|
|
|
Human gut microbiome: the second genome of human
body |
| Baoli Zhu1,Xin Wang2,Lanjuan Li3, |
| 1.CAS Key Laboratory of
Pathogenic Microbiology and Immunology, Institute of Microbiology,
Chinese Academy of Sciences, Beijing 100101, China; 2.Institute of Plant Protection
and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou
310021, China; 3.State Key Laboratory
for Diagnosis and Treatment of Infectious Diseases, the First Affiliated
Hospital, College of Medicine, Zhejiang University, Hangzhou 310003,
China; |
|
|
|
|
Abstract 21\13\60\4b\hcm0000168463.html
|
|
Issue Date: 01 August 2010
|
|
|
Ahmed, S., Macfarlane, G.T., Fite, A., McBain, A.J., Gilbert, P., and Macfarlane, S. (2007). Mucosa-Associatedbacterial diversity in relation to human terminal ileum and colonicbiopsy samples. Appl Environ Microbiol73, 7435―7442.
doi: 10.1128/AEM.01143-07
|
|
Aoi, Y., Kinoshita, T., Hata, T., Ohta, H., Obokata, H., and Tsuneda, S. (2009). Hollow-fiber membrane chamber as a device for in situenvironmental cultivation. Appl EnvironMicrobiol75, 3826―3833.
doi: 10.1128/AEM.02542-08
|
|
B?ckhed, F., Ley, R.E., Sonnenburg, J.L., Peterson, D.A., and Gordon, J.I. (2005). Host-bacterialmutualism in the human intestine. Science307, 1915―1920.
doi: 10.1126/science.1104816
|
|
Bollmann, A., Lewis, K., and Epstein, S.S. (2007). Incubationof environmental samples in a diffusion chamber increases the diversityof recovered isolates. Appl Environ Microbiol73, 6386―6390.
doi: 10.1128/AEM.01309-07
|
|
Child, M.W., Kennedy, A., Walker, A.W., Bahrami, B., Macfarlane, S., and Macfarlane, G.T. (2006). Studieson the effect of system retention time on bacterial populations colonizinga three-stage continuous culture model of the human large gut usingFISH techniques. FEMS Microbiol Ecol55, 299―310.
doi: 10.1111/j.1574-6941.2005.00016.x
|
|
Davies, J. (2001). In a map for human life, count the microbes, too. Science291, 2316.
doi: 10.1126/science.291.5512.2316b
|
|
Eckburg, P.B., Bik, E.M., Bernstein, C.N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S.R., Nelson, K.E., and Relman, D.A. (2005). Diversity of thehuman intestinal microbial flora. Science308, 1635―1638.
doi: 10.1126/science.1110591
|
|
Gaboriau-Routhiau, V., Rakotobe, S., Lécuyer, E., Mulder, I., Lan, A., Bridonneau, C., Rochet, V., Pisi, A., De Paepe, M., Brandi, G., Eberl, G., Snel, J., Kelly, D., Cerf-Bensussan, N. (2009). Thekey role of segmented filamentous bacteria in the coordinated maturationof gut helper T cell responses. Immunity31,677―689.
doi: 10.1016/j.immuni.2009.08.020
|
|
Gibson, G.R., and Wang, X. (1994). Enrichmentof bifidobacteria from human gut contents by oligofructose using continuousculture. FEMS Microbiol Lett118, 121―127.
doi: 10.1111/j.1574-6968.1994.tb06813.x
|
|
Gill, S.R., Pop, M., Deboy, R.T., Eckburg, P.B., Turnbaugh, P.J., Samuel, B.S., Gordon, J.I., Relman, D.A., Fraser-Liggett, C.M., and Nelson, K.E. (2006). Metagenomic analysis of the human distal gut microbiome. Science312, 1355―1359.
doi: 10.1126/science.1124234
|
|
Haller, D., Jobin, C. (2004). Interactionbetween resident luminal bacteria and the host: can a healthy relationshipturn sour? J Pediatr Gastroenterol Nutr38, 123―136.
doi: 10.1097/00005176-200402000-00004
|
|
Handelsman, J. (2004). Metagenomics: application of genomics to unculturedmicroorganisms. Microbiol Mol Biol Rev68, 669―685.
doi: 10.1128/MMBR.68.4.669-685.2004
|
|
Handelsman, J., Rondon, M.R., Brady, S.F., Clardy, J., and Goodman, R.M. (1998). Molecularbiological access to the chemistry of unknown soil microbes: a newfrontier for natural products. Chem Biol5, R245―R249.
doi: 10.1016/S1074-5521(98)90108-9
|
|
Hayashi, H., Sakamoto, M., and Benno, Y. (2002). Fecal microbialdiversity in a strict vegetarian as determined by molecular analysisand cultivation. Microbiol Immunol46, 819―831.
|
|
Hehemann, J.H., Correc, G., Barbeyron, T., Helbert, W., Czjzek, M., and Michel, G. (2010). Transfer of carbohydrate-activeenzymes from marine bacteria to Japanese gut microbiota. Nature464, 908―912.
doi: 10.1038/nature08937
|
|
Hold, G.L., Pryde, S.E., Russell, V.J., Furrie, E., and Flint, H.J. (2002). Assessmentof microbial diversity in human colonic samples by 16S rDNA sequenceanalysis. FEMS Microbiol Ecol39, 33―39.
doi: 10.1111/j.1574-6941.2002.tb00904.x
|
|
Hooper, L.V., and Gordon, J.I. (2001). Commensalhost-bacterial relationships in the gut. Science292, 1115―1118.
doi: 10.1126/science.1058709
|
|
Ivanov, II., Atarashi, K., Manel, N., Brodie, E.L., Shima, T., Karaoz, U., Wei, D., Goldfarb, K.C., Santee, C.A., Lynch, S.V., Tanoue, T., Imaoka, A., Itoh, K., Takeda, K., Umesaki, Y., Honda, K., Littman, D.R. (2009). Induction of intestinal Th17 cellsby segmented filamentous bacteria. Cell139,485―498.
doi: 10.1016/j.cell.2009.09.033
|
|
Ivanov, II., Frutos Rde, L., Manel, N., Yoshinaga, K., Rifkin, D.B., Sartor, R.B., Finlay, B.B., Littman, D.R. (2008). Specificmicrobiota direct the differentiation of IL-17-producing T-helpercells in the mucosa of the small intestine. Cell Host Microbe4,337―349.
doi: 10.1016/j.chom.2008.09.009
|
|
Kitahara, M., Sakamoto, M., Ike, M., Sakata, S., and Benno, Y. (2005). Bacteroides plebeius sp. nov. and Bacteroides coprocolasp. nov., isolated from human faeces. Int J Syst Evol Microbiol55, 2143―2147.
doi: 10.1099/ijs.0.63788-0
|
|
Kurokawa, K., Itoh, T., Kuwahara, T., Oshima, K., Toh, H., Toyoda, A., Takami, H., Morita, H., Sharma, V.K., Srivastava, T.P., et al.(2007). Comparative metagenomics revealed commonlyenriched gene sets in human gut microbiomes. DNA Res14, 169―181.
doi: 10.1093/dnares/dsm018
|
|
Langendijk, P.S., Schut, F., Jansen, G.J., Raangs, G.C., Kamphuis, G.R., Wilkinson, M.H.F., and Welling, G.W. (1995). Quantitative fluorescence in situ hybridization of Bifidobacteriumspp. with genus-specific 16S rRNA-targeted probes and its applicationin fecal samples. Appl Environ Microbiol61, 3069―3075.
|
|
Lederberg, J., and McCray, A.T. (2001). ‘OmeSweet ’ Omics—a genealogical treasury of words. The Scientist15, 8.
|
|
Ley, R.E., Peterson, D.A., and Gordon, J.I. (2006). Ecological and evolutionaryforces shaping microbial diversity in the human intestine. Cell124, 837―848.
doi: 10.1016/j.cell.2006.02.017
|
|
Macfarlane, G.T., and Macfarlane, S. (2007). Modelsfor intestinal fermentation: association between food components,delivery systems, bioavailability and functional interactions in thegut. Curr Opin Biotechnol18, 156―162.
doi: 10.1016/j.copbio.2007.01.011
|
|
Macfarlane, G.T., Gibson, G.R., and Cummings, J.H. (1992). Comparisonof fermentation reactions in different regions of the human colon. J Appl Bacterial72, 57―64
|
|
Macfarlane, G.T., Macfarlane, S., and Gibson, G.R. (1998). Use of a three stagecompound continuous culture systems to investigate bacterial growthand metabolism in the human colonic microbiota. Microb Ecol35, 180―187.
doi: 10.1007/s002489900072
|
|
Martinon, F., and Tschopp, J.T. (2005). NLRsjoin TLRs as innate sensors of pathogens. Trends Immunol26, 447―454.
doi: 10.1016/j.it.2005.06.004
|
|
Michelsen, K.S., Aicher, A., Mohaupt, M., Hartung, T., Dimmeler, S., Kirschning, C.J., and Schumann, R.R. (2001). The role of toll-like receptors (TLRs) in bacteria-inducedmaturation of murine dendritic cells (DCS). Peptidoglycan and lipoteichoicacid are inducers of DC maturation and require TLR2. J Biol Chem276, 25680―25686.
doi: 10.1074/jbc.M011615200
|
|
Nichols, D., Cahoon, N., Trakhtenberg, E.M., Pham, L., Mehta, A., Belanger, A., Kanigan, T., Lewis, K., and Epstein, S.S. (2010). Useof ichip for high-throughput in situ cultivation of "uncultivable"microbial species. Appl Environ Microbiol76, 2445―2450.
doi: 10.1128/AEM.01754-09
|
|
Palframan, R.J., Gibson, G.R., and Rastall, R.A. (2002). Effectof pH and dose on the growth of gut bacteria on prebiotic carbohydrates in vitro. Anaerobe8, 287―292.
doi: 10.1006/anae.2002.0434
|
|
Peterson, J., Garges, S., Giovanni, M., McInnes, P., Wang, L., Schloss, J.A., Bonazzi, V., McEwen, J.E., Wetterstrand, K.A., Deal, C., et al, and the NIH HMP Working Group. (2009). The NIH Human Microbiome Project. GenomeRes19, 2317―2323.
doi: 10.1101/gr.096651.109
|
|
Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K.S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., Yamada, T., et al, and the MetaHIT Consortium. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature464, 59―65.
doi: 10.1038/nature08821
|
|
Relman, D.A. (2002). New technologies, human-microbe interactions, and thesearch for previously unrecognized pathogens. J Infect Dis186, S254―S258.
doi: 10.1086/344935
|
|
Relman, D.A., and Falkow, S. (2001). Themeaning and impact of the human genome sequence for microbiology. Trends Microbiol9, 206―208.
doi: 10.1016/S0966-842X(01)02041-8
|
|
Savage, D.C. (1977). Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol31, 107―133.
doi: 10.1146/annurev.mi.31.100177.000543
|
|
Suau, A., Bonnet, R., Sutren, M., Godon, J.J., Gibson, G.R., Collins, M.D., and Doré, J. (1999). Direct analysis of genes encoding 16S rRNA from complexcommunities reveals many novel molecular species within the humangut. Appl Environ Microbiol65, 4799―4807.
|
|
Tap, J., Mondot, S., Levenez, F., Pelletier, E., Caron, C., Furet, J.P., Ugarte, E., Mu?oz-Tamayo, R., Paslier, D.L., Nalin, R., et al. (2009). Towards the human intestinalmicrobiota phylogenetic core. Environ Microbiol11, 2574―2584.
doi: 10.1111/j.1462-2920.2009.01982.x
|
|
Turnbaugh, P.J., Ley, R.E., Hamady, M., Fraser-Liggett, C.M., Knight, R., and Gordon, J.I. (2007). The human microbiomeproject. Nature449, 804―810.
doi: 10.1038/nature06244
|
|
Turnbaugh, P.J., Hamady, M., Yatsunenko, T., Cantarel, B.L., Duncan, A., Ley, R.E., Sogin, M.L., Jones, W.J., Roe, B.A., Affourtit, J.P., et al.(2009). A core gut microbiome in obese andlean twins. Nature457, 480―484.
doi: 10.1038/nature07540
|
|
Umesaki, Y., Okada, Y., Matsumoto, S., Imaoka, A., Setoyama, H. (1995). Segmentedfilamentous bacteria are indigenous intestinal bacteria that activateintraepithelial lymphocytes and induce MHC class II molecules andfucosyl asialo GM1 glycolipids on the small intestinal epithelialcells in the ex-germ-free mouse. MicrobiolImmunol39, 555―562.
|
|
Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., Eisen, J.A., Wu, D., Paulsen, I., Nelson, K.E., Nelson, W., et al. (2004). Environmental genome shotgun sequencing of the Sargasso Sea. Science304, 66―74.
doi: 10.1126/science.1093857
|
|
Wang, X., Gibson, G.R. (1993). Effectsof the in vitro fermentation of oligofructose and inulin by bacteriagrowing in the human large intestine. JAppl Bacteriol75, 373―380.
|
|
Wang, X., Heazlewood, S.P., Krause, D.O., and Florin, T.H. (2003). Molecular characterization of the microbial speciesthat colonize human ileal and colonic mucosa by using 16S rDNA sequenceanalysis. J Appl Microbiol95, 508―520.
doi: 10.1046/j.1365-2672.2003.02005.x
|
|
Winitz, M., Adams, R.F., Seedman, D.A., Davis, P.N., Jayko, L.G., and Hamilton, J.A. (1970). Studiesin metabolic nutrition employing chemically defined diets. II. Effectson gut microflora populations. Am J ClinNutr23, 546―559.
|
|
Yamauchi, K.E., Snel, J. (2000). Transmissionelectron microscopic demonstration of phagocytosis and intracellularprocessing of segmented filamentous bacteria by intestinal epithelialcells of the chick ileum. Infect Immun68, 6496―6504.
doi: 10.1128/IAI.68.11.6496-6504.2000
|
|
Yin, Y., Lei, F., Zhu, L., Li, S., Wu, Z., Zhang, R., Gao, G.F., Zhu, B., Wang, X. (2010). Exposure of different bacterial inocula to newborn chicken affectsgut microbiota development and ileum gene expression. ISME J4, 367―376.
doi: 10.1038/ismej.2009.128
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
| |
Shared |
|
|
|
|
| |
Discussed |
|
|
|
|
