Chicken- and duck-associated Bacteroides-Prevotella genetic markers for detecting fecal contamination in environmental water

Applied Microbiology and Biotechnology

Volumn 97, Issue 16, 2013, Pages 7427-7437

  Kobayashi, Ayano ^a   Sano, Daisuke ^a   Hatori, Jun ^a   Ishii, Satoshi ^a   Okabe, Satoshi ^a  

^a HOKKAIDO UNIVERSITY   (Japan)

Author keywords

Bacteroides Prevotella group; Chicken; Duck; Fecal contamination; Genetic markers; Real time PCR assay

Indexed keywords

BACTEROIDES-PREVOTELLA GROUP; CHICKEN; DUCK; FECAL CONTAMINATION; GENETIC MARKERS; REAL-TIME PCR ASSAY;

ASSAYS; CONTAMINATION; POLYMERASE CHAIN REACTION; RNA;

ANIMALS;

BACTERIAL DNA; BACTERIAL RNA; RNA 16S; WATER;

BACTERIUM; DNA; FECES; GENETIC MARKER; POLYMERASE CHAIN REACTION; WASTE TREATMENT; WASTEWATER; WATER POLLUTION;

ARTICLE; BACTERIUM CONTAMINATION; BACTEROIDES; CONTROLLED STUDY; COW; CROSS REACTION; DNA EXTRACTION; DUCK; FECAL COLIFORM; FECES ANALYSIS; GENETIC MARKER; LIMIT OF DETECTION; LIMIT OF QUANTITATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT; PREVOTELLA; REAL TIME POLYMERASE CHAIN REACTION; UNINDEXED SEQUENCE; WASTE WATER MANAGEMENT; WASTE WATER TREATMENT PLANT; WATER CONTAMINATION; WATER SAMPLING;

ANIMALS; BACTEROIDES; CHICKENS; CROSS REACTIONS; DNA, BACTERIAL; DUCKS; FECES; GENETIC MARKERS; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; PREVOTELLA; RNA, RIBOSOMAL, 16S; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA; WATER MICROBIOLOGY; WATER POLLUTION; WATER QUALITY;

ANAS; ANIMALIA; AVES; BACTEROIDES; PREVOTELLA; SUIDAE;

EID: 84881257809     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-012-4469-2     Document Type: Article

References (42)

1. Altschul SF, Warren G, Webb M, Eugene WM, David JL (1990) Basic local alignment search tool. J Mol Biol 215:403-410
2. Bernhard AE, Field KG (2000a) Identification of nonpoint sources of fecal pollution in coastal waters by using host-specific 16S rDNA markers from decal anaerobes. Appl Environ Microbiol 66:1587-1594 (Pubitemid 30185636)
3. Bernhard AE, Field KG (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
4. Blanch AR, Belanche-Munoz L, Bonjoch X, Ebdon J, Gantzer C, Lucena F, Ottoson J, Kourtis C, Iversen A, Kuhn I, Moce L, Muniesa M, Schwartzbrod J, Skraber S, Papageorgiou GT, Taylor H, Wallis J, Jofre J (2006) Integrated analysis of established and novel microbial and chemical methods for microbial source tracking. Appl Environ Microbiol 72:5915-5926 (Pubitemid 44414618)
5. Champagne J, Diarra MS, Rempel H, Topp E, Greer CW, Harel J, Masson L (2011) Development of a DNA microarray for Enterococcal species, virulence, and antibiotic resistance gene determinations among isolates from poultry. Appl Environ Microbiol 77:2625-2633
6. Cho JC, Kim SJ (2000) Increase in bacterial community diversity in subsurface aquifers receiving livestock wastewater input. Appl Environ Microbiol 66:956-965 (Pubitemid 30130013)
7. Devane ML, Robson B, Nourozi F, Scholes P, Gilpin BJ (2007) A PCR marker for detection in surface waters of faecal pollution derived from ducks. Water Res 41:3553-3560 (Pubitemid 47176116)
8. Dick LK, Field KG (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 (Pubitemid 39279652)
9. Dick LK, Bernhard AE, Brodeur TJ, Santo Domingo JW, Simpson JM, Walters SP, Field KG (2005) Host distributions of uncultivated fecal Bacteroidales bacteria reveal genetic markers for fecal source identification. Appl Environ Microbiol 71:3184-3191 (Pubitemid 40807229)
10. Field KG, Samadpour M (2007) Fecal source tracking, the indicator paradigm, and managing water quality. Water Res 41:3517-3538 (Pubitemid 47179855)
11. Fogarty LR, Voytek MA (2005) Comparison of Bacteroides-Prevotella 16S rRNA genetic markers for fecal samples from different animal species. Appl Environ Microbiol 71:5999-6007 (Pubitemid 41456894)
12. Fogarty LR, Haack SK, Wolcott MJ, Whitman RL (2003) Abundance and charateristics of the recreational water quality indicator bacteria Escherichia coli and enterococci in gull faeces. J Appl Microbiol 94:865-878 (Pubitemid 36555152)
13. Fremaux B, Boa T, Yost CK (2010) Quantitative real-time PCR assays for sensitive detection of Canada goose-specific fecal pollution in water sources. Appl Environ Microbiol 76:4886-4889
14. Hamilton MJ, Yan T, Sadowsky MJ (2006) Development of goose- and duck specific DNA markers to determine sources of Escherichia coli in waterways. Appl Environ Microbiol 72:4012-4019 (Pubitemid 43894865)
15. Harwood VJ, Levine AD, Scott TM, Chivukula V, Lukasik J, Farrah SR, Rose JB (2005) Validity of the indicator organism paradigm for pathogen reduction in reclaimed water and public health protection. Appl Environ Microbiol 71:3163-3170 (Pubitemid 40807226)
16. Himathongkham S, Riemann H (1999) Destruction of Salmonella typhimurium, Escherichia coli O157, H7 and Listeria monocytogenes in chicken manure by drying and/or gassing with ammonia. FEMS Microbiol Lett 171:179-182 (Pubitemid 29094679)
17. Ishii S, Hansen DL, Hicks RE, Sadowsky MJ (2007) Beach sand and sediments are temporal sinks and sources of Escherichia coli in Lake Superior. Environ Sci Tech 41:2203-2209 (Pubitemid 46595175)
18. Kassa H, Harrington B, Bisesi MS (2001) Risk of occupational exposure to Cryptosporidium, Giardia, and Campylobacter associated with the feces of giant Canada geese. Appl Occup Environ Hyg 16(9):905-909 (Pubitemid 32844000)
19. Khawaja JZ, Naeem K, Ahmed Z, Ahmad S (2005) Surveillance of avian influenza viruses in wild birds in areas adjacent to epicenter of an outbreak in federal capital territory of Pakistan. Int J Poult Sci 4:39-43
20. Kildare BJ, Leutenegger CM, McSwain BS, Bambic DG, Rajal VB, Wuertz S (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 (Pubitemid 47189599)
21. 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 (Pubitemid 43894889)
22. Loy A, Arnold R, Tischler P, Rattei T, Wagner M, Horn M (2008) probeCheck - a central resource for evaluating oligonucleotide probe coverage and specificity. Environ Microbiol 10: 2894-2896
23. Lu J, Santo Domingo JW, Lamendella R, Edge T, Hill S (2008) Phylogenetic diversity and molecular detection of gull feces. Appl Environ Microbiol 74:3969-3976 (Pubitemid 351962421)
24. Maidak BL, Olsen GJ, Larsen N, Overbeek R, McCaughey MJ, Woese CR (1997) The RDP (Ribosomal Database Project). Nucleic Acids Res 25:109-110 (Pubitemid 27303161)
25. Mieszkin S, Yala J-F, Joubrel R, Gourmelon M (2009) Phylogenetic analysis of Bacteroidales 16S rRNA gene sequences from human and animal effluents and assessment of ruminant faecal pollution by real-time PCR. J Appl Microbiol 108:974-984
26. Okabe S, Shimazu Y (2007) Persistence of host-specific Bacteroides-Prevotella 16S rRNA genetic markers in environmental waters: effects of temperature and salinity. Appl Microbiol Biotechnol 76:935-944 (Pubitemid 47340928)
27. Okabe S, Okayama N, Savichtcheva O, Ito T (2007) Quantification of host-specific Bacteroides- Prevotella 16S rRNA genetic markers for assessment of fecal pollution in freshwater. Appl Microbiol Biotechnol 74:890-901
28. Pei AY, Oberdorf WE, Nossa CW, Agarwal A, Chokshi P, Gerz EA, Jin Z, Lee P, Yang L, Poles M, Brown SM, Sotero S, Desantis T, Brodie E, Nelson K, Pei Z (2010) Diversity of 16S rRNA genes within individual prokaryotic genomes. Appl Environ Microbiol 76:3886-3897
29. Ryu H, Lu J, Vogel J, Elk M, Chavez-Ramirez F, Ashbolt N, Santo Domingo J (2012) Development and evaluation of a quantitative PCR assay targeting Sandhill Crene (Grus canadensis) fecal pollution. Appl Environ Micobiol 78:4338-4345
30. Saito N, Nei M (1987) The neighbor joining method: a new method for constructing phylogenetic trees. Mol Biol Evol 4:406-425
31. Savichtcheva O, Okabe S (2006) Alternative indicators of fecal pollution: relations with pathogens and conventional indicators, current methodologies for direct pathogen monitoring and future application perspectives. Water Res 40:2463-2476 (Pubitemid 43994104)
32. Savichtcheva O, Okayama N, Okabe S (2007) Relationships between Bacteroides 16S rRNA genetic markers and presence of bacterial enteric pathogens and conventional fecal indicators. Water Res 41:3615-3628 (Pubitemid 47176108)
33. Scott TM, Rose JB, Jenkins TM, Farrah SR, Lukasik J (2002) Microbial source tracking: current methodology and future directions. Appl Environ Microbiol 68:5796-5803 (Pubitemid 36342410)
34. Seurinck S, Defoirdt T, Verstraete W, Siciliano SD (2005) Detection and quantification of the human-specific HF183 Bacteroides 16S rRNA genetic marker with real-time PCR for assessment of human faecal pollution in freshwater. Environ Microbiol 7:249-259
35. Shanks OC, Kelty CA, Sivaganesan M, Varma M, Haugland RA (2009) Quantitative PCR for genetic markers of human fecal pollution. Appl Environ Microbiol 75:5507-5513
36. Simpson JM, Santo-Domingo JW, Reasoner DJ (2002) Microbial source tracking: state of the science. Environ Sci Technol 36:5279-5288 (Pubitemid 35462569)
37. Stephen AB, Vladimir B, Jeremy AG, Jan H, Jim H, Mikael K, Reinhold M, Tania N, Michael WP, Gregory LS, Jo V, Carl TW (2009) The MIQE guidelines: minimum information for publication of quantitative real-time pcr experiments. Clin Chem 55:611-622
38. Stoeckel DM, Stelzer EA, Dick LK (2009) Evaluation of two spike-and-recovery controls for assessment of extraction efficiency in microbial source tracking studies. Water Res 43:4820-4827
39. Thompson JD, Higgins DG, Gibson T (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties, and weight matrix choice. Nucleic Acids Res 22:4673-4680 (Pubitemid 24354800)
40. Unno T, Jang J, Han D, Kim JH, Sadowsky MJ, Kim OS, Chun J, Hur HG (2010) Use of barcoded pyrosequencing and shared OTUs to determine sources of fecal bacteria in watersheds. Environ Sci Technol 44:7777-7782
41. Weidhaas JL, Macbeth TW, Olsen RL, Harwood VJ (2011) Correlation of quantitative PCR for a poultry-specific Brevibacterium marker gene with bacterial and chemical indicators of water pollution in a watershed impacted by land application of poultry litter. Appl Environ Microbiol 77:2094-2102
42. WHO Scientific group (2011) Guidelines for drinking water quality, 4th edn. World Health Organization, Geneva