JOHN F. GRIFFITH – Microbiologist


Ph.D., Marine Environmental Biology, University of Southern California, 2006

B.S., Biology, University of Southern California, 1995

B.S., Environmental Studies, University of Southern California, 1995


Dr. Griffith is a marine microbiologist and Coordinator of Molecular Technology at SCCWRP. He earned his Ph.D. in marine biology and biological oceanography at the University of Southern California, where his dissertation research focused on indicators of fecal contamination in near-shore marine waters. Dr. Griffith joined SCCWRP in 2001. His present research efforts focus on development and evaluation of methods for detection and enumeration of fecal indicators and pathogens in fresh and marine waters, and relationships between water quality indicators and swimming-related illness. He has written over 60 articles on use of Foraminifera as bio-indicators, prokaryotic and viral diversity in marine plankton, beach water quality, microbial source tracking and relationships between water quality indicators and swimming-related illness.


Principal Scientist, Southern California Coastal Water Research Project, Costa Mesa, CA. 2010 - Present

Microbiologist, Southern California Coastal Water Research Project. Westminster, CA. 2001-2010

Research Assistant, Marine Biology Research Section, University of Southern California. Los Angeles, CA. 2000-2001

Doctoral Fellow, NSF Integrative Graduate Education and Training, Environmental Studies, Policy and Engineering - Sustainable Cities Program, University of Southern California. Los Angeles, CA. 1999-2000

Teaching Assistant, University of Southern California. Los Angeles, CA. 1995-1999

Trainee, USC Sea Grant Program. Los Angeles, CA. 1995-2001

Laboratory Assistant, University of Southern California. Los Angeles CA. 1993-1995


US EPA Scientific and Technological Achievement Award 2014
National Science Foundation IGERT Doctoral Fellowship (1998-2000)
LAS Dean's Advisory Board, University of Southern California (1994-1997)
LAS Dean's List, University of Southern California (1994, 1995)
Phi Sigma National Biological Honor Society, Chapter President (1993-1994)
Dean's List, University of California, Irvine (1993)
President's Honor Roll, Fullerton College (1992)
Golden Key National Honor Society


American Society for Microbiology
Association for the Sciences of Limnology and Oceanography
The Oceanographic Society International Water Association


Yiping Cao, Mano Sivaganesan, Catherine A. Kelty, Dan Wang, Alexandria B. Boehm, John F. Griffith, Stephen B. Weisberg, Orin C. Shanks, A human fecal contamination score for ranking recreational sites using the HF183/BacR287 quantitative real-time PCR method, In Water Research, Volume 128, 2018, Pages 148-156, ISSN 0043-1354,

Yiping Cao, Meredith R Raith, Paul D Smith, John F Griffith, Stephen B Weisberg, Alexander Schriewer, Andrew Sheldon, Chris Crompton, Geremew G Amenu, Jason Gregory, Joe Guzman, Kelly D Goodwin, Laila Othman, Mayela Manasjan, Samuel Choi, Shana Rapoport, Syreeta Steele, Tommy Nguyen, Xueyuan Yu. 2017. Regional Assessment of Human Fecal Contamination in Southern California Coastal Drainages. International Journal of Environmental Research and public Health 14: 874., doi:10.3390/ijerph14080874.

Arnold, B.F., Schiff, K.C., Ercumen, A., Benjamin-Chung, J., Steele, J.A., Griffith, J.F., Steinberg, S.J., Smith, P., McGee, C.D., Wilson, R., Nelsen, C., Weisberg, S.B., Colford, J.M. 2017. Acute Illness Among Surfers After Exposure to Seawater in Dry- and Wet-Weather Conditions. American journal of epidemiology. DOI:10.1093/aje/kwx019.

Benjamin-Chung, J., Arnold, B.F., Wade, T.J., Schiff, K., Griffith, J.F., Dufour, A.P., Weisberg, S.B. and J.M. Colford. 2017. Coliphages and gastrointestinal illness in recreational waters: pooled analysis of six coastal beach cohorts. Epidemiology 28:644. DOI:10.1097/EDE.0000000000000681 Soller, J.A., Schoen, M., Steele, J.A., Griffith, J.F., Schiff, K.C. 2017. Incidence of gastrointestinal illness following wet weather recreational exposures: Harmonization of quantitative microbial risk assessment with an epidemiologic investigation of surfers. Water Research. DOI:10.1016/j.watres.2017.05.017

Zimmer-Faust, A.G., Thulsiraj, V., Marambio-Jones, C., Cao, Y, Griffith, J.F., Holden, P.A., Jay, J.A. 2017. Effect of freshwater sediment characteristics on the persistence of fecal indicator bacteria and genetic markers within a Southern California watershed. Water Research 119:1-11., 04/2017; 119., DOI:10.1016/j.watres.2017.04.028

Arnold, B.F., Wade, T.J., Benjamin-Chung, J., Schiff, K.C., Griffith, J.F., Dufour, A.P., Weisberg, S.B., Colford, J.M. 2017. Arnold et al. Respond. American Journal of Public Health 107:10-11., DOI:10.2105/AJPH.2016.303505.

Wu, J., Y. Cao, B. Young, Y. Yuen, S. Jiang, D. Melendez, J.F. Griffith and J.R. Stewart.  2016.  Decay of Coliphages in Sewage-Contaminated Freshwater: Uncertainty and Seasonal Effects. Environmental Science & Technology. 50: 11593-11601. DOI: 10.1021/acs.est.6b03916

Maraccini, P.A., M.C. Mattioli, L.M. Sassoubre, Y. Cao, J. Griffith, J. Ervin, L.V. de Werfhorst and A.B. Boehm.  2016.  Solar Inactivation of Enterococci and Escherichia coli in Natural Waters: Effects of Water Absorbance and Depth. Environmental Science & Technology 50:5068-5076.

Cao, Y., J.F. Griffith, and S.B. Weisberg. 2016. The next generation PCR-based quantification method for ambient waters: Digital PCR. in: S.J. Bourlat (ed.), Methods in Molecular Biology Series: Marine Genomics. Springer. New York, NY.

Cao, Y., MR Raith, JF Griffith. 2016. A duplex digital PCR assay for simultaneous quantification of the Enterococcus spp. and the human Fecal-associated HF183 marker in waters. Journal of Visualized Experiments. e53611, doi:10.3791/53611 (2016)

Haugland, R. A.; Siefring, S.; Varma, M.; Oshima, K. H.; Sivaganesan, M.; Cao, Y.; Raith, M.; Griffith, J.; Weisberg, S. B.; Noble, R. T.; Blackwood, A. D.; Kinzelman, J.; Anan'eva, T.; Bushon, R. N.; Stelzer, E. A.; Harwood, V. J.; Gordon, K. V.; Sinigalliano, C.. 2016. Multi-laboratory survey of qPCR enterococci analysis method performance in U.S. Coastal and inland surface waters. J. Microbiol. Methods.

Griffith, J.F., Weisberg, S.B., Arnold, B.F., Cao, Y., Schiff, K.C. and J.M. Colford, Jr. 2015 MD. Epidemiologic evaluation of multiple alternate microbial water quality monitoring indicators at three California beaches. Water Research 94, 371-381.

Cao, Y., Griffith, J.F. and M.R. Raith. 2015. Droplet digital PCR for simultaneous quantification of general and human-associated fecal indicators for water quality assessment. Water Research 70:337-349

Love, D.C., Rodriguez, R.A., Gibbons, C.D., Griffith, J.F., Stewart, J.R. and M.D. Sobsey. 2014. Human viruses and viral indicators in marine water at two recreational beaches in southern California, USA. Journal of Water and Health 12:136-150

Yau, V., Schiff, K.C., Arnold, B.F., Griffith, J.F., Gruber, J.S., Wright, C.C., Wade, T.J., Burns, S., hayes, J.M., McGee, C., Gold, M., Cao, Y., Boehm, A.B., Weisberg, S.B. and J.M. Colford. 2014. Effect of submarine groundwater discharge on bacterial indicators and swimmer health at Avalon Beach, CA, USA. Water Research 59:23-36

Riedel, T.E., Zimmer-Faust, A.G., Thulsiraj, V., Madi, T., Hanley, K.T., Ebentier, D.L., Byappanahalli, M., Layton, B., Raith, M., Boehm, A.B., Griffith, J.F., Holden, P.A., Shanks, O.C., Weisberg, S.B., and J.A. Jay. 2014. Detection limits and cost comparisons of human- and gull-associated conventional and quantitative PCR assays in artificial waters. Journal of Environmental Management 136:112-120

Arnold, B.M., Schiff, K.C., Griffith, J.F., Gruber, J.S., Yau, V., Wright, C.C., Wade, T.J., Burns, S., Hayes, J.M., McGee, C., Gold, M., Cao, Y., Weiseberg, S.B. and J.M. Colford. 2013. Swimmer illness associated with marine water exposure and water quality indicators: Impact of widely used assumptions. Epidemiology 24:845-53. doi: 10.1097/01.ede.0000434431.06765.4a

Raith, M., Ebentier, D., Cao, Y., Griffith, J. and S. Weisberg. 2014. Factors affecting the relationship between quantitative polymerase chain reaction (qPCR) and culture-based enumeration of Enterococcus in environmental waters. Journal of Applied Microbiology 116:737-746. DOI: 10.1111/jam.12383

Cao, Y., Hagedorn, C., Shanks, O.C., Wang, D., Ervin, J., Griffith, J.F., Layton, B.A., McGee, C.D., Riedel, T.E. and S.B. Weisberg. 2013. Towards establishing a human fecal contamination index in microbial source tracking. International Journal of Chemical and Environmental Engineering Systems 4(3): 46-58

Ryu, H., Henson, M., Elk, M., Toledo-Hernandez, C., Griffith, J., Blackwood, D., Noble, R., Gourmelon, M., Glassmeyer, S. and J.W. Santo Domingo. 2013. Development of quantitative PCR assays targeting the 16S rRNA genes of Enterococcus spp. and their application to the identification of Enterococcus species in environmental samples. Applied and Environmental Microbiology 79:196-204

Ferguson, D.M., J.F. Griffith, C.D. McGee, S.B. Weisberg and C. Hagedorn. Comparison of Enterococcus species diversity in marine water and wastewater using enterolert and EPA method 1600. Journal of Environmental and Public Health In press

Bourlat, S.J., A. Borja, J. Gilbert, M.I. Taylor, N. Davies, S.B. Weisberg, J.F. Griffith, T. Lettieri, D. Field and J. Benzie. Genomics in marine monitoring: New opportunities for assessing marine health status. Marine Pollution Bulletin In press.

Cao, Y., L.C. Van De Werfhorst, E.A. Dubinsky, B.D. Badgley, M.J. Sadowsky, G.L. Andersen, J.F. Griffith and P.A. Holden. Evaluation of molecular community analysis methods for discerning fecal sources and human waste. Water Research 47:6862-6872.

Sinigalliano, C.D., J. Ervin, L.C. Van De Werfhorst, B. Badgley, E. Ballesté, J. Bartkowiak, A.B. Boehm, M. Byappanahalli, K.D. Goodwin, M. Gourmelon, J. Griffith, P.A. Holden, J.A. Jay, B.L. Layton, C. Lee, J. Lee, W.G. Meijer, R. Noble, M. Raith, H. Ryu, M.J. Sadowsky, A. Schriewer, D. Wang, D. Wanless, R. Whitman, S. Wuertz and J.W. Santo Domingo. Multi-Laboratory evaluations of the performance of Catellicoccus marimammalium PCR assays developed to target gull fecal sources. Water Research 47:6883-6896

Harwood, V.J., A.B. Boehm, L.M. Sassoubre, V. Kannappan, J.R. Stewart, T.-T. Fong, M.-P. Caprais, R.R. Converse, D. Diston, J. Ebdon, J.A. Fuhrman, M. Gourmelon, J. Gentry-Shields, J.F. Griffith, D.R. Kashian, R.T. Noble, H. Taylor and M. Wicki. Performance of viruses and bacteriophages for fecal source determination in a Multi-laboratory, comparative Study. Water Research 47:6929-6943.

Schriewer, A., K.D. Goodwin, C.D. Sinigalliano, A.M. Cox, D. Wanless, J. Bartkowiak, D.L. Ebentier, K.T. Hanley, J. Ervin, L.A. Deering, O.C. Shanks, L.A. Peed, W.G. Meijer, J.F. Griffith, J. Santodomingo, J.A. Jay, P.A. Holden and S. Wuertz. Performance evaluation of canine-associated Bacteroidales assays in a multi-laboratory comparison study. Water Research 47:6909-6920

Boehm, A.B., L.C. Van De Werfhorst, J.F. Griffith, P.A. Holden, J.A. Jay, O.C. Shanks, D. Wang and S.B. Weisberg. Performance of forty-one microbial source tracking methods: a twenty-seven lab evaluation study. Water Research 47:6812-6828.

Cao, Y., L.C. Van De Werfhorst, E.A. Scott, M.R. Raith, P.A. Holden and J.F.Griffith. Bacteroidales terminal restriction fragment length polymorphism (TRFLP) for fecal source differentiation in comparison to and in combination with universal bacteria TRFLP. Water Research 47:6944-6955.

Layton, B.A., Y. Cao, D.L. Ebentier, K. Hanley, E. Ballesté, J. Brandão, M. Byappanahalli, R. Converse, A.H. Farnleitner, J. Gentry-Shields, M.L. Gidley, M. Gourmelon, C.S. Lee, J. Lee, S. Lozach, T. Madi, W.G. Meijer, R. Noble, L. Peed, G.H. Reischer, R. Rodrigues, J.B. Rose, A. Schriewer, C. Sinigalliano, S. Srinivasan, J. Stewart, L.C. Van De Werfhorst, D. Wang, R. Whitman, S. Wuertz, J. Jay, P.A. Holden, A.B. Boehm, O. Shanks and J.F. Griffith. Performance of Human Fecal Anaerobe-Associated PCR-Based Assays in a Multi-Laboratory Method Evaluation Study. Water Research 47:6897-6908

Raith, M.R., C.A. Kelty, J.F. Griffith, A. Schriewer, S. Wuertz, S. Mieszkin, M. Gourmelon, G.H. Reischer, A.H. Farnleitner, J.S. Ervin, P.A. Holden, D.L. Ebentier, J.A. Jay, D. Wang, A.B. Boehm, T.G. Aw, J.B. Rose, E. Ballesté, W.G. Meijer, M. Sivaganesan and O.C. Shanks. Comparison of PCR and quantitative real-time PCR methods for the characterization of ruminant and cattle fecal pollution sources. Water Research 47:6921-6928

Stewart, J.R., A.B Boehm, E.A. Dubinsky, T.-T. Fong, K.D. Goodwin, J.F. Griffith, R.T. Noble, O.C. Shanks, V. Kannappan and S.B. Weisberg. Recommendations following a multi-laboratory comparison of microbial source tracking methods. Water Research 47:6829-6838.

Ebentier, D.L., K.T. Hanley, Y. Cao, B.D. Badgley, A.B. Boehm, J.S. Ervin, K.D. Goodwin, M. Gourmelon, J.F. Griffith, P.A. Holden, C.A. Kelty, S. Lozach, C. McGee, L.A. Peed, M. Raith, H. Hodon Ryu, M.J. Sadowsky, E.A. Scott, J. Santo Domingo, A. Schriewer, O.D. Sinigalliano, L.C. Van De Werfhorst, D. Wang, S. Wuertz and J.A. Jay. Evaluation of the repeatability and reproducibility of a suite of qPCR-based microbial source tracking methods. Water Research 47:6839-6848

Ryu, H., M. Henson, M. Elk, C. Toledo-Hernandez, J. Griffith, D. Blackwood, R. Noble, M. Gourmelon, S. Glassmeyer and J.W. Santo Domingo. 2013. Development of quantitative PCR assays targeting the 16S rRNA genes of Enterococcus spp. and their application to the identification of Enterococcus species in environmental samples. Applied and Environmental Microbiology 79:196-204.

Cao, Y., M. Sivaganesan, J. Kinzelman, A.D. Blackwood, R.T. Noble, R.A. Haugland, J.F. Griffith and S.B. Weisberg. 2013. Effect of platform, reference material, and quantification model on enumeration of Enterococcus by quantitative PCR methods. Water Research 47:233-241.

Converse, R.R., Griffith, J.F., Noble, R.T., Haugland, R.A., Schiff, K.C., and S.B. Weisberg. 2012. Correlation between quantitative PCR and culture-based methods for measuring Enterococcus spp. over various temporal scales at three California marine beaches. Applied and Environmental Microbiology 78:1237-1242.

McQuaig, S., Griffith, J.F. and V.J. Harwood. 2012. Association of fecal indicator bacteria with human viruses and microbial source tracking markers at coastal beaches impacted by nonpoint source pollution. Applied and Environmental Microbiology 78:6423-6432.

Dubinsky, E.A., L. Esmaili, J.R. Hull, Y. Cao, J.F. Griffith, and G. L. Andersen. 2012. Application of phylogenetic microarray analysis to discriminate sources of fecal pollution. Environmental Science and Technology 46:4340-4347.

Cao, Y., J.F. Griffith, S. Dorevitch, and S.B. Weisberg. 2012. Effectiveness of qPCR permutations, internal controls, and dilution as means for minimizing inhibition while measuring Enterococcus in environmental waters. Journal of Applied Microbiology 113:66-75.

Colford, Jr, J.M, K.C. Schiff, J.F. Griffith, V. Yau, B.F. Arnold, C.C. Wright, J.S. Gruber, T.J. Wade, S. Burns, J. Hayes, C. McGee, M. Gold, Y. Cao, R.T. Noble, R. Haugland, and S.B. Weisberg. 2012. Using rapid indicators for Enterococcus to assess the risk of illness after exposure to urban runoff contaminated marine water. Water Research 46:2176-2186.

Goodwin, K.D., M. McNay, Y. Cao, D. Ebentier, M. Madison, and J.F. Griffith. 2012. A multi-beach study of Staphylococcus aureus, MRSA, and enterococci in seawater and beach sand. Water Research 46:4195-4207.

Ryu, H., J.F. Griffith, I.U.H. Khan, S. Hill, T.A. Edge, C. Toledo-Hernandez, J. Gonzalez-Nieves, and J. Santo Domingo. 2012. Comparison of gull feces-specific assays targeting the 16S rRNA genes of Catellicoccus marimammalium and Streptococcus spp. Applied and Environmental Microbiology 78:1909-1916.

Shanks, O.C., M. Sivaganesan, L. Peed, C. Kelty, A.D. Blackwood, M.R. Greene, R. Noble, R. Bushon, E.A. Stelzer, J. Kinzelman, T. Anna'eva, C. Sinigalliano, D. Wanless, J.F. Griffith, Y. Cao, S. Weisberg, V.J. Harwood, C. Staley, K. Oshima, M. Varma and R.A. Haugland. 2011. Inter-laboratory comparison of real-time PCR protocols for quantification of general fecal indicator bacteria. Environmental Science and Technology 46:945-953.

Cao, Y., C.D. McGee, J.F. Griffith and S.B. Weisberg. 2011. Method repeatability for measuring Enterococcus in southern California beach sands. Letters in Applied Microbiology 53:656-659.

Griffith, J.F. and S.B. Weisberg. 2011. Challenges in implementing new technology for beach water quality monitoring: lessons learned from a California demonstration project. Marine Technology Society Journal 45:65-73.

Lu, J., H. Ryu, J.W. Santo Domingo, J.F. Griffith and N.A. Ashbolt. 2011. Molecular detection of Campylobacter spp. in California Gull (Larus californicus) excreta. Applied and Environmental Microbiology 77:5034-5039.

Gregory, J.B., L.F. Webster, J.F. Griffith and J.R.Stewart. 2011. Improved detection and quantitation of norovirus from water. Journal of Virological Methods 172:38-42.

Halliday, E., J.F. Griffith and R.J. Gast. 2010. Use of an exogenous plasmid standard and quantitative PCR to monitor spatial and temporal distribution of Enterococcus spp. in beach sands. Limnology and Oceanography Methods 8:146-154.

Noble, R.T., A.D. Blackwood, J.F. Griffith, C.D. McGee, and S.B. Weisberg. 2010. Comparison of rapid quantitative PCR-Based and conventional culture-based methods for enumeration of Enterococcus spp. and Escherichia coli in recreational waters. Applied and Environmental Microbiology 76:7437-7443.

Johnston, C., J. Ufnar, J. Griffith, J. Gooch, and J. Stewart. 2010. A real-time qPCR assay for the detection of the nifH gene of Methanobrevibacter smithii, a potential indicator of sewage pollution. Journal of Applied Microbiology 109:1853-1867.

Hamilton, M.J., A.Z. Hadi, J.F. Griffith, S. Ishii, and M.J. Sadowsky. 2010. Large scale analysis of virulence genes in Escherichia coli strains isolated from Avalon Bay, CA. Water Research 44:5463-73.

Lee, C.M., J.F. Griffith, W. Kaiser, and J.A. Jay. 2010. Covalently linked immunomagnetic separation/adenosine triphosphate technique (Cov-IMS/ATP) enables rapid, in-field detection and quantification of Escherichia coli and Enterococcus spp. in freshwater and marine environments. Journal of Applied Microbiology 109:324-33.

Griffith, J.F., K.C. Schiff, G.S. Lyon, and J.A. Fuhrman. 2010. Microbiological water quality at non-human influenced reference beaches in southern California during wet weather. Marine Pollution Bulletin 60:500-8.

Boehm, A.B., J. Griffith, C. McGee, T.A. Edge, H.M. Solo-Gabriele, R. Whitman, Y. Cao, M. Getrich, J.A. Jay, D. Ferguson, K.D. Goodwin, C.M. Lee, M. Madison, and S.B. Weisberg. 2009. Fecal indicator bacteria enumeration in beach sand: a comparison study of extraction methods in medium to coarse sands. Journal of Applied Microbiology 107:1740-1750.

Griffith, J.F., Y. Cao, C.D. McGee, and S.B. Weisberg. 2009. Evaluation of rapid methods and novel indicators for assessing microbiological beach water quality. Water Research 43:4900-7.

Converse, R.R., A.D. Blackwood, M. Kirs, J.F. Griffith, and R.T. Noble. 2009. Rapid QPCR-based assay for fecal Bacteroides spp. as a tool for assessing fecal contamination in recreational waters. Water Research 43:4828-37.

Colford, J.M., T.M. Wade, K.C. Schiff, C.C. Wright, J.F. Griffith, K.S. Sukhminder, S.B. Burns, J. Hayes, M.D. Sobsey, G. Lovelace, and S.B.Weisberg. 2007. Water quality indicators and the risk of illness at beaches with nonpoint sources of fecal contamination Epidemiology 18:27-35.

Griffith, J.F., L.A. Aumand, I.M. Lee, C.D. McGee, L.L. Othman, K.J. Ritter, K.O. Walker, and S.B. Weisberg. 2006. Comparison and verification of bacterial water quality indicator measurement methods using ambient coastal water samples. Environmental Monitoring and Assessment 116:335-344.

Noble, R.T., J.F. Griffith, A.D. Blackwood, J.A. Fuhrman, J.B. Gregory, X. Hernandez, X. Liang, A.A. Bera, and K. Schiff. 2006. Multi-tiered Approach Using Quantitative PCR to Track Sources of Fecal Pollution Affecting Santa Monica Bay, California. Applied and Environmental Microbiology 72:1604-1612.

Griffith, J.F., S.B. Weisberg, and C.D. McGee. 2004. Evaluation of new, rapid methods for measuring microbiological water quality. pp. 354-362 in: S.B. Weisberg and D. Elmore (eds.), Southern California Coastal Water Research Project 2003-04 Biennial Report. Westminster, CA.

Griffith, J.F., S.B. Weisberg, and C.D. McGee. 2003. Evaluation of microbial source tracking methods using mixed fecal sources in aqueous test samples. Journal of Water and Health 1:141-151.

Field, K.D., E.C. Chern, L.K. Dick, J. Fuhrman, J. Griffith, P.A. Holden, M.G. LaMontangne, J. Le, B. Olson, and M.T. Simonich. 2003. A comparative study of culture-independent, library-independent genotypic methods of fecal source tracking. Journal of Water and Health 1:181-194.

Fuhrman, J.A., J.F. Griffith, and M.S. Schwalbach. 2000. Prokaryotic and viral diversity in marine plankton. Ecological Research 17:183-194.

Stott, L.D., T.P. Hayden, and J.F. Griffith. 1996. Benthic Foraminifera at the Los Angeles County Whites Point Outfall Revisited. Journal of Foraminiferal Research 26:357-368.