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Items: 49


Large-scale implementation of standardized quantitative real-time PCR fecal source identification procedures in the Tillamook Bay Watershed.

Li X, Sivaganesan M, Kelty CA, Zimmer-Faust A, Clinton P, Reichman JR, Johnson Y, Matthews W, Bailey S, Shanks OC.

PLoS One. 2019 Jun 6;14(6):e0216827. doi: 10.1371/journal.pone.0216827. eCollection 2019.


Extended persistence of general and cattle-associated fecal indicators in marine and freshwater environment.

Korajkic A, McMinn BR, Ashbolt NJ, Sivaganesan M, Harwood VJ, Shanks OC.

Sci Total Environ. 2019 Feb 10;650(Pt 1):1292-1302. doi: 10.1016/j.scitotenv.2018.09.108. Epub 2018 Sep 9.


Comparison of somatic and F+ coliphage enumeration methods with large volume surface water samples.

McMinn BR, Rhodes ER, Huff EM, Wanjugi P, Ware MM, Nappier SP, Cyterski M, Shanks OC, Oshima K, Korajkic A.

J Virol Methods. 2018 Nov;261:63-66. doi: 10.1016/j.jviromet.2018.08.007. Epub 2018 Aug 7.


Incidence of somatic and F+ coliphage in Great Lake Basin recreational waters.

Wanjugi P, Sivaganesan M, Korajkic A, McMinn B, Kelty CA, Rhodes E, Cyterski M, Zepp R, Oshima K, Stachler E, Kinzelman J, Kurdas SR, Citriglia M, Hsu FC, Acrey B, Shanks OC.

Water Res. 2018 Sep 1;140:200-210. doi: 10.1016/j.watres.2018.04.055. Epub 2018 Apr 25.


Global Distribution of Human-Associated Fecal Genetic Markers in Reference Samples from Six Continents.

Mayer RE, Reischer GH, Ixenmaier SK, Derx J, Blaschke AP, Ebdon JE, Linke R, Egle L, Ahmed W, Blanch AR, Byamukama D, Savill M, Mushi D, Cristóbal HA, Edge TA, Schade MA, Aslan A, Brooks YM, Sommer R, Masago Y, Sato MI, Taylor HD, Rose JB, Wuertz S, Shanks OC, Piringer H, Mach RL, Savio D, Zessner M, Farnleitner AH.

Environ Sci Technol. 2018 May 1;52(9):5076-5084. doi: 10.1021/acs.est.7b04438. Epub 2018 Apr 16.


A human fecal contamination score for ranking recreational sites using the HF183/BacR287 quantitative real-time PCR method.

Cao Y, Sivaganesan M, Kelty CA, Wang D, Boehm AB, Griffith JF, Weisberg SB, Shanks OC.

Water Res. 2018 Jan 1;128:148-156. doi: 10.1016/j.watres.2017.10.071. Epub 2017 Oct 31.


Quantitative CrAssphage PCR Assays for Human Fecal Pollution Measurement.

Stachler E, Kelty C, Sivaganesan M, Li X, Bibby K, Shanks OC.

Environ Sci Technol. 2017 Aug 15;51(16):9146-9154. doi: 10.1021/acs.est.7b02703. Epub 2017 Jul 25.


Differential decomposition of bacterial and viral fecal indicators in common human pollution types.

Wanjugi P, Sivaganesan M, Korajkic A, Kelty CA, McMinn B, Ulrich R, Harwood VJ, Shanks OC.

Water Res. 2016 Nov 15;105:591-601. doi: 10.1016/j.watres.2016.09.041. Epub 2016 Sep 21.


Data Acceptance Criteria for Standardized Human-Associated Fecal Source Identification Quantitative Real-Time PCR Methods.

Shanks OC, Kelty CA, Oshiro R, Haugland RA, Madi T, Brooks L, Field KG, Sivaganesan M.

Appl Environ Microbiol. 2016 Apr 18;82(9):2773-2782. doi: 10.1128/AEM.03661-15. Print 2016 May.


Identification of Specialists and Abundance-Occupancy Relationships among Intestinal Bacteria of Aves, Mammalia, and Actinopterygii.

Green HC, Fisher JC, McLellan SL, Sogin ML, Shanks OC.

Appl Environ Microbiol. 2015 Dec 28;82(5):1496-1503. doi: 10.1128/AEM.02456-15.


Comparison of Sewage and Animal Fecal Microbiomes by Using Oligotyping Reveals Potential Human Fecal Indicators in Multiple Taxonomic Groups.

Fisher JC, Eren AM, Green HC, Shanks OC, Morrison HG, Vineis JH, Sogin ML, McLellan SL.

Appl Environ Microbiol. 2015 Oct;81(20):7023-33. doi: 10.1128/AEM.01524-15. Epub 2015 Jul 31.


Changes in bacterial and eukaryotic communities during sewage decomposition in Mississippi river water.

Korajkic A, Parfrey LW, McMinn BR, Baeza YV, VanTeuren W, Knight R, Shanks OC.

Water Res. 2015 Feb 1;69:30-39. doi: 10.1016/j.watres.2014.11.003. Epub 2014 Nov 13.


Development of rapid canine fecal source identification PCR-based assays.

Green HC, White KM, Kelty CA, Shanks OC.

Environ Sci Technol. 2014 Oct 7;48(19):11453-61. doi: 10.1021/es502637b. Epub 2014 Sep 24.


Factors affecting the presence of human-associated and fecal indicator real-time quantitative PCR genetic markers in urban-impacted recreational beaches.

Molina M, Hunter S, Cyterski M, Peed LA, Kelty CA, Sivaganesan M, Mooney T, Prieto L, Shanks OC.

Water Res. 2014 Nov 1;64:196-208. doi: 10.1016/j.watres.2014.06.036. Epub 2014 Jul 9.


Biotic interactions and sunlight affect persistence of fecal indicator bacteria and microbial source tracking genetic markers in the upper Mississippi river.

Korajkic A, McMinn BR, Shanks OC, Sivaganesan M, Fout GS, Ashbolt NJ.

Appl Environ Microbiol. 2014 Jul;80(13):3952-61. doi: 10.1128/AEM.00388-14. Epub 2014 Apr 18.


Improved HF183 quantitative real-time PCR assay for characterization of human fecal pollution in ambient surface water samples.

Green HC, Haugland RA, Varma M, Millen HT, Borchardt MA, Field KG, Walters WA, Knight R, Sivaganesan M, Kelty CA, Shanks OC.

Appl Environ Microbiol. 2014 May;80(10):3086-94. doi: 10.1128/AEM.04137-13. Epub 2014 Mar 7.


Detection limits and cost comparisons of human- and gull-associated conventional and quantitative PCR assays in artificial and environmental waters.

Riedel TE, Zimmer-Faust AG, Thulsiraj V, Madi T, Hanley KT, Ebentier DL, Byappanahalli M, Layton B, Raith M, Boehm AB, Griffith JF, Holden PA, Shanks OC, Weisberg SB, Jay JA.

J Environ Manage. 2014 Apr 1;136:112-20. doi: 10.1016/j.jenvman.2014.01.029. Epub 2014 Feb 26.


Human fecal source identification with real-time quantitative PCR.

Shanks OC, Peed L, Sivaganesan M, Haugland RA, Chern EC.

Methods Mol Biol. 2014;1096:85-99. doi: 10.1007/978-1-62703-712-9_7.


Age-related shifts in the density and distribution of genetic marker water quality indicators in cow and calf feces.

Shanks OC, Kelty CA, Peed L, Sivaganesan M, Mooney T, Jenkins M.

Appl Environ Microbiol. 2014 Mar;80(5):1588-94. doi: 10.1128/AEM.03581-13. Epub 2013 Dec 20.


Performance evaluation of canine-associated Bacteroidales assays in a multi-laboratory comparison study.

Schriewer A, Goodwin KD, Sinigalliano CD, Cox AM, Wanless D, Bartkowiak J, Ebentier DL, Hanley KT, Ervin J, Deering LA, Shanks OC, Peed LA, Meijer WG, Griffith JF, SantoDomingo J, Jay JA, Holden PA, Wuertz S.

Water Res. 2013 Nov 15;47(18):6909-20. doi: 10.1016/j.watres.2013.03.062. Epub 2013 Jul 5.


Evaluation of the repeatability and reproducibility of a suite of qPCR-based microbial source tracking methods.

Ebentier DL, Hanley KT, Cao Y, Badgley BD, Boehm AB, Ervin JS, Goodwin KD, Gourmelon M, Griffith JF, Holden PA, Kelty CA, Lozach S, McGee C, Peed LA, Raith M, Ryu H, Sadowsky MJ, Scott EA, Santo Domingo J, Schriewer A, Sinigalliano CD, Shanks OC, Van De Werfhorst LC, Wang D, Wuertz S, Jay JA.

Water Res. 2013 Nov 15;47(18):6839-48. doi: 10.1016/j.watres.2013.01.060. Epub 2013 Jul 5.


Recommendations following a multi-laboratory comparison of microbial source tracking methods.

Stewart JR, Boehm AB, Dubinsky EA, Fong TT, Goodwin KD, Griffith JF, Noble RT, Shanks OC, Vijayavel K, Weisberg SB.

Water Res. 2013 Nov 15;47(18):6829-38. doi: 10.1016/j.watres.2013.04.063. Epub 2013 Jul 10.


Enterococcus and Escherichia coli fecal source apportionment with microbial source tracking genetic markers--is it feasible?

Wang D, Farnleitner AH, Field KG, Green HC, Shanks OC, Boehm AB.

Water Res. 2013 Nov 15;47(18):6849-61. doi: 10.1016/j.watres.2013.02.058. Epub 2013 Jul 11.


Performance of forty-one microbial source tracking methods: a twenty-seven lab evaluation study.

Boehm AB, Van De Werfhorst LC, Griffith JF, Holden PA, Jay JA, Shanks OC, Wang D, Weisberg SB.

Water Res. 2013 Nov 15;47(18):6812-28. doi: 10.1016/j.watres.2012.12.046. Epub 2013 Jul 5.


Comparison of PCR and quantitative real-time PCR methods for the characterization of ruminant and cattle fecal pollution sources.

Raith MR, Kelty CA, Griffith JF, Schriewer A, Wuertz S, Mieszkin S, Gourmelon M, Reischer GH, Farnleitner AH, Ervin JS, Holden PA, Ebentier DL, Jay JA, Wang D, Boehm AB, Aw TG, Rose JB, Balleste E, Meijer WG, Sivaganesan M, Shanks OC.

Water Res. 2013 Nov 15;47(18):6921-8. doi: 10.1016/j.watres.2013.03.061. Epub 2013 Jul 5.


Characterization of fecal concentrations in human and other animal sources by physical, culture-based, and quantitative real-time PCR methods.

Ervin JS, Russell TL, Layton BA, Yamahara KM, Wang D, Sassoubre LM, Cao Y, Kelty CA, Sivaganesan M, Boehm AB, Holden PA, Weisberg SB, Shanks OC.

Water Res. 2013 Nov 15;47(18):6873-82. doi: 10.1016/j.watres.2013.02.060. Epub 2013 Jul 5.


Sewage reflects the distribution of human faecal Lachnospiraceae.

McLellan SL, Newton RJ, Vandewalle JL, Shanks OC, Huse SM, Eren AM, Sogin ML.

Environ Microbiol. 2013 Aug;15(8):2213-27. doi: 10.1111/1462-2920.12092. Epub 2013 Feb 25.


Comparison of the microbial community structures of untreated wastewaters from different geographic locales.

Shanks OC, Newton RJ, Kelty CA, Huse SM, Sogin ML, McLellan SL.

Appl Environ Microbiol. 2013 May;79(9):2906-13. doi: 10.1128/AEM.03448-12. Epub 2013 Feb 22.


Differential decay of enterococci and Escherichia coli originating from two fecal pollution sources.

Korajkic A, McMinn BR, Harwood VJ, Shanks OC, Fout GS, Ashbolt NJ.

Appl Environ Microbiol. 2013 Apr;79(7):2488-92. doi: 10.1128/AEM.03781-12. Epub 2013 Feb 1.


Dramatic improvements in beach water quality following gull removal.

Converse RR, Kinzelman JL, Sams EA, Hudgens E, Dufour AP, Ryu H, Santo-Domingo JW, Kelty CA, Shanks OC, Siefring SD, Haugland RA, Wade TJ.

Environ Sci Technol. 2012 Sep 18;46(18):10206-13. doi: 10.1021/es302306b. Epub 2012 Sep 5.


Distribution of genetic marker concentrations for fecal indicator bacteria in sewage and animal feces.

Kelty CA, Varma M, Sivaganesan M, Haugland RA, Shanks OC.

Appl Environ Microbiol. 2012 Jun;78(12):4225-32. doi: 10.1128/AEM.07819-11. Epub 2012 Apr 13.


Interlaboratory comparison of real-time PCR protocols for quantification of general fecal indicator bacteria.

Shanks OC, Sivaganesan M, Peed L, Kelty CA, Blackwood AD, Greene MR, Noble RT, Bushon RN, Stelzer EA, Kinzelman J, Anan'eva T, Sinigalliano C, Wanless D, Griffith J, Cao Y, Weisberg S, Harwood VJ, Staley C, Oshima KH, Varma M, Haugland RA.

Environ Sci Technol. 2012 Jan 17;46(2):945-53. doi: 10.1021/es2031455. Epub 2011 Dec 16. Erratum in: Environ Sci Technol. 2012 Feb 21;46(4):2478.


Differential decay of human faecal Bacteroides in marine and freshwater.

Green HC, Shanks OC, Sivaganesan M, Haugland RA, Field KG.

Environ Microbiol. 2011 Dec;13(12):3235-49. doi: 10.1111/j.1462-2920.2011.02549.x. Epub 2011 Sep 1.


Combining land use information and small stream sampling with PCR-based methods for better characterization of diffuse sources of human fecal pollution.

Peed LA, Nietch CT, Kelty CA, Meckes M, Mooney T, Sivaganesan M, Shanks OC.

Environ Sci Technol. 2011 Jul 1;45(13):5652-9. doi: 10.1021/es2003167. Epub 2011 Jun 10.


Decay of bacterial pathogens, fecal indicators, and real-time quantitative PCR genetic markers in manure-amended soils.

Rogers SW, Donnelly M, Peed L, Kelty CA, Mondal S, Zhong Z, Shanks OC.

Appl Environ Microbiol. 2011 Jul;77(14):4839-48. doi: 10.1128/AEM.02427-10. Epub 2011 Jun 3.


Community structures of fecal bacteria in cattle from different animal feeding operations.

Shanks OC, Kelty CA, Archibeque S, Jenkins M, Newton RJ, McLellan SL, Huse SM, Sogin ML.

Appl Environ Microbiol. 2011 May;77(9):2992-3001. doi: 10.1128/AEM.02988-10. Epub 2011 Mar 4.


Performance of PCR-based assays targeting Bacteroidales genetic markers of human fecal pollution in sewage and fecal samples.

Shanks OC, White K, Kelty CA, Sivaganesan M, Blannon J, Meckes M, Varma M, Haugland RA.

Environ Sci Technol. 2010 Aug 15;44(16):6281-8. doi: 10.1021/es100311n.


Improved strategies and optimization of calibration models for real-time PCR absolute quantification.

Sivaganesan M, Haugland RA, Chern EC, Shanks OC.

Water Res. 2010 Sep;44(16):4726-35. doi: 10.1016/j.watres.2010.07.066. Epub 2010 Jul 29.


Evaluation of genetic markers from the 16S rRNA gene V2 region for use in quantitative detection of selected Bacteroidales species and human fecal waste by qPCR.

Haugland RA, Varma M, Sivaganesan M, Kelty C, Peed L, Shanks OC.

Syst Appl Microbiol. 2010 Oct;33(6):348-57. doi: 10.1016/j.syapm.2010.06.001. Epub 2010 Jul 24.


Performance assessment PCR-based assays targeting bacteroidales genetic markers of bovine fecal pollution.

Shanks OC, White K, Kelty CA, Hayes S, Sivaganesan M, Jenkins M, Varma M, Haugland RA.

Appl Environ Microbiol. 2010 Mar;76(5):1359-66. doi: 10.1128/AEM.02033-09. Epub 2010 Jan 8.


Quantitative PCR for genetic markers of human fecal pollution.

Shanks OC, Kelty CA, Sivaganesan M, Varma M, Haugland RA.

Appl Environ Microbiol. 2009 Sep;75(17):5507-13. doi: 10.1128/AEM.00305-09. Epub 2009 Jul 10.


Temporal assessment of the impact of exposure to cow feces in two watersheds by multiple host-specific PCR assays.

Lee YJ, Molina M, Santo Domingo JW, Willis JD, Cyterski M, Endale DM, Shanks OC.

Appl Environ Microbiol. 2008 Nov;74(22):6839-47. doi: 10.1128/AEM.00601-08. Epub 2008 Sep 19.


A Bayesian method for calculating real-time quantitative PCR calibration curves using absolute plasmid DNA standards.

Sivaganesan M, Seifring S, Varma M, Haugland RA, Shanks OC.

BMC Bioinformatics. 2008 Feb 25;9:120. doi: 10.1186/1471-2105-9-120.


Quantitative PCR for detection and enumeration of genetic markers of bovine fecal pollution.

Shanks OC, Atikovic E, Blackwood AD, Lu J, Noble RT, Domingo JS, Seifring S, Sivaganesan M, Haugland RA.

Appl Environ Microbiol. 2008 Feb;74(3):745-52. Epub 2007 Dec 7.


Identification of chicken-specific fecal microbial sequences using a metagenomic approach.

Lu J, Santo Domingo J, Shanks OC.

Water Res. 2007 Aug;41(16):3561-74. Epub 2007 May 24.


Identification of bacterial DNA markers for the detection of human fecal pollution in water.

Shanks OC, Domingo JW, Lu J, Kelty CA, Graham JE.

Appl Environ Microbiol. 2007 Apr;73(8):2416-22. Epub 2007 Jan 5.


Basin-wide analysis of the dynamics of fecal contamination and fecal source identification in Tillamook Bay, Oregon.

Shanks OC, Nietch C, Simonich M, Younger M, Reynolds D, Field KG.

Appl Environ Microbiol. 2006 Aug;72(8):5537-46.


Competitive metagenomic DNA hybridization identifies host-specific microbial genetic markers in cow fecal samples.

Shanks OC, Santo Domingo JW, Lamendella R, Kelty CA, Graham JE.

Appl Environ Microbiol. 2006 Jun;72(6):4054-60.


Use of competitive DNA hybridization to identify differences in the genomes of bacteria.

Shanks OC, Santo Domingo JW, Graham JE.

J Microbiol Methods. 2006 Aug;66(2):321-30. Epub 2006 Feb 8.


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