Looking large, to make more, out of gut metagenomics

Current Opinion in Microbiology

Volumn 16, Issue 5, 2013, Pages 630-635

  Morrison, Mark ^a,b  

^a CSIRO   (Australia)

^b OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTIC AGENT; ENDOTOXIN; GLYCOSIDASE; PROBIOTIC AGENT; RNA 16S;

AMINO ACID METABOLISM; BIOMASS CONVERSION; CARDIOVASCULAR DISEASE; COLITIS; DNA SEQUENCE; ENTEROBACTER CLOACAE; FIRMICUTES; FOOD INDUSTRY; HUMAN; HYDROLYSIS; INFANT NUTRITION; INTESTINE FLORA; LACTATION; LIVESTOCK; METABOLIC SYNDROME X; METAGENOMICS; METHANOBREVIBACTER; METHANOGENIC ARCHAEON; MICROBIAL DIVERSITY; MICROBIOME; NECROTIZING ENTEROCOLITIS; NITROGEN METABOLISM; NONALCOHOLIC FATTY LIVER; NONHUMAN; OBESITY; REVIEW; SHORT BOWEL SYNDROME; SUCCINIVIBRIONACEAE;

ANIMALIA; RODENTIA;

ANIMALS; BIOTA; GASTROINTESTINAL TRACT; HUMANS; METAGENOME; METAGENOMICS;

EID: 84887621058     PISSN: 13695274     EISSN: 18790364     Source Type: Journal    
DOI: 10.1016/j.mib.2013.10.003     Document Type: Review

References (75)

1. Mackie R.I. Mutualistic fermentative digestion in the gastrointestinal tract: diversity and evolution. Integr Comp Biol 2002, 42:319-326.
2. Stevens C.E., Hume I.D. Comparative Physiology of the Vertebrate Digestive System 2004, 400. Cambridge University Press, Cambridge, New York.
3. Mackie R.I., White B.A., Isaacson R.E. Gastrointestinal Microbiology 1997, Chapman & Hall, New York.
4. Stahl D.A., Flesher B., Mansfield H.R., Montgomery L. Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Appl Environ Microbiol 1988, 54:1079-1084.
5. Ley R.E., Lozupone C.A., Hamady M., et al. Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol 2008, 6:776-788.
6. Rajilic-Stojanovic M., Smidt H., de Vos W.M. Diversity of the human gastrointestinal tract microbiota revisited. Environ Microbiol 2007, 9:2125-2136.
7. Samuel B.S., Hansen E.E., Manchester J.K., et al. Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proc Natl Acad Sci U S A 2007, 104:10643-10648.
8. Xu J., Bjursell M.K., Himrod J., et al. A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science 2003, 299:2074-2076.
9. Booijink C.C., Zoetendal E.G., Kleerebezem M., de Vos W.M. Microbial communities in the human small intestine: coupling diversity to metagenomics. Future Microbiol 2007, 2:285-295.
10. Gill S.R., Pop M., Deboy R.T., et al. Metagenomic analysis of the human distal gut microbiome. Science 2006, 312:1355-1359.
11. Kurokawa K., Itoh T., Kuwahara T., et al. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res 2007, 14:169-181.
12. Arumugam M., Raes J., Pelletier E., et al. Enterotypes of the human gut microbiome. Nature 2011, 473:174-180.
13. Qin J., Li R., Raes J., et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010, 464:59-65.
14. Qin J., Li Y., Cai Z., et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 2012, 490:55-60.
15. Human Microbiome Project Consortium A framework for human microbiome research. Nature 2012, 486:215-221.
16. Human Microbiome Project Consortium Structure, function and diversity of the healthy human microbiome. Nature 2012, 486:207-214.
17. Gevers D., Knight R., Petrosino J.F., et al. The Human Microbiome Project: a community resource for the healthy human microbiome. PLoS Biol 2012, 10:e1001377.
18. Sommer F., Backhed F. The gut microbiota - masters of host development and physiology. Nat Rev Microbiol 2013, 11:227-238.
19. Dusko Ehrlich S. Metagenomics of the intestinal microbiota: potential applications. Gastroenterol Clin Biol 2010, 34(Suppl 1):S23-S28.
20. Madupu R., Szpakowski S., Nelson K.E. Microbiome in human health and disease. Sci Prog 2013, 96:153-170.
21. Henao-Mejia J., Elinav E., Jin C., et al. Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity. Nature 2012, 482:179-185.
22. Tang W.H., Wang Z., Levison B.S., et al. Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk. N Engl J Med 2013, 368:1575-1584.
23. Wang Z., Klipfell E., Bennett B.J., et al. Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature 2011, 472:57-63.
24. Fukuda S., Toh H., Hase K., et al. Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature 2011, 469:543-547.
25. Devkota S., Wang Y., Musch M.W., et al. Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice. Nature 2012, 487:104-108.
26. Cho I., Yamanishi S., Cox L., et al. Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature 2012, 488:621-626.
27. Benson A.K., Kelly S.A., Legge R., et al. Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. Proc Natl Acad Sci U S A 2010, 107:18933-18938.
28. Ley R.E., Hamady M., Lozupone C., et al. Evolution of mammals and their gut microbes. Science 2008, 320:1647-1651.
29. Baker D.H. Animal models in nutrition research. J Nutr 2008, 138:391-396.
30. Bauman D.E., Harvatine K.J., Lock A.L. Nutrigenomics, rumen-derived bioactive fatty acids, and the regulation of milk fat synthesis. Annu Rev Nutr 2011, 31:299-319.
31. Bauman D.E., Perfield J.W., Harvatine K.J., Baumgard L.H. Regulation of fat synthesis by conjugated linoleic acid: lactation and the ruminant model. J Nutr 2008, 138:403-409.
32. Spurlock M.E., Gabler N.K. The development of porcine models of obesity and the metabolic syndrome. J Nutr 2008, 138:397-402.
33. Lanzas C., Ayscue P., Ivanek R., Grohn Y.T. Model or meal? Farm animal populations as models for infectious diseases of humans. Nat Rev Microbiol 2010, 8:139-148.
34. Buddington R.K., Sangild P.T. Companion animals symposium: development of the mammalian gastrointestinal tract, the resident microbiota, and the role of diet in early life. J Anim Sci 2011, 89:1506-1519.
35. Gootenberg D.B., Turnbaugh P.J. Companion animals symposium: humanized animal models of the microbiome. J Anim Sci 2011, 89:1531-1537.
36. Suchodolski J.S. Companion animals symposium: microbes and gastrointestinal health of dogs and cats. J Anim Sci 2011, 89:1520-1530.
37. Swanson K.S., Suchodolski J.S., Turnbaugh P.J. Companion animals symposium: microbes and health. J Anim Sci 2011, 89:1496-1497.
38. Kerr K.R., Beloshapka A.N., Swanson K.S. 2011 and 2012 Early Careers Achievement Awards: use of genomic biology to study companion animal intestinal microbiota. J Anim Sci 2013, 91:2504-2511.
39. Christoffersen B., Golozoubova V., Pacini G., et al. The young Gottingen minipig as a model of childhood and adolescent obesity: influence of diet and gender. Obesity (Silver Spring) 2013, 21:149-158.
40. Pedersen R., Ingerslev H.C., Sturek M., et al. Characterisation of gut microbiota in Ossabaw and Gottingen minipigs as models of obesity and metabolic syndrome. PLoS ONE 2013, 8:e56612.
41. Pang X., Hua X., Yang Q., et al. Inter-species transplantation of gut microbiota from human to pigs. ISME J 2007, 1:156-162.
42. Laycock G., Sait L., Inman C., et al. A defined intestinal colonization microbiota for gnotobiotic pigs. Vet Immunol Immunopathol 2012, 149:216-224.
43. Fei N., Zhao L. An opportunistic pathogen isolated from the gut of an obese human causes obesity in germfree mice. ISME J 2013, 7:880-884.
44. Zhao L. The gut microbiota and obesity: from correlation to causality. Nat Rev Microbiol 2013, 11:639-647.
45. Guilloteau P., Zabielski R., Hammon H.M., Metges C.C. Nutritional programming of gastrointestinal tract development. Is the pig a good model for man?. Nutr Res Rev 2010, 23:4-22.
46. Sangild P.T., Thymann T., Schmidt M., et al. Invited review: the preterm pig as a model in pediatric gastroenterology. J Anim Sci 2013, 91:4713-4729.
47. Donovan S.M., Wang M., Li M., et al. Host-microbe interactions in the neonatal intestine: role of human milk oligosaccharides. Adv Nutr 2012, 3:450S-455S.
48. Li M., Bauer L.L., Chen X., et al. Microbial composition and in vitro fermentation patterns of human milk oligosaccharides and prebiotics differ between formula-fed and sow-reared piglets. J Nutr 2012, 142:681-689.
49. Poroyko V., White J.R., Wang M., et al. Gut microbial gene expression in mother-fed and formula-fed piglets. PLoS ONE 2010, 5:e12459.
50. Poroyko V., Morowitz M., Bell T., et al. Diet creates metabolic niches in the "immature gut" that shape microbial communities. Nutr Hosp 2011, 26:1283-1295.
51. Puiman P., Stoll B., Molbak L., et al. Modulation of the gut microbiota with antibiotic treatment suppresses whole body urea production in neonatal pigs. Am J Physiol-Gastrointest Liver Physiol 2013, 304:G300-G310.
52. Burrin D., Stoll B., Moore D. Digestive Physiology of the Pig Symposium: Intestinal bile acid sensing is linked to key endocrine and metabolic signaling pathways. J Anim Sci 2013, 91:1991-2000.
53. Renfree M.B. Review: Marsupials: placental mammals with a difference. Placenta 2010, 31(Suppl):S21-S26.
54. Hume I.D. Marsupial Nutrition 1999, Cambridge University Press.
55. Kempton T.J., Murray R.M., Leng R.A. Methane production and digestibility measurements in the grey kangaroo and sheep. Aust J Biol Sci 1976, 29:209-214.
56. Madsen J., Bertelsen M.F. Methane production by red-necked wallabies (Macropus rufogriseus). J Anim Sci 2012, 90:1364-1370.
57. Morrison M. The vertebrate animal gut in context - microbiomes, methane and metagenomics. Microbiol Aust 2007, 28:107-110.
58. Morrison M., Pope P.B., Denman S.E., McSweeney C.S. Plant biomass degradation by gut microbiomes: more of the same or something new?. Curr Opin Biotechnol 2009, 20:358-363.
59. Pope P.B., Denman S.E., Jones M., et al. Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores. Proc Natl Acad Sci U S A 2010, 107:14793-14798.
60. Patil K.R., Haider P., Pope P.B., et al. Taxonomic metagenome sequence assignment with structured output models. Nat Methods 2011, 8:191-192.
61. Patil K.R., Roune L., McHardy A.C. The PhyloPythiaS web server for taxonomic assignment of metagenome sequences. PLoS ONE 2012, 7:e38581.
62. Pope P.B., Smith W., Denman S.E., et al. Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies. Science 2011, 333:646-648.
63. Evans P.N., Hinds L.A., Sly L.I., et al. Community composition and density of methanogens in the foregut of the Tammar wallaby (Macropus eugenii). Appl Environ Microbiol 2009, 75:2598-2602.
64. Gagen E.J., Denman S.E., Padmanabha J., et al. Functional gene analysis suggests different acetogen populations in the bovine rumen and tammar wallaby forestomach. Appl Environ Microbiol 2010, 76:7785-7795.
65. Omsland A., Cockrell D.C., Howe D., et al. Host cell-free growth of the Q fever bacterium Coxiella burnetii. Proc Natl Acad Sci U S A 2009, 106:4430-4434.
66. Tyson G.W., Lo I., Baker B.J., et al. Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp nov from an acidophilic microbial community. Appl Environ Microbiol 2005, 71:6319-6324.
67. Hess M., Sczyrba A., Egan R., et al. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 2011, 331:463-467.
68. Brulc J.M., Antonopoulos D.A., Miller M.E.B., et al. Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci U S A 2009, 106:1948-1953.
69. Morgavi D.P., Kelly W.J., Janssen P.H., Attwood G.T. Rumen microbial (meta) genomics and its application to ruminant production. Animal 2013, 7:184-201.
70. Kittelmann S., Seedorf H., Walters W.A., et al. Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities. PLoS ONE 2013, 8(2):e47879.
71. Fricke W.F., Seedorf H., Henne A., et al. The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H-2 for methane formation and ATP synthesis. J Bacteriol 2006, 188:642-658.
72. Borrel G., Harris H.M.B., Toney W., et al. Genome sequence of "Candidatus Methanomethylophilus alvus" Mx1201, a methanogenic archaeon from the human gut belonging to a seventh order of methanogens. J Bacteriol 2012, 194:6944-6945.
73. Paul K., Nonoh J.O., Mikulski L., Brune A. "Methanoplasmatales", Thermoplasmatales-related archaea in termite guts and other environments, are the seventh order of methanogens. Appl Environ Microbiol 2012, 78:8245-8253.
74. Neill A.R., Grime D.W., Dawson R.M.C. Conversion of choline methyl-groups through trimethylamine into methane in rumen. Biochem J 1978, 170:529-535.
75. Poulsen M., Schwab C., Jensen B.B., et al. Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen. Nat Commun 2013, 4:1428.