메뉴 건너뛰기




Volumn 5, Issue 2, 2014, Pages 192-201

Early life establishment of site-specific microbial communities in the gut

Author keywords

Fecal microbiome; Host microbial interactions; Intestinal bacterial diversity; Mucosal immunity; Neonatal microbiome

Indexed keywords

ARTICLE; BACTERIAL LOAD; BIOGEOGRAPHY; BOOTSTRAPPING; CLINICAL ARTICLE; DNA EXTRACTION; EARLY LIFE STRESS; ENTEROCOCCUS FAECALIS; FECES MICROFLORA; FEMALE; GASTROINTESTINAL TRACT; HUMAN; IMMUNE SYSTEM; INTESTINE FLORA; MALE; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MUCOSAL IMMUNITY; NEWBORN; NONHUMAN; PHYLOGENY; PRINCIPAL COMPONENT ANALYSIS; PROBABILITY; PYROSEQUENCING; REAL TIME POLYMERASE CHAIN REACTION; BACTERIA; FECES; GENETICS; INTESTINE MUCOSA; ISOLATION AND PURIFICATION; MICROBIOLOGY;

EID: 84900526712     PISSN: 19490976     EISSN: 19490984     Source Type: Journal    
DOI: 10.4161/gmic.28442     Document Type: Article
Times cited : (53)

References (46)
  • 1
    • 1542316379 scopus 로고    scopus 로고
    • Bacterial contributions to mammalian gut development
    • PMID:15001189
    • Hooper LV. Bacterial contributions to mammalian gut development. Trends Microbiol 2004; 12:129-34; PMID:15001189; http://dx.doi.org/10.1016/j.tim.2004.01.001
    • (2004) Trends Microbiol , vol.12 , pp. 129-134
    • Hooper, L.V.1
  • 2
    • 22144490199 scopus 로고    scopus 로고
    • An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system
    • PMID:16009137
    • Mazmanian SK, Liu CH, Tzianabos AO, Kasper DL. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 2005; 122:107-18; PMID:16009137; http://dx.doi.org/10.1016/j.cell.2005.05.007
    • (2005) Cell , vol.122 , pp. 107-118
    • Mazmanian, S.K.1    Liu, C.H.2    Tzianabos, A.O.3    Kasper, D.L.4
  • 3
    • 0035843993 scopus 로고    scopus 로고
    • Commensal host-bacterial relationships in the gut
    • PMID:11352068
    • Hooper LV, Gordon JI. Commensal host-bacterial relationships in the gut. Science 2001; 292:1115-8; PMID:11352068; http://dx.doi.org/10.1126/science.1058709
    • (2001) Science , vol.292 , pp. 1115-1118
    • Hooper, L.V.1    Gordon, J.I.2
  • 4
    • 0034802944 scopus 로고    scopus 로고
    • IgA responses in the intestinal mucosa against pathogenic and non-pathogenic microorganisms
    • PMID:11580989
    • Macpherson AJ, Hunziker L, McCoy K, Lamarre A. IgA responses in the intestinal mucosa against pathogenic and non-pathogenic microorganisms. Microbes Infect 2001; 3:1021-35; PMID:11580989; http://dx.doi.org/10.1016/S1286-4579(01)01460-5
    • (2001) Microbes Infect , vol.3 , pp. 1021-1035
    • McPherson, A.J.1    Hunziker, L.2    McCoy, K.3    Lamarre, A.4
  • 5
    • 0036971220 scopus 로고    scopus 로고
    • The functions of mucosal T cells in containing the indigenous commensal flora of the intestine
    • PMID:12568335
    • Macpherson AJ, Martinic MM, Harris N. The functions of mucosal T cells in containing the indigenous commensal flora of the intestine. Cell Mol Life Sci 2002; 59:2088-96; PMID:12568335; http://dx.doi.org/10.1007/s000180200009
    • (2002) Cell Mol Life Sci , vol.59 , pp. 2088-2096
    • McPherson, A.J.1    Martinic, M.M.2    Harris, N.3
  • 6
    • 0035007355 scopus 로고    scopus 로고
    • Hypothesis: Inappropriate colonization of the premature intestine can cause neonatal necrotizing enterocolitis
    • PMID:11387237
    • Claud EC, Walker WA. Hypothesis: inappropriate colonization of the premature intestine can cause neonatal necrotizing enterocolitis. FASEB J 2001; 15:1398-403; PMID:11387237; http://dx.doi.org/10.1096/fj.00-0833hyp
    • (2001) FASEB J , vol.15 , pp. 1398-1403
    • Claud, E.C.1    Walker, W.A.2
  • 8
    • 67349112373 scopus 로고    scopus 로고
    • Culture-independent identification of gut bacteria correlated with the onset of diabetes in a rat model
    • PMID:19225551
    • Roesch LF, Lorca GL, Casella G, Giongo A, Naranjo A, Pionzio AM, Li N, Mai V, Wasserfall CH, Schatz D, et al. Culture-independent identification of gut bacteria correlated with the onset of diabetes in a rat model. ISME J 2009; 3:536-48; PMID:19225551; http://dx.doi.org/10.1038/ismej.2009.5
    • (2009) ISME J , vol.3 , pp. 536-548
    • Roesch, L.F.1    Lorca, G.L.2    Casella, G.3    Giongo, A.4    Naranjo, A.5    Pionzio, A.M.6    Li, N.7    Mai, V.8    Wasserfall, C.H.9    Schatz, D.10
  • 9
    • 35348857386 scopus 로고    scopus 로고
    • Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases
    • PMID:17699621
    • Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A 2007; 104:13780-5; PMID:17699621; http://dx.doi.org/10.1073/pnas.0706625104
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 13780-13785
    • Frank, D.N.1    St Amand, A.L.2    Feldman, R.A.3    Boedeker, E.C.4    Harpaz, N.5    Pace, N.R.6
  • 11
    • 0036300743 scopus 로고    scopus 로고
    • Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces
    • PMID:12089021
    • Zoetendal EG, von Wright A, Vilpponen-Salmela T, Ben-Amor K, Akkermans AD, de Vos WM. Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces. Appl Environ Microbiol 2002; 68:3401-7; PMID:12089021; http://dx.doi.org/10.1128/AEM.68.7.3401-3407.2002
    • (2002) Appl Environ Microbiol , vol.68 , pp. 3401-3407
    • Zoetendal, E.G.1    von Wright, A.2    Vilpponen-Salmela, T.3    Ben-Amor, K.4    Akkermans, A.D.5    de Vos, W.M.6
  • 18
    • 29144464937 scopus 로고    scopus 로고
    • UniFrac: A new phylogenetic method for comparing microbial communities
    • PMID:16332807
    • Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 2005; 71:8228-35; PMID:16332807; http://dx.doi.org/10.1128/AEM.71.12.8228-8235.2005
    • (2005) Appl Environ Microbiol , vol.71 , pp. 8228-8235
    • Lozupone, C.1    Knight, R.2
  • 19
    • 0037314132 scopus 로고    scopus 로고
    • Using ecological diversity measures with bacterial communities
    • PMID:19719691
    • Hill TC, Walsh KA, Harris JA, Moffett BF. Using ecological diversity measures with bacterial communities. FEMS Microbiol Ecol 2003; 43:1-11; PMID:19719691; http://dx.doi.org/10.1111/j.1574-6941.2003.tb01040.x
    • (2003) FEMS Microbiol Ecol , vol.43 , pp. 1-11
    • Hill, T.C.1    Walsh, K.A.2    Harris, J.A.3    Moffett, B.F.4
  • 20
    • 84871162696 scopus 로고    scopus 로고
    • Necrotising enterocolitis is characterised by disrupted immune regulation and diminished mucosal regulatory (FOXP3)/effector (CD4, CD8) T cell ratios
    • PMID:22267598
    • Weitkamp JH, Koyama T, Rock MT, Correa H, Goettel JA, Matta P, Oswald-Richter K, Rosen MJ, Engelhardt BG, Moore DJ, et al. Necrotising enterocolitis is characterised by disrupted immune regulation and diminished mucosal regulatory (FOXP3)/effector (CD4, CD8) T cell ratios. Gut 2013; 62:73-82; PMID:22267598; http://dx.doi.org/10.1136/gutjnl-2011-301551
    • (2013) Gut , vol.62 , pp. 73-82
    • Weitkamp, J.H.1    Koyama, T.2    Rock, M.T.3    Correa, H.4    Goettel, J.A.5    Matta, P.6    Oswald-Richter, K.7    Rosen, M.J.8    Engelhardt, B.G.9    Moore, D.J.10
  • 22
    • 84871956840 scopus 로고    scopus 로고
    • Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization
    • PMID:22936250
    • Sharon I, Morowitz MJ, Thomas BC, Costello EK, Relman DA, Banfield JF. Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Res 2013; 23:111-20; PMID:22936250; http://dx.doi.org/10.1101/gr.142315.112
    • (2013) Genome Res , vol.23 , pp. 111-120
    • Sharon, I.1    Morowitz, M.J.2    Thomas, B.C.3    Costello, E.K.4    Relman, D.A.5    Banfield, J.F.6
  • 24
    • 77955386857 scopus 로고    scopus 로고
    • Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns
    • PMID:20566857
    • Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, Knight R. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A 2010; 107:11971-5; PMID:20566857; http://dx.doi.org/10.1073/pnas.1002601107
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 11971-11975
    • Dominguez-Bello, M.G.1    Costello, E.K.2    Contreras, M.3    Magris, M.4    Hidalgo, G.5    Fierer, N.6    Knight, R.7
  • 25
    • 33847065406 scopus 로고    scopus 로고
    • Evaluation of NucliSens easyMAG for automated nucleic acid extraction from various clinical specimens
    • PMID:17166966
    • Loens K, Bergs K, Ursi D, Goossens H, Ieven M. Evaluation of NucliSens easyMAG for automated nucleic acid extraction from various clinical specimens. J Clin Microbiol 2007; 45:421-5; PMID:17166966; http://dx.doi.org/10.1128/JCM.00894-06
    • (2007) J Clin Microbiol , vol.45 , pp. 421-425
    • Loens, K.1    Bergs, K.2    Ursi, D.3    Goossens, H.4    Ieven, M.5
  • 26
    • 77957885233 scopus 로고    scopus 로고
    • Semi-automated extraction of microbial DNA from feces for qPCR and phylogenetic microarray analysis
    • PMID:20849891
    • Nylund L, Heilig HG, Salminen S, de Vos WM, Satokari R. Semi-automated extraction of microbial DNA from feces for qPCR and phylogenetic microarray analysis. J Microbiol Methods 2010; 83:231-5; PMID:20849891; http://dx.doi.org/10.1016/j.mimet.2010.09.003
    • (2010) J Microbiol Methods , vol.83 , pp. 231-235
    • Nylund, L.1    Heilig, H.G.2    Salminen, S.3    de Vos, W.M.4    Satokari, R.5
  • 27
    • 79960228384 scopus 로고    scopus 로고
    • High prevalence of aggregative adherent Escherichia coli strains in the mucosa-associated microbiota of patients with inflammatory bowel diseases
    • PMID:21616711
    • Thomazini CM, Samegima DA, Rodrigues MA, Victoria CR, Rodrigues J. High prevalence of aggregative adherent Escherichia coli strains in the mucosa-associated microbiota of patients with inflammatory bowel diseases. Int J Med Microbiol 2011; 301:475-9; PMID:21616711; http://dx.doi.org/10.1016/j.ijmm.2011.04.015
    • (2011) Int J Med Microbiol , vol.301 , pp. 475-479
    • Thomazini, C.M.1    Samegima, D.A.2    Rodrigues, M.A.3    Victoria, C.R.4    Rodrigues, J.5
  • 28
    • 33644831090 scopus 로고    scopus 로고
    • The Crohn's disease-associated adherent-invasive Escherichia coli strain LF82 replicates in mature phagolysosomes within J774 macrophages
    • PMID:16469058
    • Bringer MA, Glasser AL, Tung CH, Méresse S, Darfeuille-Michaud A. The Crohn's disease-associated adherent-invasive Escherichia coli strain LF82 replicates in mature phagolysosomes within J774 macrophages. Cell Microbiol 2006; 8:471-84; PMID:16469058; http://dx.doi.org/10.1111/j.1462-5822.2005.00639.x
    • (2006) Cell Microbiol , vol.8 , pp. 471-484
    • Bringer, M.A.1    Glasser, A.L.2    Tung, C.H.3    Méresse, S.4    Darfeuille-Michaud, A.5
  • 29
    • 84862286169 scopus 로고    scopus 로고
    • A framework for human microbiome research
    • Human Microbiome Project Consortium. PMID:22699610
    • Human Microbiome Project Consortium. A framework for human microbiome research. Nature 2012; 486:215-21; PMID:22699610; http://dx.doi.org/10.1038/nature11209
    • (2012) Nature , vol.486 , pp. 215-221
  • 31
    • 0031784307 scopus 로고    scopus 로고
    • Comparison of phenotypic and genotypic techniques for identification of unusual aerobic pathogenic gram-negative bacilli
    • PMID:9817894
    • Tang YW, Ellis NM, Hopkins MK, Smith DH, Dodge DE, Persing DH. Comparison of phenotypic and genotypic techniques for identification of unusual aerobic pathogenic gram-negative bacilli. J Clin Microbiol 1998; 36:3674-9; PMID:9817894
    • (1998) J Clin Microbiol , vol.36 , pp. 3674-3679
    • Tang, Y.W.1    Ellis, N.M.2    Hopkins, M.K.3    Smith, D.H.4    Dodge, D.E.5    Persing, D.H.6
  • 33
    • 79960983258 scopus 로고    scopus 로고
    • Naturally transmitted segmented filamentous bacteria segregate with diabetes protection in nonobese diabetic mice
    • PMID:21709219
    • Kriegel MA, Sefik E, Hill JA, Wu HJ, Benoist C, Mathis D. Naturally transmitted segmented filamentous bacteria segregate with diabetes protection in nonobese diabetic mice. Proc Natl Acad Sci U S A 2011; 108:11548-53; PMID:21709219; http://dx.doi.org/10.1073/pnas.1108924108
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 11548-11553
    • Kriegel, M.A.1    Sefik, E.2    Hill, J.A.3    Wu, H.J.4    Benoist, C.5    Mathis, D.6
  • 34
    • 27644482283 scopus 로고    scopus 로고
    • Comprehensive algorithm for quantitative real-time polymerase chain reaction
    • PMID:16241897
    • Zhao S, Fernald RD. Comprehensive algorithm for quantitative real-time polymerase chain reaction. J Comput Biol 2005; 12:1047-64; PMID:16241897; http://dx.doi.org/10.1089/cmb.2005.12.1047
    • (2005) J Comput Biol , vol.12 , pp. 1047-1064
    • Zhao, S.1    Fernald, R.D.2
  • 36
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • PMID:20709691
    • Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010; 26:2460-1; PMID:20709691; http://dx.doi.org/10.1093/bioinformatics/btq461
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 37
    • 34548293679 scopus 로고    scopus 로고
    • Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    • PMID:17586664
    • Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007; 73:5261-7; PMID:17586664; http://dx.doi.org/10.1128/AEM.00062-07
    • (2007) Appl Environ Microbiol , vol.73 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4
  • 38
    • 73449128271 scopus 로고    scopus 로고
    • Fast UniFrac: Facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data
    • PMID:19710709
    • Hamady M, Lozupone C, Knight R. Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J 2010; 4:17-27; PMID:19710709; http://dx.doi.org/10.1038/ismej.2009.97
    • (2010) ISME J , vol.4 , pp. 17-27
    • Hamady, M.1    Lozupone, C.2    Knight, R.3
  • 39
    • 79952006773 scopus 로고    scopus 로고
    • Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
    • Human Microbiome Consortium. PMID:21212162
    • Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, et al.; Human Microbiome Consortium. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 2011; 21:494-504; PMID:21212162; http://dx.doi.org/10.1101/gr.112730.110
    • (2011) Genome Res , vol.21 , pp. 494-504
    • Haas, B.J.1    Gevers, D.2    Earl, A.M.3    Feldgarden, M.4    Ward, D.V.5    Giannoukos, G.6    Ciulla, D.7    Tabbaa, D.8    Highlander, S.K.9    Sodergren, E.10
  • 40
    • 75249107844 scopus 로고    scopus 로고
    • PyNAST: A flexible tool for aligning sequences to a template alignment
    • PMID:19914921
    • Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 2010; 26:266-7; PMID:19914921; http://dx.doi.org/10.1093/bioinformatics/btp636
    • (2010) Bioinformatics , vol.26 , pp. 266-267
    • Caporaso, J.G.1    Bittinger, K.2    Bushman, F.D.3    DeSantis, T.Z.4    Andersen, G.L.5    Knight, R.6
  • 41
    • 77951945504 scopus 로고    scopus 로고
    • Identifying biologically relevant differences between metagenomic communities
    • PMID:20130030
    • Parks DH, Beiko RG. Identifying biologically relevant differences between metagenomic communities. Bioinformatics 2010; 26:715-21; PMID:20130030; http://dx.doi.org/10.1093/bioinformatics/btq041
    • (2010) Bioinformatics , vol.26 , pp. 715-721
    • Parks, D.H.1    Beiko, R.G.2
  • 42
    • 0008475968 scopus 로고
    • Adaptation of Sorensen's K (1948) for estimating unit affinities in prairie vegetation
    • Looman J, Campbell JB. Adaptation of Sorensen's K (1948) for estimating unit affinities in prairie vegetation. Ecology 1960; 41:409-16; http://dx.doi.org/10.2307/1933315
    • (1960) Ecology , vol.41 , pp. 409-416
    • Looman, J.1    Campbell, J.B.2
  • 43
    • 84856043672 scopus 로고
    • A mathematical theory of communication
    • Shannon CE. A mathematical theory of communication. Bell Syst Tech J 1948; 27: 379-423, 623-656; http://dx.doi.org/10.1002/j.1538-7305.1948.tb01338.x.
    • (1948) Bell Syst Tech J , vol.27
    • Shannon, C.E.1
  • 45
    • 33344464667 scopus 로고
    • Measurement of diversity
    • Simpson EH. Measurement of diversity. Nature 1949; 163:688; http://dx.doi.org/10.1038/163688a0
    • (1949) Nature , vol.163 , pp. 688
    • Simpson, E.H.1
  • 46
    • 0001463548 scopus 로고
    • Non-parametric estimation of the number of classes in a population 1984
    • Chao A. Non-parametric estimation of the number of classes in a population 1984. Scand J Stat 1984; 11:265-70
    • (1984) Scand J Stat , vol.11 , pp. 265-270
    • Chao, A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.