A metabolomics pipeline for the mechanistic interrogation of the gut microbiome

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

(2020) Robert A. Quinn et al.   NATURE

A Cardiovascular Disease-Linked Gut Microbial Metabolite Acts via Adrenergic Receptors

(2020) Ina Nemet et al.   CELL

Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome

(2020) Ruben A.T. Mars et al.   CELL

Microbiota and metabolites in metabolic diseases

(2019) Patrice D. Cani   Nature Reviews Endocrinology

Identification of bioactive metabolites using activity metabolomics

(2019) Markus M. Rinschen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

(2019) Jason Lloyd-Price et al.   NATURE

Longitudinal multi-omics of host–microbe dynamics in prediabetes

(2019) Wenyu Zhou et al.   NATURE

Mapping human microbiome drug metabolism by gut bacteria and their genes

(2019) Michael Zimmermann et al.   NATURE

Neuroprotective offerings by agmatine

(2019) Nandkishor Ramdas Kotagale et al.   NEUROTOXICOLOGY

Discovery and inhibition of an interspecies gut bacterial pathway for Levodopa metabolism

(2019) Vayu Maini Rekdal et al.   SCIENCE

Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes

(2019) Hila Sberro et al.   CELL

Microbiota-derived lantibiotic restores resistance against vancomycin-resistant Enterococcus

(2019) Sohn G. Kim et al.   NATURE

Microbiomes as sources of emergent host phenotypes

(2019) J. B. Lynch et al.   SCIENCE

The emerging role of gut microbial metabolism on cardiovascular disease

(2019) Kazuyuki Kasahara et al.   CURRENT OPINION IN MICROBIOLOGY

METLIN: A Technology Platform for Identifying Knowns and Unknowns

(2018) Carlos Guijas et al.   ANALYTICAL CHEMISTRY

pymzML v2.0: introducing a highly compressed and seekable gzip format

(2018) M Kösters et al.   BIOINFORMATICS

An exclusive metabolic niche enables strain engraftment in the gut microbiota

(2018) Elizabeth Stanley Shepherd et al.   NATURE

Obesogenic diets alter metabolism in mice

(2018) Megan R. Showalter et al.   PLoS One

Emergent simplicity in microbial community assembly

(2018) Joshua E. Goldford et al.   SCIENCE

Microbially Produced Imidazole Propionate Impairs Insulin Signaling through mTORC1

(2018) Ara Koh et al.   CELL

New approach for understanding genome variations in KEGG

(2018) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites

(2017) Dylan Dodd et al.   NATURE

HMDB 4.0: the human metabolome database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

Chemical transformation of xenobiotics by the human gut microbiota

(2017) Nitzan Koppel et al.   SCIENCE

Genome composition and phylogeny of microbes predict their co-occurrence in the environment

(2017) Olga K. Kamneva   PLoS Computational Biology

From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites

(2016) Ara Koh et al.   CELL

Diet–microbiota interactions as moderators of human metabolism

(2016) Justin L. Sonnenburg et al.   NATURE

Control of Brain Development, Function, and Behavior by the Microbiome

(2015) Timothy R. Sampson et al.   Cell Host & Microbe

MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis

(2015) Hiroshi Tsugawa et al.   NATURE METHODS

Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides

(2015) M. Wu et al.   SCIENCE

Small molecules from the human microbiota

(2015) M. S. Donia et al.   SCIENCE

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production

(2014) Gary D Wu et al.   GUT

The metabolite α-ketoglutarate extends lifespan by inhibiting ATP synthase and TOR

(2014) Randall M. Chin et al.   NATURE

Long-term phenotypic evolution of bacteria

(2014) Germán Plata et al.   NATURE

Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast

(2013) Marnix H. Medema et al.   MOLECULAR BIOLOGY AND EVOLUTION

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

OCT2 and MATE1 Provide Bidirectional Agmatine Transport

(2010) Tate N. Winter et al.   MOLECULAR PHARMACEUTICS

Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites

(2009) W. R. Wikoff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Large-scale reconstruction and phylogenetic analysis of metabolic environments

(2008) E. Borenstein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA