Enhancing metaproteomics-The value of models and defined environmental microbial systems

Microbial Toluene Removal in Hypoxic Model Constructed Wetlands Occurs Predominantly via the Ring Monooxygenation Pathway

(2015) P. M. Martínez-Lavanchy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Community shifts in a well-operating agricultural biogas plant: how process variations are handled by the microbiome

(2015) Susanne Theuerl et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Context-specific metabolic network reconstruction of a naphthalene-degrading bacterial community guided by metaproteomic data

(2015) Luis Tobalina et al.   BIOINFORMATICS

New steady-state microbial community compositions and process performances in biogas reactors induced by temperature disturbances

(2015) Gang Luo et al.   Biotechnology for Biofuels

Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions

(2015) Yvonne Stolze et al.   Biotechnology for Biofuels

Identification of Putative Genes Involved in Bisphenol A Degradation Using Differential Protein Abundance Analysis of Sphingobium sp. BiD32

(2015) Nicolette A. Zhou et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Low-temperature anaerobic digestion is associated with differential methanogenic protein expression

(2015) Eoin Gunnigle et al.   FEMS MICROBIOLOGY LETTERS

Dysbiotic gut microbiota causes transmissible Crohn's disease-like ileitis independent of failure in antimicrobial defence

(2015) Monika Schaubeck et al.   GUT

The activated sludge ecosystem contains a core community of abundant organisms

(2015) Aaron M Saunders et al.   ISME Journal

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

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

Quantitative proteome analysis of Caenorhabditis elegans upon exposure to nematicidal Bacillus thuringiensis

(2015) Christian Treitz et al.   Journal of Proteomics

A Metaproteomics Approach to Elucidate Host and Pathogen Protein Expression during Catheter-Associated Urinary Tract Infections (CAUTIs)

(2015) Christian Lassek et al.   MOLECULAR & CELLULAR PROTEOMICS

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

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

(2015) Paul Wilmes et al.   PROTEOMICS

Metaproteomics of activated sludge from a wastewater treatment plant - A pilot study

(2015) Sebastian Püttker et al.   PROTEOMICS

Navigating through metaproteomics data: A logbook of database searching

(2015) Thilo Muth et al.   PROTEOMICS

Improving the quality of genome, protein sequence, and taxonomy databases: A prerequisite for microbiome meta-omics 2.0

(2015) Olivier Pible et al.   PROTEOMICS

Label-free quantification reveals major proteomic changes inPseudomonas putidaF1 during the exponential growth phase

(2015) Florian-Alexander Herbst et al.   PROTEOMICS

Metaproteomic analysis using the Galaxy framework

(2015) Pratik D. Jagtap et al.   PROTEOMICS

Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota

(2015) Weili Xiong et al.   PROTEOMICS

Early infancy microbial and metabolic alterations affect risk of childhood asthma

(2015) Marie-Claire Arrieta et al.   Science Translational Medicine

Dewatering in biological wastewater treatment: A review

(2015) Morten Lykkegaard Christensen et al.   WATER RESEARCH

MiDAS: the field guide to the microbes of activated sludge

(2015) Simon Jon McIlroy et al.   Database-The Journal of Biological Databases and Curation

Extracellular protein analysis of activated sludge and their functions in wastewater treatment plant by shotgun proteomics

(2015) Peng Zhang et al.   Scientific Reports

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

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

Cross-feeding by Bifidobacterium breve UCC2003 during co-cultivation with Bifidobacterium bifidum PRL2010 in a mucin-based medium

(2014) Muireann Egan et al.   BMC MICROBIOLOGY

Removal and fate of arsenic in the rhizosphere of Juncus effusus treating artificial wastewater in laboratory-scale constructed wetlands

(2014) Khaja Zillur Rahman et al.   ECOLOGICAL ENGINEERING

Genome Reconstruction and Gene Expression of “Candidatus Accumulibacter phosphatis” Clade IB Performing Biological Phosphorus Removal

(2014) Yanping Mao et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Diverse sulfate-reducing bacteria of the Desulfosarcina/Desulfococcus clade are the key alkane degraders at marine seeps

(2014) Sara Kleindienst et al.   ISME Journal

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

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

Reprint of “Which metaproteome? The impact of protein extraction bias on metaproteomic analyses”

(2014) Dagmar Hajkova Leary et al.   MOLECULAR AND CELLULAR PROBES

Single-molecule site-specific detection of protein phosphorylation with a nanopore

(2014) Christian B Rosen et al.   NATURE BIOTECHNOLOGY

Germ-free mice as a model to study effect of gut microbiota on host physiology

(2014) M. Grover et al.   NEUROGASTROENTEROLOGY AND MOTILITY

Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells

(2014) David Berry et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteomic investigation ofVibrio alginolyticuschallengedCaenorhabditis elegansrevealed regulation of cellular homeostasis proteins and their role in supporting innate immune system

(2014) Sellegounder Durai et al.   PROTEOMICS

A new classification paradigm of extracellular polymeric substances (EPS) in activated sludge: Separation and characterization of exopolymers between floc level and microcolony level

(2014) Bin-Bin Wang et al.   WATER RESEARCH

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

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

Subpopulation-proteomics reveal growth rate, but not cell cycling, as a major impact on protein composition in Pseudomonas putida KT2440

(2014) Sarah Lieder et al.   AMB Express

A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer

(2014) Joshua Quick et al.   GigaScience

Use of Caenorhabditis elegans as a model to study Alzheimer’s disease and other neurodegenerative diseases

(2014) Adanna G. Alexander et al.   Frontiers in Genetics

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

(2013) F. Kohrs et al.   ANAEROBE

Experimental models of the gut microbiome

(2013) Koen Venema et al.   BEST PRACTICE & RESEARCH IN CLINICAL GASTROENTEROLOGY

Ex vivo systems to study host–microbiota interactions in the gastrointestinal tract

(2013) Guus Roeselers et al.   BEST PRACTICE & RESEARCH IN CLINICAL GASTROENTEROLOGY

Gene-environment and protein-degradation signatures characterize genomic and phenotypic diversity in wild Caenorhabditis elegans populations

(2013) Rita JM Volkers et al.   BMC BIOLOGY

Bacterial Nitric Oxide Extends the Lifespan of C. elegans

(2013) Ivan Gusarov et al.   CELL

Worms need microbes too: microbiota, health and aging inCaenorhabditis elegans

(2013) Filipe Cabreiro et al.   EMBO Molecular Medicine

454 pyrosequencing analyses of bacterial and archaeal richness in 21 full-scale biogas digesters

(2013) Carina Sundberg et al.   FEMS MICROBIOLOGY ECOLOGY

Comparative genomics of two ‘Candidatus Accumulibacter’ clades performing biological phosphorus removal

(2013) Jason J Flowers et al.   ISME Journal

Metaproteomics of cellulose methanisation under thermophilic conditions reveals a surprisingly high proteolytic activity

(2013) Fan Lü et al.   ISME Journal

In-depth proteomic analysis of the human cerumen—A potential novel diagnostically relevant biofluid

(2013) Martin Andreas Feig et al.   Journal of Proteomics

Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics

(2013) Stephan A. Müller et al.   Journal of Proteomics

Metaproteomics of our microbiome — Developing insight in function and activity in man and model systems

(2013) Carolin A. Kolmeder et al.   Journal of Proteomics

Methyl-Coenzyme M Reductase from Methanogenic Archaea: Isotope Effects on the Formation and Anaerobic Oxidation of Methane

(2013) Silvan Scheller et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Metaproteome analysis of the microbial communities in agricultural biogas plants

(2013) R. Heyer et al.   New Biotechnology

Evaluating the Impact of Different Sequence Databases on Metaproteome Analysis: Insights from a Lab-Assembled Microbial Mixture

(2013) Alessandro Tanca et al.   PLoS One

A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies

(2013) Pratik Jagtap et al.   PROTEOMICS

Metagenome and metaproteome analyses of microbial communities in mesophilic biogas-producing anaerobic batch fermentations indicate concerted plant carbohydrate degradation

(2013) Angelika Hanreich et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Metagenomes obtained by ‘deep sequencing’ – what do they tell about the enhanced biological phosphorus removal communities?

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

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

Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome

(2013) Nathan P. McNulty et al.   PLOS BIOLOGY

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

Metaproteome analysis to determine the metabolically active part of a thermophilic microbial community producing biogas from agricultural biomass

(2012) Angelika Hanreich et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells

(2012) Samuel Marguerat et al.   CELL

Phosphorus recovery from wastewater through microbial processes

(2012) Zhiguo Yuan et al.   CURRENT OPINION IN BIOTECHNOLOGY

Effect of galactooligosaccharides andBifidobacterium animalisBb-12 on growth ofLactobacillus amylovorusDSM 16698, microbial community structure, and metabolite production in anin vitrocolonic model set up with human or pig microbiota

(2012) Rafael C.R. Martinez et al.   FEMS MICROBIOLOGY ECOLOGY

Association with Soil Bacteria Enhances p38-Dependent Infection Resistance in Caenorhabditis elegans

(2012) Sirena Montalvo-Katz et al.   INFECTION AND IMMUNITY

Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions

(2012) Thomas Schneider et al.   ISME Journal

Protein-SIP enables time-resolved analysis of the carbon flux in a sulfate-reducing, benzene-degrading microbial consortium

(2012) Martin Taubert et al.   ISME Journal

Effects of Long- and Short-Chain Fatty Acids on the Release of Gastrointestinal Hormones using an ex Vivo Porcine Intestinal Tissue Model

(2012) Trudy Voortman et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Proteomic profiling of the acid tolerance response (ATR) during the enhanced biomethanation process from Taihu Blue Algae with butyrate stress on anaerobic sludge

(2012) Qun Yan et al.   JOURNAL OF HAZARDOUS MATERIALS

Galacto-Oligosaccharides Have Prebiotic Activity in a Dynamic In Vitro Colon Model Using a 13C-Labeling Technique

(2012) Annet J. H. Maathuis et al.   JOURNAL OF NUTRITION

Metaproteome Analysis and Molecular Genetics of Rat Intestinal Microbiota Reveals Section and Localization Resolved Species Distribution and Enzymatic Functionalities

(2012) Sven-Bastiaan Haange et al.   JOURNAL OF PROTEOME RESEARCH

Unipept: Tryptic Peptide-Based Biodiversity Analysis of Metaproteome Samples

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

Protein-based stable isotope probing (protein-SIP) in functional metaproteomics

(2012) Jana Seifert et al.   MASS SPECTROMETRY REVIEWS

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

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

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

Proteomic tracking and analysis of a bacterial mixed culture

(2012) Sabine Kluge et al.   PROTEOMICS

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

(2012) H. Teeling et al.   SCIENCE

WebMGA: a customizable web server for fast metagenomic sequence analysis

(2011) Sitao Wu et al.   BMC GENOMICS

Microbial communities involved in enhanced biological phosphorus removal from wastewater—a model system in environmental biotechnology

(2011) Per Halkjær Nielsen et al.   CURRENT OPINION IN BIOTECHNOLOGY

Characterization of microbial biofilms in a thermophilic biogas system by high-throughput metagenome sequencing

(2011) Antje Rademacher et al.   FEMS MICROBIOLOGY ECOLOGY

A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal

(2011) Mads Albertsen et al.   ISME Journal

Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: global transcriptomic and proteomic analyses

(2011) Yujie Men et al.   ISME Journal

Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions

(2011) Christopher P Belnap et al.   ISME Journal

A metaproteomic approach gives functional insights into anaerobic digestion

(2011) F. Abram et al.   JOURNAL OF APPLIED MICROBIOLOGY

Dietary Restriction of Caenorhabditis elegans by Axenic Culture Reflects Nutritional Requirement for Constituents Provided by Metabolically Active Microbes

(2011) I. Lenaerts et al.   JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES

Quantitative Tracking of Isotope Flows in Proteomes of Microbial Communities

(2011) Chongle Pan et al.   MOLECULAR & CELLULAR PROTEOMICS

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Metaproteome analysis of sewage sludge from membrane bioreactors

(2011) Ramona Kuhn et al.   PROTEOMICS

Structure and function of the symbiosis partners of the lung lichen (Lobaria pulmonaria L. Hoffm.) analyzed by metaproteomics

(2011) Thomas Schneider et al.   PROTEOMICS

The pig: a model for human infectious diseases

(2011) François Meurens et al.   TRENDS IN MICROBIOLOGY

Metaorganisms as the new frontier

(2011) Thomas C.G. Bosch et al.   ZOOLOGY

Microbiology of ‘Candidatus Accumulibacter’ in activated sludge

(2011) Shaomei He et al.   Microbial Biotechnology

Advanced tool for characterization of microbial cultures by combining cytomics and proteomics

(2010) Nico Jehmlich et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Proteome changes of Caenorhabditis elegans upon a Staphylococcus aureus infection

(2010) Annelies Bogaerts et al.   Biology Direct

A differential proteomics study of Caenorhabditis elegans infected with Aeromonas hydrophila

(2010) Annelies Bogaerts et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Metatranscriptomic array analysis of ‘Candidatus Accumulibacter phosphatis’-enriched enhanced biological phosphorus removal sludge

(2010) Shaomei He et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2010) Robert M Morris et al.   ISME Journal

A Human Gastric Simulator (HGS) to Study Food Digestion in Human Stomach

(2010) Fanbin Kong et al.   JOURNAL OF FOOD SCIENCE

Direct Cellular Lysis/Protein Extraction Protocol for Soil Metaproteomics

(2010) Karuna Chourey et al.   JOURNAL OF PROTEOME RESEARCH

Characterization of Metaproteomics in Crop Rhizospheric Soil

(2010) Hai-Bin Wang et al.   JOURNAL OF PROTEOME RESEARCH

Diversity of methanogenic archaea in a biogas reactor fed with swine feces as the mono-substrate by mcrA analysis

(2010) Chenguang Zhu et al.   MICROBIOLOGICAL RESEARCH

Evaluating the microbial diversity of an in vitro model of the human large intestine by phylogenetic microarray analysis

(2010) M. Rajilic-Stojanovic et al.   MICROBIOLOGY-SGM

The genetics of ageing

(2010) Cynthia J. Kenyon   NATURE

Protein-based stable isotope probing

(2010) Nico Jehmlich et al.   Nature Protocols

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

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

(2010) Y. Taniguchi et al.   SCIENCE

Systems-wide temporal proteomic profiling in glucose-starved Bacillus subtilis

(2010) Andreas Otto et al.   Nature Communications

A guide to Ussing chamber studies of mouse intestine

(2009) Lane L. Clarke   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

Improving protein extraction and separation methods for investigating the metaproteome of anaerobic benzene communities within sediments

(2009) Dirk Benndorf et al.   BIODEGRADATION

Caenorhabditis elegans as an emerging model for studying the basic biology of obesity

(2009) K. T. Jones et al.   Disease Models & Mechanisms

Adaptation of protein expression byEscherichia coliin the gastrointestinal tract of gnotobiotic mice

(2009) Carl Alpert et al.   ENVIRONMENTAL MICROBIOLOGY

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

Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge

(2009) Delphine Rivière et al.   ISME Journal

Cultivation and quantitative proteomic analyses of acidophilic microbial communities

(2009) Christopher P Belnap et al.   ISME Journal

Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche

(2009) Toshiro Sato et al.   NATURE

Functional analysis of natural microbial consortia using community proteomics

(2009) Nathan C. VerBerkmoes et al.   NATURE REVIEWS MICROBIOLOGY

Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla

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

TheShigella dysenteriaeserotype 1 proteome, profiled in the host intestinal environment, reveals major metabolic modifications and increased expression of invasive proteins

(2009) Rembert Pieper et al.   PROTEOMICS

Characterization of Cytochrome 579, an Unusual Cytochrome Isolated from an Iron-Oxidizing Microbial Community

(2008) S. W. Singer et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Linking phylogenetic identities of bacteria to starch fermentation in anin vitromodel of the large intestine by RNA-based stable isotope probing

(2008) Petia Kovatcheva-Datchary et al.   ENVIRONMENTAL MICROBIOLOGY

Protein-based stable isotope probing (Protein-SIP) reveals active species within anoxic mixed cultures

(2008) Nico Jehmlich 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

Archaea diversity within a commercial biogas plant utilizing herbal biomass determined by 16S rDNA andmcrA analysis

(2008) E. Nettmann et al.   JOURNAL OF APPLIED MICROBIOLOGY

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

Sulphur transformation and deposition in the rhizosphere of Juncus effusus in a laboratory-scale constructed wetland

(2007) A. Wiessner et al.   ENVIRONMENTAL POLLUTION