Treatment regimens may compromise gut-microbiome-derived signatures for liver cirrhosis

Adverse outcomes of proton pump inhibitors in chronic liver disease: a systematic review and meta-analysis

(2020) Junna Wang et al.   Hepatology International

Impact of commonly used drugs on the composition and metabolic function of the gut microbiota

(2020) Arnau Vich Vila et al.   Nature Communications

A Universal Gut-Microbiome-Derived Signature Predicts Cirrhosis

(2020) Tae Gyu Oh et al.   Cell Metabolism

Effects of Proton Pump Inhibitors on the Gastrointestinal Microbiota in Gastroesophageal Reflux Disease

(2019) Yi-Chao Shi et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Combining amplicon sequencing and metabolomics in cirrhotic patients highlights distinctive microbiota features involved in bacterial translocation, systemic inflammation and hepatic encephalopathy

(2018) Valerio Iebba et al.   Scientific Reports

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

(2018) Nicholas A. Bokulich et al.   Microbiome

Extensive impact of non-antibiotic drugs on human gut bacteria

(2018) Lisa Maier et al.   NATURE

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Proton pump inhibitors alter the composition of the gut microbiota

(2015) Matthew A Jackson et al.   GUT

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

(2015) Kristoffer Forslund et al.   NATURE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Alterations of the human gut microbiome in liver cirrhosis

(2014) Nan Qin et al.   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2011) Daniel McDonald et al.   ISME Journal