메뉴 건너뛰기




Volumn 4, Issue , 2014, Pages

Insights into the distribution and abundance of the ubiquitous candidatus Saccharibacteria phylum following tag pyrosequencing

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; PRIMER DNA; RNA 16S;

EID: 84893837827     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep03957     Document Type: Article
Times cited : (59)

References (41)
  • 1
    • 84879678051 scopus 로고    scopus 로고
    • Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
    • doi:10.1038/nbt.2579
    • Albertsen, M. et al. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nature Biotechnol. 31, 533-538, doi:10.1038/nbt.2579 (2013
    • (2013) Nature Biotechnol , vol.31 , pp. 533-538
    • Albertsen, M.1
  • 2
    • 0035163571 scopus 로고    scopus 로고
    • Investigation of candidate division TM7, a recently recognized major lineage of the domain Bacteria, with no known pure-culture representatives
    • DOI 10.1128/AEM.67.1.411-419.2001
    • Hugenholtz, P., Tyson, G. W., Webb, R. I., Wagner, A. M. & Blackall, L. L. Investigation of Candidate Division TM7, a Recently Recognised Major Lineage of the Domain Bacteria with No Known Pure-Culture Representatives. Appl. Environ. Microbiol. 67, 411-419 (2001 (Pubitemid 32044445)
    • (2001) Applied and Environmental Microbiology , vol.67 , Issue.1 , pp. 411-419
    • Hugenholtz, P.1    Tyson, G.W.2    Webb, R.I.3    Wagner, A.M.4    Blackall, L.L.5
  • 3
    • 0029853626 scopus 로고    scopus 로고
    • Molecular biological evidence for the occurrence of uncultured members of the actinomycete line of descent in different environments and geographical locations
    • Rheims, H., Sproer, C., Rainey, F. A. & Stackebrandt, E. Molecular biological evidence for the occurrence of uncultured members of the actinomycete line of descent in different environments and geographical locations. Microbiology 142 (Pt 10), 2863-2870 (1996 (Pubitemid 26362925)
    • (1996) Microbiology , vol.142 , Issue.10 , pp. 2863-2870
    • Rheims, H.1    Sproer, C.2    Rainey, F.A.3    Stackebrandt, E.4
  • 4
    • 79959299471 scopus 로고    scopus 로고
    • In search of an uncultured human-associated TM7 bacterium in the environment
    • doi:10.1371/journal.pone.0021280
    • Dinis, J. M. et al. In search of an uncultured human-associated TM7 bacterium in the environment. PLoS ONE 6, e21280, doi:10.1371/journal.pone. 0021280 (2011
    • (2011) PLoS ONE , vol.6 , pp. 21280
    • Dinis, J.M.1
  • 5
    • 0036181778 scopus 로고    scopus 로고
    • Exploring prokaryotic diversity in the genomic era
    • Hugenholtz, P. Exploring prokaryotic diversity in the genomic era. Genome Biol. 3, REVIEWS0003 (2002
    • (2002) Genome Biol , vol.3
    • Hugenholtz, P.1
  • 6
    • 57749194898 scopus 로고    scopus 로고
    • Intestinal TM7 bacterial phylogenies in active inflammatory bowel disease
    • doi:10.1099/jmm.0.47719-0
    • Kuehbacher, T. et al. Intestinal TM7 bacterial phylogenies in active inflammatory bowel disease. J. Med. Microbiol. 57, 1569-1576, doi:10.1099/jmm.0.47719-0 (2008
    • (2008) J. Med. Microbiol , vol.57 , pp. 1569-1576
    • Kuehbacher, T.1
  • 8
    • 29144482711 scopus 로고    scopus 로고
    • Microcolony cultivation on a soil substrate membrane system recovers previously unculturable bacteria
    • Ferrari, B., Binnerup, S. J. & Gillings, M. R. Microcolony cultivation on a soil substrate membrane system recovers previously unculturable bacteria. Appl. Environ. Microbiol. 71, 8174-8720 (2005
    • (2005) Appl. Environ. Microbiol , vol.71 , pp. 8174-8720
    • Ferrari, B.1    Binnerup, S.J.2    Gillings, M.R.3
  • 9
    • 0037335696 scopus 로고    scopus 로고
    • Prevalence of bacteria of division TM7 in human subgingival plaque and their association with disease
    • DOI 10.1128/AEM.69.3.1687-1694.2003
    • Brinig, M. M., Lepp, P. W., Ouverney, C. C., Armitage, G. C. & Relman, D. A. Prevalence of bacteria of division TM7 in human subgingival plaque and their association with disease. Appl. Environ. Microbiol. 69, 1687-1694 (2003 (Pubitemid 36314312)
    • (2003) Applied and Environmental Microbiology , vol.69 , Issue.3 , pp. 1687-1694
    • Brinig, M.M.1    Lepp, P.W.2    Ouverney, C.C.3    Armitage, G.C.4    Relman, D.A.5
  • 13
    • 77449137031 scopus 로고    scopus 로고
    • The taxophysiological paradox: Changes in the intestinal microbiota of the xylophagous cockroach Cryptocercus punctulatus depending on the physiological state of the host
    • Berlanga, M., Paster, B. J. & Guerrero, R. The taxophysiological paradox: changes in the intestinal microbiota of the xylophagous cockroach Cryptocercus punctulatus depending on the physiological state of the host. Int. Microbiol. 12, 227-236 (2009
    • (2009) Int. Microbiol , vol.12 , pp. 227-236
    • Berlanga, M.1    Paster, B.J.2    Guerrero, R.3
  • 14
    • 79957576718 scopus 로고    scopus 로고
    • NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis
    • doi:10.1016/j.cell.2011.04.022
    • Elinav, E. et al. NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis. Cell 145, 745-757, doi:10.1016/j.cell.2011.04.022 (2011
    • (2011) Cell , vol.145 , pp. 745-757
    • Elinav, E.1
  • 15
    • 0142104329 scopus 로고    scopus 로고
    • Single-Cell Enumeration of an Uncultivated TM7 Subgroup in the Human Subgingival Crevice
    • DOI 10.1128/AEM.69.10.6294-6298.2003
    • Ouverney, C. C., Armitage, G. C. & Relman, D. A. Single-Cell Enumeration of an Uncultivated TM7 Subgroup in the Human Subgingival Crevice. Appl. Environ. Microbiol. 69, 6294-6298, doi:10.1128/aem.69.10.6294-6298.2003 (2003 (Pubitemid 37280358)
    • (2003) Applied and Environmental Microbiology , vol.69 , Issue.10 , pp. 6294-6298
    • Ouverney, C.C.1    Armitage, G.C.2    Relman, D.A.3
  • 16
    • 33947245553 scopus 로고    scopus 로고
    • In situ detection of protein-hydrolysing microorganisms in activated sludge
    • DOI 10.1111/j.1574-6941.2007.00279.x
    • Xia, Y., Kong, Y. & Nielsen, P. H. r. In situ detection of protein-hydrolysing microorganisms in activated sludge. FEMS Microbiol. Ecol. 60, 156-165, doi:10.1111/j.1574-6941.2007.00279.x (2007 (Pubitemid 46426582)
    • (2007) FEMS Microbiology Ecology , vol.60 , Issue.1 , pp. 156-165
    • Xia, Y.1    Kong, Y.2    Nielsen, P.H.3
  • 17
    • 84865741514 scopus 로고    scopus 로고
    • Microbiology Monographs (ed Epstein, S. ) Ch. 2 Springer
    • Sogin, M. L. in Uncultivated Microorganisms Vol. 10, Microbiology Monographs (ed Epstein, S. ) Ch. 2, 19-34 (Springer, 2009
    • (2009) Uncultivated Microorganisms , vol.10 , pp. 19-34
    • Sogin, M.L.1
  • 18
    • 84866150939 scopus 로고    scopus 로고
    • Capturing greater 16S rRNA gene sequence diversity within the domain Bacteria
    • doi:10.1128/AEM.01299-12
    • Winsley, T., van Dorst, J. M., Brown, M. V. & Ferrari, B. C. Capturing greater 16S rRNA gene sequence diversity within the domain Bacteria. Appl. Environ. Microbiol. 78, 5938-5941, doi:10.1128/AEM.01299-12 (2012
    • (2012) Appl. Environ. Microbiol , vol.78 , pp. 5938-5941
    • Winsley, T.1    Van Dorst, J.M.2    Brown, M.V.3    Ferrari, B.C.4
  • 19
    • 50249237865 scopus 로고    scopus 로고
    • Cultivating previously uncultured soil bacteria using a soil substrate membrane system
    • Ferrari, B. C., Winsley, T., Gillings, M. & Binnerup, S. Cultivating previously uncultured soil bacteria using a soil substrate membrane system. Nat. Protoc. 3, 1261-1269 (2008
    • (2008) Nat. Protoc , vol.3 , pp. 1261-1269
    • Ferrari, B.C.1    Winsley, T.2    Gillings, M.3    Binnerup, S.4
  • 20
    • 67649603157 scopus 로고    scopus 로고
    • Identification of a novel toluenedegrading bacterium from the candidate phylum TM7, as determined by DNA stable isotope probing
    • doi:10.1128/ AEM.00283-09
    • Luo, C., Xie, S., Sun,W., Li, X. & Cupples, A. M. Identification of a novel toluenedegrading bacterium from the candidate phylum TM7, as determined by DNA stable isotope probing. Appl. Environ. Microbiol. 75, 4644-4647, doi:10.1128/ AEM.00283-09 (2009
    • (2009) Appl. Environ. Microbiol , vol.75 , pp. 4644-4647
    • Luo, C.1    Sunw, X.S.2    Li, X.3    Cupples, A.M.4
  • 21
    • 78650214082 scopus 로고    scopus 로고
    • Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes
    • doi:10.1016/j.mimet.2010.10.020
    • Kim, M., Morrison, M. & Yu, Z. Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes. J. MIcrobiol. Meth. 84, 81-87, doi:10.1016/j.mimet.2010.10.020 (2011
    • (2011) J. MIcrobiol. Meth , vol.84 , pp. 81-87
    • Kim, M.1    Morrison, M.2    Yu, Z.3
  • 22
    • 84857122937 scopus 로고    scopus 로고
    • An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
    • doi:10.1038/ismej.2011.139
    • McDonald, D. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 6, 610-618, doi:10.1038/ismej.2011.139 (2012
    • (2012) ISME J , vol.6 , pp. 610-618
    • McDonald, D.1
  • 23
    • 67549099704 scopus 로고    scopus 로고
    • Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge
    • doi:10.1038/ismej.2009.2
    • Riviere, D. et al. Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge. ISME J. 3, 700-714, doi:10.1038/ismej.2009.2 (2009
    • (2009) ISME J , vol.3 , pp. 700-714
    • Riviere, D.1
  • 25
    • 84864250059 scopus 로고    scopus 로고
    • Global biogeography of SAR11marine bacteria
    • doi:10.1038/msb.2012.28
    • Brown, M. V. et al.Global biogeography of SAR11marine bacteria. Mol. Syst. Biol. 8, 595 doi:10.1038/msb.2012.28 (2012
    • (2012) Mol. Syst. Biol , vol.8 , pp. 595
    • Brown, M.V.1
  • 26
    • 84860444278 scopus 로고    scopus 로고
    • The canine oral microbiome
    • doi:10.1371/journal.pone.0036067
    • Dewhirst, F. E. et al. The canine oral microbiome. PLoS ONE 7, e36067 doi:10.1371/journal.pone.0036067 (2012
    • (2012) PLoS ONE , vol.7
    • Dewhirst, F.E.1
  • 27
    • 76949100244 scopus 로고    scopus 로고
    • Microbiomic comparison of the intestine of the earthworm Eisenia fetida fed ergovaline
    • doi:10.1007/s00284-009-9530-8
    • Rattray, R. M., Perumbakkam, S., Smith, F. & Craig, A. M. Microbiomic comparison of the intestine of the earthworm Eisenia fetida fed ergovaline. Curr. Microbiol. 60, 229-235, doi:10.1007/s00284-009-9530-8 (2010
    • (2010) Curr. Microbiol , vol.60 , pp. 229-235
    • Rattray, R.M.1    Perumbakkam, S.2    Smith, F.3    Craig, A.M.4
  • 28
    • 84857117741 scopus 로고    scopus 로고
    • Co-habiting amphibian species harbor unique skin bacterial communities in wild populations
    • doi:10.1038/ismej.2011.129
    • McKenzie, V. J., Bowers, R. M., Fierer, N., Knight, R. & Lauber, C. L. Co-habiting amphibian species harbor unique skin bacterial communities in wild populations. ISME J. 6, 588-596 doi:10.1038/ismej.2011.129 (2012
    • (2012) ISME J. , vol.6 , pp. 588-596
    • McKenzie, V.J.1    Bowers, R.M.2    Fierer, N.3    Knight, R.4    Lauber, C.L.5
  • 29
    • 84875910146 scopus 로고    scopus 로고
    • Diet and phylogeny shape the gut microbiota of Antarctic seals: A comparison of wild and captive animals
    • doi:10.1111/1462-2920.12022
    • Nelson, T. M., Rogers, T. L., Carlini, A. R. & Brown, M. V. Diet and phylogeny shape the gut microbiota of Antarctic seals: a comparison of wild and captive animals. Environ. Microbiol. 15, 1132-1145, doi:10.1111/1462-2920.12022 (2013
    • (2013) Environ. Microbiol , vol.15 , pp. 1132-1145
    • Nelson, T.M.1    Rogers, T.L.2    Carlini, A.R.3    Brown, M.V.4
  • 30
    • 35748977394 scopus 로고    scopus 로고
    • Closed-tube DNA extraction using a thermostable proteinase is highly sensitive, capable of single parasite detection
    • DOI 10.1007/s10529-007-9487-2
    • Ferrari, B. C., Power, M. L. & Bergquist, P. L. Closed-tube DNA extraction using a thermostable proteinase is highly sensitive, capable of single parasite detection. Biotechnol. Lett. 29, 1831-1837 (2007 (Pubitemid 350043619)
    • (2007) Biotechnology Letters , vol.29 , Issue.12 , pp. 1831-1837
    • Ferrari, B.C.1    Power, M.L.2    Bergquist, P.L.3
  • 33
    • 49949095159 scopus 로고    scopus 로고
    • Bacterial tagencoded FLX amplicon pyrosequencing (bTEFAP) for microbiome studies: Bacterial diversity in the ileum of newly weaned Salmonella-infected pigs
    • doi:10.1089/fpd.2008.0107
    • Dowd, S. E., Sun, Y., Wolcott, R. D., Domingo, A. & Carroll, J. A. Bacterial tagencoded FLX amplicon pyrosequencing (bTEFAP) for microbiome studies: bacterial diversity in the ileum of newly weaned Salmonella-infected pigs. Foodborne Pathog. Dis. 5, 459-472, doi:10.1089/fpd.2008.0107 (2008
    • (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
  • 35
    • 69549112742 scopus 로고    scopus 로고
    • Accurate determination of microbial diversity from 454 pyrosequencing data
    • doi:10.1038/nmeth.1361
    • Quince, C. et al. Accurate determination of microbial diversity from 454 pyrosequencing data. Nat. Meth. 6, 639-641, doi:10.1038/nmeth.1361 (2009
    • (2009) Nat. Meth , vol.6 , pp. 639-641
    • Quince, C.1
  • 36
    • 75249107844 scopus 로고    scopus 로고
    • PyNAST: A flexible tool for aligning sequences to a template alignment
    • doi:10.1093/bioinformatics/btp636
    • Caporaso, J. G. et al. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26, 266-267, doi:10.1093/bioinformatics/ btp636 (2010
    • (2010) Bioinformatics , vol.26 , pp. 266-267
    • Caporaso, J.G.1
  • 37
    • 79961181125 scopus 로고    scopus 로고
    • UCHIME improves sensitivity and speed of chimera detection
    • doi:10.1093/bioinformatics/btr381
    • Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194-2200, doi:10.1093/bioinformatics/btr381 (2011
    • (2011) Bioinformatics , vol.27 , pp. 2194-2200
    • Edgar, R.C.1    Haas, B.J.2    Clemente, J.C.3    Quince, C.4    Knight, R.5
  • 39
    • 34547322945 scopus 로고    scopus 로고
    • Characterization of filamentous bacteria, belonging to candidate phylum KSB3, that are associated with bulking in methanogenic granular sludges
    • DOI 10.1038/ismej.2007.28, PII ISMEJ200728
    • Yamada, T. et al. Characterization of filamentous bacteria, belonging to candidate phylum KSB3, that are associated with bulking inmethanogenic granular sludges. ISME J. 1, 246-255, doi:10.1038/ismej.2007.28 (2007 (Pubitemid 47145295)
    • (2007) ISME Journal , vol.1 , Issue.3 , pp. 246-255
    • Yamada, T.1    Yamauchi, T.2    Shiraishi, K.3    Hugenholtz, P.4    Ohashi, A.5    Harada, H.6    Kamagata, Y.7    Nakamura, K.8    Sekiguchi, Y.9
  • 40
    • 77949718257 scopus 로고    scopus 로고
    • FastTree 2-approximately maximumlikelihood trees for large alignments
    • doi:10.1371/journal.pone0009490
    • Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2-approximately maximumlikelihood trees for large alignments. PLoS ONE 5, e9490, doi:10.1371/ journal.pone.0009490 (2010
    • (2010) PLoS ONE , vol.5
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 41
    • 0027804103 scopus 로고
    • Non-parametric multivariate analyses of changes in community structure
    • Clarke, K. R. Non-parametric multivariate analyses of changes in community structure. Aust. J. Ecol. 18, 117-143 (1993 (Pubitemid 24409223)
    • (1993) Australian Journal of Ecology , vol.18 , Issue.1 , pp. 117-143
    • Clarke, K.R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.