Metabolome of human gut microbiome is predictive of host dysbiosis

GigaScience

Volumn 4, Issue 1, 2015, Pages 1-16

  Larsen, Peter E ^a,b   Dai1, Yang ^a  

^a University of Illinois at Chicago   (United States)

^b ARGONNE NATIONAL LABORATORY   (United States)

Author keywords

Dysbiosis; Gut microbiome; Human microbiome; Machine learning; Metabolome modeling; Metagenomics; Microbial communities

Indexed keywords

VIRULENCE FACTOR;

ANALYTICAL PARAMETERS; ARTICLE; BACTERIAL GENOME; BRAY CURTIS DISSIMILARITY INDEX; COMMUNITY STRUCTURE; DIGESTION; DYSBIOSIS; ENZYME ACTIVITY; HOST; HOST PATHOGEN INTERACTION; HUMAN; INTESTINE FLORA; LONGITUDINAL STUDY; MACHINE LEARNING; METABOLOME; METAGENOMICS; NONHUMAN; PREDICTION; PRIORITY JOURNAL; SUPPORT VECTOR MACHINE; VITAMIN METABOLISM; INTESTINE; MICROBIOLOGY; MICROFLORA;

HUMANS; INTESTINES; METABOLOME; MICROBIOTA; SUPPORT VECTOR MACHINE;

EID: 85006192496     PISSN: None     EISSN: 2047217X     Source Type: Journal    
DOI: 10.1186/s13742-015-0084-3     Document Type: Article

References (68)

1. Yoon SS, Kim EK, Lee WJ. Functional genomic and metagenomic approaches to understanding gut microbiota-animal mutualism. Curr Opin Microbiol. 2015;24:38-46.
2. Wang WL, Xu SY, Ren ZG, Tao L, Jiang JW, Zheng SS. Application of metagenomics in the human gut microbiome. World J Gastroenterol. 2015;21(3):803-14.
3. Gosalbes MJ, Abellan JJ, Durban A, Perez-Cobas AE, Latorre A, Moya A. Metagenomics of human microbiome: beyond 16 s rDNA. Clin Microbiol Infect. 2012;18 Suppl 4:47-9.
4. Bou Saab J, Losa D, Chanson M, Ruez R. Connexins in respiratory and gastrointestinal mucosal immunity. FEBS Lett. 2014;588(8):1288-96.
5. Walsh CJ, Guinane CM, O'Toole PW, Cotter PD. Beneficial modulation of the gut microbiota. FEBS Lett. 2014;588(22):4120-30.
6. Ramakrishna BS. Role of the gut microbiota in human nutrition and metabolism. J Gastroenterol Hepatol. 2013;28 Suppl 4:9-17.
7. Hennessy AA, Ross RP, Fitzgerald GF, Caplice N, Stanton C. Role of the gut in modulating lipoprotein metabolism. Curr Cardiol Rep. 2014;16(8):515.
8. Fuller M. Determination of protein and amino acid digestibility in foods including implications of gut microbial amino acid synthesis. Br J Nutr. 2012;108 Suppl 2:S238-46.
9. Dutton RJ, Turnbaugh PJ. Taking a metagenomic view of human nutrition. Curr Opin Clin Nutr Metab Care. 2012;15(5):448-54.
10. Cantorna MT, McDaniel K, Bora S, Chen J, James J. Vitamin D, immune regulation, the microbiota, and inflammatory bowel disease. Exp Biol Med (Maywood). 2014;239(11):1524-30.
11. Greer RL, Morgun A, Shulzhenko N. Bridging immunity and lipid metabolism by gut microbiota. J Allergy Clin Immunol. 2013;132(2):253-62. quiz 63.
12. Calder PC. Feeding the immune system. Proc Nutr Soc. 2013;72(3):299-309.
13. Romano-Keeler J, Weitkamp JH. Maternal influences on fetal microbial colonization and immune development. Pediatr Res. 2015;77(1-2):189-95.
14. Tamboli CP, Neut C, Desreumaux P, Colombel JF. Dysbiosis in inflammatory bowel disease. Gut. 2004;53(1):1-4.
15. Kostic AD, Xavier RJ, Gevers D. The microbiome in inflammatory bowel disease: current status and the future ahead. Gastroenterology. 2014;146(6):1489-99.
16. Cammarota G, Ianiro G, Cianci R, Bibbo S, Gasbarrini A, Curro D. The involvement of gut microbiota in inflammatory bowel disease pathogenesis: potential for therapy. Pharmacol Ther. 2015;149:191-212.
17. Han DS. Current status and prospects of intestinal microbiome studies. Intest Res. 2014;12(3):178-83.
18. Collins SM. A role for the gut microbiota in IBS. Nat Rev Gastroenterol Hepatol. 2014;11(8):497-505.
19. Dupont HL. Review article: evidence for the role of gut microbiota in irritable bowel syndrome and its potential influence on therapeutic targets. Aliment Pharmacol Ther. 2014;39(10):1033-42.
20. Collado MC, Rautava S, Isolauri E, Salminen S. Gut microbiota: a source of novel tools to reduce the risk of human disease? Pediatr Res. 2015;77(1-2):182-8.
21. McLean MH, Dieguez Jr D, Miller LM, Young HA. Does the microbiota play a role in the pathogenesis of autoimmune diseases? Gut. 2015;64(2):332-41.
22. Viaud S, Daillere R, Boneca IG, Lepage P, Pittet MJ, Ghiringhelli F, et al. Harnessing the intestinal microbiome for optimal therapeutic immunomodulation. Cancer Res. 2014;74(16):4217-21.
23. Kipanyula MJ, Seke Etet PF, Vecchio L, Farahna M, Nukenine EN, Nwabo Kamdje AH. Signaling pathways bridging microbial-triggered inflammation and cancer. Cell Signal. 2013;25(2):403-16.
24. Sanz Y, Moya-Perez A. Microbiota, inflammation and obesity. Adv Exp Med Biol. 2014;817:291-317.
25. Cox LM, Blaser MJ. Antibiotics in early life and obesity. Nat Rev Endocrinol. 2015;11(3):182-90.
26. Gohir W, Ratcliffe EM, Sloboda DM. Of the bugs that shape us: maternal obesity, the gut microbiome, and long-term disease risk. Pediatr Res. 2015;77(1-2):196-204.
27. Moran CP, Shanahan F. Gut microbiota and obesity: role in aetiology and potential therapeutic target. Best Pract Res Clin Gastroenterol. 2014;28(4):585-97.
28. Luna RA, Foster JA. Gut brain axis: diet microbiota interactions and implications for modulation of anxiety and depression. Curr Opin Biotechnol. 2015;32:35-41.
29. Fond G, Boukouaci W, Chevalier G, Regnault A, Eberl G, Hamdani N, et al. The "psychomicrobiotic": Targeting microbiota in major psychiatric disorders: A systematic review. Pathol Biol (Paris). 2015;63(1):35-42.
30. Borre YE, Moloney RD, Clarke G, Dinan TG, Cryan JF. The impact of microbiota on brain and behavior: mechanisms & therapeutic potential. Adv Exp Med Biol. 2014;817:373-403.
31. West CE, Renz H, Jenmalm MC, Kozyrskyj AL, Allen KJ, Vuillermin P, et al. The gut microbiota and inflammatory noncommunicable diseases: associations and potentials for gut microbiota therapies. J Allergy Clin Immunol. 2015;135(1):3-13. quiz 4.
32. Shanahan F, Quigley EM. Manipulation of the microbiota for treatment of IBS and IBD-challenges and controversies. Gastroenterology. 2014;146(6):1554-63.
33. Brandt LJ, Aroniadis OC. An overview of fecal microbiota transplantation: techniques, indications, and outcomes. Gastrointest Endosc. 2013;78(2):240-9.
34. Xu MQ, Cao HL, Wang WQ, Wang S, Cao XC, Yan F, et al. Fecal microbiota transplantation broadening its application beyond intestinal disorders. World J Gastroenterol. 2015;21(1):102-11.
35. Goudarzi M, Seyedjavadi SS, Goudarzi H, Mehdizadeh Aghdam E, Nazeri S. Clostridium difficile Infection: Epidemiology, Pathogenesis, Risk Factors, and Therapeutic Options. Scientifica (Cairo). 2014;2014:916826.
36. Rojo D, Hevia A, Bargiela R, Lopez P, Cuervo A, Gonzalez S, et al. Ranking the impact of human health disorders on gut metabolism: Systemic lupus erythematosus and obesity as study cases. Sci Rep-Uk. 2015;6:5.
37. Theriot CM, Koenigsknecht MJ, Carlson Jr PE, Hatton GE, Nelson AM, Li B, et al. Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection. Nat Commun. 2014;5:3114.
38. Ursell LK, Haiser HJ, Van Treuren W, Garg N, Reddivari L, Vanamala J, et al. The intestinal metabolome: an intersection between microbiota and host. Gastroenterology. 2014;146(6):1470-6.
39. Kostic AD, Gevers D, Siljander H, Vatanen T, Hyotylainen T, Hamalainen AM, et al. The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell Host Microbe. 2015;17(2):260-73.
40. MetaHIT. Metagenomics of the Human Intestinal Tract Available from: http://www.metahit.eu/.
41. HMP. Human Microbiome Project Available from: http://hmpdacc.org.
42. David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505(7484):559-63.
43. Gerber GK. The dynamic microbiome. FEBS Lett. 2014;588(22):4131-9.
44. Putignani L, Del Chierico F, Petrucca A, Vernocchi P, Dallapiccola B. The human gut microbiota: a dynamic interplay with the host from birth to senescence settled during childhood. Pediatr Res. 2014;76(1):2-10.
45. Schloissnig S, ArumugamM, Sunagawa S, MitrevaM, Tap J, Zhu A, et al. Genomic variation landscape of the human gut microbiome. Nature. 2013;493(7430):45-50.
46. The Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012 Jun 14;486 (7402):207-14.
47. Ding T, Schloss PD. Dynamics and associations of microbial community types across the human body. Nature. 2014;509(7500):357-60.
48. Lax S, Smith DP, Hampton-Marcell J, Owens SM, Handley KM, Scott NM, et al. Longitudinal analysis of microbial interaction between humans and the indoor environment. Science. 2014;345(6200):1048-52.
49. David LA, Materna AC, Friedman J, Campos-Baptista MI, Blackburn MC, Perrotta A, et al. Host lifestyle affects human microbiota on daily timescales. Genome Biol. 2014;15(7):R89.
50. Larsen PE, Scott N, Post AF, Field D, Knight R, Hamada Y, et al. Satellite remote sensing data can be used to model marine microbial metabolite turnover. ISME J. 2015;9(1):166-79.
51. Larsen PE, Collart FR, Dai Y. Predicting Ecological Roles in the Rhizosphere Using Metabolome and Transportome Modeling. PLOS ONE. 2015; doi:10.1371/journal.pone.0132837.
52. Larsen PE, Field D, Gilbert JA. Predicting bacterial community assemblages using an artificial neural network approach. Nat Methods. 2012;9(6):621-5.
53. Mumby PJ, Clarke KR, Harborne AR. Weighting species abundance estimates for marine resource assessment. Aquat Conserv. 1996;6(3):115-20.
54. Russell WR, Duncan SH, Scobbie L, Duncan G, Cantlay L, Calder AG, et al. Major phenylpropanoid-derived metabolites in the human gut can arise from microbial fermentation of protein. Mol Nutr Food Res. 2013;57(3):523-35.
55. Larque E, Sabater-Molina M, Zamora S. Biological significance of dietary polyamines. Nutrition. 2007;23(1):87-95.
56. Garenaux A, Caza M, Dozois CM. The Ins and Outs of siderophore mediated iron uptake by extra-intestinal pathogenic Escherichia coli. Vet Microbiol. 2011;153(1-2):89-98.
57. Oves-Costales D, Kadi N, Challis GL. The long-overlooked enzymology of a nonribosomal peptide synthetase-independent pathway for virulence-conferring siderophore biosynthesis. Chem Commun (Camb). 2009;21(43):6530-41.
58. Rooks MG, Veiga P, Wardwell-Scott LH, Tickle T, Segata N, Michaud M, et al. Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission. ISME J. 2014;8(7):1403-17.
59. Rossi M, Amaretti A, Raimondi S. Folate production by probiotic bacteria. Nutrients. 2011;3(1):118-34.
60. Boesjes M, Brufau G. Metabolic effects of bile acids in the gut in health and disease. Curr Med Chem. 2014;21(24):2822-9.
61. ENZYME. Enzyme nomenclature database. Available from: http://enzyme.expasy.org/.
62. Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. 2013;31(9):814
63. Larsen PE, Collart F, Field D, Meyer F, Keegan K, Henry C, et al. Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset. Microb Inform Exp. 2011;1:4.
64. R-Project. The R Project for Statistical Computing. Available from: http://www.r-project.org/.
65. e1071. Misc Functions of the Department of Statistics, Probability Theory Group. Available from: https://cran.r-project.org/web/packages/e1071/index.html.
66. Peter E Larsen, Yang Dai (2015): Supporting materials for: "Metabolome of Human Gut Microbiome is Predictive of Host Dysbiosis". GigaScience Database. http://dx.doi.org/10.5524/100163.
67. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498-504.
68. Cytoscape. Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. Available from: http://cytoscape.org/.