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  1. Content type: Meeting Report

    The National Cancer Institute (NCI) sponsored a 2-day workshop, “Next Steps in Studying the Human Microbiome and Health in Prospective Studies,” in Bethesda, Maryland, May 16–17, 2017. The workshop brought tog...

    Authors: Rashmi Sinha, Habibul Ahsan, Martin Blaser, J. Gregory Caporaso, Joseph Russell Carmical, Andrew T. Chan, Anthony Fodor, Mitchell H. Gail, Curtis C. Harris, Kathy Helzlsouer, Curtis Huttenhower, Rob Knight, Heidi H. Kong, Gabriel Y. Lai, Diane Leigh Smith Hutchinson, Loic Le Marchand…

    Citation: Microbiome 2018 6:210

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  3. Content type: Research

    The impacts of man-made chemicals, in particular of persistent organic pollutants, are multifactorial as they may affect the integrity of ecosystems, alter biodiversity and have undesirable effects on many org...

    Authors: Celso Martins, Adélia Varela, Céline C. Leclercq, Oscar Núñez, Tomáš Větrovský, Jenny Renaut, Petr Baldrian and Cristina Silva Pereira

    Citation: Microbiome 2018 6:208

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  4. Content type: Research

    Microbiome composition is linked to host functional traits including metabolism and immune function. Drivers of microbiome composition are increasingly well-characterised; however, evidence of group-level micr...

    Authors: Rachael E. Antwis, Jessica M. D. Lea, Bryony Unwin and Susanne Shultz

    Citation: Microbiome 2018 6:207

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  5. Content type: Correction

    Following publication of the original article, the authors recognized that the left and right panels in Fig. 6b had been inadvertently switched during reformatting.

    Authors: Chiranjit Mukherjee, Clifford J. Beall, Ann L. Griffen and Eugene J. Leys

    Citation: Microbiome 2018 6:206

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    The original article was published in Microbiome 2018 6:153

  6. Content type: Research

    Understanding the mechanism of the sexual dimorphism in susceptibility to obesity and metabolic syndrome (MS) is important for the development of effective interventions for MS.

    Authors: Kanakaraju Kaliannan, Ruairi C. Robertson, Kiera Murphy, Catherine Stanton, Chao Kang, Bin Wang, Lei Hao, Atul K. Bhan and Jing X. Kang

    Citation: Microbiome 2018 6:205

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  7. Content type: Research

    The International Space Station (ISS) is an ideal test bed for studying the effects of microbial persistence and succession on a closed system during long space flight. Culture-based analyses, targeted gene-ba...

    Authors: Nitin Kumar Singh, Jason M. Wood, Fathi Karouia and Kasthuri Venkateswaran

    Citation: Microbiome 2018 6:204

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    The Correction to this article has been published in Microbiome 2018 6:214

  8. Content type: Research

    The interplay between host genotype and commensal microbiota at different body sites can have important implications for health and disease. In dairy cows, polymorphism of bovine major histocompatibility compl...

    Authors: Hooman Derakhshani, Jan C. Plaizier, Jeroen De Buck, Herman W. Barkema and Ehsan Khafipour

    Citation: Microbiome 2018 6:203

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  9. Content type: Research

    Artificial gut models provide unique opportunities to study human-associated microbiota. Outstanding questions for these models’ fundamental biology include the timescales on which microbiota vary and the fact...

    Authors: Justin D. Silverman, Heather K. Durand, Rachael J. Bloom, Sayan Mukherjee and Lawrence A. David

    Citation: Microbiome 2018 6:202

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    The Correction to this article has been published in Microbiome 2018 6:212

  10. Content type: Research

    Travelers’ diarrhea (TD) is often caused by enterotoxigenic Escherichia coli, enteroaggregative E. coli, other bacterial pathogens, Norovirus, and occasionally parasites. Nevertheless, standard diagnostic methods...

    Authors: Qiyun Zhu, Christopher L. Dupont, Marcus B. Jones, Kevin M. Pham, Zhi-Dong Jiang, Herbert L. DuPont and Sarah K. Highlander

    Citation: Microbiome 2018 6:201

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  11. Content type: Research

    Mastitis, which affects nearly all lactating mammals including human, is generally thought to be caused by local infection of the mammary glands. For treatment, antibiotics are commonly prescribed, which howev...

    Authors: Chen Ma, Zheng Sun, Benhua Zeng, Shi Huang, Jie Zhao, Yong Zhang, Xiaoquan Su, Jian Xu, Hong Wei and Heping Zhang

    Citation: Microbiome 2018 6:200

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  12. Content type: Review

    Otitis media (OM) imposes a great burden of disease in indigenous populations around the world, despite a variety of treatment and prevention programs. Improved understanding of the pathogenesis of OM in indig...

    Authors: Andrea Coleman, Amanda Wood, Seweryn Bialasiewicz, Robert S. Ware, Robyn L. Marsh and Anders Cervin

    Citation: Microbiome 2018 6:199

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  13. Content type: Research

    Gut microbiome characteristics associated with HIV infection are of intense research interest but a deep understanding has been challenged by confounding factors across studied populations. Notably, a Prevotella-...

    Authors: Abigail J. S. Armstrong, Michael Shaffer, Nichole M. Nusbacher, Christine Griesmer, Suzanne Fiorillo, Jennifer M. Schneider, C. Preston Neff, Sam X. Li, Andrew P. Fontenot, Thomas Campbell, Brent E. Palmer and Catherine A. Lozupone

    Citation: Microbiome 2018 6:198

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  14. Content type: Meeting Report

    The Mid-Atlantic Microbiome Meet-up (M3) organization brings together academic, government, and industry groups to share ideas and develop best practices for microbiome research. In January of 2018, M3 held its f...

    Authors: Jacquelyn S. Meisel, Daniel J. Nasko, Brian Brubach, Victoria Cepeda-Espinoza, Jessica Chopyk, Héctor Corrada-Bravo, Marcus Fedarko, Jay Ghurye, Kiran Javkar, Nathan D. Olson, Nidhi Shah, Sarah M. Allard, Adam L. Bazinet, Nicholas H. Bergman, Alexis Brown, J. Gregory Caporaso…

    Citation: Microbiome 2018 6:197

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  15. Content type: Research

    Historically, the human womb has been thought to be sterile in healthy pregnancies, but this idea has been challenged by recent studies using DNA sequence-based methods, which have suggested that the womb is c...

    Authors: Jacob S. Leiby, Kevin McCormick, Scott Sherrill-Mix, Erik L. Clarke, Lyanna R. Kessler, Louis J. Taylor, Casey E. Hofstaedter, Aoife M. Roche, Lisa M. Mattei, Kyle Bittinger, Michal A. Elovitz, Rita Leite, Samuel Parry and Frederic D. Bushman

    Citation: Microbiome 2018 6:196

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  16. Content type: Methodology

    Several of the most devastating human diseases are caused by eukaryotic parasites transmitted by arthropod vectors or through food and water contamination. These pathogens only represent a fraction of all unic...

    Authors: Matthew V. Cannon, Haikel Bogale, Lindsay Rutt, Michael Humphrys, Poonum Korpe, Priya Duggal, Jacques Ravel and David Serre

    Citation: Microbiome 2018 6:195

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  17. Content type: Research

    The expansion of renewable energy produced by windmills and photovoltaic panels has generated a considerable electricity surplus, which can be utilized in water electrolysis systems for hydrogen production. Th...

    Authors: Alessandra Fontana, Panagiotis G. Kougias, Laura Treu, Adam Kovalovszki, Giorgio Valle, Fabrizio Cappa, Lorenzo Morelli, Irini Angelidaki and Stefano Campanaro

    Citation: Microbiome 2018 6:194

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  18. Content type: Research

    Postnatal development of early life microbiota influences immunity, metabolism, neurodevelopment, and infant health. Microbiome development occurs at multiple body sites, with distinct community compositions a...

    Authors: Alex Grier, Andrew McDavid, Bokai Wang, Xing Qiu, James Java, Sanjukta Bandyopadhyay, Hongmei Yang, Jeanne Holden-Wiltse, Haeja A Kessler, Ann L Gill, Heidie Huyck, Ann R Falsey, David J Topham, Kristin M Scheible, Mary T Caserta, Gloria S Pryhuber…

    Citation: Microbiome 2018 6:193

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  19. Content type: Research

    The identification of body site-specific microbial biomarkers and their use for classification tasks have promising applications in medicine, microbial ecology, and forensics. Previous studies have characteriz...

    Authors: Janko Tackmann, Natasha Arora, Thomas Sebastian Benedikt Schmidt, João Frederico Matias Rodrigues and Christian von Mering

    Citation: Microbiome 2018 6:192

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  20. Content type: Research

    Diversity-generating retroelements (DGRs) are genetic cassettes that selectively mutate target genes to produce hypervariable proteins. First characterized in Bordetella bacteriophage BPP-1, the DGR creates a hyp...

    Authors: Sean Benler, Ana Georgina Cobián-Güemes, Katelyn McNair, Shr-Hau Hung, Kyle Levi, Rob Edwards and Forest Rohwer

    Citation: Microbiome 2018 6:191

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  21. Content type: Research

    Pan-bacterial 16S rRNA microbiome surveys performed with massively parallel DNA sequencing technologies have transformed community microbiological studies. Current 16S profiling methods, however, fail to provi...

    Authors: Joshua P. Earl, Nithin D. Adappa, Jaroslaw Krol, Archana S. Bhat, Sergey Balashov, Rachel L. Ehrlich, James N. Palmer, Alan D. Workman, Mariel Blasetti, Bhaswati Sen, Jocelyn Hammond, Noam A. Cohen, Garth D. Ehrlich and Joshua Chang Mell

    Citation: Microbiome 2018 6:190

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  24. Content type: Research

    Paddy soil dissolved organic matter (DOM) represents a major hotspot for soil biogeochemistry, yet we know little about its chemodiversity let alone the microbial community that shapes it. Here, we leveraged u...

    Authors: Hong-Yi Li, Hang Wang, Hai-Tiao Wang, Pei-Yong Xin, Xin-Hua Xu, Yun Ma, Wei-Ping Liu, Chang-Yun Teng, Cheng-Liang Jiang, Li-Ping Lou, Wyatt Arnold, Lauren Cralle, Yong-Guan Zhu, Jin-Fang Chu, Jack A Gilbert and Zhi-Jian Zhang

    Citation: Microbiome 2018 6:187

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  26. Content type: Research

    Clostridiales and Bacteroidales are uniquely adapted to the gut environment and have co-evolved with their hosts resulting in convergent microbiome patterns within mammalian species. As a result, members of Clost...

    Authors: Adélaïde Roguet, A. Murat Eren, Ryan J Newton and Sandra L McLellan

    Citation: Microbiome 2018 6:185

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  27. Content type: Research

    Bacillus thuringiensis (Bt) crops have been cultivated at a large scale over the past several decades, which have raised concern about unintended effects on natural environments. Microbial communities typically c...

    Authors: Peng Li, Yong Xue, Jialiang Shi, Aihu Pan, Xueming Tang and Feng Ming

    Citation: Microbiome 2018 6:184

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  28. Content type: Research

    The ecological consequences of mercury (Hg) pollution—one of the major pollutants worldwide—on microbial taxonomic and functional attributes remain poorly understood and largely unexplored. Using soils from tw...

    Authors: Yu-Rong Liu, Manuel Delgado-Baquerizo, Li Bi, Jun Zhu and Ji-Zheng He

    Citation: Microbiome 2018 6:183

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  29. Content type: Research

    Microbial communities associated with indoor dust abound in the built environment. The transmission of sunlight through windows is a key building design consideration, but the effects of light exposure on dust...

    Authors: Ashkaan K. Fahimipour, Erica M. Hartmann, Andrew Siemens, Jeff Kline, David A. Levin, Hannah Wilson, Clarisse M. Betancourt-Román, GZ Brown, Mark Fretz, Dale Northcutt, Kyla N. Siemens, Curtis Huttenhower, Jessica L. Green and Kevin Van Den Wymelenberg

    Citation: Microbiome 2018 6:175

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  30. Content type: Research

    Infants born by caesarean section or receiving antibiotics are at increased risk of developing metabolic, inflammatory and immunological diseases, potentially due to disruption of normal gut microbiota at a cr...

    Authors: Katri Korpela, Anne Salonen, Outi Vepsäläinen, Marjo Suomalainen, Carolin Kolmeder, Markku Varjosalo, Sini Miettinen, Kaarina Kukkonen, Erkki Savilahti, Mikael Kuitunen and Willem M de Vos

    Citation: Microbiome 2018 6:182

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  31. Content type: Research

    Most metazoans are involved in durable relationships with microbes which can take several forms, from mutualism to parasitism. The advances of NGS technologies and bioinformatics tools have opened opportunitie...

    Authors: Cervin Guyomar, Fabrice Legeai, Emmanuelle Jousselin, Christophe Mougel, Claire Lemaitre and Jean-Christophe Simon

    Citation: Microbiome 2018 6:181

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  32. Content type: Research

    The specific interactions of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), and the lung microbiota in infection are entirely unexplored. Studies in cancer and other infectious diseas...

    Authors: Anthony M Cadena, Yixuan Ma, Tao Ding, MacKenzie Bryant, Pauline Maiello, Adam Geber, Philana Ling Lin, JoAnne L Flynn and Elodie Ghedin

    Citation: Microbiome 2018 6:180

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  33. Content type: Research

    Pediatric asthma is the most common chronic childhood disease in the USA, currently affecting ~ 7 million children. This heterogeneous syndrome is thought to encompass various disease phenotypes of clinically ...

    Authors: Marcos Pérez-Losada, Kayla J Authelet, Claire E Hoptay, Christine Kwak, Keith A Crandall and Robert J Freishtat

    Citation: Microbiome 2018 6:179

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  34. Content type: Research

    Rodents represent around 43% of all mammalian species, are widely distributed, and are the natural reservoirs of a diverse group of zoonotic viruses, including hantaviruses, Lassa viruses, and tick-borne encep...

    Authors: Zhiqiang Wu, Liang Lu, Jiang Du, Li Yang, Xianwen Ren, Bo Liu, Jinyong Jiang, Jian Yang, Jie Dong, Lilian Sun, Yafang Zhu, Yuhui Li, Dandan Zheng, Chi Zhang, Haoxiang Su, Yuting Zheng…

    Citation: Microbiome 2018 6:178

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  36. Content type: Research

    Representatives of the phylum Chloroflexi, though reportedly highly abundant in the extensive deep water habitats of both marine (SAR202 up to 30% of total prokaryotes) and freshwater (CL500-11 up to 26% of total...

    Authors: Maliheh Mehrshad, Michaela M Salcher, Yusuke Okazaki, Shin-ichi Nakano, Karel Šimek, Adrian-Stefan Andrei and Rohit Ghai

    Citation: Microbiome 2018 6:176

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  37. Content type: Research

    It is becoming evident that certain features of human microbiota, encoded by distinct autochthonous taxa, promote disease. As a result, borders between the so-called opportunistic pathogens, pathobionts, and c...

    Authors: Silke Rath, Tatjana Rud, André Karch, Dietmar Helmut Pieper and Marius Vital

    Citation: Microbiome 2018 6:174

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  38. Content type: Research

    Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cu...

    Authors: Johannes Alneberg, Christofer M. G. Karlsson, Anna-Maria Divne, Claudia Bergin, Felix Homa, Markus V. Lindh, Luisa W. Hugerth, Thijs J. G. Ettema, Stefan Bertilsson, Anders F. Andersson and Jarone Pinhassi

    Citation: Microbiome 2018 6:173

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  39. Content type: Research

    The metabolic syndrome (MetS) epidemic is associated with economic development, lifestyle transition and dysbiosis of gut microbiota, but these associations are rarely studied at the population scale. Here, we...

    Authors: Yan He, Wei Wu, Shan Wu, Hui-Min Zheng, Pan Li, Hua-Fang Sheng, Mu-Xuan Chen, Zi-Hui Chen, Gui-Yuan Ji, Zhong-Dai-Xi Zheng, Prabhakar Mujagond, Xiao-Jiao Chen, Zu-Hua Rong, Peng Chen, Li-Yi Lyu, Xian Wang…

    Citation: Microbiome 2018 6:172

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  40. Content type: Research

    Weaning is a period of marked physiological change. The introduction of solid foods and the changes in milk consumption are accompanied by significant gastrointestinal, immune, developmental, and microbial ada...

    Authors: Samanta Michelini, Biju Balakrishnan, Silvia Parolo, Alice Matone, Jane A. Mullaney, Wayne Young, Olivier Gasser, Clare Wall, Corrado Priami, Rosario Lombardo and Martin Kussmann

    Citation: Microbiome 2018 6:171

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  41. Content type: Research

    Grazing is a major modulator of biodiversity and productivity in grasslands. However, our understanding of grazing-induced changes in below-ground communities, processes, and soil productivity is limited. Here...

    Authors: Weibing Xun, Ruirui Yan, Yi Ren, Dongyan Jin, Wu Xiong, Guishan Zhang, Zhongli Cui, Xiaoping Xin and Ruifu Zhang

    Citation: Microbiome 2018 6:170

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  42. Content type: Research

    The expected increase in global surface temperature due to climate change may have a tremendous effect on the structure and function of the anaerobic food web in flooded rice field soil. Here, we used the meta...

    Authors: Jingjing Peng, Carl-Eric Wegner, Qicheng Bei, Pengfei Liu and Werner Liesack

    Citation: Microbiome 2018 6:169

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  43. Content type: Research

    Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake brines but...

    Authors: Charlotte D. Vavourakis, Adrian-Stefan Andrei, Maliheh Mehrshad, Rohit Ghai, Dimitry Y. Sorokin and Gerard Muyzer

    Citation: Microbiome 2018 6:168

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  44. Content type: Research

    Darwin’s finches are a clade of 19 species of passerine birds native to the Galápagos Islands, whose biogeography, specialized beak morphologies, and dietary choices—ranging from seeds to blood—make them a cla...

    Authors: Alice J. Michel, Lewis M. Ward, Shana K. Goffredi, Katherine S. Dawson, Daniel T. Baldassarre, Alec Brenner, Kiyoko M. Gotanda, John E. McCormack, Sean W. Mullin, Ariel O’Neill, Gabrielle S. Tender, J. Albert C. Uy, Kristie Yu, Victoria J. Orphan and Jaime A. Chaves

    Citation: Microbiome 2018 6:167

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  45. Content type: Research

    Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection (rCDI). The use of freeze-dried, encapsulated donor material for FMT (cap-FMT) allows for an easy rou...

    Authors: Christopher Staley, Thomas Kaiser, Byron P. Vaughn, Carolyn T. Graiziger, Matthew J. Hamilton, Tauseef ur Rehman, Kevin Song, Alexander Khoruts and Michael J. Sadowsky

    Citation: Microbiome 2018 6:166

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  46. Content type: Research

    Microbial processes are intricately linked to the depletion of oxygen in in-land and coastal water bodies, with devastating economic and ecological consequences. Microorganisms deplete oxygen during biomass de...

    Authors: Keith Arora-Williams, Scott W. Olesen, Benjamin P. Scandella, Kyle Delwiche, Sarah J. Spencer, Elise M. Myers, Sonali Abraham, Alyssa Sooklal and Sarah P. Preheim

    Citation: Microbiome 2018 6:165

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  47. Content type: Research

    Targeted amplicon deep sequencing (TADS) of the 16S rRNA gene is commonly used to explore and characterize bacterial microbiomes. Meanwhile, attempts to apply TADS to the detection and characterization of enti...

    Authors: Briana R. Flaherty, Eldin Talundzic, Joel Barratt, Kristine J. Kines, Christian Olsen, Meredith Lane, Mili Sheth and Richard S. Bradbury

    Citation: Microbiome 2018 6:164

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  49. Content type: Research

    Woodlice are recognized as keystone species in terrestrial ecosystems due to their role in the decomposition of organic matter. Thus, they contribute to lignocellulose degradation and nutrient cycling in the e...

    Authors: Marius Bredon, Jessica Dittmer, Cyril Noël, Bouziane Moumen and Didier Bouchon

    Citation: Microbiome 2018 6:162

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  50. Content type: Research

    Nanoarchaeota are obligate symbionts of other Archaea first discovered 16 years ago, yet little is known about this largely uncultivated taxon. While Nanoarchaeota diversity has been detected in a variety of habi...

    Authors: Jessica K. Jarett, Stephen Nayfach, Mircea Podar, William Inskeep, Natalia N. Ivanova, Jacob Munson-McGee, Frederik Schulz, Mark Young, Zackary J. Jay, Jacob P. Beam, Nikos C. Kyrpides, Rex R. Malmstrom, Ramunas Stepanauskas and Tanja Woyke

    Citation: Microbiome 2018 6:161

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