by the 11 tools can differ by over three orders of magnitude on the same datasets. Various strategies can ameliorate taxonomic misclassification, including abundance filtering, ensemble approaches, and tool intersection. Nevertheless, these strategies were often insufficient to completely eliminate false positives from environmental samples, which are especially important where they concern medically relevant species. Overall, pairing tools with different classification strategies (k-mer, alignment, marker) can combine their respective advantages.ConclusionsThis study provides positive and negative controls, titrated standards, and a guide for selecting tools for metagenomic analyses by comparing ranges of precision, accuracy, and recall. We show that proper experimental design and analysis parameters can reduce false positives, provide greater resolution of species in complex metagenomic samples, and improve the interpretation of results.

Published
2017

12. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Author

Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, TBK, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susannah G, Ivanova, Natalia N, Copeland, Alex, Clum, Alicia, Becraft, Eric D, Malmstrom, Rex R, Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M, Garrity, George M, Dodsworth, Jeremy A, Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O, Gilbert, Jack A, Nelson, William C, Hallam, Steven J, Jungbluth, Sean P, Ettema, Thijs JG, Tighe, Scott, Konstantinidis, Konstantinos T, Liu, Wen-Tso, Baker, Brett J, Rattei, Thomas, Eisen, Jonathan A, Hedlund, Brian, McMahon, Katherine D, Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H, Murat Eren, A, Schriml, Lynn, Banfield, Jillian F, Hugenholtz, Philip, and Woyke, Tanja

Subjects
Microbiology, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Cancer, Cancer Genomics, Biotechnology, Human Genome, Genome, Archaeal, Genome, Bacterial, Genomics, Metagenomics, Sequence Analysis, DNA, Genome Standards Consortium
Abstract

We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.

Published
2017

13. Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP).

Author

Tighe, Scott, Afshinnekoo, Ebrahim, Rock, Tara M, McGrath, Ken, Alexander, Noah, McIntyre, Alexa, Ahsanuddin, Sofia, Bezdan, Daniela, Green, Stefan J, Joye, Samantha, Stewart Johnson, Sarah, Baldwin, Don A, Bivens, Nathan, Ajami, Nadim, Carmical, Joseph R, Herriott, Ian Charold, Colwell, Rita, Donia, Mohamed, Foox, Jonathan, Greenfield, Nick, Hunter, Tim, Hoffman, Jessica, Hyman, Joshua, Jorgensen, Ellen, Krawczyk, Diana, Lee, Jodie, Levy, Shawn, Garcia-Reyero, Natàlia, Settles, Matthew, Thomas, Kelley, Gómez, Felipe, Schriml, Lynn, Kyrpides, Nikos, Zaikova, Elena, Penterman, Jon, and Mason, Christopher E

Subjects
Microbiology, Biological Sciences, Biotechnology, Genetics, Human Genome, Life Below Water, DNA, Bacterial, Environmental Microbiology, Extreme Environments, Metagenome, Microbiota, Molecular Typing, RNA, Bacterial, Reference Standards, Sequence Analysis, DNA, Polyzyme, extremophile, metagenomics, shotgun sequencing, whole genome, Technology, Medical and Health Sciences, Biological sciences
Abstract

The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characterization of novel microbes, 2) the evaluation of nucleic acid techniques for extremophilic samples, and 3) the identification and implementation of the appropriate bioinformatics pipelines. Here, we highlight the different ongoing projects that we have been working on, as well as details on the various methods we use to characterize the microbiome and metagenome of these complex samples. In particular, we present data of a novel multienzyme extraction protocol that we developed, called Polyzyme or MetaPolyZyme. Presently, the XMP is characterizing sample sites around the world with the intent of discovering new species, genes, and gene clusters. Once a project site is complete, the resulting data will be publically available. Sites include Lake Hillier in Western Australia, the "Door to Hell" crater in Turkmenistan, deep ocean brine lakes of the Gulf of Mexico, deep ocean sediments from Greenland, permafrost tunnels in Alaska, ancient microbial biofilms from Antarctica, Blue Lagoon Iceland, Ethiopian toxic hot springs, and the acidic hypersaline ponds in Western Australia.

Published
2017

14. Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study

Author

Foox, Jonathan, Tighe, Scott W., Nicolet, Charles M., Zook, Justin M., Byrska-Bishop, Marta, Clarke, Wayne E., Khayat, Michael M., Mahmoud, Medhat, Laaguiby, Phoebe K., Herbert, Zachary T., Warner, Derek, Grills, George S., Jen, Jin, Levy, Shawn, Xiang, Jenny, Alonso, Alicia, Zhao, Xia, Zhang, Wenwei, Teng, Fei, Zhao, Yonggang, Lu, Haorong, Schroth, Gary P., Narzisi, Giuseppe, Farmerie, William, Sedlazeck, Fritz J., Baldwin, Don A., and Mason, Christopher E.

Published
2021
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17. Genomic and morphological characterization of Knufia obscura isolated from the Mars 2020 spacecraft assembly facility

Author

Chander, Atul Munish, primary, Teixeira, Marcus Melo, additional, Singh, Nitin K., additional, Williams, Michael P., additional, Parker, Ceth W., additional, Leo, Patrick, additional, Stajich, Jason E., additional, Torok, Tamas, additional, Tighe, Scott, additional, Mason, Christopher E., additional, and Venkateswaran, Kasthuri, additional

Published
2023
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20. Assessing microbial diversity in Yellowstone National Park hot springs using a field deployable automated nucleic acid extraction system.

Author

Wood, Jason M., Urbaniak, Camilla, Parker, Ceth, Singh, Nitin Kumar, Wong, Season, Arumugam, Arunkumar, Skorupa, Dana J., Hemmah, Ashlyn, Laaguiby, Phoebe, Karouia, Fathi, Peyton, Brent M., Tighe, Scott, Venkateswaran, Kasthuri, Nelson, William C., and Xu, Guofang

Subjects
HOT springs, NUCLEIC acids, NATIONAL parks & reserves, MICROBIAL diversity, RESOURCE-limited settings, SAMPLING (Process), EXTREME environments
Abstract

Microbial diversity estimation involves extracting nucleic acids from intricate sample matrices. Preparing nucleic acid samples is time-consuming, necessitating effective cell lysis and obtaining pure, inhibitor-free nucleic acid purifications before further use. An automated system offers advantages for field deployment due to its ease of use and quick autonomous results. This is especially beneficial for rapid measurement of in situ microbial diversity in remote areas. Our study aimed to assess microbial diversity of Yellowstone hot springs using a field-deployable lab in a resource-limited remote setting and demonstrate on-site nucleic acid sample processing and sequencing. We collected microbial mat and sediment samples from several Yellowstone National Park hot springs, focusing on the Five Sister Springs (FSS), spring LNN010, and Octopus Spring (OS). The samples were processed for DNA extraction on-site and further sequenced in the lab for microbial diversity. In addition, DNA extracted from one sample was sequenced and analyzed on-site as proof-of-concept. Using either Illumina or Oxford Nanopore Technology sequencing, we found similar microbial diversities. Bacteria (over 90%) were predominant at the FSS and OS sites, with archaea accounting for less than 10%. Metagenomic results were taxonomically categorized based on the closest known organism with a sequenced genome. The dominant archaeal community member was Candidatus Caldiarchaeum subterraneum, and among bacteria, Roseiflexus sp. RS-1 was abundant in mat samples. Interestingly, Bacterium HR17 was also frequently found, suggesting the need for more research on this newly recognized bacterial community member. The presence of Bacterium HR17 in these hot springs suggests its potential role in nitrogen cycling, informing both ecological understanding and industrial potential. This pioneering study assessed the microbiome of Yellowstone hot springs in about 8-9 hours using an automated system for nucleic acid extraction. By its deployment, the system's value in elucidating the microbial diversity of extreme environments without the need to bring samples to the lab for processing had been highlighted. Sample processing and sequencing had been included in the benefits of the field-deployable lab, and the Nanopore platform had been utilized. [ABSTRACT FROM AUTHOR]

Published
2024
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21. Author Correction: Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study

Author

Foox, Jonathan, Tighe, Scott W., Nicolet, Charles M., Zook, Justin M., Byrska-Bishop, Marta, Clarke, Wayne E., Khayat, Michael M., Mahmoud, Medhat, Laaguiby, Phoebe K., Herbert, Zachary T., Warner, Derek, Grills, George S., Jen, Jin, Levy, Shawn, Xiang, Jenny, Alonso, Alicia, Zhao, Xia, Zhang, Wenwei, Teng, Fei, Zhao, Yonggang, Lu, Haorong, Schroth, Gary P., Narzisi, Giuseppe, Farmerie, William, Sedlazeck, Fritz J., Baldwin, Don A., and Mason, Christopher E.

Published
2021
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22. Field deployable automated nucleic acid extraction system enables rapid on-site measurement of microbial diversity of Yellowstone National Park hot springs

Author

Wood, Jason M., primary, Urbaniak, Camilla, additional, Parker, Ceth W., additional, Singh, Nitin Kumar, additional, Wong, Season, additional, Arumugam, Arunkumar, additional, Skorupa, Dana, additional, Hemmah, Ashlyn, additional, Laaguiby, Phoebe, additional, Karouia, Fathi, additional, Peyton, Brent, additional, Tighe, Scott, additional, and VENKATESWARAN, KASTHURI, additional

Published
2023
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23. Metagenomic Methods for Addressing NASA's Planetary Protection Policy Requirements on Future Missions: A Workshop Report

Author

Green, Stefan J., primary, Torok, Tamas, additional, Allen, Jonathan E., additional, Eloe-Fadrosh, Emiley, additional, Jackson, Scott A., additional, Jiang, Sunny C., additional, Levine, Stuart S., additional, Levy, Shawn, additional, Schriml, Lynn M., additional, Thomas, W. Kelley, additional, Wood, Jason M., additional, and Tighe, Scott W., additional

Published
2023
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24. Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics

Author

Afshinnekoo, Ebrahim, Meydan, Cem, Chowdhury, Shanin, Jaroudi, Dyala, Boyer, Collin, Bernstein, Nick, Maritz, Julia M., Reeves, Darryl, Gandara, Jorge, Chhangawala, Sagar, Ahsanuddin, Sofia, Simmons, Amber, Nessel, Timothy, Sundaresh, Bharathi, Pereira, Elizabeth, Jorgensen, Ellen, Kolokotronis, Sergios-Orestis, Kirchberger, Nell, Garcia, Isaac, Gandara, David, Dhanraj, Sean, Nawrin, Tanzina, Saletore, Yogesh, Alexander, Noah, Vijay, Priyanka, Hénaff, Elizabeth M., Zumbo, Paul, Walsh, Michael, O’Mullan, Gregory D., Tighe, Scott, Dudley, Joel T., Dunaif, Anya, Ennis, Sean, O’Halloran, Eoghan, Magalhaes, Tiago R., Boone, Braden, Jones, Angela L., Muth, Theodore R., Paolantonio, Katie Schneider, Alter, Elizabeth, Schadt, Eric E., Garbarino, Jeanne, Prill, Robert J., Carlton, Jane M., Levy, Shawn, and Mason, Christopher E.

Published
2015
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26. Cave Thiovulum (Candidatus Thiovulum stygium) differs metabolically and genomically from marine species

Author

Bizic, Mina, primary, Brad, Traian, additional, Ionescu, Danny, additional, Barbu-Tudoran, Lucian, additional, Zoccarato, Luca, additional, Aerts, Joost W., additional, Contarini, Paul-Emile, additional, Gros, Olivier, additional, Volland, Jean-Marie, additional, Popa, Radu, additional, Ody, Jessica, additional, Vellone, Daniel, additional, Flot, Jean-François, additional, Tighe, Scott, additional, and Sarbu, Serban M., additional

Published
2022
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29. Large sulfur oxidizing bacteria of the Thiovulaceae (Campylobacterota) thriving in the sulfidic groundwater of Movile Cave, in Romania

Author

Brad, Traian, primary, Bizic, Mina, additional, Ionescu, Danny, additional, Barbu-Tudoran, Lucian, additional, Aerts, Joost, additional, Popa, Radu, additional, Zoccarato, Luca, additional, Ody, Jessica, additional, Flot, Jean-François, additional, Tighe, Scott, additional, Vellone, Daniel, additional, and Sarbu, Serban, additional

Published
2022
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30. Cross-kingdom metagenomic profiling of Lake Hillier reveals pigment-rich polyextremophiles and wide-ranging metabolic adaptations

Author

Sierra, Maria A., primary, Ryon, Krista A., additional, Tierney, Braden T., additional, Foox, Jonathan, additional, Bhattacharya, Chandrima, additional, Afshin, Evan, additional, Butler, Daniel, additional, Green, Stefan J., additional, Thomas, W. Kelley, additional, Ramsdell, Jordan, additional, Bivens, Nathan J., additional, McGrath, Ken, additional, Mason, Christopher E., additional, and Tighe, Scott W., additional

Published
2022
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32. Molecular Characterization of Increased Amplicon Lengths in SARS-CoV-2 Reverse Transcription Loop-Mediated Isothermal Amplification Assays

Author

Tighe, Scott W., primary, Hayden, Andrew F., additional, Kuentzel, Marcy L., additional, Eckstrom, Korin M., additional, Foox, Jonathan, additional, Vellone, Daniel L., additional, Finstad, Kristiaan H., additional, Laaguiby, Pheobe K., additional, Hoffman, Jessica J., additional, and Chittur, Sridar V., additional

Published
2021
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33. Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications

Author

Moore, Keith J. M., primary, Cahill, Jeremy, additional, Aidelberg, Guy, additional, Aronoff, Rachel, additional, Bektaş, Ali, additional, Bezdan, Daniela, additional, Butler, Daniel J., additional, Chittur, Sridar V., additional, Codyre, Martin, additional, Federici, Fernan, additional, Tanner, Nathan A., additional, Tighe, Scott W., additional, True, Randy, additional, Ware, Sarah B., additional, Wyllie, Anne L., additional, Afshin, Evan E., additional, Bendesky, Andres, additional, Chang, Connie B., additional, Dela Rosa, Richard, additional, Elhaik, Eran, additional, Erickson, David, additional, Goldsborough, Andrew S., additional, Grills, George, additional, Hadasch, Kathrin, additional, Hayden, Andrew, additional, Her, Seong-Young, additional, Karl, Julie A., additional, Kim, Chang Hee, additional, Kriegel, Alison J., additional, Kunstman, Thomas, additional, Landau, Zeph, additional, Land, Kevin, additional, Langhorst, Bradley W., additional, Lindner, Ariel B., additional, Mayer, Benjamin E., additional, McLaughlin, Lee A., additional, McLaughlin, Matthew T., additional, Molloy, Jenny, additional, Mozsary, Christopher, additional, Nadler, Jerry L., additional, D'Silva, Melinee, additional, Ng, David, additional, O'Connor, David H., additional, Ongerth, Jerry E., additional, Osuolale, Olayinka, additional, Pinharanda, Ana, additional, Plenker, Dennis, additional, Ranjan, Ravi, additional, Rosbash, Michael, additional, Rotem, Assaf, additional, Segarra, Jacob, additional, Schürer, Stephan, additional, Sherrill-Mix, Scott, additional, Solo-Gabriele, Helena, additional, To, Shaina, additional, Vogt, Merly C., additional, Yu, Albert D., additional, and Mason, Christopher E., additional

Published
2021
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34. Evaluating particle counters

Author

O'Shaughnessy, Patrick T., Barsotti, Michael G., Fay, James W., and Tighe, Scott W.

Published
1997

36. Cave Thiovulum(CandidatusThiovulum stygium) differs metabolically and genomically from marine species

Author

Bizic, Mina, Brad, Traian, Ionescu, Danny, Barbu-Tudoran, Lucian, Zoccarato, Luca, Aerts, Joost W, Contarini, Paul-Emile, Gros, Olivier, Volland, Jean-Marie, Popa, Radu, Ody, Jessica, Vellone, Daniel, Flot, Jean-François, Tighe, Scott, and Sarbu, Serban M

Abstract

Thiovulumspp. (Campylobacterota) are large sulfur bacteria that form veil-like structures in aquatic environments. The sulfidic Movile Cave (Romania), sealed from the atmosphere for ~5 million years, has several aqueous chambers, some with low atmospheric O2(~7%). The cave’s surface-water microbial community is dominated by bacteria we identified as Thiovulum. We show that this strain, and others from subsurface environments, are phylogenetically distinct from marine Thiovulum. We assembled a closed genome of the Movile strain and confirmed its metabolism using RNAseq. We compared the genome of this strain and one we assembled from public data from the sulfidic Frasassi caves to four marine genomes, including CandidatusThiovulum karukerense and Ca. T. imperiosus, whose genomes we sequenced. Despite great spatial and temporal separation, the genomes of the Movile and Frasassi Thiovulum were highly similar, differing greatly from the very diverse marine strains. We concluded that cave Thiovulumrepresent a new species, named here CandidatusThiovulum stygium. Based on their genomes, cave Thiovulumcan switch between aerobic and anaerobic sulfide oxidation using O2and NO3-as electron acceptors, the latter likely via dissimilatory nitrate reduction to ammonia. Thus, Thiovulumis likely important to both S and N cycles in sulfidic caves. Electron microscopy analysis suggests that at least some of the short peritrichous structures typical of Thiovulumare type IV pili, for which genes were found in all strains. These pili may play a role in veil formation, by connecting adjacent cells, and in the motility of these exceptionally fast swimmers.

Published
2023
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38. Genes overexpressed in cerebral arteries following salt-induced hypertensive disease are regulated by angiotensin II, JunB, and CRE

Author

Rose, Patricia, Bond, Jeffrey, Tighe, Scott, Toth, Michael J., Wellman, Theresa L., de Montiano, Eva Maria Briso, Lewinter, Martin M., and Lounsbury, Karen M.

Subjects
Cerebral circulation -- Research, Vascular endothelium -- Research, Epithelial cells -- Research, Sodium metabolism -- Research, Gene expression -- Research, Hypertension -- Research, Renin-angiotensin system -- Research, Cerebral arteries -- Research, Cardiovascular research, Biological sciences
Abstract

Although changes in gene expression are necessary for arterial remodeling during hypertension, the genes altered and their mechanisms of regulation remain uncertain. The goal of this study was to identify cerebral artery genes altered by hypertension and define signaling pathways important in their regulation. Intact cerebral arteries from Dahl salt-sensitive normotensive and hypertensive high-salt (HS) rats were examined by immunostaining, revealing an increased phosphorylation of extracellular signal-regulated kinase 1/2 (ERKI/2) and expression of the proliferative marker Ki-67 in arteries from hypertensive animals. Arterial RNA analyzed by microarray and validated with RT-quantitative PCR revealed that jun family member junB and matricellular genes plasminogen activator inhibitor-1 (PAI-1) and osteopontin (OPN) were significantly overexpressed in HS arteries. Fisher exact test and annotation-based gene subsets showed that genes upregulated by Jun and [Ca.sup.2+]/cAMP-response element-binding protein (CREB) were overrepresented. A model of cultured rat cerebrovascular smooth muscle cells was used to test the hypothesis that angiotensin II (ANG II), JunB, and CREB are important in the regulation of genes identified in the rat hypertension model. ANG II induced a transient induction of junB and a delayed induction of PAI-1 and OPN mRNA levels, which were reduced by ERK inhibition with U-0126. Silencing junB using small-interfering RNA reduced mRNA levels of OPN but not PAI-1. The silencing of CREB reduced PAI-1 induction by ANG II but enhanced the transcription of OPN. Together, these results suggest that salt-induced hypertensive disease promotes changes in matricellular genes that are stimulated by ANG II, regulated by ERK, and selectively regulated by JunB and CREB. microarray; Dahl rat; brain arteries; mitogen-activated protein kinase signaling; transcription factors

Published
2008

39. Methods to preserve individual bacteria and microbiome samples for nucleic acid analyses without altering cellular structure or integrity

Author

Ranjan, Ravi, Green, Stefan J., Mason, Christopher, Butler, Dan, Vinas, Natalia Reyero, Hsu, Chuan-Yu, Wagner, Nicole, Thomas, W. Kelley, Simpson, Steve, Bivens, Nathan, Kehoe, Phoebe, and Tighe, Scott

Subjects
Poster Abstracts
Abstract

One of the major challenges of the microbiome studies is unavailability of a reliable preservative media for long term storage of microbes that maintains the cellular structure and integrity without causing partial lysis or cellular leakage. Such a preservative would allow for many downstream analyses without compromising DNA and RNA quality. To alleviate these technical challenges, we designed a proof of principle study which included ABRF MMRG (Metagenomics and Microbiome Research Group) Members, representing multi-institutional sites. We formulated a preservative media that was suitable for long term storage of samples, maintained cellular structure of microorganisms, exhibited no detectable DNA or RNA leakage in the solution, preserved DNA and RNA integrity, preserved Gram stain and other stainability (SYBR Green, DAPI, etc) features, and maintained enzymatic cell wall digestion by Metapolyzyme. In this proof of principle study, we preserved three Gram positive (Bacillus subtilis ATCC23857, Enterococcus faecalis OG1RF, and Staphylococcus epidermidis PCI 1200), and one Gram negative (Escherichia coli K-12 substr. MG1655) bacterial strains and evaluated for the preservation competence. For long term storage and to evaluate the features of the preservative solution, microbial reference cultures were grown to early log phase. After storage (2 ys at 4 °C), cells were evaluated using microscopy, centrifuged to check for leakage of RNA and DNA, extracted nucleic acids using various extraction kits, and evaluated on a Bioanalyzer and Fragment Analyzer. This study suggests that the MMRG preservation approach can be used for long-term storage of microbial cells without compromising the morphological and genetic integrity and can be used to enable DNA and RNA extraction efficiency studies. However, further studies are required to evaluate additional microbial strains as well as to verify any genetic changes using an in-depth comparative sequencing approach.

Published
2020

41. Cave Thiovulaceae differ metabolically and genomically from marine species

Author

Bizic, Mina, primary, Brad, Traian, additional, Ionescu, Danny, additional, Barbu-Tudoran, Lucian, additional, Aerts, Joost, additional, Popa, Radu, additional, Zoccarato, Luca, additional, Ody, Jessica, additional, Flot, Jean-François, additional, Tighe, Scott, additional, Vellone, Daniel, additional, and Sarbu, Serban M., additional

Published
2020
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42. End-to-End Protocol for the Detection of SARS-CoV-2 from Built Environments

Author

Parker, Ceth W., primary, Singh, Nitin, additional, Tighe, Scott, additional, Blachowicz, Adriana, additional, Wood, Jason M., additional, Seuylemezian, Arman, additional, Vaishampayan, Parag, additional, Urbaniak, Camilla, additional, Hendrickson, Ryan, additional, Laaguiby, Pheobe, additional, Clark, Kevin, additional, Clement, Brian G., additional, O’Hara, Niamh B., additional, Couto-Rodriguez, Mara, additional, Bezdan, Daniela, additional, Mason, Christopher E., additional, and Venkateswaran, Kasthuri, additional

Published
2020
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43. Direct RT-qPCR detection of SARS-CoV-2 RNA from patient nasopharyngeal swabs without an RNA extraction step

Author

Bruce, Emily A., primary, Huang, Meei-Li, additional, Perchetti, Garrett A., additional, Tighe, Scott, additional, Laaguiby, Pheobe, additional, Hoffman, Jessica J., additional, Gerrard, Diana L., additional, Nalla, Arun K., additional, Wei, Yulun, additional, Greninger, Alexander L., additional, Diehl, Sean A., additional, Shirley, David J., additional, Leonard, Debra G. B., additional, Huston, Christopher D., additional, Kirkpatrick, Beth D., additional, Dragon, Julie A., additional, Crothers, Jessica W., additional, Jerome, Keith R., additional, and Botten, Jason W., additional

Published
2020
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45. Evaluating the Effects of Cell Sorting on Gene Expression

Author

Box, Andrew, primary, DeLay, Monica, additional, Tighe, Scott, additional, Chittur, Sridar V., additional, Bergeron, Alan, additional, Cochran, Matthew, additional, Lopez, Peter, additional, Meyer, E. Michael, additional, Saluk, Alan, additional, Thornton, Sherry, additional, and Brundage, Kathleen, additional

Published
2020
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46. Validating an Automated Nucleic Acid Extraction Device for Omics in Space Using Whole Cell Microbial Reference Standards

Author

Urbaniak, Camilla, primary, Wong, Season, additional, Tighe, Scott, additional, Arumugam, Arunkumar, additional, Liu, Bo, additional, Parker, Ceth W., additional, Wood, Jason M., additional, Singh, Nitin K., additional, Skorupa, Dana J., additional, Peyton, Brent M., additional, Jenson, Ryan, additional, Karouia, Fathi, additional, Dragon, Julie, additional, and Venkateswaran, Kasthuri, additional

Published
2020
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47. Multi-Platform Assessment of DNA Sequencing Performance using Human and Bacterial Reference Genomes in the ABRF Next-Generation Sequencing Study

Author

Foox, Jonathan, primary, Tighe, Scott W., additional, Nicolet, Charles M., additional, Zook, Justin M., additional, Byrska-Bishop, Marta, additional, Clarke, Wayne E., additional, Khayat, Michael M., additional, Mahmoud, Medhat, additional, Laaguiby, Phoebe K., additional, Herbert, Zachary T., additional, Warner, Derek, additional, Grills, George S., additional, Jen, Jin, additional, Levy, Shawn, additional, Xiang, Jenny, additional, Alonso, Alicia, additional, Schroth, Gary P., additional, Sedlazeck, Fritz J., additional, Narzisi, Giuseppe, additional, Farmerie, William, additional, Baldwin, Don A., additional, and Mason, Christopher E., additional

Published
2020
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