Novel bile acid biosynthetic pathways are enriched in the microbiome of centenarians

Global chemical effects of the microbiome include new bile-acid conjugations

(2020) Robert A. Quinn et al.   NATURE

Bacterial metabolism of bile acids promotes generation of peripheral regulatory T cells

(2020) Clarissa Campbell et al.   NATURE

Shotgun Metagenomics of Gut Microbiota in Humans with up to Extreme Longevity and the Increasing Role of Xenobiotic Degradation

(2020) Simone Rampelli et al.   mSystems

A metabolic pathway for bile acid dehydroxylation by the gut microbiome

(2020) Masanori Funabashi et al.   NATURE

Associations of cardiovascular biomarkers and plasma albumin with exceptional survival to the highest ages

(2020) Takumi Hirata et al.   Nature Communications

Healthspan and lifespan extension by fecal microbiota transplantation into progeroid mice

(2019) Clea Bárcena et al.   NATURE MEDICINE

Streamlined Genetic Manipulation of Diverse Bacteroides and Parabacteroides Isolates from the Human Gut Microbiota

(2019) Leonor García-Bayona et al.   mBio

Regulations of bile acid metabolism in mouse models with hydrophobic bile acid composition

(2019) Akira Honda et al.   JOURNAL OF LIPID RESEARCH

Bile acid metabolites control TH17 and Treg cell differentiation

(2019) Saiyu Hang et al.   NATURE

Microbial bile acid metabolites modulate gut RORγ+ regulatory T cell homeostasis

(2019) Xinyang Song et al.   NATURE

MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data

(2018) Florian Plaza Oñate et al.   BIOINFORMATICS

Inflammaging: a new immune–metabolic viewpoint for age-related diseases

(2018) Claudio Franceschi et al.   Nature Reviews Endocrinology

Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation

(2017) Koji Atarashi et al.   SCIENCE

Gut Microbiota and Extreme Longevity

(2016) Elena Biagi et al.   CURRENT BIOLOGY

Meta-analysis of genetic variants associated with human exceptional longevity

(2016) Paola Sebastiani et al.   Aging-US

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

(2015) Dinghua Li et al.   BIOINFORMATICS

A biosynthetic pathway for a prominent class of microbiota-derived bile acids

(2015) A Sloan Devlin et al.   Nature Chemical Biology

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

(2014) Charlie G. Buffie et al.   NATURE

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Evaluation of microbial community reproducibility, stability and composition in a human distal gut chemostat model

(2013) Julie A.K. McDonald et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota

(2013) Koji Atarashi et al.   NATURE

A Versatile Medium for Cultivating Methanogenic Archaea

(2013) Saber Khelaifia et al.   PLoS One

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

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

(2012) Limin Fu et al.   BIOINFORMATICS

Gut microbiota composition correlates with diet and health in the elderly

(2012) Marcus J. Claesson et al.   NATURE

Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics

(2012) Ian Holmes et al.   PLoS One

5α-Reduced glucocorticoids: a story of natural selection

(2011) Mark Nixon et al.   JOURNAL OF ENDOCRINOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Silent Mischief: Bacteriophage Mu Insertions Contaminate Products of Escherichia coli Random Mutagenesis Performed Using Suicidal Transposon Delivery Plasmids Mobilized by Broad-Host-Range RP4 Conjugative Machinery

(2010) L. Ferrieres et al.   JOURNAL OF BACTERIOLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS