Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life

The dynamics of gut-associated microbial communities during inflammation

(2013) Sebastian E Winter et al.   EMBO REPORTS

A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4

(2013) Nicholas J. Loman et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens

(2013) Katharine M. Ng et al.   NATURE

Shallow breathing: bacterial life at low O2

(2013) Rachel L. Morris et al.   NATURE REVIEWS MICROBIOLOGY

Host-Derived Nitrate Boosts Growth of E. coli in the Inflamed Gut

(2013) S. E. Winter et al.   SCIENCE

Host sialoglycans and bacterial sialidases: a mucosal perspective

(2012) Amanda L. Lewis et al.   CELLULAR MICROBIOLOGY

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

(2012) K. C. Wrighton et al.   SCIENCE

Comparative metagenomics of microbial traits within oceanic viral communities

(2011) Itai Sharon et al.   ISME Journal

Inhibition of the cytotoxic effect of Clostridium difficile in vitro by Clostridium butyricum MIYAIRI 588 strain

(2011) T. D. H. Woo et al.   JOURNAL OF MEDICAL MICROBIOLOGY

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Streptococcus anginosusl-cysteine desulfhydrase gene expression is associated with abscess formation in BALB/c mice

(2011) Y. Takahashi et al.   Molecular Oral Microbiology

Peripheral education of the immune system by colonic commensal microbiota

(2011) Stephanie K. Lathrop et al.   NATURE

Fecal Microbiota in Premature Infants Prior to Necrotizing Enterocolitis

(2011) Volker Mai et al.   PLoS One

Gut Microbiome Metagenomics Analysis Suggests a Functional Model for the Development of Autoimmunity for Type 1 Diabetes

(2011) Christopher T. Brown et al.   PLoS One

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen

(2011) M. Hess et al.   SCIENCE

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

(2011) Christopher S Miller et al.   GENOME BIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Strain-resolved community genomic analysis of gut microbial colonization in a premature infant

(2010) M. J. Morowitz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

Intestinal Microbial Ecology in Premature Infants Assessed with Non–Culture-Based Techniques

(2009) Maka Mshvildadze et al.   JOURNAL OF PEDIATRICS

Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43

(2009) Kendle M. Maslowski et al.   NATURE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli

(2008) Matthew F. Traxler et al.   MOLECULAR MICROBIOLOGY

Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth

(2008) D. Chivian et al.   SCIENCE

Actinomyces—Gathering evidence of human colonization and infection

(2007) Val Hall   ANAEROBE