Selecting age-related functional characteristics in the human gut microbiome

Microbiome

Volumn 1, Issue 1, 2013, Pages

  Lan, Yemin ^a   Kriete, Andres ^a   Rosen, Gail L ^b  

^a DREXEL UNIVERSITY   (United States)

^b Drexel University   (United States)

Author keywords

KEGG; Metagenomics; Pfam; Supervised classification; SVM

Indexed keywords

CYANOCOBALAMIN; GLYCOSYLTRANSFERASE; OXIDOREDUCTASE;

ADULT; AGED; AGEISM; AGING; ARTICLE; CELLULAR STRESS RESPONSE; DNA DAMAGE; FUNCTIONAL STATUS; GENE; GENE ONTOLOGY; GENETIC TRANSFORMATION; HUMAN; IMMUNE SYSTEM; INFLAMMATORY BOWEL DISEASE; INTESTINE FLORA; MAJOR CLINICAL STUDY; METABOLISM; METAGENOME; METAGENOMICS; MICROBIAL GENETICS; MICROBIOME; MIDDLE AGED; NONHUMAN; OBESITY; PHYLOGENY; PREDICTION; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN FAMILY; SUPPORT VECTOR MACHINE;

EID: 84886373112     PISSN: None     EISSN: 20492618     Source Type: Journal    
DOI: 10.1186/2049-2618-1-2     Document Type: Article

References (52)

1. Whitman WB, Coleman DC, Wiebe WJ. Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 1998, 95:6578-6583. 10.1073/pnas.95.12.6578, 33863, 9618454.
2. Guerrero R, Berlanga M. Life's unity and flexibility: the ecological link. Int Microbiol 2006, 9:225-235.
3. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010, 464:59-65. 10.1038/nature08821, 20203603.
4. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, et al. Enterotypes of the human gut microbiome. Nature 2011, 473:174-180. 10.1038/nature09944, 21508958.
5. Manichanh C, Rigottier-Gois L, Bonnaud E, Gloux K, Pelletier E, Frangeul L, Nalin R, Jarrin C, Chardon P, Marteau P, Roca J, Dore J. Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut 2006, 55:205-211. 10.1136/gut.2005.073817, 1856500, 16188921.
6. Frank DN, Pace NR. Gastrointestinal microbiology enters the metagenomics era. Curr Opin Gastroenterol 2008, 24:4-10. 10.1097/MOG.0b013e3282f2b0e8, 18043225.
7. Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature 2006, 444:1022-1023. 10.1038/4441022a, 17183309.
8. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI. A core gut microbiome in obese and lean twins. Nature 2009, 457:480-484. 10.1038/nature07540, 2677729, 19043404.
9. De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, Collini S, Pieraccini G, Lionetti P. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci USA 2010, 107:14691-14696. 10.1073/pnas.1005963107, 2930426, 20679230.
10. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI. Human gut microbiome viewed across age and geography. Nature 2012, 486:222-7. 3376388, 22699611.
11. Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med 2009, 1:6ra14. 10.1126/scitranslmed.3000322, 2894525, 20368178.
12. Mitnitski AB, Graham JE, Mogilner AJ, Rockwood K. Frailty, fitness and late-life mortality in relation to chronological and biological age. BMC Geriatr 2002, 2:1. 10.1186/1471-2318-2-1, 88955, 11897015.
13. Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, Toyoda A, Takami H, Morita H, Sharma VK, Srivastava TP, Taylor TD, Noguchi H, Mori H, Ogura Y, Ehrlich DS, Itoh K, Takagi T, Sakaki Y, Hayashi T, Hattori M. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res 2007, 14:169-181. 10.1093/dnares/dsm018, 2533590, 17916580.
14. Biagi E, Nylund L, Candela M, Ostan R, Bucci L, Pini E, Nikkila J, Monti D, Satokari R, Franceschi C, Brigidi P, De Vos W. Through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians. PLoS One 2010, 5:e10667. 10.1371/journal.pone.0010667, 2871786, 20498852.
15. Claesson MJ, Cusack S, O'Sullivan O, Greene-Diniz R, de Weerd H, Flannery E, Marchesi JR, Falush D, Dinan T, Fitzgerald G, Stanton C, van Sinderen D, O'Connor M, Harnedy N, O'Connor K, Henry C, O'Mahony D, Fitzgerald AP, Shanahan F, Twomey C, Hill C, Ross RP, O'Toole PW. Composition, variability, and temporal stability of the intestinal microbiota of the elderly. Proc Natl Acad Sci USA 2011, 1:4586-4591.
16. Dominguez-Bello MG, Blaser MJ, Ley RE, Knight R. Development of the human gastrointestinal microbiota and insights from high-throughput sequencing. Gastroenterology 2011, 140:1713-1719. 10.1053/j.gastro.2011.02.011, 21530737.
17. Clemente JC, Ursell LK, Parfrey LW, Knight R. The impact of the gut microbiota on human health: an integrative view. Cell 2012, 148:1258-1270. 10.1016/j.cell.2012.01.035, 22424233.
18. Cho L, Blaser MJ. The human microbiome: at the interface of health and disease. Nat Rev Genet 2012, 13:260-270. 3418802, 22411464.
19. Sartor RB. Microbial influences in inflammatory bowel diseases. Gastroenterology 2008, 134:577-594. 10.1053/j.gastro.2007.11.059, 18242222.
20. Muegge BD, Kuczynski J, Knights D, Clemente JC, Gonzalez A, Fontana L, Henrissat B, Knight R, Gordon JI. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 2011, 332:970-974. 10.1126/science.1198719, 3303602, 21596990.
21. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE. Metagenomic analysis of the human distal gut microbiome. Science 2006, 312:1355-1359. 10.1126/science.1124234, 3027896, 16741115.
22. Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, Brulc JM, Furlan M, Desnues C, Haynes M, Li L, McDaniel L, Moran MA, Nelson KE, Nilsson C, Olson R, Paul J, Brito BR, Ruan Y, Swan BK, Stevens R, Valentine DL, Thurber RV, Wegley L, White BA, Rohwer F. Functional metagenomic profiling of nine biomes. Nature 2008, 452:629-632. 10.1038/nature06810, 18337718.
23. Greenblum S, Turnbaugh PJ, Borenstein E. Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease. Proc Natl Acad Sci USA 2012, 109:594-599. 10.1073/pnas.1116053109, 3258644, 22184244.
24. Woodmansey EJ. Intestinal bacteria and ageing. J Appl Microbiol 2007, 102:1178-1186. 10.1111/j.1365-2672.2007.03400.x, 17448153.
25. Kostic AD, Gevers D, Pedamallu CS, Michaud M, Duke F, Earl AM, Ojesina AI, Jung J, Bass AJ, Tabernero J, Baselga J, Liu C, Shivdasani RA, Ogino S, Birren BW, Huttenhower C, Garrett WS, Meyerson M. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res 2012, 22:292-298. 10.1101/gr.126573.111, 3266036, 22009990.
26. Rosen GL, Sokhansanj BA, Polikar R, Bruns MA, Russell J, Garbarine E, Essinger S, Yok N. Signal processing for metagenomics: extracting information from the soup. Curr Genomics 2009, 10:493-510. 10.2174/138920209789208255, 2808676, 20436876.
27. Madupu R, Brinkac LM, Harrow J, Wilming LG, Bohme U, Lamesch P, Hannick LI. Meeting report: a workshop on best practices in genome annotation. Database (Oxford) 2010, 2010:baq001.
28. Yok NG, Rosen GL. Combining gene prediction methods to improve metagenomic gene annotation. BMC Bioinforma 2011, 12:20.
29. Yeoman CJ, Chia N, Yildirim S, Miller MEB, Kent A, Stumpf R, Leigh SR, Nelson KE, White BA, Wilson BA. Towards an evolutionary model of animal-associated microbiomes. Entropy 2011, 13:570-594.
30. Nemergut DR, Costello EK, Hamady M, Lozupone C, Jiang L, Schmidt SK, Fierer N, Townsend AR, Cleveland CC, Stanish L, Knight R. Global patterns in the biogeography of bacterial taxa. Environ Microbiol 2011, 13:135-144. 10.1111/j.1462-2920.2010.02315.x, 21199253.
31. Natick MATLAB version 7.11 2010, Massachusetts: The MathWorks Inc, Natick.
32. R a language and environment for statistical computing 2011, Vienna, Austria: R Foundation for Statistical Computing, R.
33. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A. The Pfam protein families database. Nucleic Acids Res 2010, 38:D211-D222. Database issue, 10.1093/nar/gkp985, 2808889, 19920124.
34. Finn RD, Clements J, Eddy SR. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 2011, 39:W29-W37. Web Server issue, 10.1093/nar/gkr367, 3125773, 21593126.
35. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
36. Consortium U. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 2012, 40:D71-D75. 3245120, 22102590.
37. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. The gene ontology consortium: gene ontology: tool for the unification of biology. Nat Genet 2000, 25:25-29. 10.1038/75556, 3037419, 10802651.
38. Mitra S, Rupek P, Richter DC, Urich T, Gilbert JA, Meyer F, Wilke A, Huson DH. Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG. BMC Bioinforma 2011, 1:S21.
39. Jing LP, Huang HK, Shi HB. Improved feature selection approach TFIDF in text mining. In Proceedings of the First International Conference on Machine Learning and Cybernetics 2002, 2:944-946.
40. Peng H, Long F, Ding C. Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy. IEEE Trans Pattern Anal Mach Intell 2005, 27:1226-1238.
41. Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C. Metagenomic biomarker discovery and explanation. Genome Biol 2011, 12:R60. 10.1186/gb-2011-12-6-r60, 3218848, 21702898.
42. Duch W. Filter methods. Feature Extraction: Foundations and Applications 2006, 89-117. New York: Springer-Verlag, Guyon I, 207.
43. Legendre P, Gallagher ED. Ecologically meaningful transformations for ordination of species data. Oecologia 2001, 129:271-280.
44. Garbarine E, DePasquale J, Gadia V, Polikar R, Rosen G. Information-theoretic approaches to SVM feature selection for metagenome read classification. Comput Biol Chem 2011, 35:199-209. 10.1016/j.compbiolchem.2011.04.007, 21704267.
45. Turnbaugh PJ, Gordon JI. The core gut microbiome, energy balance and obesity. J Physiol 2009, 587:4153-4158. 10.1113/jphysiol.2009.174136, 2754355, 19491241.
46. Baik HW, Russell RM. Vitamin B12 deficiency in the elderly. Annu Rev Nutr 1999, 19:357-377. 10.1146/annurev.nutr.19.1.357, 10448529.
47. Boehm DF, Welch RA, Snyder IS. Domains of Escherichia coli hemolysin (HlyA) involved in binding of calcium and erythrocyte membranes. Infect Immun 1990, 58:1959-1964. 258750, 2187815.
48. Bork P, Hofmann K, Bucher P, Neuwald AF, Altschul SF, Koonin EV. A superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins. FASEB J 1997, 11:68-76.
49. Levine C, Hiasa H, Marians KJ. DNA gyrase and topoisomerase IV: biochemical activities, physiological roles during chromosome replication, and drug sensitivities. Biochim Biophys Acta 1998, 1400:29-43. 10.1016/S0167-4781(98)00126-2, 9748489.
50. Vericel E, Rey C, Calzada C, Haond P, Chapuy PH, Lagarde M. Age-related changes in arachidonic acid peroxidation and glutathione-peroxidase activity in human platelets. Prostaglandins 1992, 43:75-85.
51. Lee SH, Hatakeyama S, Yu SY, Bao XF, Khoo KH, Fukuda M, Fukuda M. Core 3 O-glycan synthase suppresses tumor formation and metastasis of prostate carcinoma Cells through downregulation of alpha 2 beta 1 integrin complex. Glycobiology 2008, 18:963963.
52. Stewart EJ, Madden R, Paul G, Taddei F. Aging and death in an organism that reproduces by morphologically symmetric division. PLoS Biol 2005, 3:295-300.