메뉴 건너뛰기




Volumn 15, Issue 20, 2015, Pages 3544-3552

Colonic metaproteomic signatures of active bacteria and the host in obesity

Author keywords

Composition; Intestinal microbiota; Metaproteomics; Microbiology; Obesity

Indexed keywords

PROTEOME;

EID: 84944147974     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201500049     Document Type: Article
Times cited : (64)

References (44)
  • 1
    • 84943428908 scopus 로고    scopus 로고
    • Obesity - a disease with many aetiologies disguised in the same oversized phenotype: has the overeating theory failed?
    • ePub ahead of print
    • Stenvinkel, P., Obesity - a disease with many aetiologies disguised in the same oversized phenotype: has the overeating theory failed? Nephrol. Dial. Transplant. 2014, ePub ahead of print, doi: 10.1093/ndt/gfu338.
    • (2014) Nephrol. Dial. Transplant.
    • Stenvinkel, P.1
  • 2
    • 84897138661 scopus 로고    scopus 로고
    • A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter
    • Finucane, M. M., Sharpton, T. J., Laurent, T. J., Pollard, K. S., A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter. PLoS One 2014, 9, e84689.
    • (2014) PLoS One , vol.9 , pp. e84689
    • Finucane, M.M.1    Sharpton, T.J.2    Laurent, T.J.3    Pollard, K.S.4
  • 3
    • 84909987763 scopus 로고    scopus 로고
    • Gut microbiota and obesity: role in aetiology and potential therapeutic target
    • Moran, C. P., Shanahan, F., Gut microbiota and obesity: role in aetiology and potential therapeutic target. Best Pract. Res. Clin. Gastroenterol. 2014, 28, 585-597.
    • (2014) Best Pract. Res. Clin. Gastroenterol. , vol.28 , pp. 585-597
    • Moran, C.P.1    Shanahan, F.2
  • 4
    • 84866168894 scopus 로고    scopus 로고
    • Functional interactions between the gut microbiota and host metabolism
    • Tremaroli, V., Bäckhed, F., Functional interactions between the gut microbiota and host metabolism. Nature 2012, 489, 242-249.
    • (2012) Nature , vol.489 , pp. 242-249
    • Tremaroli, V.1    Bäckhed, F.2
  • 5
    • 84875370244 scopus 로고    scopus 로고
    • Microbiota conservation and BMI signatures in adult monozygotic twins
    • Tims, S., Derom, C., Jonkers, D. M., Vlietinck, R. et al., Microbiota conservation and BMI signatures in adult monozygotic twins. ISME J. 2012, 7, 707-717.
    • (2012) ISME J , vol.7 , pp. 707-717
    • Tims, S.1    Derom, C.2    Jonkers, D.M.3    Vlietinck, R.4
  • 6
    • 84908348194 scopus 로고    scopus 로고
    • Meta-analyses of human gut microbes associated with obesity and IBD
    • Walters, W. A., Xu, Z., Knight, R., Meta-analyses of human gut microbes associated with obesity and IBD. FEBS Lett. 2014, 588, 4223-4233.
    • (2014) FEBS Lett , vol.588 , pp. 4223-4233
    • Walters, W.A.1    Xu, Z.2    Knight, R.3
  • 7
    • 84862590343 scopus 로고    scopus 로고
    • The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates
    • Zoetendal, E. G., Raes, J., van den Bogert, B., Arumugam, M. et al., The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. ISME J. 2012, 6, 1415-1426.
    • (2012) ISME J , vol.6 , pp. 1415-1426
    • Zoetendal, E.G.1    Raes, J.2    van den Bogert, B.3    Arumugam, M.4
  • 8
  • 9
    • 58549089276 scopus 로고    scopus 로고
    • Shotgun metaproteomics of the human distal gut microbiota
    • Verberkmoes, N. C., Russell, A. L., Shah, M., Godzik, A. et al., Shotgun metaproteomics of the human distal gut microbiota. ISME J. 2009, 3, 179-189.
    • (2009) ISME J , vol.3 , pp. 179-189
    • Verberkmoes, N.C.1    Russell, A.L.2    Shah, M.3    Godzik, A.4
  • 10
    • 78650780115 scopus 로고    scopus 로고
    • An iterative workflow for mining the human intestinal metaproteome
    • Rooijers, K., Kolmeder, C., Juste, C., Doré, J. et al., An iterative workflow for mining the human intestinal metaproteome. BMC Genomics 2011, 12, 1-11.
    • (2011) BMC Genomics , vol.12 , pp. 1-11
    • Rooijers, K.1    Kolmeder, C.2    Juste, C.3    Doré, J.4
  • 11
    • 84855915896 scopus 로고    scopus 로고
    • Comparative metaproteomics and diversity analysis of human intestinal microbiota testifies for its temporal stability and expression of core functions
    • Kolmeder, C. A., de Been, 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.
    • (2012) PLoS One , vol.7 , pp. e29913
    • Kolmeder, C.A.1    de Been, M.2    Nikkilä, J.3    Ritamo, I.4
  • 12
    • 84885641936 scopus 로고    scopus 로고
    • Gut microbiota disturbance during antibiotic therapy: a multiomic approach
    • Pérez-Cobas, A. E., Gosalbes, M. J., Friedrichs, A., Knecht, H. et al., Gut microbiota disturbance during antibiotic therapy: a multiomic approach. Gut 2013, 62, 1591-1601.
    • (2013) Gut , vol.62 , pp. 1591-1601
    • Pérez-Cobas, A.E.1    Gosalbes, M.J.2    Friedrichs, A.3    Knecht, H.4
  • 13
    • 84871933045 scopus 로고    scopus 로고
    • Microbiota from the distal guts of lean and obese adolescents exhibit partial functional redundancy besides clear differences in community structure
    • Ferrer, M., Ruiz, A., Lanza, F., Haange, S. et al., Microbiota from the distal guts of lean and obese adolescents exhibit partial functional redundancy besides clear differences in community structure. Environ. Microbiol. 2013, 15, 211-226.
    • (2013) Environ. Microbiol. , vol.15 , pp. 211-226
    • Ferrer, M.1    Ruiz, A.2    Lanza, F.3    Haange, S.4
  • 14
    • 84889666627 scopus 로고    scopus 로고
    • Human intestinal microbiota composition is associated with local and systemic inflammation in obesity
    • Verdam, F. J., Fuentes, S., de Jonge, C., Zoetendal, E. G. et al., Human intestinal microbiota composition is associated with local and systemic inflammation in obesity. Obesity 2013, 21, E607-E615.
    • (2013) Obesity , vol.21 , pp. E607-E615
    • Verdam, F.J.1    Fuentes, S.2    de Jonge, C.3    Zoetendal, E.G.4
  • 15
    • 84944167587 scopus 로고    scopus 로고
    • Navigating through metaproteomics data - a logbook of database searching
    • Muth, T., Kolmeder, C. A., Salojärvi, J., Keskitalo, S. et al., Navigating through metaproteomics data - a logbook of database searching. Proteomics 2015, 15, 3439-3453.
    • (2015) Proteomics , vol.15 , pp. 3439-3453
    • Muth, T.1    Kolmeder, C.A.2    Salojärvi, J.3    Keskitalo, S.4
  • 16
    • 34548178909 scopus 로고    scopus 로고
    • In-gel digestion for mass spectrometric characterization of proteins and proteomes
    • Shevchenko, A., Tomas, H., Havlis, J., Olsen, J. V. et al., In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat. Protoc. 2006, 1, 2856-2860.
    • (2006) Nat. Protoc. , vol.1 , pp. 2856-2860
    • Shevchenko, A.1    Tomas, H.2    Havlis, J.3    Olsen, J.V.4
  • 17
    • 3142702204 scopus 로고    scopus 로고
    • Tandem: matching proteins with tandem mass spectra
    • Craig, R., Beavis, R. C., Tandem: matching proteins with tandem mass spectra. Bioinformatics 2004, 20, 1466-1467.
    • (2004) Bioinformatics , vol.20 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 19
    • 38649129079 scopus 로고    scopus 로고
    • Posterior error probabilities and false discovery rates: two sides of the same coin
    • Käll, L., Storey, J. D., MacCoss, M. J., Noble, W. S., Posterior error probabilities and false discovery rates: two sides of the same coin. J. Proteome Res. 2007, 7, 40-44.
    • (2007) J. Proteome Res. , vol.7 , pp. 40-44
    • Käll, L.1    Storey, J.D.2    MacCoss, M.J.3    Noble, W.S.4
  • 20
    • 77954832678 scopus 로고    scopus 로고
    • Metaproteogenomic analysis of a dominant green sulfur bacterium from Ace Lake
    • Ng, C., DeMaere, M. Z., Williams, T. J., Lauro, F. M. et al., Metaproteogenomic analysis of a dominant green sulfur bacterium from Ace Lake. ISME J. 2010, 4, 1002-1019.
    • (2010) ISME J , vol.4 , pp. 1002-1019
    • Ng, C.1    DeMaere, M.Z.2    Williams, T.J.3    Lauro, F.M.4
  • 21
    • 84891757311 scopus 로고    scopus 로고
    • EggNOG v4.0: nested orthology inference across 3686 organisms
    • Powell, S., Forslund, K., Szklarczyk, D., Trachana, K. et al., EggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res. 2014, 42, D231-D239.
    • (2014) Nucleic Acids Res , vol.42 , pp. D231-D239
    • Powell, S.1    Forslund, K.2    Szklarczyk, D.3    Trachana, K.4
  • 22
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar, R. C., Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010, 26, 2460-2461.
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 23
    • 84924426335 scopus 로고    scopus 로고
    • The MetaProteomeAnalyzer: a powerful open-source software suite for metaproteomics data analysis and interpretation
    • 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.
    • (2015) J. Proteome Res. , vol.14 , pp. 1557-1565
    • Muth, T.1    Behne, A.2    Heyer, R.3    Kohrs, F.4
  • 24
    • 84977650745 scopus 로고    scopus 로고
    • Biostrings: string objects representing biological sequences, and matching algorithms
    • 2.32.1
    • Pages, H., Aboyoun, P., Gentleman, R., DebRoy, S., Biostrings: string objects representing biological sequences, and matching algorithms. R package version 2014, 2.32.1.
    • (2014) R package version
    • Pages, H.1    Aboyoun, P.2    Gentleman, R.3    DebRoy, S.4
  • 25
    • 84870936792 scopus 로고    scopus 로고
    • Unipept: tryptic peptide-based biodiversity analysis of metaproteome samples
    • Mesuere, B., Devreese, B., Debyser, G., Aerts, M. et al., Unipept: tryptic peptide-based biodiversity analysis of metaproteome samples. J. Proteome Res. 2012, 11, 5773-5780.
    • (2012) J. Proteome Res. , vol.11 , pp. 5773-5780
    • Mesuere, B.1    Devreese, B.2    Debyser, G.3    Aerts, M.4
  • 26
    • 84878653850 scopus 로고    scopus 로고
    • A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases
    • Lahti, L., Torrente, A., Elo, L. L., Brazma, A. et al., A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases. Nucleic Acids Res. 2013, 41, 1-10.
    • (2013) Nucleic Acids Res , vol.41 , pp. 1-10
    • Lahti, L.1    Torrente, A.2    Elo, L.L.3    Brazma, A.4
  • 27
    • 1042304216 scopus 로고    scopus 로고
    • APE: analyses of phylogenetics and evolution in R language
    • Paradis, E., Claude, J., Strimmer, K., APE: analyses of phylogenetics and evolution in R language. Bioinformatics 2004, 20, 289-290.
    • (2004) Bioinformatics , vol.20 , pp. 289-290
    • Paradis, E.1    Claude, J.2    Strimmer, K.3
  • 28
    • 84890985732 scopus 로고    scopus 로고
    • Faecal microbiota composition and host-microbe cross-talk following gastroenteritis and in postinfectious irritable bowel syndrome
    • Jalanka-Tuovinen, J., Salojärvi, J., Salonen, A., Immonen, O. et al., Faecal microbiota composition and host-microbe cross-talk following gastroenteritis and in postinfectious irritable bowel syndrome. Gut 2014, 63, 1737-1745.
    • (2014) Gut , vol.63 , pp. 1737-1745
    • Jalanka-Tuovinen, J.1    Salojärvi, J.2    Salonen, A.3    Immonen, O.4
  • 29
    • 81755176064 scopus 로고    scopus 로고
    • Strategies for metagenomic-guided whole-community proteomics of complex microbial environments
    • Cantarel, B. L., Erickson, A. R., Verberkmoes, N. C., Erickson, B. K. et al., Strategies for metagenomic-guided whole-community proteomics of complex microbial environments. PLoS One 2011, 6, e27173.
    • (2011) PLoS One , vol.6 , pp. e27173
    • Cantarel, B.L.1    Erickson, A.R.2    Verberkmoes, N.C.3    Erickson, B.K.4
  • 30
    • 68249110221 scopus 로고    scopus 로고
    • The role of pH in determining the species composition of the human colonic microbiota
    • Duncan, S. H., Louis, P., Thomson, J. M., Flint, H. J., The role of pH in determining the species composition of the human colonic microbiota. Environ. Microbiol. 2009, 11, 2112-2122.
    • (2009) Environ. Microbiol. , vol.11 , pp. 2112-2122
    • Duncan, S.H.1    Louis, P.2    Thomson, J.M.3    Flint, H.J.4
  • 31
    • 84903711427 scopus 로고    scopus 로고
    • Adiposity, gut microbiota and faecal short chain fatty acids are linked in adult humans
    • Fernandes, J., Su, W., Rahat-Rozenbloom, S., Wolever, T. et al., Adiposity, gut microbiota and faecal short chain fatty acids are linked in adult humans. Nutr. Diabetes 2014, 4, e121.
    • (2014) Nutr. Diabetes , vol.4 , pp. e121
    • Fernandes, J.1    Su, W.2    Rahat-Rozenbloom, S.3    Wolever, T.4
  • 32
    • 84858709310 scopus 로고    scopus 로고
    • Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis
    • Bahl, M. I., Bergström, A., Licht, T. R., Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis. FEMS Microbiol. Lett. 2012, 329, 193-197.
    • (2012) FEMS Microbiol. Lett. , vol.329 , pp. 193-197
    • Bahl, M.I.1    Bergström, A.2    Licht, T.R.3
  • 33
    • 84944153223 scopus 로고    scopus 로고
    • Enrichment or depletion? The impact of stool pretreatment on metaproteomic characterization of the human gut microbiota
    • Tanca, A., Palomba, A., Pisanu, S., Addis, M. F. et al., Enrichment or depletion? The impact of stool pretreatment on metaproteomic characterization of the human gut microbiota. Proteomics 2015, 15, 3473-3485.
    • (2015) Proteomics , vol.15 , pp. 3473-3485
    • Tanca, A.1    Palomba, A.2    Pisanu, S.3    Addis, M.F.4
  • 34
    • 84867026762 scopus 로고    scopus 로고
    • Bacterial proteases in IBD and IBS
    • Steck, N., Mueller, K., Schemann, M., Haller, D., Bacterial proteases in IBD and IBS. Gut 2012, 61, 1610-1618.
    • (2012) Gut , vol.61 , pp. 1610-1618
    • Steck, N.1    Mueller, K.2    Schemann, M.3    Haller, D.4
  • 35
    • 84893013094 scopus 로고    scopus 로고
    • High-fat diers gut microbiota physiology in mice
    • Daniel, H., Gholami, A. M., Berry, D., Desmarchelier, C. et al., High-fat diet alters gut microbiota physiology in mice. ISME J. 2014, 8, 295-308.
    • (2014) ISME J , vol.8 , pp. 295-308
    • Daniel, H.1    Gholami, A.M.2    Berry, D.3    Desmarchelier, C.4
  • 36
    • 14844288348 scopus 로고    scopus 로고
    • Regulation of intestinal ontogeny: effect of glucocorticoids and luminal microbes on galactosyltransferase and trehalase induction in mice
    • Nanthakumar, N. N., Dai, D., Meng, D., Chaudry, N. et al., Regulation of intestinal ontogeny: effect of glucocorticoids and luminal microbes on galactosyltransferase and trehalase induction in mice. Glycobiology 2005, 15, 221-232.
    • (2005) Glycobiology , vol.15 , pp. 221-232
    • Nanthakumar, N.N.1    Dai, D.2    Meng, D.3    Chaudry, N.4
  • 37
    • 84885927611 scopus 로고    scopus 로고
    • Trehalase as a possible marker of intestinal ischemia-reperfusion injury
    • Tóth Jr, Š, Pekárová, T., Varga, J., Tomečková, V. et al., Trehalase as a possible marker of intestinal ischemia-reperfusion injury. Acta Biochim. Pol. 2013, 60, 411-416.
    • (2013) Acta Biochim. Pol. , vol.60 , pp. 411-416
    • Tóth, S.1    Pekárová, T.2    Varga, J.3    Tomečková, V.4
  • 38
    • 79951687964 scopus 로고    scopus 로고
    • Small intestinal alterations in severely obese hyperglycemic subjects
    • Verdam, F. J., Greve, J. W. M., Roosta, S., van Eijk, H. et al., Small intestinal alterations in severely obese hyperglycemic subjects. J. Clin. Endocrinol. Metab. 2010, 96, E379-E383.
    • (2010) J. Clin. Endocrinol. Metab. , vol.96 , pp. E379-E383
    • Verdam, F.J.1    Greve, J.W.M.2    Roosta, S.3    van Eijk, H.4
  • 39
    • 84893771900 scopus 로고    scopus 로고
    • Intestinal alkaline phosphatase: novel functions and protective effects
    • Lallès, J., Intestinal alkaline phosphatase: novel functions and protective effects. Nutr. Rev. 2014, 72, 82-94.
    • (2014) Nutr. Rev. , vol.72 , pp. 82-94
    • Lallès, J.1
  • 41
    • 0026406090 scopus 로고
    • Elevated serum liver enzymes in obesity: a dilemma during clinical trials
    • Golik, A., Rubio, A., Weintraub, M., Byrne, L., Elevated serum liver enzymes in obesity: a dilemma during clinical trials. Int. J. Obes. 1991, 15, 797-801.
    • (1991) Int. J. Obes. , vol.15 , pp. 797-801
    • Golik, A.1    Rubio, A.2    Weintraub, M.3    Byrne, L.4
  • 42
    • 78149283854 scopus 로고    scopus 로고
    • Mucolytic bacteria with increased prevalence in IBD mucosa augment in vitro utilization of mucin by other bacteria
    • Png, C. W., Lindén, S. K., Gilshenan, K. S., Zoetendal, E. G. et al., Mucolytic bacteria with increased prevalence in IBD mucosa augment in vitro utilization of mucin by other bacteria. Am. J. Gastroenterol. 2010, 105, 2420-2428.
    • (2010) Am. J. Gastroenterol. , vol.105 , pp. 2420-2428
    • Png, C.W.1    Lindén, S.K.2    Gilshenan, K.S.3    Zoetendal, E.G.4
  • 43
    • 33845874101 scopus 로고    scopus 로고
    • An obesity-associated gut microbiome with increased capacity for energy harvest
    • Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V. et al., An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 2006, 444, 1027-1031.
    • (2006) Nature , vol.444 , pp. 1027-1031
    • Turnbaugh, P.J.1    Ley, R.E.2    Mahowald, M.A.3    Magrini, V.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.