Metaproteomic and Metabolomic Approaches for Characterizing the Gut Microbiome

Mass spectrometry-based fecal metabolome analysis

(2019) Jing Xu et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

Metaproteomics reveals persistent and phylum-redundant metabolic functional stability in adult human gut microbiomes of Crohn’s remission patients despite temporal variations in microbial taxa, genomes, and proteomes

(2019) J. Alfredo Blakeley-Ruiz et al.   Microbiome

1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses

(2019) Yuanqiang Zou et al.   NATURE BIOTECHNOLOGY

Targeted metabolomics of whole blood using volumetric absorptive microsampling

(2019) Miranda G.M. Kok et al.   TALANTA

Understanding mucosal and microbial functionality of the female reproductive tract by metaproteomics: Implications for HIV transmission

(2018) Alicia R. Berard et al.   AMERICAN JOURNAL OF REPRODUCTIVE IMMUNOLOGY

Comprehensive evaluation of untargeted metabolomics data processing software in feature detection, quantification and discriminating marker selection

(2018) Zhucui Li et al.   ANALYTICA CHIMICA ACTA

A review on human fecal metabolomics: Methods, applications and the human fecal metabolome database

(2018) Naama Karu et al.   ANALYTICA CHIMICA ACTA

METLIN: A Technology Platform for Identifying Knowns and Unknowns

(2018) Carlos Guijas et al.   ANALYTICAL CHEMISTRY

Metabolomics and Isotope Tracing

(2018) Cholsoon Jang et al.   CELL

High-throughput metaproteomics data analysis with Unipept: A tutorial

(2018) Bart Mesuere et al.   Journal of Proteomics

Assessing the impact of protein extraction methods for human gut metaproteomics

(2018) Xu Zhang et al.   Journal of Proteomics

Rapid Classification and Identification of Multiple Microorganisms with Accurate Statistical Significance via High-Resolution Tandem Mass Spectrometry

(2018) Gelio Alves et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Gut metabolome meets microbiome: A methodological perspective to understand the relationship between host and microbe

(2018) Santosh Lamichhane et al.   METHODS

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

Comparative metaproteomics analysis shows altered fecal microbiota signatures in patients with major depressive disorder

(2018) Zhi Chen et al.   NEUROREPORT

MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis

(2018) Jasmine Chong et al.   NUCLEIC ACIDS RESEARCH

Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle proteins in pediatric inflammatory bowel disease

(2018) Xu Zhang et al.   Nature Communications

Comparative analysis of Salivette® and paraffin gum preparations for establishment of a metaproteomics analysis pipeline for stimulated human saliva

(2018) Alexander Rabe et al.   Journal of Oral Microbiology

Metatranscriptome of human faecal microbial communities in a cohort of adult men

(2018) Galeb S. Abu-Ali et al.   Nature Microbiology

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome

(2018) Melanie Schirmer et al.   Nature Microbiology

Intestinal Metaproteomics Reveals Host-Microbiota Interactions in Subjects at Risk for Type 1 Diabetes

(2018) Patrick G. Gavin et al.   DIABETES CARE

Short-chain fatty acids: microbial metabolites that alleviate stress-induced brain-gut axis alterations

(2018) Marcel van de Wouw et al.   JOURNAL OF PHYSIOLOGY-LONDON

Computational Removal of Undesired Mass Spectral Features Possessing Repeat Units via a Kendrick Mass Filter

(2018) Ricardo R. da Silva et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

XCMS-MRM and METLIN-MRM: a cloud library and public resource for targeted analysis of small molecules

(2018) Xavier Domingo-Almenara et al.   NATURE METHODS

Separation and characterization of human microbiomes by metaproteomics

(2018) Kai Cheng et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

ProteoStorm: An Ultrafast Metaproteomics Database Search Framework

(2018) Doruk Beyter et al.   Cell Systems

Headspace Gas Monitoring of Gut Microbiota Using Targeted and Globally Optimized Targeted Secondary Electrospray Ionization Mass Spectrometry

(2018) Haorong Li et al.   ANALYTICAL CHEMISTRY

A Metabologenomic Approach Reveals Changes in the Intestinal Environment of Mice Fed on American Diet

(2018) Chiharu Ishii et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Unipept 4.0: Functional Analysis of Metaproteome Data

(2018) Robbert Gurdeep Singh et al.   JOURNAL OF PROTEOME RESEARCH

ComPIL 2.0: An Updated Comprehensive Metaproteomics Database

(2018) Sung Kyu Robin Park et al.   JOURNAL OF PROTEOME RESEARCH

New approach for understanding genome variations in KEGG

(2018) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Quantitative metaproteomics of medieval dental calculus reveals individual oral health status

(2018) Rosa R. Jersie-Christensen et al.   Nature Communications

Gut microbiome structure and metabolic activity in inflammatory bowel disease

(2018) Eric A. Franzosa et al.   Nature Microbiology

Challenges and perspectives of metaproteomic data analysis

(2017) Robert Heyer et al.   JOURNAL OF BIOTECHNOLOGY

Data acquisition workflows in liquid chromatography coupled to high resolution mass spectrometry-based metabolomics: Where do we stand?

(2017) François Fenaille et al.   JOURNAL OF CHROMATOGRAPHY A

Sample preparation optimization in fecal metabolic profiling

(2017) Olga Deda et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

Navigating freely-available software tools for metabolomics analysis

(2017) Rachel Spicer et al.   Metabolomics

The dental calculus metabolome in modern and historic samples

(2017) Irina M. Velsko et al.   Metabolomics

Typing and Characterization of Bacteria Using Bottom-up Tandem Mass Spectrometry Proteomics

(2017) Fredrik Boulund et al.   MOLECULAR & CELLULAR PROTEOMICS

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics

(2017) Zijuan Lai et al.   NATURE METHODS

Systems biology guided by XCMS Online metabolomics

(2017) Tao Huan et al.   NATURE METHODS

HMDB 4.0: the human metabolome database for 2018

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

Development of data-independent acquisition workflows for metabolomic analysis on a quadrupole-orbitrap platform

(2017) Juntuo Zhou et al.   TALANTA

Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome

(2017) Tanja V. Maier et al.   mBio

Gut flora profiling and fecal metabolite composition of colorectal cancer patients and healthy individuals

(2017) Xiaoxue Wang et al.   Experimental and Therapeutic Medicine

Significance estimation for large scale metabolomics annotations by spectral matching

(2017) Kerstin Scheubert et al.   Nature Communications

Assessing species biomass contributions in microbial communities via metaproteomics

(2017) Manuel Kleiner et al.   Nature Communications

Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis

(2017) Jaeyun Sung et al.   Nature Communications

mixOmics: An R package for ‘omics feature selection and multiple data integration

(2017) Florian Rohart et al.   PLoS Computational Biology

Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life

(2017) Weili Xiong et al.   Microbiome

Potential and active functions in the gut microbiota of a healthy human cohort

(2017) Alessandro Tanca et al.   Microbiome

MetaLab: an automated pipeline for metaproteomic data analysis

(2017) Kai Cheng et al.   Microbiome

Metabolic Fingerprints from the Human Oral Microbiome Reveal a Vast Knowledge Gap of Secreted Small Peptidic Molecules

(2017) Anna Edlund et al.   mSystems

Dark matter in host-microbiome metabolomics: Tackling the unknowns–A review

(2017) B.Y. Loulou Peisl et al.   ANALYTICA CHIMICA ACTA

Strategies for large-scale targeted metabolomics quantification by liquid chromatography-mass spectrometry

(2016) Juntuo Zhou et al.   ANALYST

In Vitro Metabolic Labeling of Intestinal Microbiota for Quantitative Metaproteomics

(2016) Xu Zhang et al.   ANALYTICAL CHEMISTRY

Peptide-Centric Approaches Provide an Alternative Perspective To Re-Examine Quantitative Proteomic Data

(2016) Zhibin Ning et al.   ANALYTICAL CHEMISTRY

Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies

(2016) Hendrik Treutler et al.   ANALYTICAL CHEMISTRY

Optimized Sample Handling Strategy for Metabolic Profiling of Human Feces

(2016) Jasmine Gratton et al.   ANALYTICAL CHEMISTRY

Simple and Integrated Spintip-Based Technology Applied for Deep Proteome Profiling

(2016) Wendong Chen et al.   ANALYTICAL CHEMISTRY

Cirrhosis related functionality characteristic of the fecal microbiota as revealed by a metaproteomic approach

(2016) Xiao Wei et al.   BMC GASTROENTEROLOGY

A comprehensive and scalable database search system for metaproteomics

(2016) Sandip Chatterjee et al.   BMC GENOMICS

Metaproteomic data analysis at a glance: advances in computational microbial community proteomics

(2016) Thilo Muth et al.   Expert Review of Proteomics

Gut Microbiota Dysbiosis as Risk and Premorbid Factors of IBD and IBS Along the Childhood–Adulthood Transition

(2016) Lorenza Putignani et al.   INFLAMMATORY BOWEL DISEASES

Environmental Microbial Community Proteomics: Status, Challenges and Perspectives

(2016) Da-Zhi Wang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A strategy for the targeted metabolomics analysis of 11 gut microbiota-host co-metabolites in rat serum, urine and feces by ultra high performance liquid chromatography–tandem mass spectrometry

(2016) Waner Hou et al.   JOURNAL OF CHROMATOGRAPHY A

Meta-omics in Inflammatory Bowel Disease Research: Applications, Challenges, and Guidelines

(2016) Mireia Valles-Colomer et al.   Journal of Crohns & Colitis

Training in metabolomics research. II. Processing and statistical analysis of metabolomics data, metabolite identification, pathway analysis, applications of metabolomics and its future

(2016) Stephen Barnes et al.   JOURNAL OF MASS SPECTROMETRY

Untargeted Metabolomics Strategies—Challenges and Emerging Directions

(2016) Alexandra C. Schrimpe-Rutledge et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health

(2016) Pamela Vernocchi et al.   Frontiers in Microbiology

The impact of sequence database choice on metaproteomic results in gut microbiota studies

(2016) Alessandro Tanca et al.   Microbiome

MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota

(2016) Xu Zhang et al.   Microbiome

Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes

(2016) Anna Heintz-Buschart et al.   Nature Microbiology

A multi-omic future for microbiome studies

(2016) Janet K. Jansson et al.   Nature Microbiology

Species–function relationships shape ecological properties of the human gut microbiome

(2016) Sara Vieira-Silva et al.   Nature Microbiology

A reference gene catalogue of the pig gut microbiome

(2016) Liang Xiao et al.   Nature Microbiology

Gut Bacteria Metabolism Impacts Immune Recovery in HIV-infected Individuals

(2016) Sergio Serrano-Villar et al.   EBioMedicine

Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation

(2016) Cecilia Noecker et al.   mSystems

Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations

(2016) Rashmi Sinha et al.   PLoS One

Toward Merging Untargeted and Targeted Methods in Mass Spectrometry-Based Metabolomics and Lipidomics

(2015) Tomas Cajka et al.   ANALYTICAL CHEMISTRY

Metabolome searcher: a high throughput tool for metabolite identification and metabolic pathway mapping directly from mass spectrometry and using genome restriction

(2015) A Ranjitha Dhanasekaran et al.   BMC BIOINFORMATICS

Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome

(2015) Saeed Shoaie et al.   Cell Metabolism

Understanding probiotics’ role in allergic children

(2015) Pamela Vernocchi et al.   Current Opinion in Allergy and Clinical Immunology

Vaginal microbiome and metabolome highlight specific signatures of bacterial vaginosis

(2015) B. Vitali et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Mass spectral similarity for untargeted metabolomics data analysis of complex mixtures

(2015) Neha Garg et al.   INTERNATIONAL JOURNAL OF MASS SPECTROMETRY

Towards biome-specific analysis of meta-omics data

(2015) Youssef Darzi et al.   ISME Journal

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

(2015) Joshua S Lichtman et al.   ISME Journal

Can NMR solve some significant challenges in metabolomics?

(2015) G.A. Nagana Gowda et al.   JOURNAL OF MAGNETIC RESONANCE

The MetaProteomeAnalyzer: A Powerful Open-Source Software Suite for Metaproteomics Data Analysis and Interpretation

(2015) Thilo Muth et al.   JOURNAL OF PROTEOME RESEARCH

A catalog of the mouse gut metagenome

(2015) Liang Xiao et al.   NATURE BIOTECHNOLOGY

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

(2015) Hiroshi Tsugawa et al.   NATURE METHODS

Sequencing and beyond: integrating molecular 'omics' for microbial community profiling

(2015) Eric A. Franzosa et al.   NATURE REVIEWS MICROBIOLOGY

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2015) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Molecular cartography of the human skin surface in 3D

(2015) Amina Bouslimani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Navigating through metaproteomics data: A logbook of database searching

(2015) Thilo Muth et al.   PROTEOMICS

Enrichment or depletion? The impact of stool pretreatment on metaproteomic characterization of the human gut microbiota

(2015) Alessandro Tanca et al.   PROTEOMICS

Colonic metaproteomic signatures of active bacteria and the host in obesity

(2015) Carolin A. Kolmeder et al.   PROTEOMICS

Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant

(2015) Brandon Brooks et al.   Frontiers in Microbiology

Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children

(2015) Chenhong Zhang et al.   EBioMedicine

RAMClust: A Novel Feature Clustering Method Enables Spectral-Matching-Based Annotation for Metabolomics Data

(2014) C. D. Broeckling et al.   ANALYTICAL CHEMISTRY

MetAssign: probabilistic annotation of metabolites from LC–MS data using a Bayesian clustering approach

(2014) Rónán Daly et al.   BIOINFORMATICS

Non-invasive fecal metabonomic detection of colorectal cancer

(2014) Lee Cheng Phua et al.   CANCER BIOLOGY & THERAPY

Identifying Small Molecules via High Resolution Mass Spectrometry: Communicating Confidence

(2014) Emma L. Schymanski et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

The Microbiome in Inflammatory Bowel Disease: Current Status and the Future Ahead

(2014) Aleksandar D. Kostic et al.   GASTROENTEROLOGY

Bacterial protein signals are associated with Crohn’s disease

(2014) Catherine Juste et al.   GUT

Development of an Enhanced Metaproteomic Approach for Deepening the Microbiome Characterization of the Human Infant Gut

(2014) Weili Xiong et al.   JOURNAL OF PROTEOME RESEARCH

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Relating the metatranscriptome and metagenome of the human gut

(2014) E. A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metaproteomics: Evaluation of protein extraction from activated sludge

(2014) Susan Hove Hansen et al.   PROTEOMICS

A straightforward and efficient analytical pipeline for metaproteome characterization

(2014) Alessandro Tanca et al.   Microbiome

Metaproteomics Analysis Reveals the Adaptation Process for the Chicken Gut Microbiota

(2013) Yue Tang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Pathview: an R/Bioconductor package for pathway-based data integration and visualization

(2013) Weijun Luo et al.   BIOINFORMATICS

Proteomics and metabolomics in inflammatory bowel disease

(2013) Yunki Yau et al.   JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY

A metaproteomic pipeline to identify newborn mouse gut phylotypes

(2013) Federica Del Chierico et al.   Journal of Proteomics

LipidBlast in silico tandem mass spectrometry database for lipid identification

(2013) Tobias Kind et al.   NATURE METHODS

A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection

(2013) Brooke L. Deatherage Kaiser et al.   PLoS One

Predicting Network Activity from High Throughput Metabolomics

(2013) Shuzhao Li et al.   PLoS Computational Biology

Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships

(2013) Ian H McHardy et al.   Microbiome

Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities

(2012) Robert L. Hettich et al.   CURRENT OPINION IN MICROBIOLOGY

Unipept: Tryptic Peptide-Based Biodiversity Analysis of Metaproteome Samples

(2012) Bart Mesuere et al.   JOURNAL OF PROTEOME RESEARCH

Translational biomarker discovery in clinical metabolomics: an introductory tutorial

(2012) Jianguo Xia et al.   Metabolomics

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

(2012) Ludovic C. Gillet et al.   MOLECULAR & CELLULAR PROTEOMICS

Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease

(2012) Luke Jostins et al.   NATURE

Comparative Metaproteomics and Diversity Analysis of Human Intestinal Microbiota Testifies for Its Temporal Stability and Expression of Core Functions

(2012) Carolin A. Kolmeder et al.   PLoS One

Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease

(2012) Alison R. Erickson et al.   PLoS One

Deep metaproteomic analysis of human salivary supernatant

(2012) Pratik Jagtap et al.   PROTEOMICS

CAMERA: An Integrated Strategy for Compound Spectra Extraction and Annotation of Liquid Chromatography/Mass Spectrometry Data Sets

(2011) Carsten Kuhl et al.   ANALYTICAL CHEMISTRY

GC/MS-based profiling of amino acids and TCA cycle-related molecules in ulcerative colitis

(2011) Makoto Ooi et al.   INFLAMMATION RESEARCH

MetAlign 3.0: performance enhancement by efficient use of advances in computer hardware

(2011) Arjen Lommen et al.   Metabolomics

Integrated Proteomic and Metabolomic Analysis of an Artificial Microbial Community for Two-Step Production of Vitamin C

(2011) Qian Ma et al.   PLoS One

Comparative Analysis of Proteome and Transcriptome Variation in Mouse

(2011) Anatole Ghazalpour et al.   PLoS Genetics

Inflammatory Bowel Disease

(2010) Arthur Kaser et al.   Annual Review of Immunology

MetPA: a web-based metabolomics tool for pathway analysis and visualization

(2010) J. Xia et al.   BIOINFORMATICS

MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

(2010) Tomáš Pluskal et al.   BMC BIOINFORMATICS

MassBank: a public repository for sharing mass spectral data for life sciences

(2010) Hisayuki Horai et al.   JOURNAL OF MASS SPECTROMETRY

An Automated Data Analysis Pipeline for GC−TOF−MS Metabonomics Studies

(2010) Wenxin Jiang et al.   JOURNAL OF PROTEOME RESEARCH

A metaproteomic analysis of the human salivary microbiota by three-dimensional peptide fractionation and tandem mass spectrometry

(2010) J.D. Rudney et al.   Molecular Oral Microbiology

MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data

(2010) J. Xia et al.   NUCLEIC ACIDS RESEARCH

Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour 'rules'

(2009) John Draper et al.   BMC BIOINFORMATICS

Metabolomics Reveals Metabolic Biomarkers of Crohn's Disease

(2009) Janet Jansson et al.   PLoS One

SIRIUS: decomposing isotope patterns for metabolite identification†

(2008) Sebastian Böcker et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Shotgun metaproteomics of the human distal gut microbiota

(2008) Nathan C Verberkmoes et al.   ISME Journal

Inter-kingdom signalling: communication between bacteria and their hosts

(2008) David T. Hughes et al.   NATURE REVIEWS MICROBIOLOGY

Symbiotic gut microbes modulate human metabolic phenotypes

(2008) M. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA