메뉴 건너뛰기




Volumn 153, Issue 1-2, 2011, Pages 124-133

Longitudinal investigation of the age-related bacterial diversity in the feces of commercial pigs

Author keywords

16S rRNA gene; Bacterial microbiome; Pig

Indexed keywords

BACTERIAL DNA; DNA 16S; RNA 16S;

EID: 80052550284     PISSN: 03781135     EISSN: 18732542     Source Type: Journal    
DOI: 10.1016/j.vetmic.2011.05.021     Document Type: Article
Times cited : (256)

References (45)
  • 1
    • 0030297089 scopus 로고    scopus 로고
    • The indigenous gastrointestinal microflora
    • Berg R.D. The indigenous gastrointestinal microflora. Trends Microbiol. 1996, 4:430-435.
    • (1996) Trends Microbiol. , vol.4 , pp. 430-435
    • Berg, R.D.1
  • 2
    • 34147182303 scopus 로고    scopus 로고
    • A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria
    • Chakravorty S., Helb D., Burday M., Connell N., Alland D. A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J. Microbiol. Methods 2007, 69:330-339.
    • (2007) J. Microbiol. Methods , vol.69 , pp. 330-339
    • Chakravorty, S.1    Helb, D.2    Burday, M.3    Connell, N.4    Alland, D.5
  • 3
    • 0036137277 scopus 로고    scopus 로고
    • DNA sequence quality trimming and vector removal
    • Chou H.H., Holmes M.H. DNA sequence quality trimming and vector removal. Bioinformatics 2001, 17:1093-1104.
    • (2001) Bioinformatics , vol.17 , pp. 1093-1104
    • Chou, H.H.1    Holmes, M.H.2
  • 4
    • 69249109724 scopus 로고    scopus 로고
    • Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine
    • Claesson M.J., O'Sullivan O., Wang Q., Nikkila J., Marchesi J.R., Smidt H., de Vos W.M., Ross R.P., O'Toole P.W. Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS One 2009, 4:e6669.
    • (2009) PLoS One , vol.4
    • Claesson, M.J.1    O'Sullivan, O.2    Wang, Q.3    Nikkila, J.4    Marchesi, J.R.5    Smidt, H.6    de Vos, W.M.7    Ross, R.P.8    O'Toole, P.W.9
  • 7
    • 56849106496 scopus 로고    scopus 로고
    • The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing
    • Dethlefsen L., Huse S., Sogin M.L., Relman D.A. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 2008, 6:e280.
    • (2008) PLoS Biol. , vol.6
    • Dethlefsen, L.1    Huse, S.2    Sogin, M.L.3    Relman, D.A.4
  • 8
    • 49949095159 scopus 로고    scopus 로고
    • Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) for microbiome studies: bacterial diversity in the ileum of newly weaned Salmonella-infected pigs
    • Dowd S.E., Sun Y., Wolcott R.D., Domingo A., Carroll J.A. Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) for microbiome studies: bacterial diversity in the ileum of newly weaned Salmonella-infected pigs. Foodborne Pathog. Dis. 2008, 5:459-472.
    • (2008) Foodborne Pathog. Dis. , vol.5 , pp. 459-472
    • Dowd, S.E.1    Sun, Y.2    Wolcott, R.D.3    Domingo, A.4    Carroll, J.A.5
  • 10
    • 35348857386 scopus 로고    scopus 로고
    • Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases
    • Frank D.N., St Amand A.L., Feldman R.A., Boedeker E.C., Harpaz N., Pace N.R. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:13780-13785.
    • (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
  • 12
    • 77956096764 scopus 로고    scopus 로고
    • Multivariate cutoff level analysis (MultiCoLA) of large community data sets
    • Gobet A., Quince C., Ramette A. Multivariate cutoff level analysis (MultiCoLA) of large community data sets. Nucleic Acids Res. 2010, 38:e155.
    • (2010) Nucleic Acids Res. , vol.38
    • Gobet, A.1    Quince, C.2    Ramette, A.3
  • 14
    • 67650021209 scopus 로고    scopus 로고
    • Microbial community profiling for human microbiome projects: tools, techniques, and challenges
    • Hamady M., Knight R. Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome Res. 2009, 19:1141-1152.
    • (2009) Genome Res. , vol.19 , pp. 1141-1152
    • Hamady, M.1    Knight, R.2
  • 15
    • 73449128271 scopus 로고    scopus 로고
    • Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data
    • 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.
    • (2010) ISME J. , vol.4 , pp. 17-27
    • Hamady, M.1    Lozupone, C.2    Knight, R.3
  • 16
    • 0036024611 scopus 로고    scopus 로고
    • Phylogenetic analysis of the human gut microbiota using 16S rDNA clone libraries and strictly anaerobic culture-based methods
    • Hayashi H., Sakamoto M., Benno Y. Phylogenetic analysis of the human gut microbiota using 16S rDNA clone libraries and strictly anaerobic culture-based methods. Microbiol. Immunol. 2002, 46:535-548.
    • (2002) Microbiol. Immunol. , vol.46 , pp. 535-548
    • Hayashi, H.1    Sakamoto, M.2    Benno, Y.3
  • 17
    • 2342453807 scopus 로고
    • Virginiamycin: a nutritional tool for swine production
    • Hedde R.D., Lindsey T.O. Virginiamycin: a nutritional tool for swine production. Agri-Practice 1986, 7:3-4.
    • (1986) Agri-Practice , vol.7 , pp. 3-4
    • Hedde, R.D.1    Lindsey, T.O.2
  • 20
    • 77955251092 scopus 로고    scopus 로고
    • Ironing out the wrinkles in the rare biosphere through improved OTU clustering
    • Huse S.M., Welch D.M., Morrison H.G., Sogin M.L. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ. Microbiol. 2010, 12:1889-1898.
    • (2010) Environ. Microbiol. , vol.12 , pp. 1889-1898
    • Huse, S.M.1    Welch, D.M.2    Morrison, H.G.3    Sogin, M.L.4
  • 21
    • 73349110099 scopus 로고    scopus 로고
    • Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates
    • Kunin V., Engelbrektson A., Ochman H., Hugenholtz P. Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ. Microbiol. 2010, 12:118-123.
    • (2010) Environ. Microbiol. , vol.12 , pp. 118-123
    • Kunin, V.1    Engelbrektson, A.2    Ochman, H.3    Hugenholtz, P.4
  • 23
    • 58149152764 scopus 로고    scopus 로고
    • The commensal microbiology of the gastrointestinal tract
    • Manson J.M., Rauch M., Gilmore M.S. The commensal microbiology of the gastrointestinal tract. Adv. Exp. Med. Biol. 2008, 635:15-28.
    • (2008) Adv. Exp. Med. Biol. , vol.635 , pp. 15-28
    • Manson, J.M.1    Rauch, M.2    Gilmore, M.S.3
  • 24
    • 3142757153 scopus 로고    scopus 로고
    • Molecular analysis of the microflora associated with dental caries
    • Munson M.A., Banerjee A., Watson T.F., Wade W.G. Molecular analysis of the microflora associated with dental caries. J. Clin. Microbiol. 2004, 42:3023-3029.
    • (2004) J. Clin. Microbiol. , vol.42 , pp. 3023-3029
    • Munson, M.A.1    Banerjee, A.2    Watson, T.F.3    Wade, W.G.4
  • 25
    • 0027460328 scopus 로고
    • Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA
    • Muyzer G., de Waal E.C., Uitterlinden A.G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 1993, 59:695-700.
    • (1993) Appl. Environ. Microbiol. , vol.59 , pp. 695-700
    • Muyzer, G.1    de Waal, E.C.2    Uitterlinden, A.G.3
  • 29
    • 0031933550 scopus 로고    scopus 로고
    • The bifidogenic nature of chicory inulin and its hydrolysis products
    • Roberfroid M.B., Van Loo J.A., Gibson G.R. The bifidogenic nature of chicory inulin and its hydrolysis products. J. Nutr. 1998, 128:11-19.
    • (1998) J. Nutr. , vol.128 , pp. 11-19
    • Roberfroid, M.B.1    Van Loo, J.A.2    Gibson, G.R.3
  • 30
    • 9444225935 scopus 로고    scopus 로고
    • Java treeview-extensible visualization of microarray data
    • Saldanha A.J. Java treeview-extensible visualization of microarray data. Bioinformatics 2004, 20:3246-3248.
    • (2004) Bioinformatics , vol.20 , pp. 3246-3248
    • Saldanha, A.J.1
  • 31
    • 0017341656 scopus 로고
    • Microbial ecology of the gastrointestinal tract
    • Savage D.C. Microbial ecology of the gastrointestinal tract. Annu. Rev. Microbiol. 1977, 31:107-133.
    • (1977) Annu. Rev. Microbiol. , vol.31 , pp. 107-133
    • Savage, D.C.1
  • 32
    • 15444362001 scopus 로고    scopus 로고
    • Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness
    • Schloss P.D., Handelsman J. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 2005, 71:1501-1506.
    • (2005) Appl. Environ. Microbiol. , vol.71 , pp. 1501-1506
    • Schloss, P.D.1    Handelsman, J.2
  • 35
    • 2942691956 scopus 로고    scopus 로고
    • Getting a grip on things: how do communities of bacterial symbionts become established in our intestine?
    • Sonnenburg J.L., Angenent L.T., Gordon J.I. Getting a grip on things: how do communities of bacterial symbionts become established in our intestine?. Nat. Immunol. 2004, 5:569-573.
    • (2004) Nat. Immunol. , vol.5 , pp. 569-573
    • Sonnenburg, J.L.1    Angenent, L.T.2    Gordon, J.I.3
  • 36
    • 0032755259 scopus 로고    scopus 로고
    • Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut
    • Suau A., Bonnet R., Sutren M., Godon J.J., Gibson G.R., Collins M.D., Dore J. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl. Environ. Microbiol. 1999, 65:4799-4807.
    • (1999) Appl. Environ. Microbiol. , vol.65 , pp. 4799-4807
    • Suau, A.1    Bonnet, R.2    Sutren, M.3    Godon, J.J.4    Gibson, G.R.5    Collins, M.D.6    Dore, J.7
  • 38
    • 78049310433 scopus 로고    scopus 로고
    • Bar-coded pyrosequencing of 16S rRNA gene amplicons reveals changes in ileal porcine bacterial communities due to high dietary zinc intake
    • Vahjen W., Pieper R., Zentek J. Bar-coded pyrosequencing of 16S rRNA gene amplicons reveals changes in ileal porcine bacterial communities due to high dietary zinc intake. Appl. Environ. Microbiol. 2010, 76:6689-6691.
    • (2010) Appl. Environ. Microbiol. , vol.76 , pp. 6689-6691
    • Vahjen, W.1    Pieper, R.2    Zentek, J.3
  • 39
    • 0029789623 scopus 로고    scopus 로고
    • A quantitative map of nucleotide substitution rates in bacterial rRNA
    • Van de Peer Y., Chapelle S., De Wachter R. A quantitative map of nucleotide substitution rates in bacterial rRNA. Nucleic Acids Res. 1996, 24:3381-3391.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 3381-3391
    • Van de Peer, Y.1    Chapelle, S.2    De Wachter, R.3
  • 40
    • 0042882421 scopus 로고    scopus 로고
    • Molecular characterization of the microbial species that colonize human ileal and colonic mucosa by using 16S rDNA sequence analysis
    • Wang X., Heazlewood S.P., Krause D.O., Florin T.H. Molecular characterization of the microbial species that colonize human ileal and colonic mucosa by using 16S rDNA sequence analysis. J. Appl. Microbiol. 2003, 95:508-520.
    • (2003) J. Appl. Microbiol. , vol.95 , pp. 508-520
    • Wang, X.1    Heazlewood, S.P.2    Krause, D.O.3    Florin, T.H.4
  • 41
    • 70350527180 scopus 로고    scopus 로고
    • Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies
    • Wang Y., Qian P.Y. Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies. PLoS One 2009, 4:e7401.
    • (2009) PLoS One , vol.4
    • Wang, Y.1    Qian, P.Y.2
  • 42
    • 65449188232 scopus 로고    scopus 로고
    • Jalview Version 2-a multiple sequence alignment editor and analysis workbench
    • Waterhouse A.M., Procter J.B., Martin D.M., Clamp M., Barton G.J. Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics 2009, 25:1189-1191.
    • (2009) Bioinformatics , vol.25 , pp. 1189-1191
    • Waterhouse, A.M.1    Procter, J.B.2    Martin, D.M.3    Clamp, M.4    Barton, G.J.5
  • 43
    • 66249145772 scopus 로고    scopus 로고
    • Statistical methods for detecting differentially abundant features in clinical metagenomic samples
    • White J.R., Nagarajan N., Pop M. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput. Biol. 2009, 5:e1000352.
    • (2009) PLoS Comput. Biol. , vol.5
    • White, J.R.1    Nagarajan, N.2    Pop, M.3
  • 44
    • 0142026205 scopus 로고    scopus 로고
    • Inaugural article: honor thy symbionts
    • Xu J., Gordon J.I. Inaugural article: honor thy symbionts. Proc. Natl. Acad. Sci. U.S.A. 2003, 100:10452-10459.
    • (2003) Proc. Natl. Acad. Sci. U.S.A. , vol.100 , pp. 10452-10459
    • Xu, J.1    Gordon, J.I.2
  • 45
    • 2442510059 scopus 로고    scopus 로고
    • Improved extraction of PCR-quality community DNA from digesta and fecal samples
    • Yu Z., Morrison M. Improved extraction of PCR-quality community DNA from digesta and fecal samples. BioTechniques 2004, 36:808-812.
    • (2004) BioTechniques , vol.36 , pp. 808-812
    • Yu, Z.1    Morrison, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.