Looking large, to make more, out of gut metagenomics
Tài liệu tham khảo
Mackie, 2002, Mutualistic fermentative digestion in the gastrointestinal tract: diversity and evolution, Integr Comp Biol, 42, 319, 10.1093/icb/42.2.319
Stevens, 2004, 400
Mackie, 1997
Stahl, 1988, Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology, Appl Environ Microbiol, 54, 1079, 10.1128/AEM.54.5.1079-1084.1988
Ley, 2008, Worlds within worlds: evolution of the vertebrate gut microbiota, Nat Rev Microbiol, 6, 776, 10.1038/nrmicro1978
Rajilic-Stojanovic, 2007, Diversity of the human gastrointestinal tract microbiota revisited, Environ Microbiol, 9, 2125, 10.1111/j.1462-2920.2007.01369.x
Samuel, 2007, Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut, Proc Natl Acad Sci U S A, 104, 10643, 10.1073/pnas.0704189104
Xu, 2003, A genomic view of the human-Bacteroides thetaiotaomicron symbiosis, Science, 299, 2074, 10.1126/science.1080029
Booijink, 2007, Microbial communities in the human small intestine: coupling diversity to metagenomics, Future Microbiol, 2, 285, 10.2217/17460913.2.3.285
Gill, 2006, Metagenomic analysis of the human distal gut microbiome, Science, 312, 1355, 10.1126/science.1124234
Kurokawa, 2007, Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes, DNA Res, 14, 169, 10.1093/dnares/dsm018
Arumugam, 2011, Enterotypes of the human gut microbiome, Nature, 473, 174, 10.1038/nature09944
Qin, 2010, A human gut microbial gene catalogue established by metagenomic sequencing, Nature, 464, 59, 10.1038/nature08821
Qin, 2012, A metagenome-wide association study of gut microbiota in type 2 diabetes, Nature, 490, 55, 10.1038/nature11450
Human Microbiome Project Consortium, 2012, A framework for human microbiome research, Nature, 486, 215, 10.1038/nature11209
Human Microbiome Project Consortium, 2012, Structure, function and diversity of the healthy human microbiome, Nature, 486, 207, 10.1038/nature11234
Gevers, 2012, The Human Microbiome Project: a community resource for the healthy human microbiome, PLoS Biol, 10, e1001377, 10.1371/journal.pbio.1001377
Sommer, 2013, The gut microbiota — masters of host development and physiology, Nat Rev Microbiol, 11, 227, 10.1038/nrmicro2974
Dusko Ehrlich, 2010, Metagenomics of the intestinal microbiota: potential applications, Gastroenterol Clin Biol, 34, S23, 10.1016/S0399-8320(10)70017-8
Madupu, 2013, Microbiome in human health and disease, Sci Prog, 96, 153, 10.3184/003685013X13683759820813
Henao-Mejia, 2012, Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity, Nature, 482, 179, 10.1038/nature10809
Tang, 2013, Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk, N Engl J Med, 368, 1575, 10.1056/NEJMoa1109400
Wang, 2011, Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease, Nature, 472, 57, 10.1038/nature09922
Fukuda, 2011, Bifidobacteria can protect from enteropathogenic infection through production of acetate, Nature, 469, 543, 10.1038/nature09646
Devkota, 2012, Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10−/− mice, Nature, 487, 104, 10.1038/nature11225
Cho, 2012, Antibiotics in early life alter the murine colonic microbiome and adiposity, Nature, 488, 621, 10.1038/nature11400
Benson, 2010, 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, 107, 18933, 10.1073/pnas.1007028107
Ley, 2008, Evolution of mammals and their gut microbes, Science, 320, 1647, 10.1126/science.1155725
Baker, 2008, Animal models in nutrition research, J Nutr, 138, 391, 10.1093/jn/138.2.391
Bauman, 2011, Nutrigenomics, rumen-derived bioactive fatty acids, and the regulation of milk fat synthesis, Annu Rev Nutr, 31, 299, 10.1146/annurev.nutr.012809.104648
Bauman, 2008, Regulation of fat synthesis by conjugated linoleic acid: lactation and the ruminant model, J Nutr, 138, 403, 10.1093/jn/138.2.403
Spurlock, 2008, The development of porcine models of obesity and the metabolic syndrome, J Nutr, 138, 397, 10.1093/jn/138.2.397
Lanzas, 2010, Model or meal? Farm animal populations as models for infectious diseases of humans, Nat Rev Microbiol, 8, 139, 10.1038/nrmicro2268
Buddington, 2011, Companion animals symposium: development of the mammalian gastrointestinal tract, the resident microbiota, and the role of diet in early life, J Anim Sci, 89, 1506, 10.2527/jas.2010-3705
Gootenberg, 2011, Companion animals symposium: humanized animal models of the microbiome, J Anim Sci, 89, 1531, 10.2527/jas.2010-3371
Suchodolski, 2011, Companion animals symposium: microbes and gastrointestinal health of dogs and cats, J Anim Sci, 89, 1520, 10.2527/jas.2010-3377
Swanson, 2011, Companion animals symposium: microbes and health, J Anim Sci, 89, 1496, 10.2527/jas.2011-3873
Kerr, 2013, 2011 and 2012 Early Careers Achievement Awards: use of genomic biology to study companion animal intestinal microbiota, J Anim Sci, 91, 2504, 10.2527/jas.2012-6225
Christoffersen, 2013, The young Gottingen minipig as a model of childhood and adolescent obesity: influence of diet and gender, Obesity (Silver Spring), 21, 149, 10.1002/oby.20249
Pedersen, 2013, Characterisation of gut microbiota in Ossabaw and Gottingen minipigs as models of obesity and metabolic syndrome, PLoS ONE, 8, e56612, 10.1371/journal.pone.0056612
Pang, 2007, Inter-species transplantation of gut microbiota from human to pigs, ISME J, 1, 156, 10.1038/ismej.2007.23
Laycock, 2012, A defined intestinal colonization microbiota for gnotobiotic pigs, Vet Immunol Immunopathol, 149, 216, 10.1016/j.vetimm.2012.07.004
Fei, 2013, An opportunistic pathogen isolated from the gut of an obese human causes obesity in germfree mice, ISME J, 7, 880, 10.1038/ismej.2012.153
Zhao, 2013, The gut microbiota and obesity: from correlation to causality, Nat Rev Microbiol, 11, 639, 10.1038/nrmicro3089
Guilloteau, 2010, Nutritional programming of gastrointestinal tract development. Is the pig a good model for man?, Nutr Res Rev, 23, 4, 10.1017/S0954422410000077
Sangild, 2013, Invited review: the preterm pig as a model in pediatric gastroenterology, J Anim Sci, 91, 4713, 10.2527/jas.2013-6359
Donovan, 2012, Host–microbe interactions in the neonatal intestine: role of human milk oligosaccharides, Adv Nutr, 3, 450S, 10.3945/an.112.001859
Li, 2012, Microbial composition and in vitro fermentation patterns of human milk oligosaccharides and prebiotics differ between formula-fed and sow-reared piglets, J Nutr, 142, 681, 10.3945/jn.111.154427
Poroyko, 2010, Gut microbial gene expression in mother-fed and formula-fed piglets, PLoS ONE, 5, e12459, 10.1371/journal.pone.0012459
Poroyko, 2011, Diet creates metabolic niches in the “immature gut” that shape microbial communities, Nutr Hosp, 26, 1283
Puiman, 2013, Modulation of the gut microbiota with antibiotic treatment suppresses whole body urea production in neonatal pigs, Am J Physiol-Gastrointest Liver Physiol, 304, G300, 10.1152/ajpgi.00229.2011
Burrin, 2013, Digestive Physiology of the Pig Symposium: Intestinal bile acid sensing is linked to key endocrine and metabolic signaling pathways, J Anim Sci, 91, 1991, 10.2527/jas.2013-6331
Renfree, 2010, Review: Marsupials: placental mammals with a difference, Placenta, 31, S21, 10.1016/j.placenta.2009.12.023
Hume, 1999
Kempton, 1976, Methane production and digestibility measurements in the grey kangaroo and sheep, Aust J Biol Sci, 29, 209, 10.1071/BI9760209
Madsen, 2012, Methane production by red-necked wallabies (Macropus rufogriseus), J Anim Sci, 90, 1364, 10.2527/jas.2011-4011
Morrison, 2007, The vertebrate animal gut in context — microbiomes, methane and metagenomics, Microbiol Aust, 28, 107, 10.1071/MA07107
Morrison, 2009, Plant biomass degradation by gut microbiomes: more of the same or something new?, Curr Opin Biotechnol, 20, 358, 10.1016/j.copbio.2009.05.004
Pope, 2010, Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores, Proc Natl Acad Sci U S A, 107, 14793, 10.1073/pnas.1005297107
Patil, 2011, Taxonomic metagenome sequence assignment with structured output models, Nat Methods, 8, 191, 10.1038/nmeth0311-191
Patil, 2012, The PhyloPythiaS web server for taxonomic assignment of metagenome sequences, PLoS ONE, 7, e38581, 10.1371/journal.pone.0038581
Pope, 2011, Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies, Science, 333, 646, 10.1126/science.1205760
Evans, 2009, Community composition and density of methanogens in the foregut of the Tammar wallaby (Macropus eugenii), Appl Environ Microbiol, 75, 2598, 10.1128/AEM.02436-08
Gagen, 2010, Functional gene analysis suggests different acetogen populations in the bovine rumen and tammar wallaby forestomach, Appl Environ Microbiol, 76, 7785, 10.1128/AEM.01679-10
Omsland, 2009, Host cell-free growth of the Q fever bacterium Coxiella burnetii, Proc Natl Acad Sci U S A, 106, 4430, 10.1073/pnas.0812074106
Tyson, 2005, Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp nov from an acidophilic microbial community, Appl Environ Microbiol, 71, 6319, 10.1128/AEM.71.10.6319-6324.2005
Hess, 2011, Metagenomic discovery of biomass-degrading genes and genomes from cow rumen, Science, 331, 463, 10.1126/science.1200387
Brulc, 2009, Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases, Proc Natl Acad Sci U S A, 106, 1948, 10.1073/pnas.0806191105
Morgavi, 2013, Rumen microbial (meta) genomics and its application to ruminant production, Animal, 7, 184, 10.1017/S1751731112000419
Kittelmann, 2013, Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities, PLoS ONE, 8, e47879, 10.1371/journal.pone.0047879
Fricke, 2006, 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, 188, 642, 10.1128/JB.188.2.642-658.2006
Borrel, 2012, Genome sequence of “Candidatus Methanomethylophilus alvus” Mx1201, a methanogenic archaeon from the human gut belonging to a seventh order of methanogens, J Bacteriol, 194, 6944, 10.1128/JB.01867-12
Paul, 2012, “Methanoplasmatales”, Thermoplasmatales-related archaea in termite guts and other environments, are the seventh order of methanogens, Appl Environ Microbiol, 78, 8245, 10.1128/AEM.02193-12
Neill, 1978, Conversion of choline methyl-groups through trimethylamine into methane in rumen, Biochem J, 170, 529, 10.1042/bj1700529
Poulsen, 2013, Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen, Nat Commun, 4, 1428, 10.1038/ncomms2432