A decade of metaproteomics: Where we stand and what the future holds

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

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

Online Peptide Fractionation Using a Multiphasic Microfluidic Liquid Chromatography Chip Improves Reproducibility and Detection Limits for Quantitation in Discovery and Targeted Proteomics

(2015) Christoph Krisp et al.   MOLECULAR & CELLULAR PROTEOMICS

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes

(2015) Jenni Hultman et al.   NATURE

In situexpression of nitrite-dependent anaerobic methane oxidation proteins byCandidatusMethylomirabilis oxyfera co-occurring with expressed anammox proteins in a contaminated aquifer

(2015) Buck T. Hanson et al.   Environmental Microbiology Reports

Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks

(2015) Hugo Roume et al.   npj Biofilms and Microbiomes

Metaproteomic Identification of Diazotrophic Methanotrophs and Their Localization in Root Tissues of Field-Grown Rice Plants

(2014) Zhihua Bao et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Integrated metagenomic and metaproteomic analyses of marine biofilm communities

(2014) Dagmar H. Leary et al.   BIOFOULING

Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics

(2014) Anke Penzlin et al.   BIOINFORMATICS

15N- and2H proteomic stable isotope probing links nitrogen flow to archaeal heterotrophic activity

(2014) Nicholas B. Justice et al.   ENVIRONMENTAL MICROBIOLOGY

Elevated temperature alters proteomic responses of individual organisms within a biofilm community

(2014) Annika C Mosier et al.   ISME Journal

Metaproteomic analysis of a winter to spring succession in coastal northwest Atlantic Ocean microbial plankton

(2014) Anna A Georges et al.   ISME Journal

Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities

(2014) Daniela S Aliaga Goltsman et al.   ISME Journal

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

Metaproteomics of soils from semiarid environment: Functional and phylogenetic information obtained with different protein extraction methods

(2014) F. Bastida et al.   Journal of Proteomics

Metaproteomic Survey of Six Aquatic Habitats: Discovering the Identities of Microbial Populations Active in Biogeochemical Cycling

(2014) Buck T. Hanson et al.   MICROBIAL ECOLOGY

Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes

(2014) A. K. Hawley 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

Metaproteomics reveals the major microbial players and their biogeochemical functions in a productive coastal system in the northern South China Sea

(2014) Hong-Po Dong et al.   Environmental Microbiology Reports

Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage

(2014) Emilie E. L. Muller et al.   Nature Communications

Stable-Isotope Probing Reveals That Hydrogen Isotope Fractionation in Proteins and Lipids in a Microbial Community Are Different and Species-Specific

(2013) Curt R. Fischer et al.   ACS Chemical Biology

Sample prefractionation with liquid isoelectric focusing enables in depth microbial metaproteome analysis of mesophilic and thermophilic biogas plants

(2013) F. Kohrs et al.   ANAEROBE

Microbial community structure and functioning in marine sediments associated with diffuse hydrothermal venting assessed by integrated meta-omics

(2013) Tim Urich et al.   ENVIRONMENTAL MICROBIOLOGY

Digging into the extracellular matrix of a complex microbial community using a combined metagenomic and metaproteomic approach

(2013) M. Albertsen et al.   WATER SCIENCE AND TECHNOLOGY

Heterotrophic Archaea Contribute to Carbon Cycling in Low-pH, Suboxic Biofilm Communities

(2012) Nicholas B. Justice et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Step-by-step strategy for protein enrichment and proteome characterisation of extracellular polymeric substances in wastewater treatment systems

(2012) Ana F. Silva et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Exploring the potential of applying proteomics for tracking bisphenol A and nonylphenol degradation in activated sludge

(2012) Neus Collado et al.   CHEMOSPHERE

Integrated metagenomic and metaproteomic analyses of an ANME-1-dominated community in marine cold seep sediments

(2012) Runar Stokke et al.   ENVIRONMENTAL MICROBIOLOGY

Gut microbiota disturbance during antibiotic therapy: a multi-omic approach

(2012) Ana Elena Pérez-Cobas et al.   GUT

A metaproteomic assessment of winter and summer bacterioplankton from Antarctic Peninsula coastal surface waters

(2012) Timothy J Williams et al.   ISME Journal

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

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

A Core Human Microbiome as Viewed through 16S rRNA Sequence Clusters

(2012) Susan M. Huse et al.   PLoS One

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

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

Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use

(2012) M. Kleiner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Substrate-Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom

(2012) H. Teeling et al.   SCIENCE

Soil-specific limitations for access and analysis of soil microbial communities by metagenomics

(2011) Nathalie Lombard et al.   FEMS MICROBIOLOGY ECOLOGY

Host–microbe relationships in inflammatory bowel disease detected by bacterial and metaproteomic analysis of the mucosal–luminal interface

(2011) Laura L. Presley et al.   INFLAMMATORY BOWEL DISEASES

454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants

(2011) Tong Zhang et al.   ISME Journal

A Metaproteomic Approach to Study Human-Microbial Ecosystems at the Mucosal Luminal Interface

(2011) Xiaoxiao Li et al.   PLoS One

Status quo in physiological proteomics of the uncultured Riftia pachyptila endosymbiont

(2011) Stephanie Markert et al.   PROTEOMICS

An integrative study of a meromictic lake ecosystem in Antarctica

(2010) Federico M Lauro et al.   ISME Journal

Metaproteogenomic analysis of a dominant green sulfur bacterium from Ace Lake, Antarctica

(2010) Charmaine Ng et al.   ISME Journal

Environmental proteomics of microbial plankton in a highly productive coastal upwelling system

(2010) Sarah M Sowell et al.   ISME Journal

Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction

(2010) Robert M Morris et al.   ISME Journal

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

Ecological distribution and population physiology defined by proteomics in a natural microbial community

(2010) Ryan S Mueller et al.   Molecular Systems Biology

Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities

(2010) V. J. Denef et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploring research frontiers in microbiology: the challenge of metagenomics in soil microbiology

(2010) Stefano Mocali et al.   RESEARCH IN MICROBIOLOGY

Metabolome-Proteome Differentiation Coupled to Microbial Divergence

(2010) P. Wilmes et al.   mBio

Radiolabelled proteomics to determine differential functioning ofAccumulibacterduring the anaerobic and aerobic phases of a bioreactor operating for enhanced biological phosphorus removal

(2009) Margaret Wexler et al.   ENVIRONMENTAL MICROBIOLOGY

Cultivation and quantitative proteomic analyses of acidophilic microbial communities

(2009) Christopher P Belnap et al.   ISME Journal

Cytochrome 572 is a conspicuous membrane protein with iron oxidation activity purified directly from a natural acidophilic microbial community

(2008) Chris Jeans et al.   ISME Journal

Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal

(2008) Paul Wilmes et al.   ISME Journal

Shotgun metaproteomics of the human distal gut microbiota

(2008) Nathan C Verberkmoes et al.   ISME Journal

Metaproteomics Provides Functional Insight into Activated Sludge Wastewater Treatment

(2008) Paul Wilmes et al.   PLoS One

Evaluation of the extracellular proteins in full-scale activated sludges

(2008) Chul Park et al.   WATER RESEARCH