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

We are living through exciting times during which we are able to unravel the “microbial dark matter” in and around us through the application of high‐resolution “meta‐omics”. Metaproteomics offers the ability to resolve the major catalytic units of microbial populations and thereby allows the establ...

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Published in:	Proteomics (Weinheim) Vol. 15; no. 20; pp. 3409 - 3417
Main Authors:	Wilmes, Paul, Heintz-Buschart, Anna, Bond, Philip L.
Format:	Journal Article
Language:	English
Published:	Germany Blackwell Publishing Ltd 01.10.2015 Wiley Subscription Services, Inc John Wiley and Sons Inc
Subjects:	Acid mine drainage Activated sludge Betaproteobacteria - genetics Biofilms Catalysis Chemical analysis Communities Community composition Cyanobacteria - genetics Dark matter Ecological function Ecosystem Fresh Water Genotypes Humans Integrated omics Intestinal microflora Leptospiraceae - genetics Metagenomics Metaproteomics Microbial activity Microbial community Microbial systems ecology Microbiology Microbiota Microorganisms Phenotypes Proteins Proteome - genetics Proteomics Seawater Soil Microbiology Viewpoint Water analysis Metagenomics Microbial systems ecology Metaproteomics Microbiology Integrated omics Microbial community
ISSN:	1615-9853, 1615-9861, 1615-9861
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Abstract	We are living through exciting times during which we are able to unravel the “microbial dark matter” in and around us through the application of high‐resolution “meta‐omics”. Metaproteomics offers the ability to resolve the major catalytic units of microbial populations and thereby allows the establishment of genotype‐phenotype linkages from in situ samples. A decade has passed since the term “metaproteomics” was first coined and corresponding analyses were carried out on mixed microbial communities. Since then metaproteomics has yielded many important insights into microbial ecosystem function in the various environmental settings where it has been applied. Although initial progress in analytical capacities and resulting numbers of proteins identified was extremely fast, this trend slowed rapidly. Here, we discuss several representative metaproteomic investigations of activated sludge, acid mine drainage biofilms, freshwater and seawater microbial communities, soil, and human gut microbiota. By using these case studies, we highlight current challenges and possible solutions for metaproteomics to realize its full potential, i.e. to enable conclusive links between microbial community composition, physiology, function, interactions, ecology, and evolution in situ.
AbstractList	We are living through exciting times during which we are able to unravel the “microbial dark matter” in and around us through the application of high‐resolution “meta‐omics”. Metaproteomics offers the ability to resolve the major catalytic units of microbial populations and thereby allows the establishment of genotype‐phenotype linkages from in situ samples. A decade has passed since the term “metaproteomics” was first coined and corresponding analyses were carried out on mixed microbial communities. Since then metaproteomics has yielded many important insights into microbial ecosystem function in the various environmental settings where it has been applied. Although initial progress in analytical capacities and resulting numbers of proteins identified was extremely fast, this trend slowed rapidly. Here, we discuss several representative metaproteomic investigations of activated sludge, acid mine drainage biofilms, freshwater and seawater microbial communities, soil, and human gut microbiota. By using these case studies, we highlight current challenges and possible solutions for metaproteomics to realize its full potential, i.e. to enable conclusive links between microbial community composition, physiology, function, interactions, ecology, and evolution in situ. We are living through exciting times during which we are able to unravel the "microbial dark matter" in and around us through the application of high-resolution "meta-omics". Metaproteomics offers the ability to resolve the major catalytic units of microbial populations and thereby allows the establishment of genotype-phenotype linkages from in situ samples. A decade has passed since the term "metaproteomics" was first coined and corresponding analyses were carried out on mixed microbial communities. Since then metaproteomics has yielded many important insights into microbial ecosystem function in the various environmental settings where it has been applied. Although initial progress in analytical capacities and resulting numbers of proteins identified was extremely fast, this trend slowed rapidly. Here, we discuss several representative metaproteomic investigations of activated sludge, acid mine drainage biofilms, freshwater and seawater microbial communities, soil, and human gut microbiota. By using these case studies, we highlight current challenges and possible solutions for metaproteomics to realize its full potential, i.e. to enable conclusive links between microbial community composition, physiology, function, interactions, ecology, and evolution in situ.We are living through exciting times during which we are able to unravel the "microbial dark matter" in and around us through the application of high-resolution "meta-omics". Metaproteomics offers the ability to resolve the major catalytic units of microbial populations and thereby allows the establishment of genotype-phenotype linkages from in situ samples. A decade has passed since the term "metaproteomics" was first coined and corresponding analyses were carried out on mixed microbial communities. Since then metaproteomics has yielded many important insights into microbial ecosystem function in the various environmental settings where it has been applied. Although initial progress in analytical capacities and resulting numbers of proteins identified was extremely fast, this trend slowed rapidly. Here, we discuss several representative metaproteomic investigations of activated sludge, acid mine drainage biofilms, freshwater and seawater microbial communities, soil, and human gut microbiota. By using these case studies, we highlight current challenges and possible solutions for metaproteomics to realize its full potential, i.e. to enable conclusive links between microbial community composition, physiology, function, interactions, ecology, and evolution in situ.
Author	Wilmes, Paul Bond, Philip L. Heintz-Buschart, Anna
AuthorAffiliation	2 Advanced Water Management Centre University of Queensland Brisbane Australia 1 Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
AuthorAffiliation_xml	– name: 1 Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg – name: 2 Advanced Water Management Centre University of Queensland Brisbane Australia
Author_xml	– sequence: 1 givenname: Paul surname: Wilmes fullname: Wilmes, Paul email: paul.wilmes@uni.lu organization: Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg – sequence: 2 givenname: Anna surname: Heintz-Buschart fullname: Heintz-Buschart, Anna organization: Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg – sequence: 3 givenname: Philip L. surname: Bond fullname: Bond, Philip L. organization: Advanced Water Management Centre, University of Queensland, Brisbane, Australia
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Cites_doi	10.1038/ismej.2014.200 10.2166/wst.2013.030 10.1126/science.1121225 10.1002/pmic.201200569 10.1016/j.chemosphere.2012.10.002 10.1007/s00248-013-0346-5 10.1111/j.1462-2920.2004.00687.x 10.1016/j.watres.2008.05.014 10.1038/nbt1247 10.1111/1758-2229.12188 10.1128/AEM.01938-12 10.1186/1746-1448-1-7 10.1038/npjbiofilms.2015.7 10.1016/j.tibtech.2006.09.002 10.1111/j.1462-2920.2012.02716.x 10.1371/journal.pone.0001778 10.1136/gut.2005.073817 10.1111/j.2041-1014.2009.00558.x 10.1038/ismej.2008.17 10.1371/journal.pone.0029913 10.1111/j.1574-6941.2011.01140.x 10.1002/pmic.201200576 10.1038/ismej.2013.234 10.1126/science.1112665 10.1038/ismej.2008.108 10.1038/ismej.2011.188 10.1126/science.1109070 10.1016/j.anaerobe.2013.11.009 10.1002/pmic.201400167 10.1021/cb400210q 10.1111/1462-2920.12488 10.1016/j.jprot.2014.02.006 10.1371/journal.pone.0034242 10.1038/nature05624 10.1371/journal.pone.0026542 10.1073/pnas.0907041107 10.1021/pr500936p 10.1038/ismej.2014.113 10.1126/science.1218344 10.1007/s00253-012-4157-2 10.1128/AEM.00969-14 10.1111/1758-2229.12239 10.1136/gutjnl-2012-303184 10.1002/ibd.21793 10.1128/mBio.00246-10 10.1111/j.1462-2920.2009.02007.x 10.1016/j.resmic.2010.04.010 10.1002/pmic.201300003 10.1038/ismej.2007.53 10.1073/pnas.1121198109 10.1641/0006-3568(2000)050[1062:LBASBA]2.0.CO;2 10.1073/pnas.1322132111 10.1007/s00442-004-1698-9 10.1038/ncomms6603 10.1021/pr060477v 10.1002/pmic.201100059 10.1073/pnas.142680199 10.1038/ismej.2012.28 10.1080/08927014.2014.977267 10.1371/journal.pone.0049138 10.1074/mcp.M114.046425 10.1126/science.1126593 10.1038/msb.2010.30 10.1038/ismej.2010.4 10.1038/ismej.2012.11 10.1038/ismej.2010.168 10.1038/ismej.2010.185 10.1038/ismej.2008.38 10.1007/s00248-006-9121-1 10.1111/1462-2920.12283 10.1038/ismej.2007.39 10.1038/ismej.2010.28 10.1038/nature14238 10.1021/pr501246w 10.1093/bioinformatics/btu267 10.1038/ismej.2009.139
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References	Hanson, B. T., Hewson, I., Madsen, E. L., Metaproteomic survey of six aquatic habitats: discovering the identities of microbial populations active in biogeochemical cycling. Microb. Ecol. 2014, 67, 520-539. Wilmes, P., Wexler, M., Bond, P. L., Metaproteomics provides functional insight into activated sludge wastewater treatment. PLoS ONE 2008, 3, e1778. Wilmes, P., Bond, P. L., The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms. Environ. Microbiol. 2004, 6, 911-920. Kohrs, F., Heyer, R., Magnussen, A., Benndorf, D. et al., Sample prefractionation with liquid isoelectric focusing enables in depth microbial metaproteome analysis of mesophilic and thermophilic biogas plants. Anaerobe 2014, 29, 59-67. Wilmes, P., Bowen, B. P., Thomas, B. C., Mueller, R. S. et al., Metabolome-proteome differentiation coupled to microbial divergence. MBio 2010, 1. Lo, I., Denef, V. J., Verberkmoes, N. C., Shah, M. B. et al., Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature 2007, 446, 537-541. Zhang, T., Shao, M.-F., Ye, L., 454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants. ISME J. 2011, 6, 1137-1147. Pérez-Cobas, A. E., Gosalbes, M. J., Friedrichs, A., Knecht, H. et al., Gut microbiota disturbance during antibiotic therapy: a multi-omic approach. Gut 2013, 62, 1591-1601. Hanson, B. T., Madsen, E. L., In situ expression of nitrite-dependent anaerobic methane oxidation proteins by Candidatus Methylomirabilis oxyfera co-occurring with expressed anammox proteins in a contaminated aquifer. Environ. Microbiol. Rep. 2015, 7, 252-264. Hansen, S. H., Stensballe, A., Nielsen, P. H., Herbst, F.-A., Metaproteomics: evaluation of protein extraction from activated sludge. Proteomics 2014, 14, 2535-2539. Bunge, J., Comment on "computational improvements reveal great bacterial diversity and high metal toxicity in soil." Science 2006, 313, 918c-918c. Schulze, W. X., Gleixner, G., Kaiser, K., Guggenberger, G. et al., A proteomic fingerprint of dissolved organic carbon and of soil particles. Oecologia 2004, 142, 335-343. Urich, T., Lanzén, A., Stokke, R., Pedersen, R. B. et al., Microbial community structure and functioning in marine sediments associated with diffuse hydrothermal venting assessed by integrated meta-omics. Environ. Microbiol. 2014, 16, 2699-2710. Daims, H., Taylor, M. W., Wagner, M., Wastewater treatment: a model system for microbial ecology. Trends Biotechnol. 2006, 24, 483-489. Mosier, A. C., Li, Z., Thomas, B. C., Hettich, R. L. et al., Elevated temperature alters proteomic responses of individual organisms within a biofilm community. ISME J. 2014, 9, 180-194. Armengaud, J., Marie Hartmann, E., Bland, C., Proteogenomics for environmental microbiology. Proteomics 2013, 13, 2731-2742. Li, Z., Wang, Y., Yao, Q., Justice, N. B. et al., Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community. Nat. Commun. 2014, 5, 1-11. Williams, T. J., Long, E., Evans, F., DeMaere, M. Z. et al., A metaproteomic assessment of winter and summer bacterioplankton from Antarctic Peninsula coastal surface waters. ISME J. 2012, 6, 1883-1900. Lauro, F. M., DeMaere, M. Z., Yau, S., Brown, M. V. et al., An integrative study of a meromictic lake ecosystem in Antarctica. ISME J. 2011, 5, 879-895. Manichanh, C., Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut 2006, 55, 205-211. Hawley, A. K., Brewer, H. M., Norbeck, A. D., Pasa-Tolic, L., Hallam, S. J., Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes. Proc. Natl. Acad. Sci. USA 2014, 111, 11395-11400. Gans, J., Wolinsky, M., Dunbar, J., Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 2005, 309, 1387-1390. Curtis, T. P., Sloan, W. T., Scannell, J. W., Estimating prokaryotic diversity and its limits. Proc. Natl. Acad. Sci. USA 2002, 99, 10494-10499. Albertsen, M., Stensballe, A., Nielsen, K. L., Nielsen, P. H., Digging into the extracellular matrix of a complex microbial community using a combined metagenomic and metaproteomic approach. Water Sci. Technol. 2013, 67, 1650-1656. Lacerda, C. M. R., Choe, L. H., Reardon, K. F., Metaproteomic analysis of a bacterial community response to cadmium exposure. J. Proteome Res. 2007, 6, 1145-1152. Silva, A. F., Carvalho, G., Soares, R., Coelho, A. V., Barreto Crespo, M. T., Step-by-step strategy for protein enrichment and proteome characterisation of extracellular polymeric substances in wastewater treatment systems. Appl. Microbiol. Biotechnol. 2012, 95, 767-776. Dong, H.-P., Hong, Y.-G., Lu, S., Xie, L.-Y., Metaproteomics reveals the major microbial players and their biogeochemical functions in a productive coastal system in the northern South China Sea. Environ. Microbiol. Rep. 2014, 6, 683-695. Verberkmoes, N. C., Russell, A. L., Shah, M., Godzik, A. et al., Shotgun metaproteomics of the human distal gut microbiota. ISME J. 2008, 3, 179-189. Kolmeder, C. A., deBeen, M., Nikkilä, J., Ritamo, I. et al., Comparative metaproteomics and diversity analysis of human intestinal microbiota testifies for its temporal stability and expression of core functions. PLoS ONE 2012, 7, e29913. Mueller, R. S., Denef, V. J., Kalnejais, L. H., Suttle, K. B. et al., Ecological distribution and population physiology defined by proteomics in a natural microbial community. Mol. Syst. Biol. 2010, 6, 1-12. Markert, S., Gardebrecht, A., Felbeck, H., Sievert, S. M. et al., Status quo in physiological proteomics of the uncultured Riftia pachyptila endosymbiont. Proteomics 2011, 11, 3106-3117. Jeans, C., Singer, S. W., Chan, C. S., Verberkmoes, N. C. et al., Cytochrome 572 is a conspicuous membrane protein with iron oxidation activity purified directly from a natural acidophilic microbial community. ISME J. 2008, 2, 542-550. Denef, V. J., Kalnejais, L. H., Mueller, R. S., Wilmes, P. et al., Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc. Natl. Acad. Sci. USA 2010, 107, 2383-2390. Penzlin, A., Lindner, M. S., Doellinger, J., Dabrowski, P. W. et al., Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics. Bioinformatics 2014, 30, i149-i156. Fischer, C. R., Bowen, B. P., Pan, C., Northen, T. R., Banfield, J. F., Stable-isotope probing reveals that hydrogen isotope fractionation in proteins and lipids in a microbial community are different and species-specific. ACS Chem. Biol. 2013, 8, 1755-1763. Aliaga Goltsman, D. S., Comolli, L. R., Thomas, B. C., Banfield, J.F., Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities. ISME J. 2015, 9, 1014-1023. Georges, A. A., El-Swais, H., Craig, S. E., Li, W. K. W., Walsh, D.A., Metaproteomic analysis of a winter to spring succession in coastal northwest Atlantic Ocean microbial plankton. ISME J. 2014, 8, 1301-1313. Kleiner, M., Wentrup, C., Lott, C., Teeling, H. et al., Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use. Proc. Natl. Acad. Sci. USA 2012, 109, E1173-E1182. Ram, R. J., Verberkmoes, N. C., Thelen, M. P., Tyson, G. W. et al., Community proteomics of a natural microbial biofilm. Science 2005, 308, 1915-1920. Martin, H. G., Ivanova, N., Kunin, V., Warnecke, F. et al., Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat. Biotechnol. 2006, 24, 1263-1269. Nicora, C. D., Anderson, B. J., Callister, S. J., Norbeck, A. D. et al., Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies. Proteomics 2013, 13, 2776-2785. Justice, N. B., Pan, C., Mueller, R., Spaulding, S. E. et al., Heterotrophic Archaea Contribute to Carbon Cycling in Low-pH, Suboxic Biofilm Communities. Appl. Environ. Microbiol. 2012, 78, 8321-8330. Stokke, R., Roalkvam, I., Lanzén, A., Haflidason, H., Steen, I.H., Integrated metagenomic and metaproteomic analyses of an ANME-1-dominated community in marine cold seep sediments. Environ. Microbiol. 2012, 14, 1333-1346. Rudney, J. D., Xie, H., Rhodus, N. L., Ondrey, F. G., Griffin, T. J., A metaproteomic analysis of the human salivary microbiota by three-dimensional peptide fractionation and tandem mass spectrometry. Mol. Oral Microbiol. 2010, 25, 38-49. Palmer, M. A., Covich, A. P., Lake, S., Biro, P. et al., Linkages between aquatic sediment biota and life above sediments as potential drivers of biodiversity and ecological processes. Bioscience 2000, 50, 1062-1075. Benndorf, D., Balcke, G. U., Harms, H., von Bergen, M., Functional metaproteome analysis of protein extracts from contaminated soil and groundwater. ISME J. 2007, 1, 224-234. Xiong, W., Giannone, R. J., Morowitz, M. J., Banfield, J. F., Hettich, R. L., Development of an enhanced metaproteomic approach for deepening the microbiome characterization of the human infant gut. J. Proteome Res. 2015, 14, 133-141. Herbst, F.-A., Bahr, A., Duarte, M., Pieper, D. H. et al., Elucidation of in situ polycyclic aromatic hydrocarbon degradation by functional metaproteomics (protein-SIP). Proteomics 2013, 13, 2910-2920. Lombard, N., Prestat, E., vanElsas, J. D., Simonet, P., Soil-specific limitations for access and analysis of soil microbial communities by metagenomics. FEMS Microbiol. Ecol. 2011, 78, 31-49. Ng, C., DeMaere, M. Z., Williams, T. J., Lauro, F. M. et al., Metaproteogenomic analysis of a dominant green sulfur bacterium from Ace Lake, Antarctica. ISME J. 2010, 4, 1002-1019. Gillet, L.C., Navarro, P., Tate, S., Roest, H. et al., Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol. Cell. 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References_xml	– reference: Rudney, J. D., Xie, H., Rhodus, N. L., Ondrey, F. G., Griffin, T. J., A metaproteomic analysis of the human salivary microbiota by three-dimensional peptide fractionation and tandem mass spectrometry. Mol. Oral Microbiol. 2010, 25, 38-49. – reference: Mocali, S., Benedetti, A., Exploring research frontiers in microbiology: the challenge of metagenomics in soil microbiology. Res. Microbiol. 2010, 161, 497-505. – reference: Mosier, A. C., Li, Z., Thomas, B. C., Hettich, R. L. et al., Elevated temperature alters proteomic responses of individual organisms within a biofilm community. ISME J. 2014, 9, 180-194. – reference: Presley, L. L., Ye, J., Li, X., LeBlanc, J. et al., Host-microbe relationships in inflammatory bowel disease detected by bacterial and metaproteomic analysis of the mucosal-luminal interface. Inflamm. Bowel Dis. 2012, 18, 409-417. – reference: Georges, A. A., El-Swais, H., Craig, S. E., Li, W. K. W., Walsh, D.A., Metaproteomic analysis of a winter to spring succession in coastal northwest Atlantic Ocean microbial plankton. ISME J. 2014, 8, 1301-1313. – reference: Morris, R. M., Nunn, B. L., Frazar, C., Goodlett, D. R. et al., Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction. ISME J. 2010, 4, 673-685. – reference: Justice, N. B., Li, Z., Wang, Y., Spaudling, S. E. et al., 15N- and 2H proteomic stable isotope probing links nitrogen flow to archaeal heterotrophic activity. Environ. Microbiol. 2014, 16, 3224-3237. – reference: Wilmes, P., Wexler, M., Bond, P. L., Metaproteomics provides functional insight into activated sludge wastewater treatment. PLoS ONE 2008, 3, e1778. – reference: Wexler, M., Richardson, D. J., Bond, P. L., Radiolabelled proteomics to determine differential functioning of Accumulibacter during the anaerobic and aerobic phases of a bioreactor operating for enhanced biological phosphorus removal. Environ. Microbiol. 2009, 11, 3029-3044. – reference: Kleiner, M., Wentrup, C., Lott, C., Teeling, H. et al., Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use. Proc. Natl. Acad. Sci. USA 2012, 109, E1173-E1182. – reference: Verberkmoes, N. C., Russell, A. L., Shah, M., Godzik, A. et al., Shotgun metaproteomics of the human distal gut microbiota. ISME J. 2008, 3, 179-189. – reference: Manichanh, C., Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut 2006, 55, 205-211. – reference: Markert, S., Gardebrecht, A., Felbeck, H., Sievert, S. M. et al., Status quo in physiological proteomics of the uncultured Riftia pachyptila endosymbiont. Proteomics 2011, 11, 3106-3117. – reference: Ng, C., DeMaere, M. Z., Williams, T. J., Lauro, F. M. et al., Metaproteogenomic analysis of a dominant green sulfur bacterium from Ace Lake, Antarctica. ISME J. 2010, 4, 1002-1019. – reference: Jeans, C., Singer, S. W., Chan, C. S., Verberkmoes, N. C. et al., Cytochrome 572 is a conspicuous membrane protein with iron oxidation activity purified directly from a natural acidophilic microbial community. ISME J. 2008, 2, 542-550. – reference: Silva, A. F., Carvalho, G., Soares, R., Coelho, A. V., Barreto Crespo, M. T., Step-by-step strategy for protein enrichment and proteome characterisation of extracellular polymeric substances in wastewater treatment systems. Appl. Microbiol. Biotechnol. 2012, 95, 767-776. – reference: Pérez-Cobas, A. E., Gosalbes, M. J., Friedrichs, A., Knecht, H. et al., Gut microbiota disturbance during antibiotic therapy: a multi-omic approach. Gut 2013, 62, 1591-1601. – reference: Li, X., LeBlanc, J., Truong, A., Vuthoori, R. et al., A Metaproteomic Approach to Study Human-Microbial Ecosystems at the Mucosal Luminal Interface. PLoS ONE 2011, 6, e26542. – reference: Mueller, R. S., Denef, V. J., Kalnejais, L. H., Suttle, K. B. et al., Ecological distribution and population physiology defined by proteomics in a natural microbial community. Mol. Syst. Biol. 2010, 6, 1-12. – reference: Pierre-Alain, M., Christophe, M., Severine, S., Houria, A. et al., Protein extraction and fingerprinting optimization of bacterial communities in natural environment. Microb. Ecol. 2007, 53, 426-434. – reference: Bastida, F., Hernández, T., García, C., Metaproteomics of soils from semiarid environment: functional and phylogenetic information obtained with different protein extraction methods. J. Proteomics 2014, 101, 31-42. – reference: Kohrs, F., Heyer, R., Magnussen, A., Benndorf, D. et al., Sample prefractionation with liquid isoelectric focusing enables in depth microbial metaproteome analysis of mesophilic and thermophilic biogas plants. Anaerobe 2014, 29, 59-67. – reference: Wilmes, P., Andersson, A. F., Lefsrud, M. G., Wexler, M. et al., Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal. ISME J. 2008, 2, 853-864. – reference: Teeling, H., Fuchs, B. M., Becher, D., Klockow, C. et al., Substrate-Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom. Science 2012, 336, 608-611. – reference: Martin, H. G., Ivanova, N., Kunin, V., Warnecke, F. et al., Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat. Biotechnol. 2006, 24, 1263-1269. – reference: Justice, N. B., Pan, C., Mueller, R., Spaulding, S. E. et al., Heterotrophic Archaea Contribute to Carbon Cycling in Low-pH, Suboxic Biofilm Communities. Appl. Environ. Microbiol. 2012, 78, 8321-8330. – reference: Erickson, A. R., Cantarel, B. L., Lamendella, R., Darzi, Y. et al., Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease. PLoS ONE 2012, 7, e49138. – reference: Park, C., Novak, J. T., Helm, R. F., Ahn, Y.-O., Esen, A., Evaluation of the extracellular proteins in full-scale activated sludges. Water Res. 2008, 42, 3879-3889. – reference: Ram, R. J., Verberkmoes, N. C., Thelen, M. P., Tyson, G. W. et al., Community proteomics of a natural microbial biofilm. Science 2005, 308, 1915-1920. – reference: Li, Z., Wang, Y., Yao, Q., Justice, N. B. et al., Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community. Nat. Commun. 2014, 5, 1-11. – reference: Benndorf, D., Balcke, G. U., Harms, H., von Bergen, M., Functional metaproteome analysis of protein extracts from contaminated soil and groundwater. ISME J. 2007, 1, 224-234. – reference: Muller, E. E. L., Pinel, N., Laczny, C. C., Hoopmann, M. R. et al., Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage. Nat. Commun. 2014, 5, 5603. – reference: Albertsen, M., Stensballe, A., Nielsen, K. L., Nielsen, P. H., Digging into the extracellular matrix of a complex microbial community using a combined metagenomic and metaproteomic approach. Water Sci. Technol. 2013, 67, 1650-1656. – reference: Roume, H., Heintz-Buschart, A., Muller, E. E. L., May, P. et al., Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks. npj Biofilms Microbiomes 2015, 1, 15007. – reference: Kolmeder, C. A., deBeen, M., Nikkilä, J., Ritamo, I. et al., Comparative metaproteomics and diversity analysis of human intestinal microbiota testifies for its temporal stability and expression of core functions. PLoS ONE 2012, 7, e29913. – reference: Lombard, N., Prestat, E., vanElsas, J. D., Simonet, P., Soil-specific limitations for access and analysis of soil microbial communities by metagenomics. FEMS Microbiol. Ecol. 2011, 78, 31-49. – reference: Roesch, L. F. W., Fulthorpe, R. R., Riva, A., Casella, G. et al., Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J. 2007, 1, 283-290. – reference: Kan, J., Hanson, T. E., Ginter, J. M., Wang, K., Chen, F., Metaproteomic analysis of Chesapeake Bay microbial communities. Saline Systems 2005, 1, 7. – reference: Herbst, F.-A., Bahr, A., Duarte, M., Pieper, D. H. et al., Elucidation of in situ polycyclic aromatic hydrocarbon degradation by functional metaproteomics (protein-SIP). Proteomics 2013, 13, 2910-2920. – reference: Hultman, J., Waldrop, M. P., Mackelprang, R., David, M. M. et al., Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes. Nature 2015, 521, 208-212. – reference: Nicora, C. D., Anderson, B. J., Callister, S. J., Norbeck, A. D. et al., Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies. Proteomics 2013, 13, 2776-2785. – reference: Volkov, I., Comment on "computational improvements reveal great bacterial diversity and high metal toxicity in soil." Science 2006, 313, 918a. – reference: Xiong, W., Giannone, R. J., Morowitz, M. J., Banfield, J. F., Hettich, R. L., Development of an enhanced metaproteomic approach for deepening the microbiome characterization of the human infant gut. J. Proteome Res. 2015, 14, 133-141. – reference: Gans, J., Wolinsky, M., Dunbar, J., Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 2005, 309, 1387-1390. – reference: Denef, V. J., Kalnejais, L. H., Mueller, R. S., Wilmes, P. et al., Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc. Natl. Acad. Sci. USA 2010, 107, 2383-2390. – reference: Curtis, T. P., Sloan, W. T., Scannell, J. W., Estimating prokaryotic diversity and its limits. Proc. Natl. Acad. Sci. USA 2002, 99, 10494-10499. – reference: Hanson, B. T., Hewson, I., Madsen, E. L., Metaproteomic survey of six aquatic habitats: discovering the identities of microbial populations active in biogeochemical cycling. Microb. Ecol. 2014, 67, 520-539. – reference: Schulze, W. X., Gleixner, G., Kaiser, K., Guggenberger, G. et al., A proteomic fingerprint of dissolved organic carbon and of soil particles. Oecologia 2004, 142, 335-343. – reference: Krisp, C., Yang, H., van Soest, R., Molloy, M.P., Online peptide fractionation using a multiphasic microfluidic liquid chromatography chip improves reproducibility and detection limits for quantitation in discovery and targeted proteomics. Mol. Cell. Proteomics 2015, 14, 1708-1719. – reference: Lauro, F. M., DeMaere, M. Z., Yau, S., Brown, M. V. et al., An integrative study of a meromictic lake ecosystem in Antarctica. ISME J. 2011, 5, 879-895. – reference: Wilmes, P., Bowen, B. P., Thomas, B. C., Mueller, R. S. et al., Metabolome-proteome differentiation coupled to microbial divergence. MBio 2010, 1. – reference: Lo, I., Denef, V. J., Verberkmoes, N. C., Shah, M. B. et al., Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature 2007, 446, 537-541. – reference: Leary, D. H., Li, R. W., Hamdan, L. J., Hervey, W. J. et al., Integrated metagenomic and metaproteomic analyses of marine biofilm communities. Biofouling 2014, 30, 1211-1223. – reference: Huse, S. M., Ye, Y., Zhou, Y., Fodor, A. A., A core human microbiome as viewed through 16S rRNA sequence clusters. PLoS ONE 2012, 7, e34242. – reference: Bao, Z., Okubo, T., Kubota, K., Kasahara, Y. et al., Metaproteomic identification of diazotrophic methanotrophs and their localization in root tissues of field-grown rice plants. Appl. Environ. Microbiol. 2014, 80, 5043-5052. – reference: Belnap, C. P., Pan, C., Verberkmoes, N. C., Power, M. E. et al., Cultivation and quantitative proteomic analyses of acidophilic microbial communities. ISME J. 2009, 4, 520-530. – reference: Hawley, A. K., Brewer, H. M., Norbeck, A. D., Pasa-Tolic, L., Hallam, S. J., Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes. Proc. Natl. Acad. Sci. USA 2014, 111, 11395-11400. – reference: Daims, H., Taylor, M. W., Wagner, M., Wastewater treatment: a model system for microbial ecology. Trends Biotechnol. 2006, 24, 483-489. – reference: Wilmes, P., Bond, P. L., The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms. Environ. Microbiol. 2004, 6, 911-920. – reference: Williams, T. J., Long, E., Evans, F., DeMaere, M. Z. et al., A metaproteomic assessment of winter and summer bacterioplankton from Antarctic Peninsula coastal surface waters. ISME J. 2012, 6, 1883-1900. – reference: Hanson, B. T., Madsen, E. L., In situ expression of nitrite-dependent anaerobic methane oxidation proteins by Candidatus Methylomirabilis oxyfera co-occurring with expressed anammox proteins in a contaminated aquifer. Environ. Microbiol. Rep. 2015, 7, 252-264. – reference: Collado, N., Buttiglieri, G., Kolvenbach, B. A., Comas, J. et al., Exploring the potential of applying proteomics for tracking bisphenol A and nonylphenol degradation in activated sludge. Chemosphere 2013, 90, 2309-2314. – reference: Urich, T., Lanzén, A., Stokke, R., Pedersen, R. B. et al., Microbial community structure and functioning in marine sediments associated with diffuse hydrothermal venting assessed by integrated meta-omics. Environ. Microbiol. 2014, 16, 2699-2710. – reference: Palmer, M. A., Covich, A. P., Lake, S., Biro, P. et al., Linkages between aquatic sediment biota and life above sediments as potential drivers of biodiversity and ecological processes. Bioscience 2000, 50, 1062-1075. – reference: Muth, T., Behne, A., Heyer, R., Kohrs, F. et al., The MetaProteomeAnalyzer: a powerful open-source software suite for metaproteomics data analysis and interpretation. J. Proteome Res. 2015, 14, 1557-1565. – reference: Lacerda, C. M. R., Choe, L. H., Reardon, K. F., Metaproteomic analysis of a bacterial community response to cadmium exposure. J. Proteome Res. 2007, 6, 1145-1152. – reference: Hansen, S. H., Stensballe, A., Nielsen, P. H., Herbst, F.-A., Metaproteomics: evaluation of protein extraction from activated sludge. Proteomics 2014, 14, 2535-2539. – reference: Aliaga Goltsman, D. S., Comolli, L. R., Thomas, B. C., Banfield, J.F., Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities. ISME J. 2015, 9, 1014-1023. – reference: Bunge, J., Comment on "computational improvements reveal great bacterial diversity and high metal toxicity in soil." Science 2006, 313, 918c-918c. – reference: Dong, H.-P., Hong, Y.-G., Lu, S., Xie, L.-Y., Metaproteomics reveals the major microbial players and their biogeochemical functions in a productive coastal system in the northern South China Sea. Environ. Microbiol. Rep. 2014, 6, 683-695. – reference: Gillet, L.C., Navarro, P., Tate, S., Roest, H. et al., Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol. Cell. Proteomics 2012, O111.016717. – reference: Penzlin, A., Lindner, M. S., Doellinger, J., Dabrowski, P. W. et al., Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics. Bioinformatics 2014, 30, i149-i156. – reference: Zhang, T., Shao, M.-F., Ye, L., 454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants. ISME J. 2011, 6, 1137-1147. – reference: Stokke, R., Roalkvam, I., Lanzén, A., Haflidason, H., Steen, I.H., Integrated metagenomic and metaproteomic analyses of an ANME-1-dominated community in marine cold seep sediments. Environ. Microbiol. 2012, 14, 1333-1346. – reference: Armengaud, J., Marie Hartmann, E., Bland, C., Proteogenomics for environmental microbiology. Proteomics 2013, 13, 2731-2742. – reference: Fischer, C. R., Bowen, B. P., Pan, C., Northen, T. R., Banfield, J. F., Stable-isotope probing reveals that hydrogen isotope fractionation in proteins and lipids in a microbial community are different and species-specific. ACS Chem. Biol. 2013, 8, 1755-1763. – reference: Sowell, S. M., Abraham, P. E., Shah, M., Verberkmoes, N. C. et al., Environmental proteomics of microbial plankton in a highly productive coastal upwelling system. ISME J 2011, 5, 856-865. – volume: 142 start-page: 335 year: 2004 end-page: 343 article-title: A proteomic fingerprint of dissolved organic carbon and of soil particles publication-title: Oecologia – volume: 4 start-page: 520 year: 2009 end-page: 530 article-title: Cultivation and quantitative proteomic analyses of acidophilic microbial communities publication-title: ISME J. – volume: 4 start-page: 1002 year: 2010 end-page: 1019 article-title: Metaproteogenomic analysis of a dominant green sulfur bacterium from Ace Lake, Antarctica publication-title: ISME J. – volume: 313 start-page: 918a year: 2006 article-title: Comment on “computational improvements reveal great bacterial diversity and high metal toxicity in soil publication-title: Science – volume: 107 start-page: 2383 year: 2010 end-page: 2390 article-title: Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities publication-title: Proc. Natl. Acad. Sci. USA – volume: 161 start-page: 497 year: 2010 end-page: 505 article-title: Exploring research frontiers in microbiology: the challenge of metagenomics in soil microbiology publication-title: Res. Microbiol. – volume: 16 start-page: 2699 year: 2014 end-page: 2710 article-title: Microbial community structure and functioning in marine sediments associated with diffuse hydrothermal venting assessed by integrated meta‐omics publication-title: Environ. Microbiol. – volume: 42 start-page: 3879 year: 2008 end-page: 3889 article-title: Evaluation of the extracellular proteins in full‐scale activated sludges publication-title: Water Res. – volume: 14 start-page: 1333 year: 2012 end-page: 1346 article-title: Integrated metagenomic and metaproteomic analyses of an ANME‐1‐dominated community in marine cold seep sediments publication-title: Environ. Microbiol. – volume: 18 start-page: 409 year: 2012 end-page: 417 article-title: Host–microbe relationships in inflammatory bowel disease detected by bacterial and metaproteomic analysis of the mucosal–luminal interface publication-title: Inflamm. Bowel Dis. – volume: 6 start-page: 683 year: 2014 end-page: 695 article-title: Metaproteomics reveals the major microbial players and their biogeochemical functions in a productive coastal system in the northern South China Sea publication-title: Environ. Microbiol. Rep. – volume: 111 start-page: 11395 year: 2014 end-page: 11400 article-title: Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes publication-title: Proc. Natl. Acad. Sci. USA – volume: 6 start-page: 1749 year: 2012 end-page: 1762 article-title: Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions – volume: 7 start-page: e49138 year: 2012 article-title: Integrated Metagenomics/Metaproteomics Reveals Human Host‐Microbiota Signatures of Crohn's Disease publication-title: PLoS ONE – volume: 29 start-page: 59 year: 2014 end-page: 67 article-title: Sample prefractionation with liquid isoelectric focusing enables in depth microbial metaproteome analysis of mesophilic and thermophilic biogas plants publication-title: Anaerobe – volume: 313 start-page: 918c year: 2006 end-page: 918c article-title: Comment on “computational improvements reveal great bacterial diversity and high metal toxicity in soil publication-title: Science – volume: 99 start-page: 10494 year: 2002 end-page: 10499 article-title: Estimating prokaryotic diversity and its limits publication-title: Proc. Natl. Acad. Sci. USA – volume: 521 start-page: 208 year: 2015 end-page: 212 article-title: Multi‐omics of permafrost, active layer and thermokarst bog soil microbiomes publication-title: Nature – volume: 336 start-page: 608 year: 2012 end-page: 611 article-title: Substrate‐Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom publication-title: Science – volume: 1 start-page: 283 year: 2007 end-page: 290 article-title: Pyrosequencing enumerates and contrasts soil microbial diversity publication-title: ISME J. – volume: 67 start-page: 1650 year: 2013 end-page: 1656 article-title: Digging into the extracellular matrix of a complex microbial community using a combined metagenomic and metaproteomic approach publication-title: Water Sci. Technol. – volume: 25 start-page: 38 year: 2010 end-page: 49 article-title: A metaproteomic analysis of the human salivary microbiota by three‐dimensional peptide fractionation and tandem mass spectrometry publication-title: Mol. Oral Microbiol. – volume: 4 start-page: 673 year: 2010 end-page: 685 article-title: Comparative metaproteomics reveals ocean‐scale shifts in microbial nutrient utilization and energy transduction publication-title: ISME J. – volume: 6 start-page: 911 year: 2004 end-page: 920 article-title: The application of two‐dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms publication-title: Environ. Microbiol. – volume: 1 start-page: 224 year: 2007 end-page: 234 article-title: Functional metaproteome analysis of protein extracts from contaminated soil and groundwater publication-title: ISME J. – volume: 62 start-page: 1591 year: 2013 end-page: 1601 article-title: Gut microbiota disturbance during antibiotic therapy: a multi‐omic approach publication-title: Gut – volume: 24 start-page: 1263 year: 2006 end-page: 1269 article-title: Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities publication-title: Nat. Biotechnol. – volume: 3 start-page: e1778 year: 2008 article-title: Metaproteomics provides functional insight into activated sludge wastewater treatment publication-title: PLoS ONE – volume: 11 start-page: 3029 year: 2009 end-page: 3044 article-title: Radiolabelled proteomics to determine differential functioning of Accumulibacter during the anaerobic and aerobic phases of a bioreactor operating for enhanced biological phosphorus removal publication-title: Environ. Microbiol. – volume: 5 start-page: 879 year: 2011 end-page: 895 article-title: An integrative study of a meromictic lake ecosystem in Antarctica publication-title: ISME J. – volume: 7 start-page: 252 year: 2015 end-page: 264 article-title: In situ expression of nitrite‐dependent anaerobic methane oxidation proteins by Candidatus Methylomirabilis oxyfera co‐occurring with expressed anammox proteins in a contaminated aquifer publication-title: Environ. Microbiol. Rep. – volume: 6 start-page: 1883 year: 2012 end-page: 1900 article-title: A metaproteomic assessment of winter and summer bacterioplankton from Antarctic Peninsula coastal surface waters publication-title: ISME J. – volume: 24 start-page: 483 year: 2006 end-page: 489 article-title: Wastewater treatment: a model system for microbial ecology publication-title: Trends Biotechnol. – volume: 55 start-page: 205 year: 2006 end-page: 211 article-title: Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach publication-title: Gut – volume: 13 start-page: 2776 year: 2013 end-page: 2785 article-title: Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies publication-title: Proteomics – volume: 1 start-page: 15007 year: 2015 article-title: Comparative integrated omics: identification of key functionalities in microbial community‐wide metabolic networks publication-title: npj Biofilms Microbiomes – volume: 308 start-page: 1915 year: 2005 end-page: 1920 article-title: Community proteomics of a natural microbial biofilm publication-title: Science – volume: 2 start-page: 853 year: 2008 end-page: 864 article-title: Community proteogenomics highlights microbial strain‐variant protein expression within activated sludge performing enhanced biological phosphorus removal publication-title: ISME J. – volume: 78 start-page: 8321 year: 2012 end-page: 8330 article-title: Heterotrophic Archaea Contribute to Carbon Cycling in Low‐pH, Suboxic Biofilm Communities publication-title: Appl. Environ. Microbiol. – volume: 446 start-page: 537 year: 2007 end-page: 541 article-title: Strain‐resolved community proteomics reveals recombining genomes of acidophilic bacteria publication-title: Nature – volume: 13 start-page: 2910 year: 2013 end-page: 2920 article-title: Elucidation of in situ polycyclic aromatic hydrocarbon degradation by functional metaproteomics (protein‐SIP) publication-title: Proteomics – volume: 30 start-page: i149 year: 2014 end-page: i156 article-title: Pipasic: similarity and expression correction for strain‐level identification and quantification in metaproteomics publication-title: Bioinformatics – volume: 78 start-page: 31 year: 2011 end-page: 49 article-title: Soil‐specific limitations for access and analysis of soil microbial communities by metagenomics publication-title: FEMS Microbiol. Ecol. – volume: 14 start-page: 2535 year: 2014 end-page: 2539 article-title: Metaproteomics: evaluation of protein extraction from activated sludge publication-title: Proteomics – volume: 6 start-page: 1145 year: 2007 end-page: 1152 article-title: Metaproteomic analysis of a bacterial community response to cadmium exposure publication-title: J. Proteome Res. – volume: 109 start-page: E1173 year: 2012 end-page: E1182 article-title: Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use publication-title: Proc. Natl. Acad. Sci. USA – volume: 90 start-page: 2309 year: 2013 end-page: 2314 article-title: Exploring the potential of applying proteomics for tracking bisphenol A and nonylphenol degradation in activated sludge publication-title: Chemosphere – volume: 6 start-page: e26542 year: 2011 article-title: A Metaproteomic Approach to Study Human‐Microbial Ecosystems at the Mucosal Luminal Interface publication-title: PLoS ONE – volume: 2 start-page: 542 year: 2008 end-page: 550 article-title: Cytochrome 572 is a conspicuous membrane protein with iron oxidation activity purified directly from a natural acidophilic microbial community publication-title: ISME J. – volume: 67 start-page: 520 year: 2014 end-page: 539 article-title: Metaproteomic survey of six aquatic habitats: discovering the identities of microbial populations active in biogeochemical cycling publication-title: Microb. Ecol. – volume: 1 start-page: 7 year: 2005 article-title: Metaproteomic analysis of Chesapeake Bay microbial communities publication-title: Saline Systems – volume: 8 start-page: 1755 year: 2013 end-page: 1763 article-title: Stable‐isotope probing reveals that hydrogen isotope fractionation in proteins and lipids in a microbial community are different and species‐specific publication-title: ACS Chem. Biol. – volume: 8 start-page: 1301 year: 2014 end-page: 1313 article-title: Metaproteomic analysis of a winter to spring succession in coastal northwest Atlantic Ocean microbial plankton publication-title: ISME J. – volume: 7 start-page: e34242 year: 2012 article-title: A core human microbiome as viewed through 16S rRNA sequence clusters publication-title: PLoS ONE – volume: 9 start-page: 180 year: 2014 end-page: 194 article-title: Elevated temperature alters proteomic responses of individual organisms within a biofilm community publication-title: ISME J. – volume: 6 start-page: 1137 year: 2011 end-page: 1147 article-title: 454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants publication-title: ISME J. – volume: 13 start-page: 2731 year: 2013 end-page: 2742 article-title: Proteogenomics for environmental microbiology publication-title: Proteomics – volume: 53 start-page: 426 year: 2007 end-page: 434 article-title: Protein extraction and fingerprinting optimization of bacterial communities in natural environment publication-title: Microb. Ecol. – volume: 7 start-page: e29913 year: 2012 article-title: Comparative metaproteomics and diversity analysis of human intestinal microbiota testifies for its temporal stability and expression of core functions publication-title: PLoS ONE – volume: 101 start-page: 31 year: 2014 end-page: 42 article-title: Metaproteomics of soils from semiarid environment: functional and phylogenetic information obtained with different protein extraction methods publication-title: J. Proteomics – volume: 11 start-page: 3106 year: 2011 end-page: 3117 article-title: Status quo in physiological proteomics of the uncultured Riftia pachyptila endosymbiont publication-title: Proteomics – volume: 9 start-page: 1014 year: 2015 end-page: 1023 article-title: Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities publication-title: ISME J. – volume: 14 start-page: 133 year: 2015 end-page: 141 article-title: Development of an enhanced metaproteomic approach for deepening the microbiome characterization of the human infant gut publication-title: J. Proteome Res. – year: 2012 article-title: Targeted data extraction of the MS/MS spectra generated by data‐independent acquisition: a new concept for consistent and accurate proteome analysis publication-title: Mol. Cell. Proteomics – volume: 16 start-page: 3224 year: 2014 end-page: 3237 article-title: 15N‐ and 2H proteomic stable isotope probing links nitrogen flow to archaeal heterotrophic activity publication-title: Environ. Microbiol. – volume: 6 start-page: 1 year: 2010 end-page: 12 article-title: Ecological distribution and population physiology defined by proteomics in a natural microbial community publication-title: Mol. Syst. Biol. – volume: 3 start-page: 179 year: 2008 end-page: 189 article-title: Shotgun metaproteomics of the human distal gut microbiota publication-title: ISME J. – volume: 309 start-page: 1387 year: 2005 end-page: 1390 article-title: Computational improvements reveal great bacterial diversity and high metal toxicity in soil publication-title: Science – volume: 14 start-page: 1708 year: 2015 end-page: 1719 article-title: Online peptide fractionation using a multiphasic microfluidic liquid chromatography chip improves reproducibility and detection limits for quantitation in discovery and targeted proteomics publication-title: Mol. Cell. Proteomics – volume: 30 start-page: 1211 year: 2014 end-page: 1223 article-title: Integrated metagenomic and metaproteomic analyses of marine biofilm communities publication-title: Biofouling – volume: 80 start-page: 5043 year: 2014 end-page: 5052 article-title: Metaproteomic identification of diazotrophic methanotrophs and their localization in root tissues of field‐grown rice plants publication-title: Appl. Environ. Microbiol. – volume: 1 year: 2010 article-title: Metabolome‐proteome differentiation coupled to microbial divergence publication-title: MBio – volume: 50 start-page: 1062 year: 2000 end-page: 1075 article-title: Linkages between aquatic sediment biota and life above sediments as potential drivers of biodiversity and ecological processes publication-title: Bioscience – volume: 5 start-page: 5603 year: 2014 article-title: Community‐integrated omics links dominance of a microbial generalist to fine‐tuned resource usage publication-title: Nat. Commun. – volume: 5 start-page: 1 year: 2014 end-page: 11 article-title: Diverse and divergent protein post‐translational modifications in two growth stages of a natural microbial community publication-title: Nat. Commun. – volume: 5 start-page: 856 year: 2011 end-page: 865 article-title: Environmental proteomics of microbial plankton in a highly productive coastal upwelling system publication-title: ISME J – volume: 14 start-page: 1557 year: 2015 end-page: 1565 article-title: The MetaProteomeAnalyzer: a powerful open‐source software suite for metaproteomics data analysis and interpretation publication-title: J. Proteome Res. – volume: 95 start-page: 767 year: 2012 end-page: 776 article-title: Step‐by‐step strategy for protein enrichment and proteome characterisation of extracellular polymeric substances in wastewater treatment systems publication-title: Appl. Microbiol. Biotechnol. – ident: e_1_2_10_26_1 doi: 10.1038/ismej.2014.200 – ident: e_1_2_10_13_1 doi: 10.2166/wst.2013.030 – ident: e_1_2_10_50_1 doi: 10.1126/science.1121225 – ident: e_1_2_10_46_1 doi: 10.1002/pmic.201200569 – ident: e_1_2_10_11_1 doi: 10.1016/j.chemosphere.2012.10.002 – ident: e_1_2_10_42_1 doi: 10.1007/s00248-013-0346-5 – ident: e_1_2_10_3_1 doi: 10.1111/j.1462-2920.2004.00687.x – ident: e_1_2_10_14_1 doi: 10.1016/j.watres.2008.05.014 – ident: e_1_2_10_7_1 doi: 10.1038/nbt1247 – ident: e_1_2_10_28_1 doi: 10.1111/1758-2229.12188 – ident: e_1_2_10_20_1 doi: 10.1128/AEM.01938-12 – ident: e_1_2_10_27_1 doi: 10.1186/1746-1448-1-7 – ident: e_1_2_10_70_1 doi: 10.1038/npjbiofilms.2015.7 – ident: e_1_2_10_5_1 doi: 10.1016/j.tibtech.2006.09.002 – ident: e_1_2_10_38_1 doi: 10.1111/j.1462-2920.2012.02716.x – ident: e_1_2_10_6_1 doi: 10.1371/journal.pone.0001778 – ident: e_1_2_10_62_1 doi: 10.1136/gut.2005.073817 – ident: e_1_2_10_79_1 doi: 10.1111/j.2041-1014.2009.00558.x – ident: e_1_2_10_16_1 doi: 10.1038/ismej.2008.17 – ident: e_1_2_10_64_1 doi: 10.1371/journal.pone.0029913 – ident: e_1_2_10_48_1 doi: 10.1111/j.1574-6941.2011.01140.x – ident: e_1_2_10_2_1 doi: 10.1002/pmic.201200576 – ident: e_1_2_10_29_1 doi: 10.1038/ismej.2013.234 – ident: e_1_2_10_51_1 doi: 10.1126/science.1112665 – year: 2012 ident: e_1_2_10_67_1 article-title: Targeted data extraction of the MS/MS spectra generated by data‐independent acquisition: a new concept for consistent and accurate proteome analysis publication-title: Mol. Cell. Proteomics – ident: e_1_2_10_60_1 doi: 10.1038/ismej.2008.108 – ident: e_1_2_10_74_1 doi: 10.1038/ismej.2011.188 – ident: e_1_2_10_4_1 doi: 10.1126/science.1109070 – ident: e_1_2_10_66_1 doi: 10.1016/j.anaerobe.2013.11.009 – ident: e_1_2_10_12_1 doi: 10.1002/pmic.201400167 – ident: e_1_2_10_21_1 doi: 10.1021/cb400210q – ident: e_1_2_10_22_1 doi: 10.1111/1462-2920.12488 – ident: e_1_2_10_52_1 doi: 10.1016/j.jprot.2014.02.006 – ident: e_1_2_10_78_1 doi: 10.1371/journal.pone.0034242 – ident: e_1_2_10_17_1 doi: 10.1038/nature05624 – ident: e_1_2_10_58_1 doi: 10.1371/journal.pone.0026542 – ident: e_1_2_10_18_1 doi: 10.1073/pnas.0907041107 – ident: e_1_2_10_61_1 doi: 10.1021/pr500936p – ident: e_1_2_10_25_1 doi: 10.1038/ismej.2014.113 – ident: e_1_2_10_32_1 doi: 10.1126/science.1218344 – ident: e_1_2_10_15_1 doi: 10.1007/s00253-012-4157-2 – ident: e_1_2_10_56_1 doi: 10.1128/AEM.00969-14 – ident: e_1_2_10_45_1 doi: 10.1111/1758-2229.12239 – ident: e_1_2_10_65_1 doi: 10.1136/gutjnl-2012-303184 – ident: e_1_2_10_59_1 doi: 10.1002/ibd.21793 – ident: e_1_2_10_73_1 doi: 10.1128/mBio.00246-10 – ident: e_1_2_10_9_1 doi: 10.1111/j.1462-2920.2009.02007.x – ident: e_1_2_10_47_1 doi: 10.1016/j.resmic.2010.04.010 – ident: e_1_2_10_53_1 doi: 10.1002/pmic.201300003 – ident: e_1_2_10_77_1 doi: 10.1038/ismej.2007.53 – ident: e_1_2_10_35_1 doi: 10.1073/pnas.1121198109 – ident: e_1_2_10_76_1 doi: 10.1641/0006-3568(2000)050[1062:LBASBA]2.0.CO;2 – ident: e_1_2_10_33_1 doi: 10.1073/pnas.1322132111 – ident: e_1_2_10_54_1 doi: 10.1007/s00442-004-1698-9 – ident: e_1_2_10_69_1 doi: 10.1038/ncomms6603 – ident: e_1_2_10_10_1 doi: 10.1021/pr060477v – ident: e_1_2_10_36_1 doi: 10.1002/pmic.201100059 – ident: e_1_2_10_75_1 doi: 10.1073/pnas.142680199 – ident: e_1_2_10_39_1 doi: 10.1038/ismej.2012.28 – volume: 5 start-page: 1 year: 2014 ident: e_1_2_10_23_1 article-title: Diverse and divergent protein post‐translational modifications in two growth stages of a natural microbial community publication-title: Nat. Commun. – ident: e_1_2_10_34_1 doi: 10.1080/08927014.2014.977267 – ident: e_1_2_10_63_1 doi: 10.1371/journal.pone.0049138 – ident: e_1_2_10_68_1 doi: 10.1074/mcp.M114.046425 – ident: e_1_2_10_49_1 doi: 10.1126/science.1126593 – ident: e_1_2_10_19_1 doi: 10.1038/msb.2010.30 – ident: e_1_2_10_31_1 doi: 10.1038/ismej.2010.4 – ident: e_1_2_10_55_1 doi: 10.1038/ismej.2012.11 – ident: e_1_2_10_30_1 doi: 10.1038/ismej.2010.168 – ident: e_1_2_10_43_1 doi: 10.1038/ismej.2010.185 – ident: e_1_2_10_8_1 doi: 10.1038/ismej.2008.38 – ident: e_1_2_10_40_1 doi: 10.1007/s00248-006-9121-1 – ident: e_1_2_10_37_1 doi: 10.1111/1462-2920.12283 – ident: e_1_2_10_41_1 doi: 10.1038/ismej.2007.39 – ident: e_1_2_10_44_1 doi: 10.1038/ismej.2010.28 – ident: e_1_2_10_57_1 doi: 10.1038/nature14238 – ident: e_1_2_10_71_1 doi: 10.1021/pr501246w – ident: e_1_2_10_72_1 doi: 10.1093/bioinformatics/btu267 – ident: e_1_2_10_24_1 doi: 10.1038/ismej.2009.139
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Snippet	We are living through exciting times during which we are able to unravel the “microbial dark matter” in and around us through the application of... We are living through exciting times during which we are able to unravel the "microbial dark matter" in and around us through the application of...
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SubjectTerms	Acid mine drainage Activated sludge Betaproteobacteria - genetics Biofilms Catalysis Chemical analysis Communities Community composition Cyanobacteria - genetics Dark matter Ecological function Ecosystem Fresh Water Genotypes Humans Integrated omics Intestinal microflora Leptospiraceae - genetics Metagenomics Metaproteomics Microbial activity Microbial community Microbial systems ecology Microbiology Microbiota Microorganisms Phenotypes Proteins Proteome - genetics Proteomics Seawater Soil Microbiology Viewpoint Water analysis
Title	A decade of metaproteomics: Where we stand and what the future holds
URI	https://api.istex.fr/ark:/67375/WNG-13J8VB60-T/fulltext.pdf https://onlinelibrary.wiley.com/doi/abs/10.1002%2Fpmic.201500183 https://www.ncbi.nlm.nih.gov/pubmed/26315987 https://www.proquest.com/docview/2035648986 https://www.proquest.com/docview/1722927718 https://www.proquest.com/docview/1727680974 https://pubmed.ncbi.nlm.nih.gov/PMC5049639
Volume	15
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