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  1. Preterm infants represent a unique patient population that is born functionally immature and must accomplish development under the influence of a hospital environment. Neonatal necrotizing enterocolitis (NEC) ...

    Authors: Erika C Claud, Kevin P Keegan, Jennifer M Brulc, Lei Lu, Daniela Bartels, Elizabeth Glass, Eugene B Chang, Folker Meyer and Dionysios A Antonopoulos
    Citation: Microbiome 2013 1:20
    Content type: Research Published on:

  2. The lung microbiome of healthy individuals frequently harbors oral organisms. Despite evidence that microaspiration is commonly associated with smoking-related lung diseases, the effects of lung microbiome enr...

    Authors: Leopoldo N Segal, Alexander V Alekseyenko, Jose C Clemente, Rohan Kulkarni, Benjamin Wu, Hao Chen, Kenneth I Berger, Roberta M Goldring, William N Rom, Martin J Blaser and Michael D Weiden
    Citation: Microbiome 2013 1:19
    Content type: Research Published on:

    The Erratum to this article has been published in Microbiome 2014 2:21

  3. Antimicrobial use is thought to suppress the intestinal microbiota, thereby impairing colonization resistance and allowing Clostridium difficile to infect the gut. Additional risk factors such as proton-pump inhi...

    Authors: Caroline Vincent, David A Stephens, Vivian G Loo, Thaddeus J Edens, Marcel A Behr, Ken Dewar and Amee R Manges
    Citation: Microbiome 2013 1:18
    Content type: Research Published on:

  4. Consistent compositional shifts in the gut microbiota are observed in IBD and other chronic intestinal disorders and may contribute to pathogenesis. The identities of microbial biomolecular mechanisms and meta...

    Authors: Ian H McHardy, Maryam Goudarzi, Maomeng Tong, Paul M Ruegger, Emma Schwager, John R Weger, Thomas G Graeber, Justin L Sonnenburg, Steve Horvath, Curtis Huttenhower, Dermot PB McGovern, Albert J Fornace Jr., James Borneman and Jonathan Braun
    Citation: Microbiome 2013 1:17
    Content type: Research Published on:

  5. Numerous cancers have been linked to microorganisms. Given that colorectal cancer is a leading cause of cancer deaths and the colon is continuously exposed to a high diversity of microbes, the relationship bet...

    Authors: René L Warren, Douglas J Freeman, Stephen Pleasance, Peter Watson, Richard A Moore, Kyla Cochrane, Emma Allen-Vercoe and Robert A Holt
    Citation: Microbiome 2013 1:16
    Content type: Research Published on:

  6. The aberrant inflammation that is the hallmark of the inflammatory bowel diseases (IBD) is associated with several factors, including changes in the intestinal microbiota. Here, we confirmed that an intestinal...

    Authors: Nabeetha A Nagalingam, Courtney J Robinson, Ingrid L Bergin, Kathryn A Eaton, Gary B Huffnagle and Vincent B Young
    Citation: Microbiome 2013 1:15
    Content type: Research Published on:

  7. Large-scale ‘meta-omic’ projects are greatly advancing our knowledge of the human microbiome and its specific role in governing health and disease states. A myriad of ongoing studies aim at identifying links b...

    Authors: Joëlle V Fritz, Mahesh S Desai, Pranjul Shah, Jochen G Schneider and Paul Wilmes
    Citation: Microbiome 2013 1:14
    Content type: Review Published on:

  8. Necrotizing enterocolitis (NEC) is a devastating intestinal disease that afflicts 10% of extremely preterm infants. The contribution of early intestinal colonization to NEC onset is not understood, and predict...

    Authors: Ardythe L Morrow, Anne J Lagomarcino, Kurt R Schibler, Diana H Taft, Zhuoteng Yu, Bo Wang, Mekibib Altaye, Michael Wagner, Dirk Gevers, Doyle V Ward, Michael A Kennedy, Curtis Huttenhower and David S Newburg
    Citation: Microbiome 2013 1:13
    Content type: Research Published on:

  9. Bacterial vaginosis (BV), the most common vaginal condition of reproductive-aged women, is associated with a highly diverse and heterogeneous microbiota. Here we present a proof-of-principle analysis to uncove...

    Authors: Jean M Macklaim, Andrew D Fernandes, Julia M Di Bella, Jo-Anne Hammond, Gregor Reid and Gregory B Gloor
    Citation: Microbiome 2013 1:12
    Content type: Research Published on:

  10. Recent advances in next-generation DNA sequencing enable rapid high-throughput quantitation of microbial community composition in human samples, opening up a new field of microbiomics. One of the promises of t...

    Authors: Alexander Statnikov, Mikael Henaff, Varun Narendra, Kranti Konganti, Zhiguo Li, Liying Yang, Zhiheng Pei, Martin J Blaser, Constantin F Aliferis and Alexander V Alekseyenko
    Citation: Microbiome 2013 1:11
    Content type: Research Published on:

  12. The indigenous gut microbiota are thought to play a crucial role in the development and maintenance of the abnormal inflammatory responses that are the hallmark of inflammatory bowel disease. Direct tests of t...

    Authors: Vincent B Young, Laura H Raffals, Susan M Huse, Marius Vital, Dongjuan Dai, Patrick D Schloss, Jennifer M Brulc, Dionysios A Antonopoulos, Rose L Arrieta, John H Kwon, K Gautham Reddy, Nathaniel A Hubert, Sharon L Grim, Joseph H Vineis, Sushila Dalal, Hilary G Morrison…
    Citation: Microbiome 2013 1:9
    Content type: Research Published on:

  13. Butyrate, which is produced by the human microbiome, is essential for awell-functioning colon. Bacteria that produce butyrate are phylogeneticallydiverse, which hinders their accurate detection based on conven...

    Authors: Marius Vital, Christopher R Penton, Qiong Wang, Vincent B Young, Dion A Antonopoulos, Mitchell L Sogin, Hilary G Morrison, Laura Raffals, Eugene B Chang, Gary B Huffnagle, Thomas M Schmidt, James R Cole and James M Tiedje
    Citation: Microbiome 2013 1:8
    Content type: Research Published on:

  14. Murine norovirus (MNV) is the most common gastrointestinal pathogen of research mice and can alter research outcomes in biomedical mouse models of inflammatory bowel disease (IBD). Despite indications that an ...

    Authors: Adam M Nelson, Michael D Elftman, Amelia K Pinto, Megan Baldridge, Patrick Hooper, Justin Kuczynski, Joseph F Petrosino, Vincent B Young and Christiane E Wobus
    Citation: Microbiome 2013 1:7
    Content type: Research Published on:

  15. Besides the development of comprehensive tools for high-throughput 16S ribosomal RNA amplicon sequence analysis, there exists a growing need for protocols emphasizing alternative phylogenetic markers such as t...

    Authors: James Robert White, Cynthia Maddox, Owen White, Samuel V Angiuoli and W Florian Fricke
    Citation: Microbiome 2013 1:6
    Content type: Methodology Published on:

  16. Viruses are important drivers of ecosystem functions, yet little is known about the vast majority of viruses. Viral shotgun metagenomics enables the investigation of broad ecological questions in phage communi...

    Authors: Heather K Allen, John Bunge, James A Foster, Darrell O Bayles and Thaddeus B Stanton
    Citation: Microbiome 2013 1:5
    Content type: Research Published on:

  17. The use of culture-independent nucleic acid techniques, such as ribosomal RNA gene cloning library analysis, has unveiled the tremendous microbial diversity that exists in natural environments. In sharp contra...

    Authors: Weimin Gao, Dena Navarroli, Jared Naimark, Weiwen Zhang, Shih-hui Chao and Deirdre R Meldrum
    Citation: Microbiome 2013 1:4
    Content type: Methodology Published on:

  18. Fecal bacteriotherapy (‘stool transplant’) can be effective in treating recurrent Clostridium difficile infection, but concerns of donor infection transmission and patient acceptance limit its use. Here we descri...

    Authors: Elaine O Petrof, Gregory B Gloor, Stephen J Vanner, Scott J Weese, David Carter, Michelle C Daigneault, Eric M Brown, Kathleen Schroeter and Emma Allen-Vercoe
    Citation: Microbiome 2013 1:3
    Content type: Methodology Published on:
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