Mapping human microbiome drug metabolism by gut bacteria and their genes

Separating host and microbiome contributions to drug pharmacokinetics and toxicity

(2019) Michael Zimmermann et al.   SCIENCE

Extensive impact of non-antibiotic drugs on human gut bacteria

(2018) Lisa Maier et al.   NATURE

Drug pharmacomicrobiomics and toxicomicrobiomics: from scattered reports to systematic studies of drug–microbiome interactions

(2018) Ramy K. Aziz et al.   Expert Opinion on Drug Metabolism & Toxicology

Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug

(2017) Hao Wu et al.   NATURE MEDICINE

DrugBank 5.0: a major update to the DrugBank database for 2018

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

Vaginal bacteria modify HIV tenofovir microbicide efficacy in African women

(2017) Nichole R. Klatt et al.   SCIENCE

Gut microbiome interactions with drug metabolism, efficacy, and toxicity

(2017) Ian D. Wilson et al.   Translational Research

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Antimicrobial peptide resistance mediates resilience of prominent gut commensals during inflammation

(2015) T. W. Cullen et al.   SCIENCE

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED

(2015) James Kaminski et al.   PLoS Computational Biology

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

On the Colonic Bacterial Metabolism of Azo-Bonded Prodrugsof 5-Aminosalicylic Acid

(2014) Tiago Sousa et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

Clostridium scindens: a human gut microbe with a high potential to convert glucocorticoids into androgens

(2013) Jason M. Ridlon et al.   JOURNAL OF LIPID RESEARCH

Predicting and Manipulating Cardiac Drug Inactivation by the Human Gut Bacterium Eggerthella lenta

(2013) H. J. Haiser et al.   SCIENCE

The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens

(2012) K. J. Forsberg et al.   SCIENCE

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Identifying microbial fitness determinants by insertion sequencing using genome-wide transposon mutant libraries

(2011) Andrew L Goodman et al.   Nature Protocols

Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

(2011) A. L. Goodman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Alleviating Cancer Drug Toxicity by Inhibiting a Bacterial Enzyme

(2010) B. D. Wallace et al.   SCIENCE

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat

(2009) Andrew L. Goodman et al.   Cell Host & Microbe

Intestinal Microbiota Regulate Xenobiotic Metabolism in the Liver

(2009) Britta Björkholm et al.   PLoS One

Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism

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

Starch Catabolism by a Prominent Human Gut Symbiont Is Directed by the Recognition of Amylose Helices

(2008) Nicole M. Koropatkin et al.   STRUCTURE