Evaluation of molecular community analysis methods for discerning fecal sources and human waste

Water Research

Volumn 47, Issue 18, 2013, Pages 6862-6872

  Cao, Yiping ^a   Van De Werfhorst, Laurie C ^b   Dubinsky, Eric A ^c   Badgley, Brian D ^d,e   Sadowsky, Michael J ^d   Andersen, Gary L ^c   Griffith, John F ^a   Holden, Patricia A ^b  

^a SOUTHERN CALIFORNIA COASTAL WATER RESEARCH PROJECT   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^d UNIVERSITY OF MINNESOTA   (United States)

^e VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

Author keywords

Microbial community analysis; Microbial source tracking; Next generation sequencing; PhyloChip; TRFLP

Indexed keywords

GEOGRAPHICAL REGIONS; MICROORGANISMS; PHYLOGENETIC;

ANALYSIS METHOD; DUAL SOURCE; HUMAN FECES; MICROBIAL COMMUNITY ANALYSIS; MICROBIAL SOURCE TRACKING; NEXT-GENERATION SEQUENCING; PHYLOCHIP; SINGLE SOURCE; TERMINAL RESTRICTION FRAGMENT POLYMORPHISM; TERMINAL RESTRICTION FRAGMENTS;

SEWAGE;

BIOTIC FACTOR; DEER; FECES; MICROBIAL COMMUNITY; MOLECULAR ANALYSIS; PERTURBATION; PHYLOGENETICS; PIG; SEWAGE;

ARTICLE; CHICKEN; CONTROLLED STUDY; DEER; DOG; DONOR; EVALUATION; FECES ANALYSIS; GENE SEQUENCE; GOOSE; HORSE; HUMAN; MICROARRAY ANALYSIS; MICROBIAL COMMUNITY; NONHUMAN; PHYLOGENY; PIGEON; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SENSITIVITY AND SPECIFICITY; SEWAGE; UNITED STATES; WASTE;

CALIFORNIA; UNITED STATES;

ANSER; CANIS FAMILIARIS; CERVIDAE; COLUMBA; ENTEROCOCCUS; EQUIDAE; GALLUS GALLUS; SUIDAE;

MICROBIAL COMMUNITY ANALYSIS; MICROBIAL SOURCE TRACKING; NEXT GENERATION SEQUENCING; PHYLOCHIP; TRFLP;

ANIMALS; BIRDS; DNA FINGERPRINTING; DNA, BACTERIAL; ENVIRONMENTAL MONITORING; FECES; HUMANS; MAMMALS; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RNA, RIBOSOMAL, 16S; SEWAGE; WATER MICROBIOLOGY; WATER POLLUTION;

EID: 84887176578     PISSN: 00431354     EISSN: 18792448     Source Type: Journal    
DOI: 10.1016/j.watres.2013.02.061     Document Type: Article

References (24)

1. Boehm A.B., Van De Werfhorst L.C., Griffith J.F., Holden P.A., Jay J.A., Shanks O.C., Wang D., Weisberg S.B. Performance of forty-one microbial source tracking methods: a twenty-seven lab evaluation study. Water Research 2013, this issue.
2. Cao Y., Cherr G.N., Córdova-Kreylos A.L., Fan T.W.-M., Green P.G., Higashi R.M., LaMontagne M.G., Scow K.M., Vines C.A., Yuan J., Holden P.A. Relationships between sediment microbial communities and pollutants in two California salt marshes. Microbial Ecology 2006, 52(4):619-633.
3. Cao Y., Van De Werfhorst L.C., Scott E., Raith M., Holden P.A., Griffith J.F. Bacteroidales terminal restriction fragment length polymorphism (TRFLP) for fecal source differentiation in comparison to and in combination with universal Bacteria TRFLP. Water Research 2013, this issue.
4. Cao Y., Van De Werfhorst L.C., Sercu B., Murray J.L.S., Holden P.A. Application of an integrated community analysis approach for microbial source tracking in a coastal creek. Environmental Science & Technology 2011, 45(17):7195-7201.
5. Cao Y., Wu C.H., Andersen G.L., Holden P.A. Community analysis-based methods. Microbial Source Tracking: Methods, Applications, and Case Studies 2011, 251-282. Springer, New York, NY. C. Hagedorn, A. Blanch, V. Harwood (Eds.).
6. Cole J.R., Wang Q., Cardenas E., Fish J., Chai B., Farris R.J., Kulam-Syed-Mohideen A.S., McGarrell D.M., Marsh T., Garrity G.M., Tiedje J.M. The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Research 2009, 37(suppl 1):D141-D145.
7. Dubinsky E.A., Esmaili L., Hulls J.R., Cao Y., Griffith J.F., Andersen G.L. Application of phylogenetic microarray analysis to discriminate sources of fecal pollution. Environmental Science & Technology 2012, 46(8):4340-4347.
8. Edgar R.C., Haas B.J., Clemente J.C., Quince C., Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011, 27(16):2194-2200.
9. Ervin J.S., Russell T.L., Layton B.A., Yamahara K.M., Wang D., Sassoubre L.M., Cao Y., Kelty C.A., Sivaganesan M., Boehm A.B., Holden P.A., Weisberg S.B., Shanks O.C. Characterization of fecal concentrations in human and other animal sources by physical, culture, and quantitative real-time PCR methods. Water Research 2013, this issue.
10. Field K.G., Chern E.C., Dick L.K., Fuhrman J., Griffith J., Holden P.A., LaMontagne M.G., Olson B., Simonich M.T. A comparative study of culture-independent, library-independent genotypic methods of fecal source tracking. Journal of Water and Health 2003, 1:181-194.
11. Harwood V.J., Levine A.D., Scott T.M., Chivukula V., Lukasik J., Farrah S.R., Rose J.B. Validity of the indicator organism paradigm for pathogen reduction in reclaimed water and public health protection. Applied and Environmental Microbiology 2005, 71(6):3163-3170.
12. Huber J.A., Mark Welch D.B., Morrison H.G., Huse S.M., Neal P.R., Butterfield D.A., Sogin M.L. Microbial population structures in the deep marine biosphere. Science 2007, 318(5847):97-100.
13. Knights D., Kuczynski J., Charlson E.S., Zaneveld J., Mozer M.C., Collman R.G., Bushman F.D., Knight R., Kelley S.T. Bayesian community-wide culture-independent microbial source tracking. Nature Methods 2011, 8(9):761-763.
14. Lee J.E., Lee S., Sung J., Ko G. Analysis of human and animal fecal microbiota for microbial source tracking. ISME Journal 2011, 5(2):362-365.
15. Ley R.E., Hamady M., Lozupone C., Turnbaugh P.J., Ramey R.R., Bircher J.S., Schlegel M.L., Tucker T.A., Schrenzel M.D., Knight R., Gordon J.I. Evolution of mammals and their gut microbes. Science 2008, 32:1647-1651.
16. Liu W.-T., Marsh T.L., Cheng H., Forney L.J. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Applied and Environmental Microbiology 1997, 63(11):4516-4522.
17. McLellan S.L., Huse S.M., Mueller-Spitz S.R., Andreishcheva E.N., Sogin M.L. Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent. Environmental Microbiology 2010, 12(2):378-392.
18. Schloss P.D., Westcott S.L., Ryabin T., Hall J.R., Hartmann M., Hollister E.B., Lesniewski R.A., Oakley B.B., Parks D.H., Robinson C.J., Sahl J.W., Stres B., Thallinger G.G., Van Horn D.J., Weber C.F. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 2009, 75(23):7537-7541.
19. Shanks O.C., Kelty C.A., Archibeque S., Jenkins M., Newton R.J., McLellan S.L., Huse S.M., Sogin M.L. Community structures of fecal bacteria in cattle from different animal feeding operations. Applied and Environmental Microbiology 2011, 77(9):2992-3001.
20. U.S.EPA Method 1600: Enterococci in Water by Membrane Filtration Using Membrane-Enterococcus Indoxyl-β-D-glucoside Agar (mEI) 2002, EPA-821-R-02-022, Washington, D.C.
21. Unno T., Di D.Y.W., Jang J., Suh Y.S., Sadowsky M.J., Hur H.-G. Integrated online system for a pyrosequencing-based microbial source tracking method that targets Bacteroidetes 16S rDNA. Environmental Science & Technology 2011, 46(1):93-98.
22. Unno T., Jang J., Han D., Kim J.H., Sadowsky M.J., Kim O.-S., Chun J., Hur H.-G. Use of barcoded pyrosequencing and shared OTUs to determine sources of fecal bacteria in watersheds. Environmental Science & Technology 2010, 44(20):7777-7782.
23. Walters S.P., Yamahara K.M., Boehm A.B. Persistence of nucleic acid markers of health-relevant organisms in seawater microcosms: Implications for their use in assessing risk in recreational waters. Water Research 2009, 43(19):4929-4939.
24. Wood J., Scott K.P., Avguštin G., Newbold C.J., Flint H.J. Estimation of the relative abundance of different bacteroides and prevotella ribotypes in gut samples by restriction enzyme profiling of PCR-amplified 16S rRNA gene sequences. Applied and Environmental Microbiology 1998, 64(10):3683-3689.