A meta-proteomics approach to study the interspecies interactions affecting microbial biofilm development in a model community

[1]  S. Sørensen,et al.  Low‐abundant species facilitates specific spatial organization that promotes multispecies biofilm formation , 2017, Environmental microbiology.

[2]  S. Sørensen,et al.  Distinct gene expression profile of Xanthomonas retroflexus engaged in synergistic multispecies biofilm formation , 2016, The ISME Journal.

[3]  L. Jensen,et al.  Metaproteomics of saliva identifies human protein markers specific for individuals with periodontitis and dental caries compared to orally healthy controls , 2016, PeerJ.

[4]  Dazhi Wang,et al.  Environmental Microbial Community Proteomics: Status, Challenges and Perspectives , 2016, International journal of molecular sciences.

[5]  Marco Y. Hein,et al.  The Perseus computational platform for comprehensive analysis of (prote)omics data , 2016, Nature Methods.

[6]  Philipp E. Geyer,et al.  Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome , 2016, Genome Medicine.

[7]  José A. Dianes,et al.  2016 update of the PRIDE database and its related tools , 2016, Nucleic Acids Res..

[8]  S. Sørensen,et al.  Interspecific bacterial interactions are reflected in multispecies biofilm spatial organization , 2016 .

[9]  Fusheng Chen,et al.  Global insights into acetic acid resistance mechanisms and genetic stability of Acetobacter pasteurianus strains by comparative genomics , 2015, Scientific Reports.

[10]  J. Grossmann,et al.  Proteomic profiling of host-biofilm interactions in an oral infection model resembling the periodontal pocket , 2015, Scientific Reports.

[11]  Adriana Ambrosini,et al.  Plant growth-promoting bacteria as inoculants in agricultural soils , 2015, Genetics and molecular biology.

[12]  Etienne Yergeau,et al.  Metaproteomics of aquatic microbial communities in a deep and stratified estuary , 2015, Proteomics.

[13]  S. Aymerich,et al.  Pathogens protection against the action of disinfectants in multispecies biofilms , 2015, Front. Microbiol..

[14]  F. Fang,et al.  Extracellular protein analysis of activated sludge and their functions in wastewater treatment plant by shotgun proteomics , 2015, Scientific Reports.

[15]  Ryan S. Mueller,et al.  Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant , 2015, Front. Microbiol..

[16]  B. Xi,et al.  Metaproteomics reveals major microbial players and their biodegradation functions in a large-scale aerobic composting plant , 2015, Microbial biotechnology.

[17]  A. Papadimitropoulos,et al.  Establishment of an oral infection model resembling the periodontal pocket in a perfusion bioreactor system , 2015, Virulence.

[18]  Annika C. Mosier,et al.  Elevated temperature alters proteomic responses of individual organisms within a biofilm community , 2014, The ISME Journal.

[19]  S. Sørensen,et al.  High prevalence of biofilm synergy among bacterial soil isolates in cocultures indicates bacterial interspecific cooperation , 2014, The ISME Journal.

[20]  K. Konstantinidis,et al.  Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities. , 2014, Environmental microbiology reports.

[21]  Marco Y. Hein,et al.  Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ * , 2014, Molecular & Cellular Proteomics.

[22]  Oscar Cerda,et al.  Characterization of the Arginine Decarboxylase Gene (ORF HP0422, speA) Involved in Acid Tolerance in Helicobacter pylori , 2014, Helicobacter.

[23]  M. Mann,et al.  Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells , 2014, Nature Methods.

[24]  Fangfang Xia,et al.  The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) , 2013, Nucleic Acids Res..

[25]  Stefan Schuster,et al.  Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria , 2013, The ISME Journal.

[26]  S. Sørensen,et al.  High-Throughput Screening of Multispecies Biofilm Formation and Quantitative PCR-Based Assessment of Individual Species Proportions, Useful for Exploring Interspecific Bacterial Interactions , 2014, Microbial Ecology.

[27]  B. Kjellerup,et al.  Applications of biofilms in bioremediation and biotransformation of persistent organic pollutants, pharmaceuticals/personal care products, and heavy metals , 2013, Applied Microbiology and Biotechnology.

[28]  Thomas Bjarnsholt,et al.  The in vivo biofilm. , 2013, Trends in microbiology.

[29]  W. Giordano,et al.  The Role of Bacterial Biofilms and Surface Components in Plant-Bacterial Associations , 2013, International journal of molecular sciences.

[30]  Chongle Pan,et al.  Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities. , 2013, Analytical chemistry.

[31]  Amadou Sarr,et al.  Loss in microbial diversity affects nitrogen cycling in soil , 2013, The ISME Journal.

[32]  Wenying Shou,et al.  Strong inter-population cooperation leads to partner intermixing in microbial communities , 2013, eLife.

[33]  S. Sørensen,et al.  The ability of soil bacteria to receive the conjugative IncP1 plasmid, pKJK10, is different in a mixed community compared to single strains. , 2013, FEMS microbiology letters.

[34]  Richard J. Lavallee,et al.  Optimized fast and sensitive acquisition methods for shotgun proteomics on a quadrupole orbitrap mass spectrometer. , 2012, Journal of proteome research.

[35]  M. Selbach,et al.  Global quantification of mammalian gene expression control , 2011, Nature.

[36]  Sheng Lin,et al.  Characterization of metaproteomics in crop rhizospheric soil. , 2011, Journal of proteome research.

[37]  V. Cooper,et al.  Ecological succession in long-term experimentally evolved biofilms produces synergistic communities , 2011, The ISME Journal.

[38]  M. Mann,et al.  Andromeda: a peptide search engine integrated into the MaxQuant environment. , 2011, Journal of proteome research.

[39]  M. Vieira,et al.  A review of current and emergent biofilm control strategies , 2010 .

[40]  Chongle Pan,et al.  Cultivation and quantitative proteomic analyses of acidophilic microbial communities , 2010, The ISME Journal.

[41]  J. Keller,et al.  Initial development and structure of biofilms on microbial fuel cell anodes , 2010, BMC Microbiology.

[42]  Hadley Wickham,et al.  ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .

[43]  Paul Stoodley,et al.  Evolving concepts in biofilm infections , 2009, Cellular microbiology.

[44]  Vincent J. Denef,et al.  Systems Biology: Functional analysis of natural microbial consortia using community proteomics , 2009, Nature Reviews Microbiology.

[45]  P. Stewart,et al.  Escherichia coli O157:H7 requires colonizing partner to adhere and persist in a capillary flow cell. , 2009, Environmental science & technology.

[46]  M. Mann,et al.  MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification , 2008, Nature Biotechnology.

[47]  Rick L. Stevens,et al.  The RAST Server: Rapid Annotations using Subsystems Technology , 2008, BMC Genomics.

[48]  C. Fuqua,et al.  Biofilm formation by plant-associated bacteria. , 2007, Annual review of microbiology.

[49]  Martin A Hamilton,et al.  Comparative evaluation of biofilm disinfectant efficacy tests. , 2007, Journal of microbiological methods.

[50]  Steven P Gygi,et al.  Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry , 2007, Nature Methods.

[51]  J. R. Lobry,et al.  SeqinR 1.0-2: A Contributed Package to the R Project for Statistical Computing Devoted to Biological Sequences Retrieval and Analysis , 2007 .

[52]  A. Griffin,et al.  Social evolution theory for microorganisms , 2006, Nature Reviews Microbiology.

[53]  J. Slonczewski,et al.  Polyamine stress at high pH in Escherichia coli K-12 , 2005, BMC Microbiology.

[54]  Lennart Martens,et al.  DBToolkit: processing protein databases for peptide-centric proteomics , 2005, Bioinform..

[55]  John W. Foster,et al.  Escherichia coli Glutamate- and Arginine-Dependent Acid Resistance Systems Increase Internal pH and Reverse Transmembrane Potential , 2004, Journal of bacteriology.

[56]  J. Frank,et al.  Behavior of Listeria monocytogenes in a Pseudomonas putida biofilm on a condensate-forming surface. , 2004, Journal of food protection.

[57]  J. Bruno,et al.  Inclusion of facilitation into ecological theory , 2003 .

[58]  R. Tibshirani,et al.  Significance analysis of microarrays applied to the ionizing radiation response , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[59]  C. Potera Studying slime. , 1998, Environmental health perspectives.

[60]  J. Knappe,et al.  Reconstitution and Characterization of the Polynuclear Iron-Sulfur Cluster in Pyruvate Formate-lyase-activating Enzyme , 1998, The Journal of Biological Chemistry.

[61]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[62]  H. A. Barker,et al.  Lysine 2,3-aminomutase. Purification and properties of a pyridoxal phosphate and S-adenosylmethionine-activated enzyme. , 1970, The Journal of biological chemistry.