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  1. Invasive methods requiring general anaesthesia are needed to sample the lung microbiota in young children who do not expectorate. This poses substantial challenges to longitudinal study of paediatric airway mi...

    Authors: R. L. Marsh, M. Kaestli, A. B. Chang, M. J. Binks, C. E. Pope, L. R. Hoffman and H. C. Smith-Vaughan
    Citation: Microbiome 2016 4:37
  2. Upper respiratory infections (URI) and their complications are a major healthcare burden for pediatric populations. Although the microbiology of the nasopharynx is an important determinant of the complications...

    Authors: Clark A. Santee, Nabeetha A. Nagalingam, Ali A. Faruqi, Gregory P. DeMuri, James E. Gern, Ellen R. Wald and Susan V. Lynch
    Citation: Microbiome 2016 4:34
  3. The fermentation of dietary fiber to various organic acids is a beneficial function provided by the microbiota in the human large intestine. In particular, butyric acid contributes to host health by facilitati...

    Authors: A. Venkataraman, J. R. Sieber, A. W. Schmidt, C. Waldron, K. R. Theis and T. M. Schmidt
    Citation: Microbiome 2016 4:33
  4. The National Heart, Lung, and Blood Institute (NHLBI) of the National Institutes of Health convened a Working Group on the Microbiome in Cardiovascular, Pulmonary and Hematologic Health and Diseases from June ...

    Authors: Shimian Zou, Lis Caler, Sandra Colombini-Hatch, Simone Glynn and Pothur Srinivas
    Citation: Microbiome 2016 4:32
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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...

    Citation: Microbiome 2016 4:24

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

  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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

    The original article was published in Microbiome 2015 3:40

  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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

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