Meta-omics analysis of elite athletes identifies a performance-enhancing microbe that functions via lactate metabolism

Current understanding of the human microbiome

(2018) Jack A Gilbert et al.   NATURE MEDICINE

Diet, Genetics, and the Gut Microbiome Drive Dynamic Changes in Plasma Metabolites

(2018) Shiho Fujisaka et al.   Cell Reports

Environment dominates over host genetics in shaping human gut microbiota

(2018) Daphna Rothschild et al.   NATURE

Community characteristics of the gut microbiomes of competitive cyclists

(2017) Lauren M. Petersen et al.   Microbiome

Phylo.io: Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web

(2016) Oscar Robinson et al.   MOLECULAR BIOLOGY AND EVOLUTION

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Exercise and associated dietary extremes impact on gut microbial diversity

(2014) Siobhan F Clarke et al.   GUT

Longitudinal analysis of microbial interaction between humans and the indoor environment

(2014) S. Lax et al.   SCIENCE

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Olfactory receptor responding to gut microbiota-derived signals plays a role in renin secretion and blood pressure regulation

(2013) Jennifer L. Pluznick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

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

(2012) Junjie Qin et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Short-chain fatty acids and ketones directly regulate sympathetic nervous system via G protein-coupled receptor 41 (GPR41)

(2011) I. Kimura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2009) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH