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  1. 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
    Content type: Research Published on:

  2. 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
    Content type: Research Published on:

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

  3. 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
    Content type: Research Published on:

  4. 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
    Content type: Research Published on:

  5. 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
    Content type: Review Published on:

  6. 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
    Content type: Research Published on:

    The Correction to this article has been published in Microbiome 2020 8:50

  7. 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
    Content type: Meeting Report Published on:

  8. 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
    Content type: Research Published on:

  9. 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
    Content type: Methodology Published on:

  10. 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
    Content type: Research Published on:

  11. 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
    Content type: Research Published on:

  12. 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
    Content type: Research Published on:

  13. 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
    Content type: Research Published on:

  14. 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
    Content type: Research Published on:

  17. 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-Tao 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
    Content type: Research Published on:

    The Correction to this article has been published in Microbiome 2020 8:169

  19. 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
    Content type: Research Published on:

  20. 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
    Content type: Research Published on:

  21. 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
    Content type: Research Published on:

  22. 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
    Content type: Research Published on:

  23. 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
    Content type: Research Published on:

  24. 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
    Content type: Research Published on:

  25. 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
    Content type: Research Published on:

  26. 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
    Content type: Research Published on:

  27. 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
    Content type: Research Published on:

  29. 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
    Content type: Research Published on:

  30. 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
    Content type: Research Published on:

  31. 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
    Content type: Research Published on:

  32. 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
    Content type: Research Published on:

  33. 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
    Content type: Research Published on:

  34. 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
    Content type: Research Published on:

  35. 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
    Content type: Research Published on:

  36. 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
    Content type: Research Published on:

  37. 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
    Content type: Research Published on:

  38. 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
    Content type: Research Published on:

  39. 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
    Content type: Research Published on:

  40. 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
    Content type: Research Published on:

  42. 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
    Content type: Research Published on:

  43. 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
    Content type: Research Published on:

  44. Here, we summarize a symposium entitled “Microbiology of the Built Environment: Implications for Health and Design” that was presented at the National Council for Science and the Environment (NCSE) 17th Nation...

    Authors: Ashleigh Bope, Mark H. Weir, Amy Pruden, Michael Morowitz, Jade Mitchell and Karen C. Dannemiller
    Citation: Microbiome 2018 6:160
    Content type: Meeting Report Published on:

  47. Preterm infants are at risk of developing intestinal dysbiosis with an increased proportion of Gammaproteobacteria. In this study, we sought the clinical determinants of the relative abundance of feces-associa...

    Authors: Thao T. B. Ho, Maureen W. Groer, Bradley Kane, Alyson L. Yee, Benjamin A. Torres, Jack A. Gilbert and Akhil Maheshwari
    Citation: Microbiome 2018 6:157
    Content type: Research Published on:

  48. Plants are capable of building up beneficial rhizosphere communities as is evidenced by disease-suppressive soils. However, it is not known how and why soil bacterial communities are impacted by plant exposure...

    Authors: Jun Yuan, Jun Zhao, Tao Wen, Mengli Zhao, Rong Li, Pim Goossens, Qiwei Huang, Yang Bai, Jorge M. Vivanco, George A. Kowalchuk, Roeland L. Berendsen and Qirong Shen
    Citation: Microbiome 2018 6:156
    Content type: Research Published on:

  49. Recent advances in sequencing technologies and bioinformatics tools have allowed for large-scale microbiome studies that are rapidly advancing medical research. However, small changes in technique or analysis ...

    Authors: Jeffrey M. Bender, Fan Li, Helty Adisetiyo, David Lee, Sara Zabih, Long Hung, Thomas A. Wilkinson, Pia S. Pannaraj, Rosemary C. She, Jennifer Dien Bard, Nicole H. Tobin and Grace M. Aldrovandi
    Citation: Microbiome 2018 6:155
    Content type: Methodology Published on:

  50. Sequencing of the 16S rRNA gene has been the standard for studying the composition of microbial communities. While it allows identification of bacteria at the level of species, this method does not usually pro...

    Authors: Chiranjit Mukherjee, Clifford J. Beall, Ann L. Griffen and Eugene J. Leys
    Citation: Microbiome 2018 6:153
    Content type: Research Published on:

    The Correction to this article has been published in Microbiome 2018 6:206

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