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  1. Clostridium difficile is the most common known cause of antibiotic-associated diarrhea. Upon the disturbance of gut microbiota by antibiotics, C. difficile establishes growth and relea...

    Authors: Manli Y. Davis, Husen Zhang, Lera E. Brannan, Robert J. Carman and James H. Boone
    Citation: Microbiome 2016 4:53
  2. Whole genome amplification (WGA) is a challenging, key step in metagenomic studies of samples containing minute amounts of DNA, such as samples from low biomass environments. It is well known that multiple dis...

    Authors: Maria Hammond, Felix Homa, Helene Andersson-Svahn, Thijs J. G. Ettema and Haakan N. Joensson
    Citation: Microbiome 2016 4:52
  3. Elucidating the role of gut microbiota in physiological and pathological processes has recently emerged as a key research aim in life sciences. In this respect, metaproteomics, the study of the whole protein c...

    Authors: Alessandro Tanca, Antonio Palomba, Cristina Fraumene, Daniela Pagnozzi, Valeria Manghina, Massimo Deligios, Thilo Muth, Erdmann Rapp, Lennart Martens, Maria Filippa Addis and Sergio Uzzau
    Citation: Microbiome 2016 4:51
  4. End-stage renal disease (ESRD) is associated with uremia and increased systemic inflammation. Alteration of the intestinal microbiota may facilitate translocation of endotoxins into the systemic circulation le...

    Authors: Janice Crespo-Salgado, V. Matti Vehaskari, Tyrus Stewart, Michael Ferris, Qiang Zhang, Guangdi Wang, Eugene E. Blanchard, Christopher M. Taylor, Mahmoud Kallash, Larry A. Greenbaum and Diego H. Aviles
    Citation: Microbiome 2016 4:50
  5. Post-translational modification (PTM) of proteins is one important strategy employed by bacteria for environmental adaptation. However, PTM profiles in deep-sea microbes remain largely unexplored.

    Authors: Weipeng Zhang, Jin Sun, Huiluo Cao, Renmao Tian, Lin Cai, Wei Ding and Pei-Yuan Qian
    Citation: Microbiome 2016 4:49
  6. Fresh sprouted seeds have been associated with a number of large outbreaks caused by Salmonella and Shiga toxin-producing E. coli. However, the high number of commensal bacteria found on sprouted seeds hampers th...

    Authors: Heike Margot, Roger Stephan and Taurai Tasara
    Citation: Microbiome 2016 4:48
  7. We investigated whether the carriage of Blastocystis in IBS patients was associated with differences in the faecal microbiota. Forty patients with diarrhoea-predominant IBS (26 Blastocystis-positive and 14 Blasto...

    Authors: Robyn Nagel, Rebecca J. Traub, Richard J. N. Allcock, Marcella M. S. Kwan and Helle Bielefeldt-Ohmann
    Citation: Microbiome 2016 4:47
  8. Although the common, silver, and bighead carps are native and sparsely distributed in Eurasia, these fish have become abundant and invasive in North America. An understanding of the biology of these species ma...

    Authors: Jessica J. Eichmiller, Matthew J. Hamilton, Christopher Staley, Michael J. Sadowsky and Peter W. Sorensen
    Citation: Microbiome 2016 4:44
  9. The editors of Microbiome would like to thank all our reviewers who have contributed to the journal in 2015.

    Authors: Jacques Ravel and Eric Wommack
    Citation: Microbiome 2016 4:43
  10. Reduced microbial diversity in human intestines has been implicated in various conditions such as diabetes, colorectal cancer, and inflammatory bowel disease. The role of physical fitness in the context of hum...

    Authors: Mehrbod Estaki, Jason Pither, Peter Baumeister, Jonathan P. Little, Sandeep K. Gill, Sanjoy Ghosh, Zahra Ahmadi-Vand, Katelyn R. Marsden and Deanna L. Gibson
    Citation: Microbiome 2016 4:42
  11. The human gut microbiota directly affects human health, and its alteration can lead to gastrointestinal abnormalities and inflammation. Rett syndrome (RTT), a progressive neurological disorder mainly caused by...

    Authors: Francesco Strati, Duccio Cavalieri, Davide Albanese, Claudio De Felice, Claudio Donati, Joussef Hayek, Olivier Jousson, Silvia Leoncini, Massimo Pindo, Daniela Renzi, Lisa Rizzetto, Irene Stefanini, Antonio Calabrò and Carlotta De Filippo
    Citation: Microbiome 2016 4:41
  12. In this manuscript, we investigate the “stones best left unturned” of sample storage and preparation and their implications for the next-generation sequencing of infant faecal microbial communities by the 16S ...

    Authors: Alexander G. Shaw, Kathleen Sim, Elizabeth Powell, Emma Cornwell, Teresa Cramer, Zoë E. McClure, Ming-Shi Li and J. Simon Kroll
    Citation: Microbiome 2016 4:40
  13. Antibiotics are a mainstay of treatment for bacterial infections worldwide, yet the effects of typical antibiotic prescriptions on human indigenous microbiota have not been thoroughly evaluated. We examined th...

    Authors: Shira R. Abeles, Marcus B. Jones, Tasha M. Santiago-Rodriguez, Melissa Ly, Niels Klitgord, Shibu Yooseph, Karen E. Nelson and David T. Pride
    Citation: Microbiome 2016 4:39
  14. Studies of environmental microbiota typically target only specific groups of microorganisms, with most focusing on bacteria through taxonomic classification of 16S rRNA gene sequences. For a more holistic unde...

    Authors: Miguel I. Uyaguari-Diaz, Michael Chan, Bonnie L. Chaban, Matthew A. Croxen, Jan F. Finke, Janet E. Hill, Michael A. Peabody, Thea Van Rossum, Curtis A. Suttle, Fiona S. L. Brinkman, Judith Isaac-Renton, Natalie A. Prystajecky and Patrick Tang
    Citation: Microbiome 2016 4:20
  15. Longitudinal studies of the lung microbiome are challenging due to the invasive nature of sample collection. In addition, studies of the lung microbiome in human disease are usually performed after disease ons...

    Authors: Alison Morris, Joseph N. Paulson, Hisham Talukder, Laura Tipton, Heather Kling, Lijia Cui, Adam Fitch, Mihai Pop, Karen A. Norris and Elodie Ghedin
    Citation: Microbiome 2016 4:38
  16. 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
  17. Our view of host-associated microbiota remains incomplete due to the presence of as yet uncultured constituents. The Bacteroidales family S24-7 is a prominent example of one of these groups. Marker gene surveys i...

    Authors: Kate L. Ormerod, David L. A. Wood, Nancy Lachner, Shaan L. Gellatly, Joshua N. Daly, Jeremy D. Parsons, Cristiana G. O. Dal’Molin, Robin W. Palfreyman, Lars K. Nielsen, Matthew A. Cooper, Mark Morrison, Philip M. Hansbro and Philip Hugenholtz
    Citation: Microbiome 2016 4:36
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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

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

  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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

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