This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Bernhard, A. E.
Right arrow Articles by Field, K. G.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Bernhard, A. E.
Right arrow Articles by Field, K. G.
Agricola
Right arrow Articles by Bernhard, A. E.
Right arrow Articles by Field, K. G.

 Previous Article  |  Next Article 

Applied and Environmental Microbiology, October 2000, p. 4571-4574, Vol. 66, No. 10
0099-2240/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.

A PCR Assay To Discriminate Human and Ruminant Feces on the Basis of Host Differences in Bacteroides-Prevotella Genes Encoding 16S rRNA

Anne E. Bernhard and Katharine G. Field*

Department of Microbiology, Oregon State University, Corvallis, Oregon 97330

Received 14 April 2000/Accepted 26 July 2000

Our purpose was to develop a rapid, inexpensive method of diagnosing the source of fecal pollution in water. In previous research, we identified Bacteroides-Prevotella ribosomal DNA (rDNA) PCR markers based on analysis. These markers length heterogeneity PCR and terminal restriction fragment length polymorphism distinguish cow from human feces. Here, we recovered 16S rDNA clones from natural waters that were close phylogenetic relatives of the markers. From the sequence data, we designed specific PCR primers that discriminate human and ruminant sources of fecal contamination.

* Corresponding author. Mailing address: Dept. of Microbiology, 220 Nash Hall, Oregon State University, Corvallis, OR 97331. Phone: (541) 737-1837. Fax: (541) 737-0496. E-mail: fieldk{at}bcc.orst.edu.

Applied and Environmental Microbiology, October 2000, p. 4571-4574, Vol. 66, No. 10
0099-2240/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.


This article has been cited by other articles:

  • Rosario, K., Symonds, E. M., Sinigalliano, C., Stewart, J., Breitbart, M. (2009). Pepper Mild Mottle Virus as an Indicator of Fecal Pollution. Appl. Environ. Microbiol. 75: 7261-7267 [Abstract] [Full Text]  
  • Lu, J., Santo Domingo, J. W., Hill, S., Edge, T. A. (2009). Microbial Diversity and Host-Specific Sequences of Canada Goose Feces. Appl. Environ. Microbiol. 75: 5919-5926 [Abstract] [Full Text]  
  • Lamendella, R., Santo Domingo, J. W., Yannarell, A. C., Ghosh, S., Di Giovanni, G., Mackie, R. I., Oerther, D. B. (2009). Evaluation of Swine-Specific PCR Assays Used for Fecal Source Tracking and Analysis of Molecular Diversity of Swine-Specific "Bacteroidales" Populations. Appl. Environ. Microbiol. 75: 5787-5796 [Abstract] [Full Text]  
  • Marti, R., Dabert, P., Pourcher, A.-M. (2009). Pig Manure Contamination Marker Selection Based on the Influence of Biological Treatment on the Dominant Fecal Microbial Groups. Appl. Environ. Microbiol. 75: 4967-4974 [Abstract] [Full Text]  
  • McQuaig, S. M., Scott, T. M., Lukasik, J. O., Paul, J. H., Harwood, V. J. (2009). Quantification of Human Polyomaviruses JC Virus and BK Virus by TaqMan Quantitative PCR and Comparison to Other Water Quality Indicators in Water and Fecal Samples. Appl. Environ. Microbiol. 75: 3379-3388 [Abstract] [Full Text]  
  • Bell, A., Layton, A. C., McKay, L., Williams, D., Gentry, R., Sayler, G. S. (2009). Factors Influencing the Persistence of Fecal Bacteroides in Stream Water. J. Environ. Qual. 38: 1224-1232 [Abstract] [Full Text]  
  • Jeter, S. N., McDermott, C. M., Bower, P. A., Kinzelman, J. L., Bootsma, M. J., Goetz, G. W., McLellan, S. L. (2009). Bacteroidales Diversity in Ring-Billed Gulls (Laurus delawarensis) Residing at Lake Michigan Beaches. Appl. Environ. Microbiol. 75: 1525-1533 [Abstract] [Full Text]  
  • Lee, Y.-J., Molina, M., Santo Domingo, J. W., Willis, J. D., Cyterski, M., Endale, D. M., Shanks, O. C. (2008). Temporal Assessment of the Impact of Exposure to Cow Feces in Two Watersheds by Multiple Host-Specific PCR Assays. Appl. Environ. Microbiol. 74: 6839-6847 [Abstract] [Full Text]  
  • Ahmed, W., Huygens, F., Goonetilleke, A., Gardner, T. (2008). Real-Time PCR Detection of Pathogenic Microorganisms in Roof-Harvested Rainwater in Southeast Queensland, Australia. Appl. Environ. Microbiol. 74: 5490-5496 [Abstract] [Full Text]  
  • Lu, J., Santo Domingo, J. W., Lamendella, R., Edge, T., Hill, S. (2008). Phylogenetic Diversity and Molecular Detection of Bacteria in Gull Feces. Appl. Environ. Microbiol. 74: 3969-3976 [Abstract] [Full Text]  
  • Ahmed, W., Stewart, J., Powell, D., Gardner, T. (2008). Evaluation of the Host-Specificity and Prevalence of Enterococci Surface Protein (esp) Marker in Sewage and its Application for Sourcing Human Fecal Pollution. J. Environ. Qual. 37: 1583-1588 [Abstract] [Full Text]  
  • Hong, P.-Y., Wu, J.-H., Liu, W.-T. (2008). Relative Abundance of Bacteroides spp. in Stools and Wastewaters as Determined by Hierarchical Oligonucleotide Primer Extension. Appl. Environ. Microbiol. 74: 2882-2893 [Abstract] [Full Text]  
  • Ueki, A., Abe, K., Kaku, N., Watanabe, K., Ueki, K. (2008). Bacteroides propionicifaciens sp. nov., isolated from rice-straw residue in a methanogenic reactor treating waste from cattle farms. Int. J. Syst. Evol. Microbiol. 58: 346-352 [Abstract] [Full Text]  
  • Lamendella, R., Domingo, J. W. S., Kelty, C., Oerther, D. B. (2008). Bifidobacteria in Feces and Environmental Waters. Appl. Environ. Microbiol. 74: 575-584 [Abstract] [Full Text]  
  • Shanks, O. C., Atikovic, E., Blackwood, A. D., Lu, J., Noble, R. T., Domingo, J. S., Seifring, S., Sivaganesan, M., Haugland, R. A. (2008). Quantitative PCR for Detection and Enumeration of Genetic Markers of Bovine Fecal Pollution. Appl. Environ. Microbiol. 74: 745-752 [Abstract] [Full Text]  
  • Ufnar, J. A., Wang, S. Y., Ufnar, D. F., Ellender, R. D. (2007). Methanobrevibacter ruminantium as an Indicator of Domesticated-Ruminant Fecal Pollution in Surface Waters. Appl. Environ. Microbiol. 73: 7118-7121 [Abstract] [Full Text]  
  • Dickerson, J. W. Jr., Crozier, J. B., Hagedorn, C., Hassall, A. (2007). Assessment of the 16S-23S rDNA Intergenic Spacer Region in Enterococcus spp. for Microbial Source Tracking. J. Environ. Qual. 36: 1661-1669 [Abstract] [Full Text]  
  • Ufnar, J. A., Ufnar, D. F., Wang, S. Y., Ellender, R. D. (2007). Development of a Swine-Specific Fecal Pollution Marker Based on Host Differences in Methanogen mcrA Genes. Appl. Environ. Microbiol. 73: 5209-5217 [Abstract] [Full Text]  
  • Gourmelon, M., Caprais, M. P., Segura, R., Le Mennec, C., Lozach, S., Piriou, J. Y., Rince, A. (2007). Evaluation of Two Library-Independent Microbial Source Tracking Methods To Identify Sources of Fecal Contamination in French Estuaries. Appl. Environ. Microbiol. 73: 4857-4866 [Abstract] [Full Text]  
  • Shanks, O. C., Domingo, J. W. S., Lu, J., Kelty, C. A., Graham, J. E. (2007). Identification of Bacterial DNA Markers for the Detection of Human Fecal Pollution in Water. Appl. Environ. Microbiol. 73: 2416-2422 [Abstract] [Full Text]  
  • Stoeckel, D. M., Harwood, V. J. (2007). Performance, Design, and Analysis in Microbial Source Tracking Studies. Appl. Environ. Microbiol. 73: 2405-2415 [Full Text]  
  • Vogel, J. R., Stoeckel, D. M., Lamendella, R., Zelt, R. B., Santo Domingo, J. W., Walker, S. R., Oerther, D. B. (2007). Identifying Fecal Sources in a Selected Catchment Reach Using Multiple Source-Tracking Tools. J. Environ. Qual. 36: 718-729 [Abstract] [Full Text]  
  • Yan, T., Hamilton, M. J., Sadowsky, M. J. (2007). High-Throughput and Quantitative Procedure for Determining Sources of Escherichia coli in Waterways by Using Host-Specific DNA Marker Genes. Appl. Environ. Microbiol. 73: 890-896 [Abstract] [Full Text]  
  • McQuaig, S. M., Scott, T. M., Harwood, V. J., Farrah, S. R., Lukasik, J. O. (2006). Detection of Human-Derived Fecal Pollution in Environmental Waters by Use of a PCR-Based Human Polyomavirus Assay. Appl. Environ. Microbiol. 72: 7567-7574 [Abstract] [Full Text]  
  • Shanks, O. C., Nietch, C., Simonich, M., Younger, M., Reynolds, D., Field, K. G. (2006). Basin-Wide Analysis of the Dynamics of Fecal Contamination and Fecal Source Identification in Tillamook Bay, Oregon. Appl. Environ. Microbiol. 72: 5537-5546 [Abstract] [Full Text]  
  • Reischer, G. H., Kasper, D. C., Steinborn, R., Mach, R. L., Farnleitner, A. H. (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 [Abstract] [Full Text]  
  • Walters, S. P., Field, K. G. (2006). Persistence and growth of fecal bacteroidales assessed by bromodeoxyuridine immunocapture.. Appl. Environ. Microbiol. 72: 4532-4539 [Abstract] [Full Text]  
  • Hamilton, M. J., Yan, T., Sadowsky, M. J. (2006). Development of Goose- and Duck-Specific DNA Markers To Determine Sources of Escherichia coli in Waterways.. Appl. Environ. Microbiol. 72: 4012-4019 [Abstract] [Full Text]  
  • Shanks, O. C., Santo Domingo, J. W., Lamendella, R., Kelty, C. A., Graham, J. E. (2006). Competitive metagenomic DNA hybridization identifies host-specific microbial genetic markers in cow fecal samples.. Appl. Environ. Microbiol. 72: 4054-4060 [Abstract] [Full Text]  
  • Layton, A., McKay, L., Williams, D., Garrett, V., Gentry, R., Sayler, G. (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 [Abstract] [Full Text]  
  • Soule, M., Kuhn, E., Loge, F., Gay, J., Call, D. R. (2006). Using DNA microarrays to identify library-independent markers for bacterial source tracking.. Appl. Environ. Microbiol. 72: 1843-1851 [Abstract] [Full Text]  
  • Noble, R. T., Griffith, J. F., Blackwood, A. D., Fuhrman, J. A., Gregory, J. B., Hernandez, X., Liang, X., Bera, A. A., Schiff, K. (2006). Multitiered Approach Using Quantitative PCR To Track Sources of Fecal Pollution Affecting Santa Monica Bay, California. Appl. Environ. Microbiol. 72: 1604-1612 [Abstract] [Full Text]  
  • Bower, P. A., Scopel, C. O., Jensen, E. T., Depas, M. M., McLellan, S. L. (2005). Detection of Genetic Markers of Fecal Indicator Bacteria in Lake Michigan and Determination of Their Relationship to Escherichia coli Densities Using Standard Microbiological Methods. Appl. Environ. Microbiol. 71: 8305-8313 [Abstract] [Full Text]  
  • Fogarty, L. R., Voytek, M. A. (2005). Comparison of Bacteroides-Prevotella 16S rRNA Genetic Markers for Fecal Samples from Different Animal Species. Appl. Environ. Microbiol. 71: 5999-6007 [Abstract] [Full Text]  
  • Ahmed, W., Neller, R., Katouli, M. (2005). Host Species-Specific Metabolic Fingerprint Database for Enterococci and Escherichia coli and Its Application To Identify Sources of Fecal Contamination in Surface Waters. Appl. Environ. Microbiol. 71: 4461-4468 [Abstract] [Full Text]  
  • Carson, C. A., Christiansen, J. M., Yampara-Iquise, H., Benson, V. W., Baffaut, C., Davis, J. V., Broz, R. R., Kurtz, W. B., Rogers, W. M., Fales, W. H. (2005). Specificity of a Bacteroides thetaiotaomicron Marker for Human Feces. Appl. Environ. Microbiol. 71: 4945-4949 [Abstract] [Full Text]  
  • Dick, L. K., Simonich, M. T., Field, K. G. (2005). Microplate Subtractive Hybridization To Enrich for Bacteroidales Genetic Markers for Fecal Source Identification. Appl. Environ. Microbiol. 71: 3179-3183 [Abstract] [Full Text]  
  • Dick, L. K., Bernhard, A. E., Brodeur, T. J., Santo Domingo, J. W., Simpson, J. M., Walters, S. P., Field, K. G. (2005). Host Distributions of Uncultivated Fecal Bacteroidales Bacteria Reveal Genetic Markers for Fecal Source Identification. Appl. Environ. Microbiol. 71: 3184-3191 [Abstract] [Full Text]  
  • Nielsen, J. L., Schramm, A., Bernhard, A. E., van den Engh, G. J., Stahl, D. A. (2004). Flow Cytometry-Assisted Cloning of Specific Sequence Motifs from Complex 16S rRNA Gene Libraries. Appl. Environ. Microbiol. 70: 7550-7554 [Abstract] [Full Text]  
  • Dick, L. K., Field, K. G. (2004). Rapid Estimation of Numbers of Fecal Bacteroidetes by Use of a Quantitative PCR Assay for 16S rRNA Genes. Appl. Environ. Microbiol. 70: 5695-5697 [Abstract] [Full Text]  
  • Wiggins, B. A., Cash, P. W., Creamer, W. S., Dart, S. E., Garcia, P. P., Gerecke, T. M., Han, J., Henry, B. L., Hoover, K. B., Johnson, E. L., Jones, K. C., McCarthy, J. G., McDonough, J. A., Mercer, S. A., Noto, M. J., Park, H., Phillips, M. S., Purner, S. M., Smith, B. M., Stevens, E. N., Varner, A. K. (2003). Use of Antibiotic Resistance Analysis for Representativeness Testing of Multiwatershed Libraries. Appl. Environ. Microbiol. 69: 3399-3405 [Abstract] [Full Text]  
  • Carson, C. A., Shear, B. L., Ellersieck, M. R., Schnell, J. D. (2003). Comparison of Ribotyping and Repetitive Extragenic Palindromic-PCR for Identification of Fecal Escherichia coli from Humans and Animals. Appl. Environ. Microbiol. 69: 1836-1839 [Abstract] [Full Text]  
  • Jenkins, M. B., Hartel, P. G., Olexa, T. J., Stuedemann, J. A. (2003). Putative Temporal Variability of Escherichia coli Ribotypes from Yearling Steers. J. Environ. Qual. 32: 305-309 [Abstract] [Full Text]  
  • Scott, T. M., Rose, J. B., Jenkins, T. M., Farrah, S. R., Lukasik, J. (2002). Microbial Source Tracking: Current Methodology and Future Directions. Appl. Environ. Microbiol. 68: 5796-5803 [Full Text]  
  • Hartel, P. G., Summer, J. D., Hill, J. L., Collins, J. V., Entry, J. A., Segars, W. I. (2002). Geographic Variability of Escherichia coli Ribotypes from Animals in Idaho and Georgia. J. Environ. Qual. 31: 1273-1278 [Abstract] [Full Text]  
  • Graves, A. K., Hagedorn, C., Teetor, A., Mahal, M., Booth, A. M., Reneau, R. B. Jr. (2002). Antibiotic Resistance Profiles to Determine Sources of Fecal Contamination in a Rural Virginia Watershed. J. Environ. Qual. 31: 1300-1308 [Abstract] [Full Text]  
  • Carson, C. A., Shear, B. L., Ellersieck, M. R., Asfaw, A. (2001). Identification of Fecal Escherichia coli from Humans and Animals by Ribotyping. Appl. Environ. Microbiol. 67: 1503-1507 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»