Comparison of Bacteroides-Prevotella 16S rRNA genetic markers for fecal samples from different animal species

Applied and Environmental Microbiology

Volumn 71, Issue 10, 2005, Pages 5999-6007

  Fogarty, Lisa R ^a   Voytek, Mary A ^a  

^a U S GEOLOGICAL SURVEY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; GENES; GENETIC ENGINEERING; GROUNDWATER; MOLECULAR BIOLOGY; RNA; SURFACE WATERS;

ANIMAL SPECIES; FECAL SAMPLES; GENETIC MARKERS; POLYMORPHISM;

BIOMARKERS;

DNA; DRINKING WATER; RNA 16S;

FECES; GENETIC MARKER; POLLUTION;

ARTICLE; BACTEROIDES; BIRD; CHICKEN; COW; DEER; DOG; FECES; GEOGRAPHIC DISTRIBUTION; GOOSE; HORSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PREVOTELLA; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SWINE; TERMINAL RESTRICTION FRAGMENT LENGTH POLYMORPHISM; WATER CONTAMINATION; WATER QUALITY;

ANIMALS; BACTEROIDES; CATTLE; DNA, BACTERIAL; DOGS; FECES; GENETIC MARKERS; HUMANS; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; PREVOTELLA; RNA, RIBOSOMAL, 16S; SPECIES SPECIFICITY; WATER MICROBIOLOGY; WATER POLLUTION;

ANIMALIA; ANSER; ANSER SP.; AVES; BACTERIA (MICROORGANISMS); BACTEROIDES; CANIS FAMILIARIS; CERVIDAE; EQUIDAE; EQUUS CABALLUS; GALLUS GALLUS; PREVOTELLA; SUS SCROFA;

EID: 26844510666     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.71.10.5999-6007.2005     Document Type: Article

References (37)

1. Allsop, K., and D. J. Stickler. 1985. An assessment of Bacteroides fragilis group organisms as indicators of human faecal pollution. J. Appl. Bacteriol. 58:95-99.
2. Bernhard, A. E., and K. G. Field. 2000. 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.
3. Bernhard, A. E., and K. G. Field. 2000. 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.
4. Bernhard, A. E., T. Goyard, M. T. Simonich, and K. G. Field. 2003. Application of a rapid method for identifying fecal pollution sources in a multi-use estuary. Water Res. 37:909-913.
5. Blackwood, C. B., T. Marsh, S. Kim, and E. A. Paul. 2003. Terminal restriction fragment length polymorphism data analysis for quantitative comparison of microbial communities. Appl. Environ. Microbiol. 69:926-932.
6. Carrillo, M., E. Estrada, and T. C. Hazen. 1985. Survival and enumeration of the fecal indicators Bifidobacterium adolescente and Escherichia coli in a tropical rain forest watershed. Appl. Environ. Microbiol. 50:468-476.
7. Carson, C. A., B. L. Shear, M. R. Ellersieck, and A. Asfaw. 2001. Identification of fecal Escherichia coli from humans and animals by ribotyping. Appl. Environ. Microbiol. 67:1503-1507.
8. Centers for Disease Control and Prevention. 2002. Surveillance for waterborne disease outbreaks-United States, 1999-2000. Morb. Mortal. Wkly. Rep. 51:1-28
9. Dombek, P. E., L. K. Johnson, S. T. Zimmerley, and M. J. Sadowsky. 2000. Use of repetitive DNA sequences and the PCR to differentiate Escherichia coli isolates from human and animal sources. Appl. Environ. Microbiol. 66:2572-2577.
10. Dunbar, J., L. O. Ticknor, and C. R. Kuske. 2000. Assessment of microbial diversity in four southwestern United States soils by 16S rRNA gene terminal restriction fragment analysis. Appl. Environ. Microbiol. 66:2943-2950.
11. Dunbar, J., L. O. Ticknor, and C. R. Kuske. 2001. Phylogenetic specificity and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities. Appl. Environ. Microbiol. 67:190-197.
12. Field, K., E. C Chern, L. K. Dick, J. Fuhrman, J. Griffith, P. A. Holden, M. G. LaMontagne, J. Le, B. Olson, and M. T. Simonich. 2003. A comparative study of culture-independent, library-independent genotypic methods of fecal source tracking. J. Water Health 1:181-194.
13. Fiksdal, L., J. S. Maki, S. J. LaCroix, and J. T. Staley. 1985. Survival and detection of Bacteroides spp., prospective indicator bacteria. tAppl. Environ. Microbiol. 49:148-150.
14. Fogarty, L. R., S. K. Haack, M. J. Wolcott, and R. L. Whitman. 2003. Abundance and characteristics of the recreational water quality indicator bacteria Escherichia coli and enterococci in gull faeces. J. Appl. Microbiol. 94:865-878.
15. Hagedorn, C., S. L. Robinson, J. R. Filtz, S. M. Grubbs, T. A. Angier, and R. B. Reneau, Jr. 1999. Determining sources of fecal pollution in a rural Virginia watershed with antibiotic resistance patterns in fecal streptococci. Appl. Environ. Microbiol. 65:5522-5531.
16. Harwood, V. J, J. Whitlock, and V. Withington. 2000. Classification of antibiotic resistance patterns of indicator bacteria by discriminant analysis: Use in predicting the source of fecal contamination in subtropical waters. Appl. Environ. Microbiol. 66:3698-3704.
17. Kaplan, C. W., J. C. Astaire, M. E. Sanders, Bandaru, S. Reddy, and C. L. Kitts. 2001. 16S ribosomal DNA terminal restriction fragment pattern analysis of bacterial communities in feces of rats fed Lactobacillus acidophilus. Appl. Environ. Microbiol. 67:1935-1939.
18. Kitts, C. L. 2001. Terminal restriction fragment patterns: A tool for comparing microbial communities and assessing community dynamics. Curr. Issues Intest. Microbiol. 2:17-25.
19. Kreader, C. A. 1998. Persistence of PCR-detectable Bacteroides distasonis from human feces in river water. Appl. Environ. Microbiol. 64:4103-4105.
20. 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.
21. Malakoff, D. 2002. Water quality. Microbiologists on the trail of polluting bacteria. Science 295:2352-2353.
22. Marsh, T. L. 1999. Terminal restriction fragment length polymorphism (T-RFLP): an emerging method for characterizing diversity among homologous populations of amplification products. Curr. Opin. Microbiol. 2:323-327.
23. McOrist, A. L., M. Jackson, and A. R. Bird. 2002. A comparison of five methods for extraction of bacterial DNA from human faecal samples. J. Microbiol. Methods 50:131-139.
24. Nagashima, K., T. Hisada, M. Sato, and J. Mochizuki. 2003. Application of new primer-enzyme combinations to terminal restriction fragment length polymorphism profiling of bacterial populations in human feces. Appl. Environ. Microbiol. 69:1251-1262.
25. Parveen, S., N. C. Hodge, R. E. Stall, S. R. Farrah, and M. L. Tamplin. 2001. Phenotypic and genotypic characterization of human and nonhuman Escherichia coli. Water Res. 35:379-386.
26. Rhodes, M. W., and H. Kator. 1988. Survival of Escherichia coli and Salmonella spp. in estuarine environments. Appl. Environ. Microbiol. 54:2902-2907.
27. Rose, J. B., and D. J. Grimes. 2001. Reevaluation of microbial water quality: powerful new tools for detection and risk assessment. ASM Press, Washington, D.C.
28. Salyers, A. A. 1984. Bacteroides of the human lower intestinal tract. Annu. Rev. Microbiol. 38:293-313.
29. Sghir, A., G. Gramet, A. Suau, V. Rochet, P. Pochart, and J. Dore. 2000. Quantification of bacterial groups within human fecal flora by oligonucleotide probe hybridization. Appl. Environ. Microbiol. 66:2263-2266.
30. Stoeckel, D. M., M. V. Mathes, K. E. Hyer, C. Hagedorn, H. Kator, J. Lukasik, T. L. O'Brien, T. W. Fenger, M. Samadpour, K. M. Strickler, and B. A. Wiggins. 2004. Comparison of seven protocols to identify fecal contamination sources using Escherichia coli. Environ. Sci. Technol. 38:6109-6117.
31. Suau, A., R. Bonnet, M. Sutren, J. J. Godon, G. R. Gibson, M. D. Collins, and J. Dore. 1999. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl. Environ. Microbiol. 65:4799-4807.
32. Tannok, G. W. 1997. Modification of the normal microbiota by diet, stress, antimicrobial agents, and probiotics, p. 434-465. In R. J. Mackie and B. A. White (ed.) Gastrointestinal microbiology, vol. 2: gastrointestinal microbes and host interactions. Academic Press, New York, NY.
33. U.S. Environmental Protection Agency. 2000. The quality of our nation's waters. EPA841-S-00-0011-20. U.S. Environmental Protection Agency, Washington, DC.
34. U.S. Environmental Protection Agency. 1986. Ambient water quality criteria for bacteria-1986. EPA440-5-84-002. U.S. Environmental Protection Agency, Washington, DC.
35. Vispo, C., and W. H. Karasov. 1997. The interaction of avian gut microbes and their host: an elusive symbiosis, p 115-155. In R. I. Mackie and B. A. White (ed.), Gastrointestinal microbiology, vol. 1: gastrointestinal ecosystems and fermentations. Academic Press, New York, NY.
36. Wiggins, B. A., P. W. Cash, W. S. Creamer, S. E. Dart, P. P. Garcia, T. M. Gerecke, J. Man, B. L. Henry, K. B. Hoover, E. L. Johnson, K. C. Jones, J. G. McCarthy, J. A. McDonough, S. A. Mercer, M. J. Note, H. Park, M. S. Phillips, S. M. Purner, B. M. Smith, E. N. Stevens, and A. K. Varner. 2003. Use of antibiotic resistance analysis for representativeness testing of multiwatershed libraries. Appl. Environ. Microbiol. 69:3399-3405.
37. Wood, J., K. P. Scott, G. Avgustin, C. J. Newbold, and H. J. Flint. 1998. Estimation of the relative abundance of different Bacleroides and Prevotella ribotypes in gut samples by restriction enzyme profiling of PCR-amplified 16S rRNA gene sequences. Appl. Environ. Microbiol. 64:3683-3689.