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  1. The Atacama Desert is one of the driest deserts in the world and its soil, with extremely low moisture, organic carbon content, and oxidizing conditions, is considered to be at the dry limit for life.

    Authors: Alexander Crits-Christoph, Courtney K Robinson, Tyler Barnum, W Florian Fricke, Alfonso F Davila, Bruno Jedynak, Christopher P McKay and Jocelyne DiRuggiero

    Citation: Microbiome 2013 1:28

    Content type: Research

    Published on:

  2. Cystic fibrosis (CF) is caused by inherited mutations in the cystic fibrosis transmembrane conductance regulator gene and results in a lung environment that is highly conducive to polymicrobial infection. Over...

    Authors: Katherine E Price, Thomas H Hampton, Alex H Gifford, Emily L Dolben, Deborah A Hogan, Hilary G Morrison, Mitchell L Sogin and George A O’Toole

    Citation: Microbiome 2013 1:27

    Content type: Research

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  3. Regardless of infection route, the intestine is the primary site for HIV-1 infection establishment and results in significant mucosal CD4+ T lymphocyte depletion, induces an inflammatory state that propagates ...

    Authors: Ian H McHardy, Xiaoxiao Li, Maomeng Tong, Paul Ruegger, Jonathan Jacobs, James Borneman, Peter Anton and Jonathan Braun

    Citation: Microbiome 2013 1:26

    Content type: Research

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  4. Our knowledge of microbial diversity in the human oral cavity has vastly expanded during the last two decades of research. However, much of what is known about the behavior of oral species to date derives from...

    Authors: Anna Edlund, Youngik Yang, Adam P Hall, Lihong Guo, Renate Lux, Xuesong He, Karen E Nelson, Kenneth H Nealson, Shibu Yooseph, Wenyuan Shi and Jeffrey S McLean

    Citation: Microbiome 2013 1:25

    Content type: Methodology

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  5. Formation of operational taxonomic units (OTU) is a common approach to data aggregation in microbial ecology studies based on amplification and sequencing of individual gene targets. The de novo assembly of OTU s...

    Authors: Matthew G Links, Bonnie Chaban, Sean M Hemmingsen, Kevin Muirhead and Janet E Hill

    Citation: Microbiome 2013 1:23

    Content type: Methodology

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  6. Sediments are massive reservoirs of carbon compounds and host a large fraction of microbial life. Microorganisms within terrestrial aquifer sediments control buried organic carbon turnover, degrade organic con...

    Authors: Laura A Hug, Cindy J Castelle, Kelly C Wrighton, Brian C Thomas, Itai Sharon, Kyle R Frischkorn, Kenneth H Williams, Susannah G Tringe and Jillian F Banfield

    Citation: Microbiome 2013 1:22

    Content type: Research

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  7. Soil is among the most diverse and complex environments in the world. Soil microorganisms play an essential role in biogeochemical cycles and affect plant growth and crop production. However, our knowledge of ...

    Authors: Nicolás Rascovan, Belén Carbonetto, Santiago Revale, Marina D Reinert, Roberto Alvarez, Alicia M Godeas, Roxana Colombo, Mario Aguilar, María Victoria Novas, Leopoldo Iannone, Alicia M Zelada, Alejandro Pardo, Gustavo Schrauf, Alejandro Mentaberry and Martín P Vazquez

    Citation: Microbiome 2013 1:21

    Content type: Microbiome Announcement

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  8. 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

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  9. 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

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

  10. 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

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  11. 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

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  12. 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

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  13. 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

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  14. 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

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  15. 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

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  16. 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

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  17. 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

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  18. 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

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  19. 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

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  20. 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

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  21. 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:

  22. 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:

  23. 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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