Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations

Butyrate-Producing Bacteria, Including Mucin Degraders, from the Swine Intestinal Tract

(2013) Uri Y. Levine et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2013) Katharine M. Ng et al.   NATURE

Bacterial colonization factors control specificity and stability of the gut microbiota

(2013) S. Melanie Lee et al.   NATURE

The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates

(2012) Erwin G Zoetendal et al.   ISME Journal

Complex Carbohydrate Utilization by the Healthy Human Microbiome

(2012) Brandi L. Cantarel et al.   PLoS One

In-feed antibiotic effects on the swine intestinal microbiome

(2012) T. Looft et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial shifts in the swine distal gut in response to the treatment with antimicrobial growth promoter, tylosin

(2012) H. B. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Comparative fecal metagenomics unveils unique functional capacity of the swine gut

(2011) Regina Lamendella et al.   BMC MICROBIOLOGY

Review: The use of direct fed microbials to mitigate pathogens and enhance production in cattle

(2011) T. A. McAllister et al.   CANADIAN JOURNAL OF ANIMAL SCIENCE

Bacteria and host interactions in the gut epithelial barrier

(2011) Hiroshi Ashida et al.   Nature Chemical Biology

Impaired Carbohydrate Digestion and Transport and Mucosal Dysbiosis in the Intestines of Children with Autism and Gastrointestinal Disturbances

(2011) Brent L. Williams et al.   PLoS One

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

Antibiotics in Feed Induce Prophages in Swine Fecal Microbiomes

(2011) H. K. Allen et al.   mBio

Effect of apple intake on fecal microbiota and metabolites in humans

(2010) Kenji Shinohara et al.   ANAEROBE

Identifying biologically relevant differences between metagenomic communities

(2010) Donovan H. Parks et al.   BIOINFORMATICS

High temporal and inter-individual variation detected in the human ileal microbiota

(2010) Carien C. G. M. Booijink et al.   ENVIRONMENTAL MICROBIOLOGY

Spatial organization of intestinal microbiota in the mouse ascending colon

(2010) Gerardo M Nava et al.   ISME Journal

Draft Genome Sequence of Turicibacter sanguinis PC909, Isolated from Human Feces

(2010) P. O. Cuiv et al.   JOURNAL OF BACTERIOLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Resistant starch, large bowel fermentation and a broader perspective of prebiotics and probiotics

(2010) A. Bird et al.   Beneficial Microbes

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Systematic artifacts in metagenomes from complex microbial communities

(2009) Vicente Gomez-Alvarez et al.   ISME Journal

Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis

(2009) D A Hill et al.   Mucosal Immunology

Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla

(2009) M. A. Mahowald et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

(2009) James Robert White et al.   PLoS Computational Biology

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex

(2008) Micah Hamady et al.   NATURE METHODS

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH

ARDB--Antibiotic Resistance Genes Database

(2008) B. Liu et al.   NUCLEIC ACIDS RESEARCH