Articles

An in vitrobiofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome

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

Opportunities and challenges for gut microbiome studies in the Indian population

The gut microbiome is a complex ecosystem that affects the development, immunological responses and nutritional status of the host. Efforts are being made to unravel the complex interaction between the gut mic...

Authors: Sudarshan Anand Shetty, Nachiket Prakash Marathe and Yogesh S Shouche

mPUMA: a computational approach to microbiota analysis by de novo assembly of operational taxonomic units based on protein-coding barcode sequences

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

Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling

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

The PAMPA datasets: a metagenomic survey of microbial communities in Argentinean pampean soils

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

Bacterial community structure and functional contributions to emergence of health or necrotizing enterocolitis in preterm infants

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

Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation

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

Reductions in intestinal Clostridiales precede the development of nosocomial Clostridium difficile infection

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

Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships

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

Co-occurrence of anaerobic bacteria in colorectal carcinomas

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

The effects of intestinal microbial community structure on disease manifestation in IL-10^-/- mice infected with Helicobacter hepaticus

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

From meta-omics to causality: experimental models for human microbiome research

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

Early microbial and metabolomic signatures predict later onset of necrotizing enterocolitis in preterm infants

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

Comparative meta-RNA-seq of the vaginal microbiota and differential expression by Lactobacillus iners in health and dysbiosis

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

A comprehensive evaluation of multicategory classification methods for microbiomic data

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

Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform

High-throughput sequencing of 16S rRNA gene amplicons has revolutionized the capacity and depth of microbial community profiling. Several sequencing platforms are available, but most phylogenetic studies are p...

Authors: Erin B Fichot and R Sean Norman

Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis

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…

A gene-targeted approach to investigate the intestinal butyrate-producing bacterialcommunity

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

Murine norovirus infection does not cause major disruptions in the murine intestinal microbiota

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

CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota

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

Estimation of viral richness from shotgun metagenomes using a frequency count approach

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

Microbe observation and cultivation array (MOCA) for cultivating and analyzing environmental microbiota

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

Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut

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

Selecting age-related functional characteristics in the human gut microbiome

Human gut microbial functions are often associated with various diseases and host physiologies. Aging, a less explored factor, is also suspected to affect or be affected by microbiome alterations. By combining...

Authors: Yemin Lan, Andres Kriete and Gail L Rosen

Microbiome, demystifying the role of microbial communities in the biosphere

Authors: K Eric Wommack and Jacques Ravel