메뉴 건너뛰기




Volumn 49, Issue 4, 2011, Pages 585-594

Microbial community analysis and identification of alternative host-specific fecal indicators in fecal and river water samples using pyrosequencing

Author keywords

bacteroidales; microbial source tracking; potential fecal indicator; pyrosequencing

Indexed keywords

BACTERIAL DNA; RNA 16S;

EID: 80052287608     PISSN: 12258873     EISSN: 19763794     Source Type: Journal    
DOI: 10.1007/s12275-011-0530-6     Document Type: Article
Times cited : (34)

References (44)
  • 1
    • 71549133364 scopus 로고    scopus 로고
    • Evaluation of multiple sewage-associated bacteroides PCR markers for sewage pollution tracking
    • Ahmed, W., A. Goonetilleke, D. Powell, and T. Gardner. 2009. Evaluation of multiple sewage-associated bacteroides PCR markers for sewage pollution tracking. Water Res. 43, 4872-4877.
    • (2009) Water Res , vol.43 , pp. 4872-4877
    • Ahmed, W.1    Goonetilleke, A.2    Powell, D.3    Gardner, T.4
  • 3
    • 11244279103 scopus 로고    scopus 로고
    • Comparison of three PCR primer sets for identification of vanB gene carriage in feces and correlation with carriage of vancomycinresistant Enterococci: Interference by vanB-containing anaerobic Bacilli
    • Ballard, S. A., E. A. Grabsch, P. D. Johnson, and M. L. Grayson. 2005. Comparison of three PCR primer sets for identification of vanB gene carriage in feces and correlation with carriage of vancomycinresistant Enterococci: Interference by vanB-containing anaerobic Bacilli. Antimicrob. Agents Chemother. 49, 77-81.
    • (2005) Antimicrob. Agents Chemother , vol.49 , pp. 77-81
    • Ballard, S.A.1    Grabsch, E.A.2    Johnson, P.D.3    Grayson, M.L.4
  • 4
    • 0034126848 scopus 로고    scopus 로고
    • Identification of nonpoint sources of fecal pollution in coastal waters by using host-specific 16S ribosomal DNA genetic markers from fecal anaerobes
    • Bernhard, A. E. and K. G. Field. 2000a. Identification of nonpoint sources of fecal pollution in coastal waters by using host-specific 16S ribosomal DNA genetic markers from fecal anaerobes. Appl. Environ. Microbiol. 66, 1587-1594.
    • (2000) Appl. Environ. Microbiol , vol.66 , pp. 1587-1594
    • Bernhard, A.E.1    Field, K.G.2
  • 5
    • 0033774937 scopus 로고    scopus 로고
    • A PCR assay to discriminate human and ruminant feces on the basis of host differences in bacteroides-prevotella genes encoding 16S rRNA
    • Bernhard, A. E. and K. G. Field. 2000b. A PCR assay to discriminate human and ruminant feces on the basis of host differences in bacteroides-prevotella genes encoding 16S rRNA. Appl. Environ. Microbiol. 66, 4571-4574.
    • (2000) Appl. Environ. Microbiol , vol.66 , pp. 4571-4574
    • Bernhard, A.E.1    Field, K.G.2
  • 7
    • 35648991375 scopus 로고    scopus 로고
    • Eztaxon: A web-based tool for the identification of prokaryotes based on 16S ribosomal rRNA gene sequences
    • Chun, J., J. H. Lee, Y. Jung, M. Kim, S. Kim, B. K. Kim, and Y. W. Lim. 2007. Eztaxon: A web-based tool for the identification of prokaryotes based on 16S ribosomal rRNA gene sequences. Int. J. Syst. Evol. Microbiol. 57, 2259-2261.
    • (2007) Int. J. Syst. Evol. Microbiol , vol.57 , pp. 2259-2261
    • Chun, J.1    Lee, J.H.2    Jung, Y.3    Kim, M.4    Kim, S.5    Kim, B.K.6    Lim, Y.W.7
  • 8
    • 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. O'sullivan, Q. Wang, J. Nikkila, J. R. Marchesi, H. Smidt, W. M. de Vos, R. P. Ross, and P. W. O'Toole. 2009. Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS One 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
  • 9
    • 2942707955 scopus 로고    scopus 로고
    • Atopostipes suicloacale gen. nov., sp. nov., isolated from an underground swine manure storage pit
    • Cotta, M. A., T. R. Whitehead, M. D. Collins, and P. A. Lawson. 2004. Atopostipes suicloacale gen. nov., sp. nov., isolated from an underground swine manure storage pit. Anaerobe 10, 191-195.
    • (2004) Anaerobe , vol.10 , pp. 191-195
    • Cotta, M.A.1    Whitehead, T.R.2    Collins, M.D.3    Lawson, P.A.4
  • 10
    • 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., S. Huse, M. L. Sogin, and D. A. Relman. 2008. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 6, e280.
    • (2008) PLoS Biol , vol.6
    • Dethlefsen, L.1    Huse, S.2    Sogin, M.L.3    Relman, D.A.4
  • 12
    • 49549107771 scopus 로고    scopus 로고
    • Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded flx amplicon pyrosequencing (btefap)
    • Dowd, S. E., T. R. Callaway, R. D. Wolcott, Y. Sun, T. McKeehan, R. G. Hagevoort, and T. S. Edrington. 2008a. Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded flx amplicon pyrosequencing (btefap). BMC Microbiol. 8, 125.
    • (2008) BMC Microbiol , vol.8 , pp. 125
    • Dowd, S.E.1    Callaway, T.R.2    Wolcott, R.D.3    Sun, Y.4    McKeehan, T.5    Hagevoort, R.G.6    Edrington, T.S.7
  • 13
    • 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., Y. Sun, R. D. Wolcott, A. Domingo, and J. A. Carroll. 2008b. Bacterial tag-encoded FLX amplicon pyrosequencing (btefap) for microbiome studies: Bacterial diversity in the ileum of newly weaned salmonella-infected pigs. Foodborne Pathog. Dis. 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
  • 17
    • 77954254522 scopus 로고    scopus 로고
    • Improvement of the representation of bifidobacteria in fecal microbiota metagenomic libraries by application of the cpn60 universal primer cocktail
    • Hill, J. E., W. M. U. Fernando, G. A. Zello, R. T. Tyler, W. J. Dahl, and A. G. V. Kessel. 2010. Improvement of the representation of bifidobacteria in fecal microbiota metagenomic libraries by application of the cpn60 universal primer cocktail. Appl. Environ. Microbiol. 76, 4550-4552.
    • (2010) Appl. Environ. Microbiol , vol.76 , pp. 4550-4552
    • Hill, J.E.1    Fernando, W.M.U.2    Zello, G.A.3    Tyler, R.T.4    Dahl, W.J.5    Kessel, A.G.V.6
  • 18
    • 58149133908 scopus 로고    scopus 로고
    • Molecular identification of fecal pollution sources in water supplies by host-specific fecal DNA markers and terminal restriction fragment length polymorphism profiles of 16S rRNA gene
    • Jeong, J. Y., K. I. Gil, K. H. Lee, and J. O. Ka. 2008. Molecular identification of fecal pollution sources in water supplies by host-specific fecal DNA markers and terminal restriction fragment length polymorphism profiles of 16S rRNA gene. J. Microbiol. 46, 599-607.
    • (2008) J. Microbiol , vol.46 , pp. 599-607
    • Jeong, J.Y.1    Gil, K.I.2    Lee, K.H.3    Ka, J.O.4
  • 19
    • 77649199697 scopus 로고    scopus 로고
    • Quantitative analysis of human and cow-specific 16S rRNA gene markers for assessment of fecal pollution in river waters by real-time PCR
    • Jeong, J. Y., H. D. Park, K. H. Lee, J. H. Hwang, and J. O. Ka. 2010. Quantitative analysis of human and cow-specific 16S rRNA gene markers for assessment of fecal pollution in river waters by real-time PCR. J. Microbiol. Biotechnol. 20, 245-253.
    • (2010) J. Microbiol. Biotechnol , vol.20 , pp. 245-253
    • Jeong, J.Y.1    Park, H.D.2    Lee, K.H.3    Hwang, J.H.4    Ka, J.O.5
  • 20
    • 77951700268 scopus 로고    scopus 로고
    • Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent clostridium difficile-associated diarrhea
    • Khoruts, A., J. Dicksved, J. K. Jansson, and M. J. Sadowsky. 2010. Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent clostridium difficile-associated diarrhea. J. Clin. Gastroenterol. 44, 354-360.
    • (2010) J. Clin. Gastroenterol , vol.44 , pp. 354-360
    • Khoruts, A.1    Dicksved, J.2    Jansson, J.K.3    Sadowsky, M.J.4
  • 21
    • 34547597968 scopus 로고    scopus 로고
    • 16S rRNA-based assays for quantitative detection of universal, human-, cow-, and dog-specific fecal bacteroidales: A bayesian approach
    • Kildare, B. J., C. M. Leutenegger, B. S. McSwain, D. G. Bambic, V. B. Rajal, and S. Wuertz. 2007. 16S rRNA-based assays for quantitative detection of universal, human-, cow-, and dog-specific fecal bacteroidales: A bayesian approach. Water Res. 41, 3701-3715.
    • (2007) Water Res , vol.41 , pp. 3701-3715
    • Kildare, B.J.1    Leutenegger, C.M.2    McSwain, B.S.3    Bambic, D.G.4    Rajal, V.B.5    Wuertz, S.6
  • 22
    • 32044463785 scopus 로고    scopus 로고
    • Representational difference analysis and real-time PCR for strain-specific quantification of Lactobacillus sobrius sp. Nov
    • Konstantinov, S. R., H. Smidt, and W. M. de Vos. 2005. Representational difference analysis and real-time PCR for strain-specific quantification of Lactobacillus sobrius sp. Nov. Appl. Environ. Microbiol. 71, 7578-7581.
    • (2005) Appl. Environ. Microbiol , vol.71 , pp. 7578-7581
    • Konstantinov, S.R.1    Smidt, H.2    de Vos, W.M.3
  • 23
    • 0028906052 scopus 로고
    • Design and evaluation of bacteroides DNA probes for the specific detection of human fecal pollution
    • Kreader, C. A. 1995. Design and evaluation of bacteroides DNA probes for the specific detection of human fecal pollution. Appl. Environ. Microbiol. 61, 1171-1179.
    • (1995) Appl. Environ. Microbiol , vol.61 , pp. 1171-1179
    • Kreader, C.A.1
  • 24
    • 33745153077 scopus 로고    scopus 로고
    • Development of bacteroides 16S rRNA gene taqman-based real-time PCR assays for estimation of total, human, and bovine fecal pollution in water
    • Layton, A., L. McKay, D. Williams, V. Garrett, R. Gentry, and G. Sayler. 2006. Development of bacteroides 16S rRNA gene taqman-based real-time PCR assays for estimation of total, human, and bovine fecal pollution in water. Appl. Environ. Microbiol. 72, 4214-4224.
    • (2006) Appl. Environ. Microbiol , vol.72 , pp. 4214-4224
    • Layton, A.1    McKay, L.2    Williams, D.3    Garrett, V.4    Gentry, R.5    Sayler, G.6
  • 26
    • 77649220428 scopus 로고    scopus 로고
    • Evaluation of Lactobacillus sobrius/L. amylovorus as a new microbial marker of pig manure
    • Marti, R., P. Dabert, C. Ziebal, and A. M. Pourcher. 2010. Evaluation of Lactobacillus sobrius/L. amylovorus as a new microbial marker of pig manure. Appl. Environ. Microbiol. 76, 1456-1461.
    • (2010) Appl. Environ. Microbiol , vol.76 , pp. 1456-1461
    • Marti, R.1    Dabert, P.2    Ziebal, C.3    Pourcher, A.M.4
  • 27
    • 69949188278 scopus 로고    scopus 로고
    • Lack of specificity for PCR assays targeting human bacteroides 16S rRNA gene: Cross-amplification with fish feces
    • McLain, J. E., H. Ryu, L. Kabiri-Badr, C. M. Rock, and M. Abbaszadegan. 2009. Lack of specificity for PCR assays targeting human bacteroides 16S rRNA gene: Cross-amplification with fish feces. FEMS Microbiol. Lett. 299, 38-43.
    • (2009) FEMS Microbiol. Lett , vol.299 , pp. 38-43
    • McLain, J.E.1    Ryu, H.2    Kabiri-Badr, L.3    Rock, C.M.4    Abbaszadegan, M.5
  • 28
    • 77649110123 scopus 로고    scopus 로고
    • Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent
    • McLellan, S. L., S. M. Huse, S. R. Mueller-Spitz, E. N. Andreishcheva, and M. L. Sogin. 2009. Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent. Environ. Microbiol. 12, 378-392.
    • (2009) Environ. Microbiol , vol.12 , pp. 378-392
    • McLellan, S.L.1    Huse, S.M.2    Mueller-Spitz, S.R.3    Andreishcheva, E.N.4    Sogin, M.L.5
  • 29
    • 66249125965 scopus 로고    scopus 로고
    • Estimation of pig fecal contamination in a river catchment by real-time PCR using two pig-specific bacteroidales 16S rRNA genetic markers
    • Mieszkin, S., J. P. Furet, G. Corthier, and M. Gourmelon. 2009. Estimation of pig fecal contamination in a river catchment by real-time PCR using two pig-specific bacteroidales 16S rRNA genetic markers. Appl. Environ. Microbiol. 75, 3045-3054.
    • (2009) Appl. Environ. Microbiol , vol.75 , pp. 3045-3054
    • Mieszkin, S.1    Furet, J.P.2    Corthier, G.3    Gourmelon, M.4
  • 30
    • 67649603926 scopus 로고    scopus 로고
    • Barcoded pyrosequencing reveals shared bacterial community properties along the temperature gradients of two alkaline hot springs in yellowstone national park
    • Miller, S. R., A. L. Strong, K. L. Jones, and M. C. Ungerer. 2009. Barcoded pyrosequencing reveals shared bacterial community properties along the temperature gradients of two alkaline hot springs in yellowstone national park. Appl. Environ. Microbiol. 75, 4565-4572.
    • (2009) Appl. Environ. Microbiol , vol.75 , pp. 4565-4572
    • Miller, S.R.1    Strong, A.L.2    Jones, K.L.3    Ungerer, M.C.4
  • 31
    • 69449092649 scopus 로고    scopus 로고
    • Parasutterella excrementihominis gen. Nov., sp. Nov., a member of the family alcaligenaceae isolated from human faeces
    • Nagai, F., M. Morotomi, H. Sakon, and R. Tanaka. 2009. Parasutterella excrementihominis gen. Nov., sp. Nov., a member of the family alcaligenaceae isolated from human faeces. Int. J. Syst. Evol. Microbiol. 59, 1793-1797.
    • (2009) Int. J. Syst. Evol. Microbiol , vol.59 , pp. 1793-1797
    • Nagai, F.1    Morotomi, M.2    Sakon, H.3    Tanaka, R.4
  • 32
    • 33847312252 scopus 로고    scopus 로고
    • Quantification of host-specific bacteroides-prevotella 16S rRNA genetic markers for assessment of fecal pollution in freshwater
    • Okabe, S., N. Okayama, O. Savichtcheva, and T. Ito. 2007. Quantification of host-specific bacteroides-prevotella 16S rRNA genetic markers for assessment of fecal pollution in freshwater. Appl. Microbiol. Biotechnol. 74, 890-901.
    • (2007) Appl. Microbiol. Biotechnol , vol.74 , pp. 890-901
    • Okabe, S.1    Okayama, N.2    Savichtcheva, O.3    Ito, T.4
  • 34
    • 33947640155 scopus 로고    scopus 로고
    • A quantitative real-time PCR assay for the highly sensitive and specific detection of human faecal influence in spring water from a large alpine catchment area
    • Reischer, G. H., D. C. Kasper, R. Steinborn, A. H. Farnleitner, and R. L. Mach. 2007. A quantitative real-time PCR assay for the highly sensitive and specific detection of human faecal influence in spring water from a large alpine catchment area. Lett. Appl. Microbiol. 44, 351-356.
    • (2007) Lett. Appl. Microbiol , vol.44 , pp. 351-356
    • Reischer, G.H.1    Kasper, D.C.2    Steinborn, R.3    Farnleitner, A.H.4    Mach, R.L.5
  • 35
    • 33747329331 scopus 로고    scopus 로고
    • Quantitative PCR method for sensitive detection of ruminant fecal pollution in freshwater and evaluation of this method in alpine karstic regions
    • Reischer, G. H., D. C. Kasper, R. Steinborn, R. L. Mach, and A. H. Farnleitner. 2006. Quantitative PCR method for sensitive detection of ruminant fecal pollution in freshwater and evaluation of this method in alpine karstic regions. Appl. Environ. Microbiol. 72, 5610-5614.
    • (2006) Appl. Environ. Microbiol , vol.72 , pp. 5610-5614
    • Reischer, G.H.1    Kasper, D.C.2    Steinborn, R.3    Mach, R.L.4    Farnleitner, A.H.5
  • 36
    • 0019486796 scopus 로고
    • Assessment of bifidobacteria as indicators of human fecal pollution
    • Resnick, I. G. and M. A. Levin. 1981. Assessment of bifidobacteria as indicators of human fecal pollution. Appl. Environ. Microbiol. 42, 433-438.
    • (1981) Appl. Environ. Microbiol , vol.42 , pp. 433-438
    • Resnick, I.G.1    Levin, M.A.2
  • 37
    • 47249135018 scopus 로고    scopus 로고
    • Sutterella parvirubra sp. nov. and Megamonas funiformis sp. nov., isolated from human faeces
    • Sakon, H., F. Nagai, M. Morotomi, and R. Tanaka. 2008. Sutterella parvirubra sp. nov. and Megamonas funiformis sp. nov., isolated from human faeces. Int. J. Syst. Evol. Microbiol. 58, 970-975.
    • (2008) Int. J. Syst. Evol. Microbiol , vol.58 , pp. 970-975
    • Sakon, H.1    Nagai, F.2    Morotomi, M.3    Tanaka, R.4
  • 39
    • 72949107142 scopus 로고    scopus 로고
    • Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities
    • Schloss, P. D., S. L. Westcott, T. Ryabin, J. R. Hall, M. Hartmann, E. B. Hollister, R. A. Lesniewski, and et al. 2009. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537-7541.
    • (2009) Appl. Environ. Microbiol , vol.75 , pp. 7537-7541
    • Schloss, P.D.1    Westcott, S.L.2    Ryabin, T.3    Hall, J.R.4    Hartmann, M.5    Hollister, E.B.6    Lesniewski, R.A.7
  • 40
    • 0035376988 scopus 로고    scopus 로고
    • Detection of toxigenicity by a probe for the microcystin synthetase a gene (mcyA) of the cyanobacterial genus microcystis: Comparison of toxicities with 16S rRNA and phycocyanin operon (phycocyanin intergenic spacer) phylogenies
    • Tillett, D., D. L. Parker, and B. A. Neilan. 2001. Detection of toxigenicity by a probe for the microcystin synthetase a gene (mcyA) of the cyanobacterial genus microcystis: Comparison of toxicities with 16S rRNA and phycocyanin operon (phycocyanin intergenic spacer) phylogenies. Appl. Environ. Microbiol. 67, 2810-2818.
    • (2001) Appl. Environ. Microbiol , vol.67 , pp. 2810-2818
    • Tillett, D.1    Parker, D.L.2    Neilan, B.A.3
  • 41
    • 34547702305 scopus 로고    scopus 로고
    • Genetic diversity and population structure of Escherichia coli isolated from freshwater beaches
    • Walk, S. T., E. W. Alm, L. M. Calhoun, J. M. Mladonicky, and T. S. Whittam. 2007. Genetic diversity and population structure of Escherichia coli isolated from freshwater beaches. Environ. Microbiol. 9, 2274-2288.
    • (2007) Environ. Microbiol , vol.9 , pp. 2274-2288
    • Walk, S.T.1    Alm, E.W.2    Calhoun, L.M.3    Mladonicky, J.M.4    Whittam, T.S.5
  • 42
    • 34548293679 scopus 로고    scopus 로고
    • Naive bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    • Wang, Q., G. M. Garrity, J. M. Tiedje, and J. R. Cole. 2007. Naive bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261-5267.
    • (2007) Appl. Environ. Microbiol , vol.73 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4
  • 43
    • 27744480824 scopus 로고    scopus 로고
    • A similarity measure based on species proportions
    • Yue, J. C. and M. K. Clayton. 2005. A similarity measure based on species proportions. Comm. Statist. Theory Methods 34, 2123-2131.
    • (2005) Comm. Statist. Theory Methods , vol.34 , pp. 2123-2131
    • Yue, J.C.1    Clayton, M.K.2
  • 44
    • 58549117517 scopus 로고    scopus 로고
    • Development of Faecalibacterium 16S rRNA gene marker for identification of human faeces
    • Zheng, G., H. Yampara-Iquise, J. E. Jones, and C. Andrew Carson. 2009. Development of Faecalibacterium 16S rRNA gene marker for identification of human faeces. J. Appl. Microbiol. 106, 634-641.
    • (2009) J. Appl. Microbiol , vol.106 , pp. 634-641
    • Zheng, G.1    Yampara-Iquise, H.2    Jones, J.E.3    Andrew Carson, C.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.