1887

Chapter 8 : The Future of Microbial Source Tracking Studies

Authors: Michael J. Sadowsky1, Douglas R. Call2, Jorge W. Santo Domingo3
VIEW AFFILIATIONS HIDE AFFILIATIONS
Affiliations: 1: Department of Soil, Water & Climate and BioTechnology Institute, University of Minnesota, 1991 Upper Buford Circle, 439 BorH, St. Paul, MN 55108; 2: Department of Veterinary Microbiology & Pathology, Washington State University, Pullman, WA 99164-7040; 3: U.S. Environmental Protection Agency, ORD/NRMRL/WSWRD/MCCB, 26 West Martin Luther King Dr., MS 387, Cincinnati, OH 45268
Content Type: Monograph
Publication Year: 2007

Category: Environmental Microbiology; Applied and Industrial Microbiology

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Preview Magnify
Zoom in
Zoomout

The Future of Microbial Source Tracking Studies, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555815769/9781555813741_Chap08-1.gif /docserver/preview/fulltext/10.1128/9781555815769/9781555813741_Chap08-2.gif

Abstract:

This chapter summarizes some of the challenges that people interested in source identification are currently facing, provides information on the microbial ecology of the gut and potential microorganisms to use in source-tracking studies, discusses research tools that will likely improve marker discovery, and offers some suggestions on the future needs for determining sources of microorganisms impacting waterways. There is considerable debate as to the choice of organism(s) to be used as an indicator of fecal contamination of waterways and for microbial source tracking (MST) studies. There are four basic types of digestive systems in animals: simple stomach or monogastric (man, pig), equine-modified simple stomach (horse), ruminant or polygastric (sheep, cow, goat, deer), and avian (chicken, turkey). Genome sequence analyses, as well as the emergence of other ‘’omic ‘’ based technologies including metagenomics, proteomics, and transcriptomics, will enhance one’s understanding of the molecular and biochemical diversity of the animal GI tract. While genome sequence information for protozoa is not as wide ranging as that for bacteria and viruses, sequence analyses have shown strong host dependence due to the lack of biosynthetic pathways. The study of the gut metagenome has clear implications to human health. In this study, sequencing analysis of cloned transcripts showed the presence of transcripts linked to sulfur, carbon, and nitrogen biogeochemical processes. Results from the microbial characterization of animal intestinal tracts have suggested that anatomical and physiological differences found in different digestive systems may lead to conditions that affect the structure of gut microbial communities.

Citation: Sadowsky M, Call D, Santo Domingo J. 2007. The Future of Microbial Source Tracking Studies, p 235-277. In Santo Domingo J, Sadowsky M, Doyle M (ed), Microbial Source Tracking. ASM Press, Washington, DC. doi: 10.1128/9781555815769.ch8
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

The Future of Microbial Source Tracking Studies
[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555815769.ch08-1,webId=/content/author/10.1128/9781555815769.ch08-1,properties={foaf_givenname=Michael J., foaf_name=Michael J. Sadowsky, foaf_surname=Sadowsky, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555815769.ch08-aff1]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555815769.ch08-2,webId=/content/author/10.1128/9781555815769.ch08-2,properties={foaf_givenname=Douglas R., foaf_name=Douglas R. Call, foaf_surname=Call, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555815769.ch08-aff2]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555815769.ch08-3,webId=/content/author/10.1128/9781555815769.ch08-3,properties={foaf_givenname=Jorge W., foaf_name=Jorge W. Santo Domingo, foaf_surname=Santo Domingo, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555815769.ch08-aff3]]}]]
Citation: Sadowsky M, Call D, Santo Domingo J. 2007. The Future of Microbial Source Tracking Studies, p 235-277. In Santo Domingo J, Sadowsky M, Doyle M (ed), Microbial Source Tracking. ASM Press, Washington, DC. doi: 10.1128/9781555815769.ch8
/content/10.1128/9781555815769.ch08.ch08fig01
Figure 1
One strategy for identifying library-independent MST markers using microarrays and comparative genomics.
10.1128/9781555815769/f0256-01_thmb.gif
10.1128/9781555815769/f0256-01.gif
Image of Figure 1
Figure 1

One strategy for identifying library-independent MST markers using microarrays and comparative genomics.

Citation: Sadowsky M, Call D, Santo Domingo J. 2007. The Future of Microbial Source Tracking Studies, p 235-277. In Santo Domingo J, Sadowsky M, Doyle M (ed), Microbial Source Tracking. ASM Press, Washington, DC. doi: 10.1128/9781555815769.ch8
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555815769.ch08
1. Abrahamsen, M. S.,, T. J. Templeton,, S. Enomoto,, J. E. Abrahante,, G. Zhu,, C. A. Lancto,, M. Deng,, C. Liu,, G. Widmer,, S. Tzipori,, G. A. Buck,, P. Xu,, A.T. Bankier,, P. H. Dear,, B. A. Konfortov,, H. F. Spriggs,, L. Iyer,, V. Anantharaman,, L. Aravind, and, V. Kapur. 2004. Complete genome sequence of the Apicomplexan, Cryptosporidium parvum. Science 304: 441– 445.
2. Abrahamsen, M. S.,, V. Kapur,, S. Tzipori, and, G. A. Buck. 2004. The genome of Cryptosporidium hominis. Nature 431: 1107– 1112.
3. Alland, D.,, T. S. Whittam,, M. B. Murray,, M. D. Cave,, M. H. Hazbon,, K. Dix,, M. Kokoris,, A. Duesterhoeft,, J. A. Eisen,, C. M. Fraser, and, R. D. Fleischmann. 2003. Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis. J. Bacteriol. 185: 3392– 3399.
4. Alverdy, J.,, O. Zaborina, and, L. Wu. 2005. The impact of stress and nutrition on bacterial-host interactions at the intestinal epithelial surface. Curr. Opin. Clin. Nutr. Metab. Care 8: 205– 209.
5. Amit-Romach, E.,, D. Sklan, and, Z. Uni. 2004. Microflora ecology of the chicken intestine using 16S ribosomal DNA primers. Poult. Sci. 83: 1093– 1098.
6. Anderson, K. L.,, J. E. Whitlock, and, V. J. Harwood. 2005. Persistence and differential survival of fecal indicator bacteria in subtropical waters and sediments. Appl. Environ. Microbiol. 71: 3041– 3048.
7. Andrews-Polymenis, H. L.,, W. Rabsch,, S. Porwollik,, M. McClelland,, C. Rosetti,, L. G. Adams, and, A. J. Baumler. 2004. Host restriction of Salmonella enterica serotype Typhimurium pigeon isolates does not correlate with loss of discrete genes. J. Bacteriol. 186: 2619– 2628.
8. Arroyo, L. G.,, S. A. Kruth,, B. M. Willey,, H. R. Staempfli,, D. E. Low, and, J. S. Weese. 2005. PCR ribotyping of Clostridium difficile isolates originating from human and animal sources. J. Med. Microbiol. 54: 163– 166.
9. Bäckhed, F.,, R. E. Ley,, J. L. Sonnenburg,, D. A. Peterson, and, J. I. Gordon. 2005. Host-bacterial mutualism in the human intestine. Science 307: 1915– 1920.
10. Beerens, H.,, B. Hass Brac de la Perriere, and, F. Gavini. 2000. Evaluation of the hygienic quality of raw milk based on the presence of bifidobacteria: the cow as a source of faecal contamination. Int. J. Food Microbiol. 54: 163– 169.
11. 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.
12. 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 coding for 16S rRNA. Appl. Environ. Microbiol. 66: 4571– 4574.
13. Berrilli, F.,, D. Di Cave,, C. De Liberato,, A. Franco,, P. Scaramozzino, and, P. Orecchia. 2004. Genotype characterisation of Giardia duodenalis isolates from domestic and farm animals by SSU-rRNA gene sequencing. Vet. Parasitol. 122: 193– 199.
14. Biavati, B., and, P. Mattarelli. 1991. Bifidobacterium ruminantium sp. nov. and Bifido-bacterium merycicum sp. nov. from the rumens of cattle. Int. J. Syst. Bacteriol. 41: 163– 168.
15. Blackstone, G. M.,, J. L. Nordstrom,, M. C. L. Vickery,, M. D. Bowen,, R. F. Meyer, and, A. DePaola. 2003. Detection of pathogenic Vibrio parahaemolyticus in oyster enrichments by real-time PCR. J. Microbiol. Methods 53: 149– 155.
16. Blanch, A. R.,, L. Belanche-Munoz,, X. Bonjoch,, J. Ebdon,, C. Gantzer,, F. Lucena,, J. Ottoson,, C. Kourtis,, A. Iversen,, I. Kuhn,, L. Moce,, M. Muniesa,, J. Schwartzbrod,, S. Skraber,, G. Papageorgiou,, H. D. Taylor,, J. Wallis, and, J. Jofre. 2005. Tracking the origin of faecal pollution in surface water: an ongoing project within the European Union research programme. J. Water Health 2: 249– 260.
17. Bonjoch, X.,, E. Ballesté, and, A. R. Blanch. 2004. Multiplex PCR with 16S rRNA gene-targeted primers of Bifidobacterium spp. to identify sources of fecal pollution. Appl. Environ. Microbiol. 70: 3171– 3175.
18. Borucki, M., and, D. R. Call. 2003. Listeria monocytogenes serotype identification using PCR. J. Clin. Microbiol. 41: 5537– 5540.
19. Borucki, M.,, M. Krug,, W. Muraoka, and, D. Call. 2003. Discrimination among Listeria monocytogenes isolates using a mixed genome DNA microarray. Vet. Microbiol. 92: 351– 362.
20. Botero, L. M.,, S. D’Imperio,, M. Burr,, T. R. McDermott,, M. Young, and, D.J. Hassett. 2005. Poly(A) polymerase modification and reverse transcriptase PCR amplification of environmental RNA. Appl. Environ. Microbiol. 71: 1267– 1275.
21. Breitbart, M.,, I. Hewson,, B. Felts,, J. M. Mahaffy,, J. Nulton,, P. Salamon, and, F. Rohwer. 2003. Metagenomic analyses of an uncultured viral community from human feces. J. Bacteriol. 185: 6220– 6223.
22. Brinkman, N. E.,, R. A. Haugland,, L. J. Wymer,, M. Byappanahalli,, R. L. Whitman, and, S. J. Vesper. 2003. Evaluation of a rapid, quantitative real-time PCR method for enumeration of pathogenic Candida cells in water. Appl. Environ. Microbiol. 69: 1775– 1782.
23. Brooks, S. P.,, M. McAllister,, M. Sandoz, and, M. L. Kalmokoff. 2003. Culture-independent phylogenetic analysis of the faecal flora of the rat. Can. J. Microbiol. 49: 589– 601.
24. Bueschel, D. M.,, B. H. Jost,, S. J. Billington,, H. T. Trinh, and, J. G. Songer. 2003. Prevalence of cpb2, encoding beta2 toxin, in Clostridium perfringens field isolates: correlation of genotype with phenotype. Vet. Microbiol. 94: 121– 129.
25. Byappanahalli, M., and, R. Fujioka. 2004. Indigenous soil bacteria and low moisture may limit but allow faecal bacteria to multiply and become a minor population in tropical soils. Water Sci. Technol. 50: 27– 32.
26. Byappanahalli, M. N.,, R. L. Whitman,, D. A. Shively,, M. J. Sadowsky, and, S. Ishii. 2006. Population structure, persistence, and seasonality of autochthonous Escherichia coli in temperate, coastal forest soil from a Great Lakes watershed. Environ. Microbiol. 8: 504– 513.
27. Call, D.,, M. Borucki, and, T. Besser. 2003. Mixed-genome microarrays reveal multiple serotype and lineage-specific differences among strains of Listeria monocytogenes. J. Clin. Microbiol. 41: 632– 639.
28. Cann, A. J.,, S. E. Fandrich, and, S. Heaphy. 2005. Analysis of the virus population present in equine faeces indicates the presence of hundreds of uncharacterized virus genomes. Virus Genes 30: 151– 156.
29. Carson, C. A.,, B. L. Shear,, M. R. Ellersieck, and, J. D. Schnell. 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.
30. Carson, C. A.,, J. M. Christiansen,, H. Yampara-Iquise,, V. W. Benson,, C. Baffaut,, J. V. Davis,, R. R. Broz,, W. B. Kurtz,, W. M. Rogers, and, W. H. Fales. 2005. Specificity of a Bacteroides thetaiotaomicron marker for human feces. Appl. Environ. Microbiol. 71: 4945– 4949.
31. Chan, K.,, S. Baker,, C. C. Kim,, C. S. Detweiler,, G. Dougan, and, S. Falkow. 2003. Genomic comparison of Salmonella enterica serovars and Salmonella bongori by use of an S. enterica serovar Typhimurium DNA microarray. J. Bacteriol. 185: 553– 563.
32. Chern, E. C.,, Y. L. Tsai, and, B. H. Olson. 2004. Occurrence of genes associated with enterotoxigenic and enterohemorrhagic Escherichia coli in agricultural waste lagoons. Appl. Environ. Microbiol. 70: 356– 362.
33. Cho, J., and, J. M. Tiedje. 2001. Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays. Appl. Environ. Microbiol. 67: 3677– 3682.
34. Craun, G. F.,, R. L. Calderon, and, M. F. Craun. 2005. Outbreaks associated with recreational water in the United States. Int. J. Environ. Health Res. 15: 243– 262.
35. Crump, B. C.,, G. W. Kling,, M. Bahr, and, J. E. Hobbie. 2003. Bacterioplankton community shifts in an arctic lake correlate with seasonal changes in organic matter source. Appl. Environ. Microbiol. 69: 2253– 2268.
36. Daly, K.,, C. S. Stewart,, H. J. Flint, and, S. P. Shirazi-Beechey. 2001. Bacterial diversity within the equine large intestine as revealed by molecular analysis of cloned 16S rRNA genes. FEMS Microbiol. Ecol. 38: 141– 151.
37. Dawson, D. 2005. Foodborne protozoan parasites. Int. J. Food Microbiol. 103: 207– 227.
38. Delcenserie, V.,, N. Bechoux,, T. Leonard,, B. China, and, G. Daube. 2004. Discrimination between Bifidobacterium species from human and animal origin by PCR-restriction fragment length polymorphism. J. Food Prot. 67: 1284– 1288.
39. Delong, E. F. 2005. Microbial community genomics in the ocean. Nat. Rev. Microbiol. 3: 459– 469.
40. Diamant, E.,, Y. Palti,, R. Gur-Arie,, H. Cohen,, E. M. Hallerman, and, Y. Kashi. 2004. Phylogeny and strain typing of Escherichia coli, inferred from variation at mononucleotide repeat loci. Appl. Environ. Microbiol. 70: 2464– 2473.
41. Dick, L. K., and, K. G. Field. 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.
42. Dick, L. K.,, M.T. Simonich, and, K. G. Field. 2005. Microplate subtractive hybridization to enrich for Bacteroidales genetic markers for fecal source identification. Appl. Environ. Microbiol. 71: 3179– 3183.
43. Dick, L. K.,, A. E. Bernhard,, T. J. Brodeur,, J. W. Santo Domingo,, J. M. Simpson,, S. P. Walters, and, K. G. Field. 2005. Host distributions of uncultivated fecal Bacteroidales bacteria reveal genetic markers for fecal source identification. Appl. Environ. Microbiol. 71: 3184– 3191.
44. Dobrindt, U. 2005. (Patho-) Genomics of Escherichia coli. Int. J. Med. Microbiol. 295: 357– 371.
45. 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.
46. Dorrell, N.,, J. A. Mangan,, K. G. Laing,, J. Hinds,, D. Linton,, H. Al-Ghusein,, B. G. Barrell,, J. Parkhill,, N. G. Stoker,, A. V. Karlyshev,, P. D. Butcher, and, B. W. Wren. 2001. Whole genome comparison of Campylobacter jejuni human isolates using a low-cost microarray reveals extensive genetic diversity. Genome Res. 11: 1706– 1715.
47. Dunny, G. M. 1990. Genetic functions and cell-cell interactions in the pheromone-inducible plasmid transfer system of Enterococcus faecalis. Mol. Microbiol. 4: 689– 696.
48. Eckburg, P. B.,, E. M. Bik,, C. N. Bernstein,, E. Purdom,, L. Dethlefsen,, M. Sargent,, S. R. Gill,, K. E. Nelson, and, D. A. Relman. 2005. Diversity of the human intestinal microbial flora. Science 308: 1635– 1638.
49. Edsall, G. S.,, S. Gaines, and, M. Landy. 1960. Studies on infection and immunity in experimental typhoid fever. I. Typhoid fever in chimpanzees orally infected with Salmonella typhosa. J. Exp. Med. 112: 143– 166.
50. Egert, M.,, U. Stingl,, L. D. Bruun,, B. Wagner,, A. Brune, and, M. W. Friedrich. 2005. Structure and topology of microbial communities in the major gut compartments of Melolontha melolontha larvae (Coleoptera: Scarabaeidae). Appl. Environ. Microbiol. 71: 4556– 4566.
51. Eyers, L.,, I. George,, L. Schuler,, B. Stenuit,, S. N. Agathos, and, S. E. Fantroussi. 2004. Environmental genomics: exploring the unmined richness of microbes to degrade xenobiotics. Appl. Microbiol. Biotechnol. 66: 123– 130.
52. Fay, J. 2006. Human genome: which proteins contribute to human-chimpanzee differences? Eur. J. Hum. Genet. 14: 506.
53. Field, D., and, C. Wills. 1996. Long, polymorphic microsatellites in simple organisms. Proc. R. Soc. Lond. B Biol. Sci. 263: 209– 215.
54. Field, K. G.,, 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.
55. Fierer, N.,, J. A. Jackson,, R. Vilgalys, and, R. B. Jackson. 2005. Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Appl. Environ. Microbiol. 71: 4117– 4120.
56. Fiksdal, L.,, J. S. Maki,, S. J. LaCroix, and, J. T. Staley. 1985. Survival and detection of Bacteroides spp., prospective indicator bacteria. Appl. Environ. Microbiol. 49: 148– 150.
57. Finegold, S. M.,, H. R. Attebery, and, V. L. Sutter. 1974. Effect of diet on human fecal flora: comparison of Japanese and American diets. Am. J. Clin. Nutr. 27: 1456– 1469.
58. Fitzgerald, J. R.,, D. E. Sturdevant,, S. M. Mackie,, S. R. Gill, and, J. M. Musser. 2001. Evolutionary genomics of Staphylococcus aureus: insights into the origin of methicillin-resistant strains and the toxic shock syndrome epidemic. Proc. Natl. Acad. Sci. USA 98: 8821– 8826.
59. Fong, T. T., and, E. K. Lipp. 2005. Enteric viruses of humans and animals in aquatic environments: health risks, detection, and potential water quality assessment tools. Microbiol. Mol. Biol. Rev. 69: 357– 371.
60. Fong, T.-T.,, D. W. Griffin, and, E. K. Lipp. 2005. Molecular assays for targeting human and bovine enteric viruses in coastal waters and their application for library-independent source tracking. Appl. Environ. Microbiol. 71: 2070– 2078.
61. Foulds, I. V.,, A. Granacki,, C. Xiao,, U. J. Krull,, A. Castle, and, P. A. Horgen. 2002. Quantification of microcystin-producing cyanobacteria and E. coli in water by 5’-nuclease PCR. J. Appl. Microbiol. 93: 825– 834.
62. Frahm, E., and, U. Obst. 2003. Application of the fluorogenic probe technique (TaqMan PCR) to the detection of Enterococcus spp. and Escherichia coli in water samples. J. Microbiol. Methods 52: 123– 131.
63. Franks, A. H.,, H. J. Harmsen,, G. C. Raangs,, G. J. Jansen,, F. Schut, and, G. W. Welling. 1998. Variations of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol. 64: 3336– 3345.
64. Fujioka, R. S. 2001. Monitoring coastal marine waters for spore-forming bacteria of faecal and soil origin to determine point from non-point source pollution. Water Sci. Technol. 44: 181– 188.
65. Gajadhar, A. A., and, J. R. Allen. 2004. Factors contributing to the public health and economic importance of waterborne zoonotic parasites. Vet. Parasitol. 126: 3– 14.
66. Galbraith, E. A.,, D. A. Antonopoulos, and, B. A. White. 2004. Suppressive subtractive hybridization as a tool for identifying genetic diversity in an environmental metagenome: the rumen as a model. Environ. Microbiol. 6: 928– 937.
67. Gavini, F.,, A. M. Pourcher,, C. Neut,, D. Monget,, C. Romond,, C. Oger, and, D. Izard. 1991. Phenotypic differentiation of bifidobacteria of human and animal origins. Int. J. Syst. Bacteriol. 41: 548– 557.
68. Germond, J. E.,, O. Mamin, and, B. Mollet. 2002. Species specific identification of nine human Bifidobacterium spp. in feces. Syst. Appl. Microbiol. 25: 536– 543.
69. Gibbs, R. A.,, G. M. Weinstock,, M. L. Metzker,, D. M. Muzny,, E. J. Sodergren,, S. Scherer,, G. Scott,, D. Steffen,, K. C. Worley,, P. E. Burch,, G. Okwuonu,, S. Hines,, L. Lewis,, C. DeRamo,, O. Delgado,, S. Dugan-Rocha,, G. Miner,, M. Morgan,, A. Hawes,, R. Gill,, R. A. Holt,, M. D. Adams,, P. G. Amanatides,, H. Baden-Tillson,, M. Barnstead,, S. Chin,, C. A. Evans,, S. Ferriera,, C. Fosler,, A. Glodek,, Z. Gu,, D. Jennings,, C. L. Kraft,, T. Nguyen,, C. M. Pfannkoch,, C. Sitter,, G. G. Sutton,, J. C. Venter,, T. Woodage,, D. Smith,, H.-M. Lee,, E. Gustafson,, P. Cahill,, A. Kana,, L. Doucette-Stamm,, K. Weinstock,, K. Fechtel,, R. B. Weiss,, D. M. Dunn,, E. D. Green,, R. W. Blakesley,, G. G. Bouffard,, P. J. de Jong,, K. Osoegawa,, B. Zhu,, M. Marra,, J. Schein,, I. Bosdet,, C. Fjell,, S. Jones,, M. Krzywinski,, C. Mathewson,, A. Siddiqui,, N. Wye,, J. McPherson,, S. Zhao,, C. M. Fraser,, J. Shetty,, S. Shatsman,, K. Geer,, Y. Chen,, S. Abramzon,, W. C. Nierman,, P. H. Havlak,, R. Chen,, K. J. Durbin,, A. Egan,, Y. Ren,, X.-Z. Song,, B. Li,, Y. Liu,, X. Qin,, S. Cawley,, K. C. Worley,, A.J. Cooney,, L. M. D’Souza,, K. Martin,, J. Q. Wu,, M. L. Gonzalez-Garay,, A. R. Jackson,, K. J. Kalafus,, M. P. McLeod,, A. Milosavljevic,, D. Virk,, A. Volkov,, D. A. Wheeler,, Z. Zhang,, J. A. Bailey,, E. E. Eichler,, E. Tuzun,, E. Birney,, E. Mongin,, A. Ureta-Vidal,, C. Woodwark,, E. Zdobnov,, P. Bork,, M. Suyama,, D. Torrents,, M. Alexandersson,, B. J. Trask,, J. M. Young,, H. Huang,, H. Wang,, H. Xing,, S. Daniels,, D. Gietzen,, J. Schmidt,, K. Stevens,, U. Vitt,, J. Wingrove,, F. Camara,, M. Mar Alba,, J. F. Abril,, R. Guigo,, A. Smit,, I. Dubchak,, E. M. Rubin,, O. Couronne,, A. Poliakov,, N. Hubner,, D. Ganten,, C. Goesele,, O. Hummel,, T. Kreitler,, Y.-A. Lee,, J. Monti,, H. Schulz,, H. Zimdahl,, H. Himmelbauer,, H. Lehrach,, H. J. Jacob,, S. Bromberg,, J. Gullings-Handley,, M. I. Jensen-Seaman,, A. E. Kwitek,, J. Lazar,, D. Pasko,, P. J. Tonellato,, S. Twigger,, C. P. Ponting,, J. M. Duarte,, S. Rice,, L. Goodstadt,, S. A. Beatson,, R. D. Emes,, E. E. Winter,, C. Webber,, P. Brandt,, G. Nyakatura,, M. Adetobi,, F. Chiaromonte,, L. Elnitski,, P. Eswara,, R. C. Hardison,, M. Hou,, D. Kolbe,, K. Makova,, W. Miller,, A. Nekrutenko,, C. Riemer,, S. Schwartz,, J. Taylor,, S. Yang,, Y. Zhang,, K. Lindpaintner,, T. D. Andrews,, M. Caccamo,, M. Clamp,, L. Clarke,, V. Curwen,, R. Durbin,, E. Eyras,, S. M. Searle,, G. M. Cooper,, S. Batzoglou,, M. Brudno,, A. Sidow,, E. A. Stone,, B. A. Payseur,, G. Bourque,, C. Lopez-Otin,, X. S. Puente,, K. Chakrabarti,, S. Chatterji,, C. Dewey,, L. Pachter,, N. Bray,, V. B. Yap,, A. Caspi,, G. Tesler,, P. A. Pevzner,, D. Haussler,, K. M. Roskin,, R. Baertsch,, H. Clawson,, T. S. Furey,, A. S. Hinrichs,, D. Karolchik,, W. J. Kent,, K. R. Rosenbloom,, H. Trumbower,, M. Weirauch,, D. N. Cooper,, P. D. Stenson,, B. Ma,, M. Brent,, M. Arumugam,, D. Shteynberg,, R. R. Copley,, M. S. Taylor,, H. Riethman,, U. Mudunuri,, J. Peterson,, M. Guyer,, A. Felsenfeld,, S. Old,, S. Mockrin, and, F. Collins. 2004. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428: 493– 521.
70. Gillespie, D. E.,, S. F. Brady,, A. D. Bettermann,, N. P. Cianciotto,, M. R. Liles,, M. R. Rondon,, J. Clardy,, R. M. Goodman, and, J. Handelsman. 2002. Isolation of antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA. Appl. Environ. Microbiol. 68: 4301– 4306.
71. Glockner, F. O.,, E. Zaichikov,, N. Belkova,, L. Denissova,, J. Pernthaler,, A. Pernthaler, and, R. Amann. 2000. Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria. Appl. Environ. Microbiol. 66: 5053– 5065.
72. Goodgame, R. 2003. Emerging causes of traveler’s diarrhea: Cryptosporidium, Cyclospora, Isospora, and Microsporidia. Curr. Infect. Dis. Rep. 5: 66– 73.
73. Gordon, D. M. 2001. Geographical structure and host specificity in bacteria and the implications for tracing the source of coliform contamination. Microbiology 147: 1079– 1085.
74. Griffiths, N. J.,, J. R. Walton,, G. B. Edwards,, M. Bennett,, B. China,, J. Mainil,, S. Vandevenne, and, C. A. Hart. 1997. The prevalence of Clostridium perfringens in the horse. Rev. Med. Microbiol. 8: S52– S54.
75. Guarner, F., and, J. R. Malagelada. 2003. Gut flora in health and disease. Lancet 361: 512– 519.
76. Gur-Arie, R.,, C. J. Cohen,, Y. Eitan,, L. Shelef,, E. M. Hallerman, and, Y. Kashi. 2000. Simple sequence repeats in Escherichia coli: abundance, distribution, composition, and polymorphism. Genome Res. 10: 62– 71.
77. Guy, R. A.,, C. Xiao, and, P. A. Horgen. 2004. Real-time PCR assay for detection and genotype differentiation of Giardia lamblia in stool specimens. J. Clin. Microbiol. 42: 3317– 3320.
78. Haarman, M., and, J. Knol. 2005. Quantitative real-time PCR assays to identify and quantify fecal Bifidobacterium species in infants receiving a prebiotic infant formula. Appl. Environ. Microbiol. 71: 2318– 2324.
79. Hajishengallis, G.,, H. Nawar,, R. I. Tapping,, M. W. Russell, and, T. D. Connell. 2004. The type II heat-labile enterotoxins LT-IIa and LT-IIb and their respective B pentamers differentially induce and regulate cytokine production in human monocytic cells. Infect. Immun. 72: 6351– 6358.
80. Hakenbeck, R.,, N. Balmelle,, B. Weber,, C. Gardes,, W. Keck, and, A. de Saizieu. 2001. Mosaic genes and mosaic chromosomes: intra- and interspecies genomic variation of Streptococcus pneumoniae. Infect. Immun. 69: 2477– 2486.
81. Hamilton, M. J.,, T. Yan, and, M. J. Sadowsky. 2006. Development of goose- and duck-specific DNA markers to determine sources of Escherichia coli in waterways. Appl. Environ. Microbiol. 72: 4012– 4019.
82. Handelsman, J. 2004. Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 68: 669– 685.
83. Haugland, R. A.,, S. C. Siefring,, L. J. Wymer,, K. P. Brenne, and, A. P. Dufour. 2005. Comparison of Enterococcus measurements in freshwater at two recreational beaches by quantitative polymerase chain reaction and membrane filter culture analysis. Water Res. 39: 559– 568.
84. Hooper, L. V., and, J. I. Gordon. 2001. Glycans as legislators of host-microbial interactions: spanning the spectrum from symbiosis to pathogenicity. Glycobiology 11: 1– 10.
85. Hopkins, K. L.,, M. Desai,, J. A. Frost,, J. Stanley, and, J. M. Logan. 2004. Fluorescent amplified fragment length polymorphism genotyping of Campylobacter jejuni and Campylobacter coli strains and its relationship with host specificity, serotyping, and phage typing. J. Clin. Microbiol. 42: 229– 235.
86. Ishii, S.,, W. B. Ksoll,, R. E. Hicks, and, M.J. Sadowsky. 2006. Presence and growth of naturalized Escherichia coli in temperate soils from Lake Superior watersheds. Appl. Environ. Microbiol. 72: 612– 621.
87. Jasinska, A., and, W. J. Krzyzosiak. 2004. Repetitive sequences that shape the human transcriptome. FEBS Lett. 567: 136– 141.
88. Jeffreys, A. J.,, V. Wilson, and, S. L. Thein. 1985. Hypervariable “minisatellite” regions in human DNA. Nature 314: 67– 73.
89. Jeffreys, A. J.,, V. Wilson,, R. Newumann, and, J. Keyte. 1988. Amplification of human minisatellites by the polymerase chain reaction: towards DNA fingerprinting of single cells. Nucleic Acids Res. 16: 10953– 10971.
90. Johnson, A. P. 1994. The pathogenicity of enterococci. J. Antimicrob. Chemother. 33: 1083– 1089.
91. Johnson, L. K.,, M. B. Brown,, E. A. Carruthers,, J. A. Ferguson,, P. E. Dombek, and, M.J. Sadowsky. 2004. Sample size, library composition, and genotypic diversity among natural populations of Escherichia coli from different animals influence accuracy of determining sources of fecal pollution. Appl. Environ. Microbiol. 70: 4478– 4485.
92. Jungblut, P. R.,, E. C. Müller,, J. Mattow, and, S. H. E. Kaufmann. 2001. Proteomics reveals open reading frames in Mycobacterium tuberculosis H37Rv not predicted by genomics. Infect. Immun. 69: 5905– 5907.
93. Khatib, L. A.,, Y. L. Tsai, and, B. H. Olson. 2002. A biomarker for the identification of cattle fecal pollution in water using the LTIIa toxin gene from enterotoxigenic Escherichia coli. Appl. Microbiol. Biotechnol. 59: 97– 104.
94. Khatib, L. A.,, Y. L. Tsai, and, B. H. Olson. 2003. A biomarker for the identification of swine fecal pollution in water, using the STII toxin gene from enterotoxigenic Escherichia coli. Appl. Microbiol. Biotechnol. 63: 231– 238.
95. Klietmann, W. F., and, K. L. Ruoff. 2001. Bioterrorism: implications for the clinical microbiologist. Clin. Microbiol. Rev. 14: 364– 381.
96. Knietsch, A.,, T. Waschkowitz,, S. Bowien,, A. Henne, and, R. Daniel. 2003. Construction and screening of metagenomic libraries derived from enrichment cultures: generation of a gene bank for genes conferring alcohol oxidoreductase activity on Escherichia coli. Appl. Environ. Microbiol. 69: 1408– 1416.
97. Kuwahara, T.,, A. Yamashita,, H. Hirakawa,, H. Nakayama,, H. Toh,, N. Okada,, S. Kuhara,, M. Hattori,, T. Hayashi, and, Y. Ohnishi. 2004. Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation. Proc. Natl. Acad. Sci. USA 101: 14919– 14924.
98. Lalle, M.,, E. Jimenez-Cardosa,, S. M. Caccio, and, E. Pozio. 2005. Genotyping of Giardia duodenalis from humans and dogs from Mexico using a beta-giardin nested polymerase chain reaction assay. J. Parasitol. 91: 203– 205.
99. Larue, R.,, Z. Yu,, V. A. Parisi,, A. R. Egan, and, M. Morrison. 2005. Novel microbial diversity adherent to plant biomass in the herbivore gastrointestinal tract, as revealed by ribosomal intergenic spacer analysis and rrs gene sequencing. Environ. Microbiol. 7: 530– 543.
100. Lebuhn, M.,, M. Effenberger,, G. Garces,, A. Gronauer, and, P. A. Wilderer. 2004. Evaluating real-time PCR for the quantification of distinct pathogens and indicator organisms in environmental samples. Water Sci. Technol. 50: 263– 270.
101. Lee, S. J.,, D. Y. Lee,, T. Y. Kim,, B. H. Kim,, J. Lee, and, S. Y. Lee. 2005. Metabolic engineering of Escherichia coli for enhanced production of succinic acid, based on genome comparison and in silico gene knockout simulation. Appl. Environ. Microbiol. 71: 7880– 7887.
102. Lee, S. W.,, K. Won,, H. K. Lim,, J. C. Kim,, G. J. Choi, and, K. Y. Cho. 2004. Screening for novel lipolytic enzymes from uncultured soil microorganisms. Appl. Microbiol. Biotechnol. 65: 720– 726.
103. Lengeler, J. W. 2000. Metabolic networks: a signal-oriented approach to cellular models. Biol. Chem. 381: 911– 920.
104. Leser, T. D.,, R. H. Lindecrona,, T. K. Jensen,, B. B. Jensen, and, K. Møller. 2000. Changes in bacterial community structure in the colon of pigs fed different experimental diets and after infection with Brachyspira hyodysenteriae. Appl. Environ. Microbiol. 66: 3290– 3296.
105. Leser, T. D.,, J. Z. Amenuvor,, T. K. Jensen,, R. H. Lindecrona,, M. Boye, and, K. Møller. 2002. Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. Appl. Environ. Microbiol. 68: 673– 690.
106. Li, T. X.,, J. Wang,, Y. Bai,, X. Sun, and, Z. Lu. 2004. A novel method for screening species-specific gDNA probes for species identification. Nucleic Acids Res. 32: e45.
107. Liang, X.,, X. Q. Pham,, M. V. Olson, and, S. Lory. 2001. Identification of a genomic island present in the majority of pathogenic isolates of Pseudomonas aeruginosa. J. Bacteriol. 183: 843– 853.
108. Lu, J.,, U. Idris,, B. Harmon,, C. Hofacre,, J. J. Maurer, and, M. D. Lee. 2003. Diversity and succession of the intestinal bacterial community of the maturing broiler chicken. Appl. Environ. Microbiol. 69: 6816– 6824.
109. Ludwig, W., and, K. H. Schleifer. 2000. How quantitative is quantitative PCR with respect to cell counts? Syst. Appl. Microbiol. 23: 556– 562.
110. Lyon, W.J. 2001. TaqMan PCR for detection of Vibrio cholerae O1, O139, non-O1, and non-O139 in pure cultures, raw oysters, and synthetic seawater. Appl. Environ. Microbiol. 67: 4685– 4693.
111. Mai, V. 2004. Dietary modification of the intestinal microbiota. Nutr. Rev. 62: 235– 242.
112. Maroncle, N.,, D. Balestrino,, C. Rich, and, C. Forestier. 2002. Identification of Klebsiella pneumoniae genes involved in intestinal colonization and adhesion using signature-tagged mutagenesis. Infect. Immun. 70: 4729– 4734.
113. Marteau, P.,, P. Pochart,, J. Doré,, C. Béra-Maillet,, A. Bernalier, and, G. Corthier. 2001. Comparative study of bacterial groups within the human cecal and fecal microbiota. Appl. Environ. Microbiol. 67: 4939– 4942.
114. Matsuki, T.,, K. Watanabe,, R. Tanaka,, M. Fukuda, and, H. Oyaizu. 1999. Distribution of bifidobacterial species in human intestinal microflora examined with 16S rRNA-gene-targeted species-specific primers. Appl. Environ. Microbiol. 65: 4506– 4512.
115. Matsuki, T.,, K. Watanabe,, J. Fujimoto,, Y. Miyamoto,, T. Takada,, K. Matsumoto,, H. Oyaizu, and, R. Tanaka. 2002. Development of 16S rRNA-gene-targeted group-specific primers for the detection and identification of predominant bacteria in human feces. Appl. Environ. Microbiol. 68: 5445– 5451.
116. Matsuki, T.,, K. Watanabe, and, R. Tanaka. 2003. Genus- and species-specific PCR primers for the detection and identification of bifidobacteria. Curr. Issues Intest. Microbiol. 4: 61– 69.
117. Matsuki, T.,, K. Watanabe,, J. Fujimoto,, T. Takada, and, R. Tanaka. 2004. Use of 16S rRNA gene-targeted group-specific primers for real-time PCR analysis of predominant bacteria in human feces. Appl. Environ. Microbiol. 70: 7220– 7228.
118. McDougald, L. R. 1998. Intestinal protozoa important to poultry. Poult. Sci. 77: 1156– 1158.
119. McLellan, S. L. 2004. Genetic diversity of Escherichia coli isolated from urban rivers and beach water. Appl. Environ. Microbiol. 70: 4658– 4665.
120. McLellan, S. L.,, A. D. Daniels, and, A. K. Salmore. 2003. Genetic characterization of Escherichia coli populations from host sources of fecal pollution by using DNA fingerprinting. Appl. Environ. Microbiol. 69: 2587– 2594.
121. Mikkelsen, L. L.,, C. Bendixen,, M. Jakobsen, and, B. B. Jensen. 2003. Enumeration of bifidobacteria in gastrointestinal samples from piglets. Appl. Environ. Microbiol. 69: 654– 658.
122. Mikkelsen, T. S.,, L. W. Hillier,, E. E. Eichler,, M. C. Zody,, D. B. Jaffe,, S.-P. Yang,, W. Enard,, I. Hellmann,, K. Lindblad-Toh,, T. K. Altheide,, N. Archidiacono,, P. Bork,, J. Butler,, J. L. Chang,, Z. Cheng,, A. T. Chinwalla,, P. deJong,, K. D. Delehaunty,, C. C. Fronick,, L. L. Fulton,, Y. Gilad,, G. Glusman,, S. Gnerre,, T. A. Graves,, T. Hayakawa,, K. E. Hayden,, X. Huang,, H. Ji,, W. J. Kent,, M.-C. King,, E.J. Kulbokas III,, M. K. Lee,, G. Liu,, C. Lopez-Otin,, K. D. Makova,, O. Man,, E. R. Mardis,, E. Mauceli,, T. L. Miner,, W. E. Nash,, J. O. Nelson,, S. Pääbo,, N.J. Patterson,, C. S. Pohl,, K. S. Pollard,, K. Prüfer,, X. S. Puente,, D. Reich,, M. Rocchi,, K. Rosenbloom,, M. Ruvolo,, D. J. Richter,, S. F. Schaffner,, A. F. A. Smit,, S. M. Smith,, M. Suyama,, J. Taylor,, D. Torrents,, E. Tuzun,, A. Varki,, G. Velasco,, M. Ventura,, J. W. Wallis,, M. C. Wendl,, R. K. Wilson,, E. S. Lander, and, R. H. Waterston ( The Chimpanzee Sequencing and Analysis Consortium). 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69– 87.
123. Moore, W. E. C., and, L. V. Holdeman. 1974. Human fecal flora: the normal flora of 20 Japanese-Hawaiians. Appl. Microbiol. 27: 961– 979.
124. Mostowy, S.,, C. Cleto,, D. R. Sherman, and, M. A. Behr. 2004. The Mycobacterium tuberculosis complex transcriptome of attenuation. Tuberculosis 84: 197– 204.
125. Moune, S.,, P. Caumette,, R. Matheron, and, J. C. Willison. 2003. Molecular sequence analysis of prokaryotic diversity in the anoxic sediments underlying cyanobacterial mats of two hypersaline ponds in Mediterranean salterns. FEMS Microbiol. Ecol. 44: 117– 130.
126. Muller, T.,, A. Ulrich,, E. M. Ott, and, M. Muller. 2001. Identification of plant-associated enterococci. J. Appl. Microbiol. 91: 268– 278.
127. Mutch, D. M.,, R. Simmering,, D. Donnicola,, G. Fotopoulos,, J. A. Holzwarth,, G. Williamson, and, I. Corthesy-Theulaz. 2004. Impact of commensal microbiota on murine gastrointestinal tract gene ontologies. Physiol. Genomics 19: 22– 31.
128. Nakamura, Y.,, M. Leppert,, P. O’Connell,, R. Wolff,, T. Holm,, M. Culver,, C. Martin,, E. Fujimoto,, M. Hoff,, E. Kumlin, and, R.W hite. 1987. Variable number tandem repeat (VNTR) markers for human gene mapping. Science 235: 1616– 1622.
129. Nystrom, T. 2001. Not quite dead enough: on bacterial life, culturability, senescence, and death. Arch. Microbiol. 176: 159– 164.
130. O’Sullivan, L. A.,, A. J. Weightman, and, J. C. Fry. 2002. New degenerate Cytophaga-Flexibacter-Bacteroides-specific 16S ribosomal DNA-targeted oligonucleotide probes reveal high bacterial diversity in River Taff epilithon. Appl. Environ. Microbiol. 68: 201– 210.
131. Pardon, P.,, R. Scanchis,, J. Marly,, F. Lantier,, M. Pepin, and, M. Popoff. 1988. Ovine sal-monellosis caused by Salmonella abortus ovis. Ann. Rech. Vet. 19: 221– 235. (In French.)
132. Parveen, S.,, K. M. Portier,, K. Robinson,, L. Edmiston, and, M. L. Tamplin. 1999. Discriminant analysis of ribotype profiles of Escherichia coli for differentiating human and nonhuman sources of fecal pollution. Appl. Environ. Microbiol. 65: 3142– 3147.
133. Paulsen, I. T.,, L. Banerjei,, G. S. Myers,, K. E. Nelson,, R. Seshadri,, T. D. Read,, D. E. Fouts,, J. A. Eisen,, S. R. Gill,, J. F. Heidelberg,, H. Tettelin,, R. J. Dodson,, L. Umayam,, L. Brinkac,, M. Beanan,, S. Daugherty,, R. T. DeBoy,, S. Durkin,, J. Kolonay,, R. Madupu,, W. Nelson,, J. Vamathevan,, B. Tran,, J. Upton,, T. Hansen,, J. Shetty,, H. Khouri,, T. Utterback,, D. Radune,, K. A. Ketchum,, B. A. Dougherty, and, C. M. Fraser. 2003. Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. Science 299: 2071– 2074.
134. Piel, J.,, D. Butzke,, N. Fusetani,, D. Hui,, M. Platzer,, G. Wen, and, S. Matsunaga. 2005. Exploring the chemistry of uncultivated bacterial symbionts: antitumor polyketides of the pederin family. J. Nat. Prod. 68: 472– 479.
135. Poretsky, R. S.,, N. Bano,, A. Buchan,, G. LeCleir,, J. Kleikemper,, M. Pickering,, W. M. Pate,, M.-A. Moran, and, J. T. Hollibaugh. 2005. Analysis of microbial gene transcripts in environmental samples. Appl. Environ. Microbiol. 71: 4121– 4126.
136. Ram, R. J.,, N. C. VerBerkmoes,, M. P. Thelen,, G. W. Tyson,, B. J. Baker,, R. C. Blake II,, M. Shah,, R. L. Hettich, and, J. F. Banfield. 2005. Community proteomics of a natural microbial biofilm. Science 308: 1915– 1920.
137. Rasmussen, T. B.,, M. E. Skindersoe,, T. Bjarnsholt,, R. K. Phipps,, K. B. Christensen,, P. O. Jensen,, J. B. Andersen,, B. Koch,, T. O. Larsen,, M. Hentzer,, L. Eberl,, N. Hoiby, and, M. Givskov. 2005. Identity and effects of quorum-sensing inhibitors produced by Penicillium species. Microbiology 151: 1325– 1340.
138. Rawls, J. F.,, B. S. Samuel, and, J. I. Gordon. 2004. Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota. Proc. Natl. Acad. Sci. USA 101: 4596– 4601.
139. Rebrikov, D. V.,, S. M. Desai,, P. D. Siebert, and, S. A. Lukyanov. 2004. Suppression subtractive hybridization. Methods Mol. Biol. 258: 107– 134.
140. Remold, S. K., and, R. E. Lenski. 2001. Contribution of individual random mutations to genotype-by-environment interactions in Escherichia coli. Proc. Natl. Acad. Sci. USA 98: 11388– 11393.
141. Rondon, M. R.,, P. R. August,, A. D. Bettermann,, S. F. Brady,, T. H. Grossman,, M. R. Liles,, K. A. Loiacono,, B. A. Lynch,, I. A. MacNeil,, C. Minor,, C. L. Tiong,, M. Gilman,, M. S. Osburne,, J. Clardy,, J. Handelsman, and, R. M. Goodman. 2000. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66: 2541– 2547.
142. Sano, E.,, S. Carlson,, L. Wegley, and, F. Rohwer. 2004. Movement of viruses between biomes. Appl. Environ. Microbiol. 70: 5842– 5846.
143. Santo Domingo, J. W.,, S. C. Siefring, and, R. A. Haugland. 2003. Real-time PCR method to detect Enterococcus faecalis in water. Biotechnol. Lett. 25: 261– 265.
144. Schell, M. A.,, M. Karmirantzou,, B. Snel,, D. Vilanova,, B. Berger,, G. Pessi,, M. C. Zwahlen,, F. Desiere,, P. Bork,, M. Delley,, R. D. Pridmore, and, F. Arigoni. 2002. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc. Natl. Acad. Sci. USA 29: 14422– 14427.
145. Schirmer, A.,, R. Gadkari,, C. D. Reeves,, F. Ibrahim,, E. F. DeLong, and, C. Richard Hutchinson. 2005. Metagenomic analysis reveals diverse polyketide synthase gene clusters in microorganisms associated with the marine sponge Discodermia dissolute. Appl. Environ. Microbiol. 71: 4840– 4849.
146. Schmeisser, C.,, C. Stöckigt,, C. Raasch,, J. Wingender,, K. N.T immis,, D. F. Wenderoth,, H.-C. Flemming,, H. Liesegang,, R. A. Schmitz,, K.-E. Jaeger, and, W. R. Streit. 2003. Metagenome survey of biofilms in drinking-water networks. Appl. Environ. Microbiol. 69: 7298– 7309.
147. Scott, T. M.,, T. M.J enkins,, J. Lukasik, and, J. B. Rose. 2005. Potential use of a host associated molecular marker in Enterococcus faecium as an index of human fecal pollution. Environ. Sci. Technol. 19: 145– 152.
148. Seksik, P.,, L. Rigottier-Gois,, G. Gramet,, M. Sutren,, P. Pochart,, P. Marteau,, R. Jian, and, J. Dore. 2003. Alterations of the dominant faecal bacterial groups in patients with Crohn’s disease of the colon. Gut 52: 237– 242.
149. 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.
150. Shanks, O. C.,, J. W. Santo Domingo, and, J. E. Graham. Use of competitive DNA hybridization to identify differences in the genomes of bacteria. J. Microbiol. Methods 66: 321– 330.
151. Shanks, O. C.,, J. W. Santo Domingo, and, J. E. Graham. 2006. Competitive metagenomic DNA hybridization identifies host-specific microbial genetic markers in cattle fecal samples. Appl. Environ. Microbiol. 72: 4054– 4060.
152. Simpson, J. M.,, J. W. Santo Domingo, and, D.J. Reasoner. 2002. Microbial source tracking: state of the science. Environ. Sci. Technol. 36: 5279– 5288.
153. Simpson, J. M.,, J. W. Santo Domingo, and, D.J. Reasoner. 2004. Assessment of equine fecal contamination: the search for alternative bacterial source-tracking targets. FEMS Microbiol. Ecol. 47: 65– 75.
154. Sinton, L. W.,, A. M. Donnison, and, C. M. Hastie. 1993. Faecal streptococci as faecal pollution indicators: a review. Part II: sanitary significance, survival, and use. N. Z.J. Mar. Freshwater Res. 27: 117– 137.
155. Sjoling, S., and, D. A. Cowan. 2003. High 16S rDNA bacterial diversity in glacial melt-water lake sediment, Bratina Island, Antarctica. Extremophiles 7: 275– 282.
156. Somer, L.,, Y. Danin-Poleg,, E. Diamant,, R. Gur-Arie,, Y. Palti, and, Y. Kashi. 2005. Amplified intergenic locus polymorphism as a basis for bacterial typing of Listeria spp. and Escherichia coli. Appl. Environ. Microbiol. 71: 3144– 3152.
157. Soule, M.,, K. Cain,, S. LaFrentz, and, D. R. Call. 2005. Combining suppression subtractive hybridization and microarrays to map the intraspecies phylogeny of Flavobacterium psychrophilum. Infect. Immun. 73: 3799– 3802.
158. Soule, M.,, S. LaFrentz,, K. Cain,, S. LaPatra, and, D. R. Call. 2005. Polymorphisms in 16S rRNA genes of Flavobacterium psychrophilum correlate with elastin hydrolysis and tetracycline resistance. Dis. Aquat. Organ. 65: 209– 216.
159. Soule, M.,, E. Kuhn,, F. Loge,, J. Gay, and, D. R. Call. 2006. Using DNA microarrays to identify library-independent markers for bacterial source tracking. Appl. Environ. Microbiol. 72: 1843– 1851.
160. Southern, E.,, K. Mir, and, M. Shchepinov. 1999. Molecular interactions on microarrays. Nat. Genet. 21: 5– 9.
161. Stewart, J. R.,, J. Vinjé,, S.J. G. Oudejans,, G. I. Scott, and, M. D. Sobsey. 2006. Sequence variation among group III F-specific RNA coliphages from water samples and swine lagoons. Appl. Environ. Microbiol. 72: 1226– 1230.
162. Sutherland, G. R., and, R. I. Richards. 1995. Simple tandem DNA repeats and human genetic disease. Proc. Natl. Acad. Sci. USA 92: 3636– 3641.
163. Švec, P.,, L. A. Devriese,, I. Sedlacek, M. Baele,, M. Vancanneyt, F. Haesebrouck,, J. Swings, and J. Doskar. 2002. Characterization of yellow-pigmented and motile enterococci isolated from intestines of the garden snail Helix aspersa. J. Appl. Microbiol. 92: 951– 957.
164. Švec, P.,, M. Vancanneyt,, L. A. Devriese,, S. M. Naser,, C. Snauwaert,, K. Lefebvre,, B. Hoste, and, J. Swings. 2005. Enterococcus aquimarinus sp. nov., isolated from sea water. Int. J. Syst. Evol. Microbiol. 55: 2183– 2187.
165. Taboada, E. N.,, R. R. Acedillo,, C. D. Carrillo,, W. A. Findlay,, D. T. Medeiros,, O. L. Mykytczuk,, M. J. Roberts,, C. A. Valencia,, J. M. Farber, and, J. H. Nash. 2004. Large-scale comparative genomics meta-analysis of Campylobacter jejuni isolates reveals low level of genome plasticity. J. Clin. Microbiol. 42: 4566– 4576.
166. Tajima, K.,, R. I. Aminov,, T. Nagamine,, K. Ogata,, M. Nakamura,, H. Matsui, and, Y. Benno. 1999. Rumen bacterial diversity as determined by sequence analysis of 16S rDNA libraries. FEMS Microbiol. Ecol. 29: 159– 169.
167. Taylor, D. N.,, J. M. Bied,, J. S. Munro, and, R. A. Feldman. 1982. Salmonella dublin infections in the United States, 1979–1980. J. Infect. Dis. 146: 322– 327.
168. Tendolkar, P. M.,, A. S. Baghdayan, and, N. Shankar. 2005. The N-terminal domain of enterococcal surface protein, Esp, is sufficient for Esp-mediated biofilm enhancement in Enterococcus faecalis. J. Bacteriol. 187: 6213– 6222.
169. Todorov, J. R.,, A. Y. Chistoserdov, and, J. Y. Aller. 2000. Molecular analysis of microbial communities in mobile deltaic muds of Southeastern Papua New Guinea. FEMS Microbiol. Ecol. 33: 147– 155.
170. Trovatelli, L. D., and, D. Matteuzzi. 1976. Presence of bifidobacteria in the rumen of calves fed different rations. Appl. Environ. Microbiol. 32: 470– 473.
171. Trusova, M. Y., and, M. I. Gladyshev. 2002. Phylogenetic diversity of winter bacterio-plankton of eutrophic Siberian reservoirs as revealed by 16S rRNA gene sequence. Microb. Ecol. 44: 252– 259.
172. Tyagi, S., and, F. R. Kramer. 1996. Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14: 303– 308.
173. Tyagi, S.,, D. P. Bratu, and, F. R. Kramer. 1998. Multicolor molecular beacons for allele discrimination. Nat. Biotechnol. 16: 49– 53.
174. U.S. Environmental Protection Agency. 2005. Microbial Source Tracking Guide Document. EPA-600/R-05/064. Office of Research and Development, U.S. Environmental Protection Agency, Washington, D.C.
175. van Belkum, A. 2003. Molecular diagnostics in medical microbiology: yesterday, today and tomorrow. Curr. Opin. Pharmacol. 3: 497– 501.
176. van Belkum, A.,, S. Scherer,, L. van Alphen, and, H. Verbrugh. 1998. Short-sequence DNA repeats in prokaryotic genomes. Microbiol. Mol. Biol. Rev. 62: 275– 293.
177. van Belkum, A.,, M. Struelens,, A. de Visser,, H. Verbrugh, and, M.T ibayrenc. 2001. Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology. Clin. Microbiol. Rev. 14: 547– 560.
178. van Kessel, J. S.,, J. S. Karns, and, M. L. Perdue. 2003. Using a portable real-time PCR assay to detect Salmonella in raw milk. J. Food Prot. 66: 1762– 1767.
179. Venter, J. C.,, K. Remington,, J. F. Heidelberg,, A. L. Halpern,, D. Rusch,, J. A. Eisen,, D. Wu,, I. Paulsen,, K. E. Nelson,, W. Nelson,, D. E. Fouts,, S. Levy,, A. H. Knap,, M. W. Lomas,, K. Nealson,, O. White,, J. Peterson,, J. Hoffman,, R. Parsons,, H. Baden-Tillson,, C. Pfannkoch,, Y.-H. Rogers, and, H. O. Smith. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66– 74.
180. Versalovic, J.,, M. Schneider,, F. J. de Bruijn, and, J. R. Lupski. 1994. Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol. Cell. Biol. 5: 25– 40.
181. Volker, U., and, M. Hecker. 2005. From genomics via proteomics to cellular physiology of the Gram-positive model organism Bacillus subtilis. Cell. Microbiol. 7: 1077– 1085.
182. Walter, J.,, M. Mangold, and, G. W. Tannock. 2005. Construction, analysis, and β-glucanase screening of a bacterial artificial chromosome library from the large-bowel microbiota of mice. Appl. Environ. Microbiol. 71: 2347– 2354.
183. Wang, M.,, S. Ahrné,, B.J eppsson, and, G. Molin. 2005. Comparison of bacterial diversity along the human intestinal tract by direct cloning and sequencing of 16S rRNA genes. FEMS Microbiol. Ecol. 54: 219– 231.
184. Wang, X.,, S. P. Heazlewood,, D. O. Krause, and, T. H. Florin. 2003. Molecular characterization of the microbial species that colonize human ileal and colonic mucosa by using 16S rDNA sequence analysis. J. Appl. Microbiol. 95: 508– 520.
185. Washburn, M. P., and, J. R. Yates III. 2000. Analysis of the microbial proteome. Curr. Opin. Microbiol. 3: 292– 297.
186. Wei, J.,, M. B. Goldberg,, V. Burland,, M. M. Venkatesan,, W. Deng,, G. Fournier,, G. F. Mayhew,, G. Plunkett III,, D. J. Rose,, A. Darling,, B. Mau,, N. T. Perna,, S. M. Payne,, L. J. Runyen-Janecky,, S. Zhou,, D. C. Schwartz, and, F. R. Blattner. 2003. Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infect. Immun. 71: 2775– 2786.
187. Whitman, R. L.,, D. A. Shively,, H. Pawlik,, M.B. Nevers, and, M. N. Byappanahalli. 2003. Occurrence of Escherichia coli and enterococci in Cladophora (Chlorophyta) in nearshore water and beach sand of Lake Michigan. Appl. Environ. Microbiol. 69: 4714– 4719.
188. Whitman, W. B.,, D. C. Coleman, and, W. J. Wiebe. 1998. Prokaryotes: the unseen majority. Proc. Natl. Acad. Sci. USA 95: 6578– 6583.
189. Whittam, T. S. 1996. Genetic variation and evolutionary processes in natural populations of Escherichia coli, p. 2708– 2720. In F. C. Neidhardt,, R. C. Curtiss III,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter, and, H. E. Umbarger (ed.), Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed. American Society for Microbiology, Washington, D.C.
190. Wiedmann, M.,, J. L. Bruce,, C. Keating,, A. E. Johnson,, P. L. McDonough, and, C. A. Batt. 1997. Ribotypes and virulence gene polymorphisms suggest three distinct Listeria monocytogenes lineages with differences in pathogenic potential. Infect. Immun. 65: 2707– 2716.
191. Willard, M. D.,, R. B. Simpson,, N. D. Cohen, and, J. S. Clancy. 2000. Effects of dietary fructooligosaccharide on selected bacterial populations in feces of dogs. Am. J. Vet. Res. 61: 820– 825.
192. Wolffs, P.,, B. Norling, and, P. Radstrom. 2005. Risk assessment of false-positive quantitative real-time PCR results in food, due to detection of DNA originating from dead cells. J. Microbiol. Methods 60: 315– 323.
193. Xu, J.,, M. K. Bjursell,, J. Himrod,, S. Deng,, L. K. Carmichael,, H. C. Chiang,, L. V. Hooper, and, J. L. Gordon. 2003. A genomic view of the human -Bacteroides thetaio-taomicron symbiosis. Science 299: 2074– 2076.
194. Xu, P.,, G. Widmer,, Y. Wang,, L. S. Ozaki,, J. M. Alves,, M. G. Serrano,, D. Puiu,, P. Manque,, D. Akiyoshi,, A. J. Mackey,, W. R. Pearson,, P. H. Dear,, A. T. Bankier,, D. L. Peterson,, M. S. Abrahamsen,, V. Kapur,, S. Tzipori, and, G. A. Buck. 2004. The genome of Cryptosporidium hominis. Nature 431: 1107– 1112.
195. Yun, J., and, S. Ryu. 2005. Screening for novel enzymes from metagenome and SIGEX, as a way to improve it. Microb. Cell Fact. 4: 8.
196. Zhu, X. Y.,, T. Zhong,, Y. Pandya, and, R. D.J oerger. 2002. 16S rRNA-based analysis of microbiota from the cecum of broiler chickens. Appl. Environ. Microbiol. 68: 124– 137.
197. Zhu, Y.-L,, Q.-J. Song,, D. L. Hyten,, C. P. Van Tassell,, L. K. Matukumalli,, D. R. Grimm,, S. M. Hyatt,, E. W. Fickus,, N. D. Young, and, P. B. Cregan. 2003. Single nucleotide polymorphisms (SNPs) in soybean. Genetics 163: 1123– 1134.

Back to top
This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error