Profiling the human intestinal environment under physiological conditions

Human metabolome variation along the upper intestinal tract

(2023) Jacob Folz et al.   Nature Metabolism

Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota

(2022) Andrés Aranda-Díaz et al.   Cell Host & Microbe

Optimization of the 16S rRNA sequencing analysis pipeline for studying in vitro communities of gut commensals

(2022) Arianna I. Celis et al.   iScience

Carbohydrate-active enzymes (CAZymes) in the gut microbiome

(2022) Jacob F. Wardman et al.   NATURE REVIEWS MICROBIOLOGY

The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

(2022) et al.   SCIENCE

Deciphering Active Prophages from Metagenomes

(2022) Kristopher Kieft et al.   mSystems

sangeranalyseR: Simple and Interactive Processing of Sanger Sequencing Data in R

(2021) Kuan-Hao Chao et al.   Genome Biology and Evolution

VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

(2021) Jiarong Guo et al.   Microbiome

A new parallel high-pressure packing system enables rapid multiplexed production of capillary columns

(2021) Johannes B. Müller-Reif et al.   MOLECULAR & CELLULAR PROTEOMICS

Rapid ordering of barcoded transposon insertion libraries of anaerobic bacteria

(2021) Anthony L. Shiver et al.   Nature Protocols

Dominant Bacterial Phyla from the Human Gut Show Widespread Ability To Transform and Conjugate Bile Acids

(2021) L. N. Lucas et al.   mSystems

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

(2021) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Mapping the Segmental Microbiomes in the Human Small Bowel in Comparison with Stool: A REIMAGINE Study

(2020) Gabriela G. S. Leite et al.   DIGESTIVE DISEASES AND SCIENCES

Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics

(2020) Kendra J. Adams et al.   JOURNAL OF PROTEOME RESEARCH

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

(2020) Robert A. Quinn et al.   NATURE

Distinct microbial and immune niches of the human colon

(2020) Kylie R. James et al.   NATURE IMMUNOLOGY

Bile acid metabolism is altered in multiple sclerosis and supplementation ameliorates neuroinflammation

(2020) Pavan Bhargava et al.   JOURNAL OF CLINICAL INVESTIGATION

Current Sampling Methods for Gut Microbiota: A Call for More Precise Devices

(2020) Qiang Tang et al.   Frontiers in Cellular and Infection Microbiology

VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

(2020) Kristopher Kieft et al.   Microbiome

Mimicking prophage induction in the body: induction in the lab with pH gradients

(2020) Taylor Miller-Ensminger et al.   PeerJ

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

(2020) Stephen Nayfach et al.   NATURE BIOTECHNOLOGY

Taxonomic profiling and populational patterns of bacterial bile salt hydrolase (BSH) genes based on worldwide human gut microbiome

(2019) Ziwei Song et al.   Microbiome

Advances in the physiology of gastric emptying

(2019) Raj K. Goyal et al.   NEUROGASTROENTEROLOGY AND MOTILITY

Perspective and Guidelines for Metaproteomics in Microbiome Studies

(2019) Xu Zhang et al.   JOURNAL OF PROTEOME RESEARCH

Composition of the mucosa-associated microbiota along the entire gastrointestinal tract of human individuals

(2019) FER Vuik et al.   United European Gastroenterology Journal

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

A Comprehensive Plasma Metabolomics Dataset for a Cohort of Mouse Knockouts within the International Mouse Phenotyping Consortium

(2019) Dinesh K. Barupal et al.   Metabolites

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

(2019) Pierre-Alain Chaumeil et al.   BIOINFORMATICS

The relationship between fecal bile acids and microbiome community structure in pediatric Crohn’s disease

(2019) Jessica Connors et al.   ISME Journal

Inhibition of histone deacetylase 1 (HDAC1) and HDAC2 enhances CRISPR/Cas9 genome editing

(2019) Bin Liu et al.   NUCLEIC ACIDS RESEARCH

Animal models to study bile acid metabolism

(2018) Jianing Li et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Latent variable modeling for the microbiome

(2018) Kris Sankaran et al.   BIOSTATISTICS

Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features

(2018) Niv Zmora et al.   CELL

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

Evaluation of FASP, SP3, and iST Protocols for Proteomic Sample Preparation in the Low Microgram Range

(2017) Malte Sielaff et al.   JOURNAL OF PROTEOME RESEARCH

Microbial Ecology along the Gastrointestinal Tract

(2017) Ethan T. Hillman et al.   MICROBES AND ENVIRONMENTS

dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation

(2017) Le Huang et al.   NUCLEIC ACIDS RESEARCH

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

The Human Intestinal Microbiome in Health and Disease

(2016) Susan V. Lynch et al.   NEW ENGLAND JOURNAL OF MEDICINE

Obeticholic acid, a synthetic bile acid agonist of the farnesoid X receptor, attenuates experimental autoimmune encephalomyelitis

(2016) Peggy P. Ho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plasma Proteome Profiling to Assess Human Health and Disease

(2016) Philipp E. Geyer et al.   Cell Systems

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

(2015) Dinghua Li et al.   BIOINFORMATICS

Quantitative Imaging of Gut Microbiota Spatial Organization

(2015) Kristen A. Earle et al.   Cell Host & Microbe

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

The effect of microbial colonization on the host proteome varies by gastrointestinal location

(2015) Joshua S Lichtman et al.   ISME Journal

topicmodels: AnRPackage for Fitting Topic Models

(2015) Bettina Grün et al.   Journal of Statistical Software

Gastrointestinal pH and Transit Time Profiling in Healthy Volunteers Using the IntelliCap System Confirms Ileo-Colonic Release of ColoPulse Tablets

(2015) Jacoba M. Maurer et al.   PLoS One

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

Characterization of Romboutsia ilealis gen. nov., sp. nov., isolated from the gastro-intestinal tract of a rat, and proposal for the reclassification of five closely related members of the genus Clostridium into the genera Romboutsia gen. nov., Intestinibacter gen. nov., Terrisporobacter gen. nov. and Asaccharospora gen. nov.

(2014) J. Gerritsen et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

Bile acids are nutrient signaling hormones

(2014) Huiping Zhou et al.   STEROIDS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Host-centric Proteomics of Stool: A Novel Strategy Focused on intestinal Responses to the Gut Microbiota

(2013) Joshua S. Lichtman et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

SprayQc: A Real-Time LC–MS/MS Quality Monitoring System To Maximize Uptime Using Off the Shelf Components

(2012) Richard A. Scheltema et al.   JOURNAL OF PROTEOME RESEARCH

Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10 −/− mice

(2012) Suzanne Devkota et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Second-generation colon capsule endoscopy compared with colonoscopy

(2011) Cristiano Spada et al.   GASTROINTESTINAL ENDOSCOPY

Advances in human proteomics at high scale with the SOMAscan proteomics platform

(2011) Larry Gold et al.   New Biotechnology

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

High temporal and inter-individual variation detected in the human ileal microbiota

(2010) Carien C. G. M. Booijink et al.   ENVIRONMENTAL MICROBIOLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Lipid extraction by methyl-tert-butyl ether for high-throughput lipidomics

(2008) Vitali Matyash et al.   JOURNAL OF LIPID RESEARCH

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY