张晨虹, 杨鑫 . 微生物组与人体健康研究策略及方法[J]. 诊断学理论与实践, 2019 , 18(03) : 250 -257 . DOI: 10.16150/j.1671-2870.2019.03.003
| [1] | Obesity: preventing and managing the global epidemic. Report of a WHO consultation[J]. World Health Organ Tech Rep Ser, 2000, 894:i-xii,1-253. |
| [2] | Morabia A, Abel T. The WHO report "Preventing chronic diseases: a vital investment" and us[J]. Soz Praventivmed, 2006, 51(2):74. |
| [3] | Willett WC. Overview and perspective in human nutrition[J]. Asia Pac J Clin Nutr, 2008, 17(Suppl 1):1-4. |
| [4] | Kell DB. Metabolomics and systems biology: making sense of the soup[J]. Curr Opin Microbiol, 2004, 7(3):296-307. |
| [5] | The Science of Synthesis: Exploring the Social Implications of General Systems Theory(Book)[M]. Choice: Current Reviews for Academic Libraries, 2004,1114. |
| [6] | Wayne LG. International Committee on Systematic Bacteriology: announcement of the report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics[J]. Zentralbl Bakteriol Mikrobiol Hyg A, 1988, 268(4):433-434. |
| [7] | Rasko DA, Rosovitz MJ, Myers GS, et al. The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates[J]. J Bacteriol, 2008, 190(20):6881-6893. |
| [8] | Smokvina T, Wels M, Polka J, et al. Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity[J]. PLoS One, 2013, 8(7):e68731. |
| [9] | Turnbaugh PJ, Ley RE, Mahowald MA, et al. An obesity-associated gut microbiome with increased capacity for energy harvest[J]. Nature, 2006, 444(7122):1027-1031. |
| [10] | Zhao L. The gut microbiota and obesity: from correlation to causality[M]. Nat Rev Microbiol, 2013:639-647. |
| [11] | Zhao L. The gut microbiota and obesity: from correlation to causality[J]. Nat Rev Microbiol, 2013, 11(9):639-647. |
| [12] | Fei N, Zhao L. An opportunistic pathogen isolated from the gut of an obese human causes obesity in germfree mice[J]. ISME J, 2013, 7(4):880-884. |
| [13] | Zhang C, Yin A, Li H, et al. Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children[J]. EBioMedicine, 2015, 2(8):968-984. |
| [14] | Zhao L, Zhang F, Ding X, et al. Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes[J]. Science, 2018, 359(6380):1151-1156. |
| [15] | Merriman B, Ion Torrent R&D Team, Rothberg JM. Progress in ion torrent semiconductor chip based sequencing[J]. Electrophoresis, 2012, 33(23):3397-3417. |
| [16] | Garrido-Cardenas JA, Manzano-Agugliaro F. The metagenomics worldwide research[J]. Curr Genet, 2017, 63(5):819-829. |
| [17] | Integrative HMP iHMP Research Network Consortium. The Integrative Human Microbiome Project[J]. Nature, 2019, 569(7758):641-648. |
| [18] | Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome[J]. Nature, 2012, 486(7402):207-214. |
| [19] | Li J, Jia H, Cai X, et al. An integrated catalog of refe-rence genes in the human gut microbiome[J]. Nat Biote-chnol, 2014, 32(8):834-841. |
| [20] | Dubilier N, McFall-Ngai M, Zhao L. Microbiology: Create a global microbiome effort[J]. Nature, 2015, 526(7575):631-634. |
| [21] | Handelsman J, Rondon MR, Brady SF, et al. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products[J]. Chem Biol, 1998, 5(10):R245-R249. |
| [22] | Chen K, Pachter L. Bioinformatics for whole-genome shotgun sequencing of microbial communities[J]. PLoS Comput Biol, 2005, 1(2):106-112. |
| [23] | Gill SR, Pop M, Deboy RT, et al. Metagenomic analysis of the human distal gut microbiome[J]. Science, 2006, 312(5778):1355-1359. |
| [24] | Poinar HN, Schwarz C, Qi J, et al. Metagenomics to paleo-genomics: large-scale sequencing of mammoth DNA[J]. Science, 2006, 311(5759):392-394. |
| [25] | Xiong X, Frank DN, Robertson CE, et al. Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing[J]. PLoS One, 2012, 7(4):e36009. |
| [26] | Nicholson JK, Lindon JC, Holmes E. 'Metabonomics': understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data[J]. Xenobiotica, 1999, 29(11):1181-1189. |
| [27] | Nicholson JK, Holmes E, Wilson ID. Gut microorganisms, mammalian metabolism and personalized health care[J]. Nat Rev Microbiol, 2005, 3(5):431-438. |
| [28] | Rezzi S, Ramadan Z, Fay LB, et al. Nutritional metabonomics: applications and perspectives[J]. J Proteome Res, 2007, 6(2):513-525. |
| [29] | Dumas ME, Maibaum EC, Teague C, et al. Assessment of analytical reproducibility of 1H NMR spectroscopy based metabonomics for large-scale epidemiological research: the INTERMAP Study[J]. Anal Chem, 2006, 78(7):2199-2208. |
| [30] | Holmes E, Loo RL, Stamler J, et al. Human metabolic phenotype diversity and its association with diet and blood pressure[J]. Nature, 2008, 453(7193):396-400. |
| [31] | Rezzi S, Ramadan Z, Martin FP, et al. Human metabolic phenotypes link directly to specific dietary preferences in healthy individuals[J]. J Proteome Res, 2007, 6(11):4469-4477. |
| [32] | Robosky LC, Wells DF, Egnash LA, et al. Communication regarding metabonomic identification of two distinct phenotypes in Sprague-Dawley (Crl:CD(SD)) rats[J]. Toxicol Sci, 2006, 91(1):309. |
| [33] | Stella C, Beckwith-Hall B, Cloarec O, et al. Susceptibility of human metabolic phenotypes to dietary modulation[J]. J Proteome Res, 2006, 5(10):2780-2788. |
| [34] | Wan Q, Wang Y, Tang H. Quantitative 13C Traces of Glucose Fate in Hepatitis B Virus-Infected Hepatocytes[J]. Anal Chem, 2017, 89(6):3293-3299. |
| [35] | Liu F, Zhang N, Li Z, et al. Chondroitin sulfate disaccharides modified the structure and function of the murine gut microbiome under healthy and stressed conditions[J]. Sci Rep, 2017, 7(1):6783. |
| [36] | Rabot S, Membrez M, Bruneau A, et al. Germ-free C57BL/6J mice are resistant to high-fat-diet-induced insulin resistance and have altered cholesterol metabolism[J]. FASEB J, 2010, 24(12):4948-4959. |
| [37] | Cani PD, Possemiers S, Van de Wiele T, et al. Changes in gut microbiota control inflammation in obese mice through a mechanism involving GLP-2-driven improvement of gut permeability[J]. Gut, 2009, 58(8):1091-1103. |
| [38] | Maslowski KM, Vieira AT, Ng A, et al. Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43[J]. Nature, 2009, 461(7268):1282-1286. |
| [39] | Smith PM, Howitt MR, Panikov N, et al. The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis[J]. Science, 2013, 341(6145):569-573. |
| [40] | Furusawa Y, Obata Y, Fukuda S, et al. Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells[J]. Nature, 2013, 504(7480):446-450. |
| [41] | Rezzi S, Ramadan Z, Martin FP, et al. Human metabolic phenotypes link directly to specific dietary preferences in healthy individuals[J]. J Proteome Res, 2007, 6(11):4469-4477. |
| [42] | Kaeberlein T, Lewis K, Epstein SS. Isolating "uncultivable" microorganisms in pure culture in a simulated natural environment[J]. Science, 2002, 296(5570):1127-1129. |
| [43] | Nichols D, Cahoon N, Trakhtenberg EM, et al. Use of ichip for high-throughput in situ cultivation of "uncultivable" microbial species[J]. Appl Environ Microbiol, 2010, 76(8):2445-2450. |
| [44] | Lagier JC, Dubourg G, Million M, et al. Culturing the human microbiota and culturomics[J]. Nat Rev Microbiol, 2018:540-550. |
| [45] | Krasny L, Hynek R, Hochel I. Identification of bacteria using mass spectrometry techniques[J]. Int J Mass Spectrom, 2013, 353:67-79. |
| [46] | Fenselau C, Demirev PA. Characterization of intact microorganisms by MALDI mass spectrometry[J]. Mass Spect-rom Rev, 2001, 20(4):157-171. |
| [47] | Seng P, Drancourt M, Gouriet F, et al. Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry[J]. Clin Infect Dis, 2009, 49(4):543-551. |
| [48] | Seng P, Abat C, Rolain JM, et al. Identification of rare pathogenic bacteria in a clinical microbiology laboratory: impact of matrix-assisted laser desorption ionization-time of flight mass spectrometry[J]. J Clin Microbiol, 2013, 51(7):2182-2194. |
| [49] | Lagier JC, Hugon P, Khelaifia S, et al. The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota[J]. Clin Microbiol Rev, 2015, 28(1):237-264. |
| [50] | Zou Y, Xue W, Luo G, et al. 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses[J]. Nat Biotechnol, 2019, 37(2):179-185. |
| [51] | van der Ark KCH, van Heck RGA, Martins Dos Santos VAP, et al. More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes[J]. Microbiome, 2017, 5(1):78. |
| [52] | Zarecki R, Oberhardt MA, Reshef L, et al. A novel nutritional predictor links microbial fastidiousness with lo-wered ubiquity, growth rate, and cooperativeness[J]. PLoS Comput Biol, 2014, 10(7):e1003726. |
| [53] | Zilber-Rosenberg I, Rosenberg E. Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution[J]. FEMS Microbiol Rev, 2008, 32(5):723-735. |
/
| 〈 |
|
〉 |
