High throughput sequencing methods for microbiome profiling: application to food animal systems

Defining the "core microbiome" of the microbial communities in the tonsils of healthy pigs

(2012) Beth A Lowe et al.   BMC MICROBIOLOGY

Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis

(2012) Martin Iain Bahl et al.   FEMS MICROBIOLOGY LETTERS

A framework for human microbiome research

(2012)   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Insights into the bovine rumen plasmidome

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

Community Structures of Fecal Bacteria in Cattle from Different Animal Feeding Operations

(2011) Orin C. Shanks et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads

(2011) Andrea K. Bartram et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Identification of a novel astrovirus in domestic sheep in Hungary

(2011) Gábor Reuter et al.   ARCHIVES OF VIROLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing

(2011) Samuel V Angiuoli et al.   BMC BIOINFORMATICS

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

(2011) Bo Liu et al.   BMC GENOMICS

Analysis of 16S rRNA environmental sequences using MEGAN

(2011) Suparna Mitra et al.   BMC GENOMICS

Comparative fecal metagenomics unveils unique functional capacity of the swine gut

(2011) Regina Lamendella et al.   BMC MICROBIOLOGY

Characterization of the rumen microbiota of pre-ruminant calves using metagenomic tools

(2011) Robert W. Li et al.   ENVIRONMENTAL MICROBIOLOGY

Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome

(2011) Margret E. Berg Miller et al.   ENVIRONMENTAL MICROBIOLOGY

Molecular diversity of the foregut bacteria community in the dromedary camel (Camelus dromedarius)

(2011) Anjas A. Samsudin et al.   ENVIRONMENTAL MICROBIOLOGY

Bacterial Community Analysis of Beef Cattle Feedlots Reveals That Pen Surface Is Distinct from Feces

(2011) Lisa M. Durso et al.   Foodborne Pathogens and Disease

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Effect of Sample Storage Conditions on Culture-Independent Bacterial Community Measures in Cystic Fibrosis Sputum Specimens

(2011) J. Zhao et al.   JOURNAL OF CLINICAL MICROBIOLOGY

The Fecal Virome of Pigs on a High-Density Farm

(2011) T. Shan et al.   JOURNAL OF VIROLOGY

IMG/M: the integrated metagenome data management and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

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

(2011) M. Hess et al.   SCIENCE

METAREP: JCVI metagenomics reports—an open source tool for high-performance comparative metagenomics

(2010) Johannes Goll et al.   BIOINFORMATICS

Bacterial diversity in faeces from polar bear (Ursus maritimus) in Arctic Svalbard

(2010) Trine Glad et al.   BMC MICROBIOLOGY

Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags

(2010) Gary D Wu et al.   BMC MICROBIOLOGY

Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples

(2010) Christian L. Lauber et al.   FEMS MICROBIOLOGY LETTERS

UniFrac: an effective distance metric for microbial community comparison

(2010) Catherine Lozupone et al.   ISME Journal

Virulence-associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach

(2010) Lisa M. Durso et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

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

CRISPR/Cas, the Immune System of Bacteria and Archaea

(2010) P. Horvath et al.   SCIENCE

A Catalog of Reference Genomes from the Human Microbiome

(2010) et al.   SCIENCE

Microbial communities in the tonsils of healthy pigs

(2010) Beth A. Lowe et al.   VETERINARY MICROBIOLOGY

Metagenomic analysis of the turkey gut RNA virus community

(2010) J Michael Day et al.   Virology Journal

The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data

(2010) David M. Tanenbaum et al.   Standards in Genomic Sciences

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads

(2009) Wolfgang Gerlach et al.   BMC BIOINFORMATICS

Rumen microbial diversity in Svalbard reindeer, with particular emphasis on methanogenic archaea

(2009) Monica A. Sundset et al.   FEMS MICROBIOLOGY ECOLOGY

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Metagenomic study of the oral microbiota by Illumina high-throughput sequencing

(2009) Vladimir Lazarevic et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Microbial Fuel Cells and Microbial Ecology: Applications in Ruminant Health and Production Research

(2009) Orianna Bretschger et al.   MICROBIAL ECOLOGY

The integrated microbial genomes system: an expanding comparative analysis resource

(2009) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases

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

Critical Evaluation of Two Primers Commonly Used for Amplification of Bacterial 16S rRNA Genes

(2008) J. A. Frank et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP)

(2008) Scot E Dowd et al.   BMC MICROBIOLOGY

An Invitation to the Marriage of Metagenomics and Metabolomics

(2008) Peter J. Turnbaugh et al.   CELL

MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes

(2008) H. Noguchi et al.   DNA RESEARCH

Analysis of bacterial diversity in the canine duodenum, jejunum, ileum, and colon by comparative 16S rRNA gene analysis

(2008) Jan S. Suchodolski et al.   FEMS MICROBIOLOGY ECOLOGY

Evaluating different approaches that test whether microbial communities have the same structure

(2008) Patrick D Schloss   ISME Journal

Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology

(2008) Erik K Binga et al.   ISME Journal

Comparison of the Cecal Microbiota of Domestic and Wild Turkeys

(2008) Alexandra J Scupham et al.   MICROBIAL ECOLOGY

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

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

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

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE