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  1. The gut microbiota has been shown to be closely associated with human health and disease. While next-generation sequencing can be readily used to profile the microbiota taxonomy and metabolic potential, metapr...

    Authors: Xu Zhang, Zhibin Ning, Janice Mayne, Jasmine I. Moore, Jennifer Li, James Butcher, Shelley Ann Deeke, Rui Chen, Cheng-Kang Chiang, Ming Wen, David Mack, Alain Stintzi and Daniel Figeys

    Citation: Microbiome 2016 4:31

    Content type: Methodology

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  2. Gastrointestinal disturbances are among symptoms commonly reported by individuals diagnosed with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). However, whether ME/CFS is associated with an alter...

    Authors: Ludovic Giloteaux, Julia K. Goodrich, William A. Walters, Susan M. Levine, Ruth E. Ley and Maureen R. Hanson

    Citation: Microbiome 2016 4:30

    Content type: Research

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  3. Recent studies have suggested that bacteria associated with the placenta—a “placental microbiome”—may be important in reproductive health and disease. However, a challenge in working with specimens with low ba...

    Authors: Abigail P. Lauder, Aoife M. Roche, Scott Sherrill-Mix, Aubrey Bailey, Alice L. Laughlin, Kyle Bittinger, Rita Leite, Michal A. Elovitz, Samuel Parry and Frederic D. Bushman

    Citation: Microbiome 2016 4:29

    Content type: Research

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  4. Next-generation 16S ribosomal RNA gene sequencing is widely used to determine the relative composition of the mammalian gut microbiomes. However, in the absence of a reference, this does not reveal alterations...

    Authors: Frank Stämmler, Joachim Gläsner, Andreas Hiergeist, Ernst Holler, Daniela Weber, Peter J. Oefner, André Gessner and Rainer Spang

    Citation: Microbiome 2016 4:28

    Content type: Methodology

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  5. This proof-of-principle study examines whether postnatal, low-dose exposure to environmental chemicals modifies the composition of gut microbiome. Three chemicals that are widely used in personal care products...

    Authors: Jianzhong Hu, Vincent Raikhel, Kalpana Gopalakrishnan, Heriberto Fernandez-Hernandez, Luca Lambertini, Fabiana Manservisi, Laura Falcioni, Luciano Bua, Fiorella Belpoggi, Susan L.Teitelbaum and Jia Chen

    Citation: Microbiome 2016 4:26

    Content type: Research

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  6. Periodontal disease is highly prevalent amongst domestic cats, causing pain, gingival bleeding, reduced food intake, loss of teeth and possibly impacts on overall systemic health. Diet has been suggested to pl...

    Authors: Christina J. Adler, Richard Malik, Gina V. Browne and Jacqueline M. Norris

    Citation: Microbiome 2016 4:23

    Content type: Research

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  7. The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is a novel, interdisciplinary initiative comprised of experts across many fields, including genomics, data ana...

    Authors:

    Citation: Microbiome 2016 4:24

    Content type: Meeting Report

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    The Erratum to this article has been published in Microbiome 2016 4:45

  8. For potential future human missions to the Moon or Mars and sustained presence in the International Space Station, a safe enclosed habitat environment for astronauts is required. Potential microbial contaminat...

    Authors: Teresa Mayer, Adriana Blachowicz, Alexander J. Probst, Parag Vaishampayan, Aleksandra Checinska, Tiffany Swarmer, Pablo de Leon and Kasthuri Venkateswaran

    Citation: Microbiome 2016 4:22

    Content type: Research

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  9. Alterations in intestinal microbiota have been correlated with a growing number of diseases. Investigating the faecal microbiota is widely used as a non-invasive and ethically simple proxy for intestinal biops...

    Authors: Cian J. Hill, Jillian R. M. Brown, Denise B. Lynch, Ian B. Jeffery, C. Anthony Ryan, R. Paul Ross, Catherine Stanton and Paul W. O’Toole

    Citation: Microbiome 2016 4:19

    Content type: Methodology

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  10. The 16s rRNA gene is so far the most widely used marker for taxonomical classification and separation of prokaryotes. Since it is universally conserved among prokaryotes, it is possible to use this gene to cla...

    Authors: Yemin Lan, Gail Rosen and Ruth Hershberg

    Citation: Microbiome 2016 4:18

    Content type: Research

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  11. The development of anti-islet cell autoimmunity precedes clinical type 1 diabetes and occurs very early in life. During this early period, dietary factors strongly impact on the composition of the gut microbio...

    Authors: David Endesfelder, Marion Engel, Austin G. Davis-Richardson, Alexandria N. Ardissone, Peter Achenbach, Sandra Hummel, Christiane Winkler, Mark Atkinson, Desmond Schatz, Eric Triplett, Anette-Gabriele Ziegler and Wolfgang zu Castell

    Citation: Microbiome 2016 4:17

    Content type: Research

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  12. The epidemiology of bacterial vaginosis (BV) suggests it is sexually transmissible, yet no transmissible agent has been identified. It is probable that BV-associated bacterial communities are transferred from ...

    Authors: Marcela Zozaya, Michael J. Ferris, Julia D. Siren, Rebecca Lillis, Leann Myers, M. Jacques Nsuami, A. Murat Eren, Jonathan Brown, Christopher M. Taylor and David H. Martin

    Citation: Microbiome 2016 4:16

    Content type: Research

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  13. Chronic granulomatous disease (CGD) is caused by defects in nicotinamide adenine dinucleotide phosphate oxidase 2 (NOX2) complex subunits (gp91 phox (a.k.a. Nox2), p47 ...

    Authors: E. Liana Falcone, Loreto Abusleme, Muthulekha Swamydas, Michail S. Lionakis, Li Ding, Amy P. Hsu, Adrian M. Zelazny, Niki M. Moutsopoulos, Douglas B. Kuhns, Clay Deming, Mariam Quiñones, Julia A. Segre, Clare E. Bryant and Steven M. Holland

    Citation: Microbiome 2016 4:13

    Content type: Research

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  14. The Neolithic revolution—the transition of our species from hunter and gatherer to cultivator—began approximately 14,000 years ago and is essentially complete for macroscopic food. Humans remain largely pre-Ne...

    Authors: David S. Thaler

    Citation: Microbiome 2016 4:14

    Content type: Review

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  15. Since 1982, specific serotypes of Shiga toxin-producing Escherichia coli (STEC) have been recognized as significant foodborne pathogens acquired from contaminated beef and, more recently, other food products. Cat...

    Authors: Jessica Chopyk, Ryan M. Moore, Zachary DiSpirito, Zachary R. Stromberg, Gentry L. Lewis, David G. Renter, Natalia Cernicchiaro, Rodney A. Moxley and K. Eric Wommack

    Citation: Microbiome 2016 4:9

    Content type: Research

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  16. Clostridium difficile infection (CDI) is the leading infectious cause of nosocomial diarrhea. Hospitalized patients are at increased risk of developing CDI because they are exposed to

    Authors: Caroline Vincent, Mark A. Miller, Thaddeus J. Edens, Sudeep Mehrotra, Ken Dewar and Amee R. Manges

    Citation: Microbiome 2016 4:12

    Content type: Research

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  17. Fungi play critical roles in many ecosystems, cause serious diseases in plants and animals, and pose significant threats to human health and structural integrity problems in built environments. While most fung...

    Authors: Jennifer Fouquier, Jai Ram Rideout, Evan Bolyen, John Chase, Arron Shiffer, Daniel McDonald, Rob Knight, J Gregory Caporaso and Scott T. Kelley

    Citation: Microbiome 2016 4:11

    Content type: Software

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  18. Architects are enthusiastic about “bioinformed design” as occupant well-being is a primary measure of architectural success. However, architects are also under mounting pressure to create more sustainable buil...

    Authors: G. Z. Brown, Jeff Kline, Gwynne Mhuireach, Dale Northcutt and Jason Stenson

    Citation: Microbiome 2016 4:6

    Content type: Commentary

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  19. Lower respiratory tract infection (LRTI) is a major contributor to respiratory failure requiring intubation and mechanical ventilation. LRTI also occurs during mechanical ventilation, increasing the morbidity ...

    Authors: Brendan J. Kelly, Ize Imai, Kyle Bittinger, Alice Laughlin, Barry D. Fuchs, Frederic D. Bushman and Ronald G. Collman

    Citation: Microbiome 2016 4:7

    Content type: Research

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  20. While 16S ribosomal RNA (rRNA) sequencing has been used to characterize the lung’s bacterial microbiota in human immunodeficiency virus (HIV)-infected individuals, taxonomic studies provide limited information...

    Authors: Sushma K. Cribbs, Karan Uppal, Shuzhao Li, Dean P. Jones, Laurence Huang, Laura Tipton, Adam Fitch, Ruth M. Greenblatt, Lawrence Kingsley, David M. Guidot, Elodie Ghedin and Alison Morris

    Citation: Microbiome 2016 4:3

    Content type: Research

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  21. Metatranscriptomics is emerging as a powerful technology for the functional characterization of complex microbial communities (microbiomes). Use of unbiased RNA-sequencing can reveal both the taxonomic composi...

    Authors: Yue Jiang, Xuejian Xiong, Jayne Danska and John Parkinson

    Citation: Microbiome 2016 4:2

    Content type: Research

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  22. A variety of different sampling devices are currently available to acquire air samples for the study of the microbiome of the air. All have a degree of technical complexity that limits deployment. Here, we eva...

    Authors: Julian Gordon, Prasanthi Gandhi, Gajendra Shekhawat, Angel Frazier, Jarrad Hampton-Marcell and Jack A. Gilbert

    Citation: Microbiome 2015 3:79

    Content type: Methodology

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  23. Each day people are exposed to millions of bioaerosols, including whole microorganisms, which can have both beneficial and detrimental effects. The next chapter in understanding the airborne microbiome of the ...

    Authors: Aaron J. Prussin II and Linsey C. Marr

    Citation: Microbiome 2015 3:78

    Content type: Review

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  24. Authors: W. Florian Fricke, Yang Song, An-Jiang Wang, Allen Smith, Viktoriya Grinchuk, Chenlin Pei, Bing Ma, Nonghua Lu, Joseph F. Urban Jr., Terez Shea-Donohue and Aiping Zhao

    Citation: Microbiome 2015 3:77

    Content type: Erratum

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    The original article was published in Microbiome 2015 3:40

  25. The Tasmanian devil, the world’s largest carnivorous marsupial, is at risk of extinction due to devil facial tumour disease (DFTD), a fatal contagious cancer. The Save the Tasmanian Devil Program has establish...

    Authors: Yuanyuan Cheng, Samantha Fox, David Pemberton, Carolyn Hogg, Anthony T. Papenfuss and Katherine Belov

    Citation: Microbiome 2015 3:76

    Content type: Research

    Published on:

  26. Westernized lifestyle and hygienic behavior have contributed to dramatic changes in the human-associated microbiota. This particularly relates to indoor activities such as house cleaning. We therefore investig...

    Authors: Ekaterina Avershina, Anuradha Ravi, Ola Storrø, Torbjørn Øien, Roar Johnsen and Knut Rudi

    Citation: Microbiome 2015 3:65

    Content type: Research

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  27. The etiology of dental caries is multifactorial, but frequent consumption of free sugars, notably sucrose, appears to be a major factor driving the supragingival microbiota in the direction of dysbiosis. Recen...

    Authors: Joel D. Rudney, Pratik D. Jagtap, Cavan S. Reilly, Ruoqiong Chen, Todd W. Markowski, LeeAnn Higgins, James E. Johnson and Timothy J. Griffin

    Citation: Microbiome 2015 3:69

    Content type: Research

    Published on:

  28. Fecal microbiota transplantation is an effective treatment for recurrent Clostridium difficile infection and is being investigated as a treatment for other microbiota-associated diseases. To facilitate these a...

    Authors: Abbas Kazerouni, James Burgess, Laura J. Burns and Lawrence M. Wein

    Citation: Microbiome 2015 3:75

    Content type: Research

    Published on:

  29. The microbiome of the built environment (MoBE) is a relatively new area of study. While some knowledge has been gained regarding impacts of the MoBE on the human microbiome and disease vulnerability, there is ...

    Authors: Andrew J. Hoisington, Lisa A. Brenner, Kerry A. Kinney, Teodor T. Postolache and Christopher A. Lowry

    Citation: Microbiome 2015 3:60

    Content type: Review

    Published on:

  30. Viral infections such as influenza have been shown to predispose hosts to increased colonization of the respiratory tract by pathogenic bacteria and secondary bacterial pneumonia. To examine how viral infectio...

    Authors: Y. Tarabichi, K. Li, S. Hu, C. Nguyen, X. Wang, D. Elashoff, K. Saira, Bryan Frank, Monika Bihan, E. Ghedin, Barbara A. Methé and Jane C. Deng

    Citation: Microbiome 2015 3:74

    Content type: Research

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  31. Aphids are known to live in symbiosis with specific bacteria, called endosymbionts which can be classified as obligate or accessory. Buchnera aphidicola is generally the only obligatory symbiont present in aphids...

    Authors: Caroline De Clerck, Akiko Fujiwara, Pauline Joncour, Simon Léonard, Marie-Line Félix, Frédéric Francis, M. Haissam Jijakli, Tsutomu Tsuchida and Sébastien Massart

    Citation: Microbiome 2015 3:63

    Content type: Research

    Published on:

  32. The quantified self community brings together enthusiasts who are using technological devices to monitor their health and social media to share their personal data with others online. In light of the growing p...

    Authors: Carine Gimbert and François-Joseph Lapointe

    Citation: Microbiome 2015 3:70

    Content type: Commentary

    Published on:

  33. We previously showed that stool samples of pre-adolescent and adolescent US children diagnosed with diarrhea-predominant IBS (IBS-D) had different compositions of microbiota and metabolites compared to healthy...

    Authors: Vijay Shankar, Nicholas V. Reo and Oleg Paliy

    Citation: Microbiome 2015 3:73

    Content type: Short report

    Published on:

  34. A wide variety of specialty textiles are used in health care settings for bedding, clothing, and privacy. The ability of textiles to host or otherwise sequester microbes has been well documented; however, thei...

    Authors: Alina Handorean, Charles E. Robertson, J. Kirk Harris, Daniel Frank, Natalie Hull, Cassandra Kotter, Mark J. Stevens, Darrel Baumgardner, Norman R. Pace and Mark Hernandez

    Citation: Microbiome 2015 3:72

    Content type: Research

    Published on:

  35. Recent studies posit a reciprocal dependency between the microbiomes associated with humans and indoor environments. However, none of these metagenome surveys has considered the viability of constituent microo...

    Authors: Thomas Weinmaier, Alexander J. Probst, Myron T. La Duc, Doina Ciobanu, Jan-Fang Cheng, Natalia Ivanova, Thomas Rattei and Parag Vaishampayan

    Citation: Microbiome 2015 3:62

    Content type: Research

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  36. The Sloan Symposium, “Microbiology of the Indoor Environment,” was held to facilitate dialog on biological research between scientists and practitioners in the field which was complementary to the adjoining ac...

    Authors: Hal Levin, Martin Täubel and Mark Hernandez

    Citation: Microbiome 2015 3:68

    Content type: Meeting Report

    Published on:

  37. Lowering water heater temperature set points and using less drinking water are common approaches to conserving water and energy; yet, there are discrepancies in past literature regarding the effects of water h...

    Authors: William J. Rhoads, Pan Ji, Amy Pruden and Marc A. Edwards

    Citation: Microbiome 2015 3:67

    Content type: Research

    Published on:

  38. Microorganisms are distributed on surfaces within homes, workplaces, and schools, with the potential to impact human health and disease. University campuses represent a unique opportunity to explore the distri...

    Authors: Ashley A. Ross and Josh D. Neufeld

    Citation: Microbiome 2015 3:66

    Content type: Research

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  39. Newborns delivered by C-section acquire human skin microbes just after birth, but the sources remain unknown. We hypothesized that the operating room (OR) environment contains human skin bacteria that could be...

    Authors: Hakdong Shin, Zhiheng Pei, Keith A. Martinez II, Juana I. Rivera-Vinas, Keimari Mendez, Humberto Cavallin and Maria G. Dominguez-Bello

    Citation: Microbiome 2015 3:59

    Content type: Research

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    The Erratum to this article has been published in Microbiome 2016 4:4

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