Skip to main content


Page 36 of 36

  1. Humans can spend the majority of their time indoors, but little is known about the interactions between the human and built-environment microbiomes or the forces that drive microbial community assembly in the ...

    Authors: James F Meadow, Adam E Altrichter, Steven W Kembel, Maxwell Moriyama, Timothy K O’Connor, Ann M Womack, G Z Brown, Jessica L Green and Brendan J M Bohannan
    Citation: Microbiome 2014 2:7
  2. To take advantage of affordable high-throughput next-generation sequencing technologies to characterize microbial community composition often requires the development of improved methods to overcome technical ...

    Authors: Douglas W Fadrosh, Bing Ma, Pawel Gajer, Naomi Sengamalay, Sandra Ott, Rebecca M Brotman and Jacques Ravel
    Citation: Microbiome 2014 2:6
  3. Mucosal biopsy is the most common sampling technique used to assess microbial communities associated with the intestinal mucosa. Biopsies disrupt the epithelium and can be associated with complications such as...

    Authors: Susan M Huse, Vincent B Young, Hilary G Morrison, Dionysios A Antonopoulos, John Kwon, Sushila Dalal, Rose Arrieta, Nathaniel A Hubert, Lici Shen, Joseph H Vineis, Jason C Koval, Mitchell L Sogin, Eugene B Chang and Laura E Raffals
    Citation: Microbiome 2014 2:5
  4. This study was undertaken to characterize the vaginal microbiota throughout normal human pregnancy using sequence-based techniques. We compared the vaginal microbial composition of non-pregnant patients with a...

    Authors: Roberto Romero, Sonia S Hassan, Pawel Gajer, Adi L Tarca, Douglas W Fadrosh, Lorraine Nikita, Marisa Galuppi, Ronald F Lamont, Piya Chaemsaithong, Jezid Miranda, Tinnakorn Chaiworapongsa and Jacques Ravel
    Citation: Microbiome 2014 2:4

    The Erratum to this article has been published in Microbiome 2014 2:10

  5. Shotgun metagenomics has become an important tool for investigating the ecology of microorganisms. Underlying these investigations is the assumption that metagenome sequence data accurately estimates the censu...

    Authors: Rachel Marine, Coleen McCarren, Vansay Vorrasane, Dan Nasko, Erin Crowgey, Shawn W Polson and K Eric Wommack
    Citation: Microbiome 2014 2:3
  6. The source inoculum of gastrointestinal tract (GIT) microbes is largely influenced by delivery mode in full-term infants, but these influences may be decoupled in very low birth weight (VLBW, <1,500 g) neonate...

    Authors: Brandon Brooks, Brian A Firek, Christopher S Miller, Itai Sharon, Brian C Thomas, Robyn Baker, Michael J Morowitz and Jillian F Banfield
    Citation: Microbiome 2014 2:1
  7. Psoriasis is a common chronic inflammatory disease of the skin. We sought to characterize and compare the cutaneous microbiota of psoriatic lesions (lesion group), unaffected contralateral skin from psoriatic ...

    Authors: Alexander V Alekseyenko, Guillermo I Perez-Perez, Aieska De Souza, Bruce Strober, Zhan Gao, Monika Bihan, Kelvin Li, Barbara A Methé and Martin J Blaser
    Citation: Microbiome 2013 1:31
  8. The premature infant gut has low individual but high inter-individual microbial diversity compared with adults. Based on prior 16S rRNA gene surveys, many species from this environment are expected to be simil...

    Authors: Christopher T Brown, Itai Sharon, Brian C Thomas, Cindy J Castelle, Michael J Morowitz and Jillian F Banfield
    Citation: Microbiome 2013 1:30
  9. Bacterial vaginosis (BV) is a common gynecologic diagnosis characterized by dysbiosis of the vaginal microbiota. It is often accompanied by vaginal symptoms such as odor and discharge, but can be asymptomatic....

    Authors: Jacques Ravel, Rebecca M Brotman, Pawel Gajer, Bing Ma, Melissa Nandy, Douglas W Fadrosh, Joyce Sakamoto, Sara SK Koenig, Li Fu, Xia Zhou, Roxana J Hickey, Jane R Schwebke and Larry J Forney
    Citation: Microbiome 2013 1:29
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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

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

  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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

Annual Journal Metrics

  • 2022 Citation Impact
    15.5 - 2-year Impact Factor
    19.4 - 5-year Impact Factor
    2.998 - SNIP (Source Normalized Impact per Paper)
    3.709 - SJR (SCImago Journal Rank)

    2023 Speed
    41 days submission to first editorial decision for all manuscripts (Median)
    196 days submission to accept (Median)

    2023 Usage
    7,051 Altmetric mentions