Fecal source tracking based on fecal coliform concentration and bacterial community structure in the Bong stream, Korea

  • Soon Bum Shin
  • Ji Hee Lee
  • Chi Won Lim
  • Kwang Tae Son
  • Sang Hyeon JeongEmail author
Research Article


Fecal source tracking of the Bong stream, a representative inland pollutant around the drainage basin of Gangjin Bay (an area where shellfish are grown for export), was performed three times in four confluence areas with 13 sampling sites by analyzing fecal coliform concentrations and two types of bacterial community structures. Identification of the origin of major fecal pollution in the area that inflowed simultaneously via several branch streams was difficult using fecal source tracking based on fecal coliform concentration. Bacterial community analyses using high-throughput sequencing showed that the dominant groups in the entire bacterial community at the class level were Beta-, Gamma-, and Alpha-proteobacteria; Flavobacteriia; and Bacteroidia, and the most abundant groups in the Bacteroidales-specific community at the genus level were Prevotella and Bacteroides. Hierarchical clustering and Bray–Curtis dissimilarity analysis for fecal source tracking indicated that the Bacteroidales-specific community was superior in water environments compared with analysis of the entire bacterial community. Conversely, when the degree of fecal pollution in the sample was low, fecal source tracking based on the entire bacterial community was more reliable. These results suggest that fecal source tracking based on bacterial communities is a useful tool for identifying the origin of fecal pollution in a large stream and implementing systematic guidelines for the establishment of an effective management plan to reduce fecal pollution sources.


Fecal source tracking Fecal coliform Bacterial community structure Bacteroidales Bong stream 



This work was supported by the National Institute of Fisheries Science (NIFS, R2018056).

Supplementary material

11356_2018_3995_MOESM1_ESM.docx (384 kb)
Supplementary Material (DOCX 384 kb)


  1. Ackerman D, Weisberg SB (2003) Relationship between rainfall and beach bacterial concentrations on Santa Monica Bay beaches. J Water Health 1(2):85–89CrossRefGoogle Scholar
  2. Allsop K, Stickler DJ (1985) An assessment of Bacteroides fragilis group organisms as indicators of human faecal pollution. J Appl Microbiol 58(1):95–99Google Scholar
  3. APHA (American Public Health Association) (1970) Recommended procedures for the examination of seawater and shellfish. American Public Health Association, Washington DCGoogle Scholar
  4. Aslan-Yılmaz A, Okuş E, Övez S (2004) Bacteriological indicators of anthropogenic impact prior to and during the recovery of water quality in an extremely polluted estuary, Golden Horn, Turkey. Mar Pollut Bull 49(11–12):951–958CrossRefGoogle Scholar
  5. Bernhard AE, Field KG (2000a) 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(4):1587–1594CrossRefGoogle Scholar
  6. Bernhard AE, Field KG (2000b) A PCR assay to discriminate human and ruminant feces based on host differences in Bacteroides–Prevotella 16S ribosomal DNA. Appl Environ Microbiol 66(10):4571–4574CrossRefGoogle Scholar
  7. Bryan FL (1977) Diseases transmitted by foods contaminated by wastewater. J Food Prot 40(1):45–56CrossRefGoogle Scholar
  8. Chao A (1984) Nonparametric estimation of the number of classes in a population. Scand J Stat 11:265–270Google Scholar
  9. Chigbu P, Gordon S, Strange T (2004) Influence of inter-annual variations in climatic factors on fecal coliform levels in Mississippi Sound. Water Res 38(20):4341–4352CrossRefGoogle Scholar
  10. Daly K, Stewart CS, Flint HJ, Shirazi-Beechey SP (2001) Bacterial diversity within the equine large intestine as revealed by molecular analysis of cloned 16S rRNA genes. FEMS Microbiol Ecol 38:141–151CrossRefGoogle Scholar
  11. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA (2005) Diversity of the human intestinal microbial flora. Science 308(5728):1635–1638CrossRefGoogle Scholar
  12. Ellender RD, Mapp JB, Middlebrooks BL, Cook DW, Cake EW (1980) Natural enterovirus and fecal coliform contamination of Gulf Coast oysters. J Food Prot 43(2):105–110CrossRefGoogle Scholar
  13. Fiksdal L, Maki JS, LaCroix SJ, Staley JT (1985) Survival and detection of Bacteroides spp., prospective indicator bacteria. Appl Environ Microbiol 49(1):148–150Google Scholar
  14. Fogarty LR, Voytek MA (2005) Comparison of Bacteroides–Prevotella 16S rRNA genetic markers for fecal samples from different animal species. Appl Environ Microbiol 71(10):5999–6007CrossRefGoogle Scholar
  15. Gerba CP, Goyal SM (1978) Detection and occurrence of enteric viruses in shellfish: a review. J Food Prot 41(9):743–754CrossRefGoogle Scholar
  16. Glasoe S, Christy A (2004) Coastal urbanization and microbial contamination of shellfish growing areas. Puget Sound Action Team, State of Washington, WashingtonGoogle Scholar
  17. Gorvitovskaia A, Holmes SP, Huse SM (2016) Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle. Microbiome 4(1):15CrossRefGoogle Scholar
  18. Ha KS, Yoo HD, Shim KB, Kim JH, Lee TS, Kim PH, Ju JY, Lee HJ (2011) Evaluation of the influence of inland pollution sources on shellfish growing areas after rainfall events in Geoje bay, Korea. Korean J Fish Aquat Sci 44(6):612–621Google Scholar
  19. Harwood VJ, Staley C, Badgley BD, Borges K, Korajkic A (2014) Microbial source tracking markers for detection of fecal contamination in environmental waters: relationships between pathogens and human health outcomes. FEMS Microbiol Rev 38(1):1–40CrossRefGoogle Scholar
  20. Hold GL, Pryde SE, Russell VJ, Furrie E, Flint HJ (2002) Assessment of microbial diversity in human colonic samples by 16S rDNA sequence analysis. FEMS Microbiol Ecol 39:33–39CrossRefGoogle Scholar
  21. Hong H, Qiu J, Liang Y (2010) Environmental factors influencing the distribution of total and fecal coliform bacteria in six water storage reservoirs in the Pearl River Delta Region, China. J Environ Sci 22(5):663–668CrossRefGoogle Scholar
  22. Keim BD, Faiers GE, Muller RA, Grymes JM, Rohli RV (1995) Long-term trends of precipitation and runoff in Louisiana, USA. Int J Climatol 15(5):531–541CrossRefGoogle Scholar
  23. Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO (2013) Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41(1):e1CrossRefGoogle Scholar
  24. Kwon JY, Park KBW, Song KC, Lee HJ, Park JH, Kim JD, Son KT (2008) Evaluation of the bacteriological quality of a shellfish-growing area in Kamak Bay, Korea. Fish Aquat Sci 11(1):7–14Google Scholar
  25. 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(6):4214–4224CrossRefGoogle Scholar
  26. Lee TS, Oh EG, Yu HD, Ha KS, Yu HS, Byun HS, Kim JH (2010) Impact of rainfall events on the bacteriological water quality of the shellfish growing area in Korea. Korean J Fish Aquat Sci 43(5):406–414Google Scholar
  27. Lee DY, Lee H, Trevors JT, Weir SC, Thomas JL, Habash M (2014) Characterization of sources and loadings of fecal pollutants using microbial source tracking assays in urban and rural areas of the Grand River Watershed, Southwestern Ontario. Water Res 53:123–131CrossRefGoogle Scholar
  28. Leser TD, Amenuvor JZ, Jensen TK, Lindecrona RH, Boye M, Møller K (2002) Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. Appl Environ Microbiol 68(2):673–690CrossRefGoogle Scholar
  29. Lipp EK, Rose JB (1997) The role of seafood in foodborne diseases in the United States of America. Rev Sci Tech OIE 16(2):620–640CrossRefGoogle Scholar
  30. Mallin MA, Williams KE, Esham EC, Lowe RP (2000) Effect of human development on bacteriological water quality in coastal watersheds. Ecol Appl 10(4):1047–1056CrossRefGoogle Scholar
  31. Martinez-Manzanares E, Morinigo MA, Castro D, Balebona MC, Munoz MA, Borrego JJ (1992) Relationship between indicators of fecal pollution in shellfish-growing water and the occurrence of human pathogenic microorganisms in shellfish. J Food Prot 55(8):609–614CrossRefGoogle Scholar
  32. McLellan SL, Eren AM (2014) Discovering new indicators of fecal pollution. Trends Microbiol 22(12):697–706CrossRefGoogle Scholar
  33. Meays CL, Broersma K, Nordin R, Mazumder A (2004) Source tracking fecal bacteria in water: a critical review of current methods. J Environ Manag 73(1):71–79CrossRefGoogle Scholar
  34. Mieszkin S, Furet JP, Corthier G, Gourmelon M (2009) Estimation of pig fecal contamination in a river catchment by real-time PCR using two pig-specific Bacteroidales 16S rRNA genetic markers. Appl Environ Microbiol 75(10):3045–3054CrossRefGoogle Scholar
  35. MOF (Ministry of Oceans and Fisheries) (2015) Korean Shellfish Sanitation Program (KSSP). Ministry of Oceans and Fisheries, SejongGoogle Scholar
  36. Mok JS, Lee KJ, Kim PH, Lee TS, Lee HJ, Jung YJ, Kim JH (2016) Bacteriological quality evaluation of seawater and oysters from the Jaranman-Saryangdo area, a designated shellfish growing area in Korea: impact of inland pollution sources. Mar Pollut Bull 108(1–2):147–154CrossRefGoogle Scholar
  37. Mulholland PJ, Best GR, Coutant CC, Hornberger GM, Meyer JL, Robinson PJ, Stenberg JR, Turner RE, Vera-Herrera F, Wetzel RG (1997) Effects of climate change on freshwater ecosystems of the South-Eastern United States and the Gulf Coast of Mexico. Hydrol Process 11(8):949–970CrossRefGoogle Scholar
  38. Naemura LG, Seidler RJ (1978) Significance of low-temperature growth associated with the fecal coliform response, indole production, and pectin liquefaction in Klebsiella. Appl Environ Microbiol 35(2):392–396Google Scholar
  39. 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(4):935–944CrossRefGoogle Scholar
  40. Okabe S, Okayama N, Savichtcheva O, Ito T (2007) Quantification of host-specific BacteroidesPrevotella 16S rRNA genetic markers for assessment of fecal pollution in freshwater. Appl Microbiol Biotechnol 74(4):890–901CrossRefGoogle Scholar
  41. Oksanen J, Blanchet FG, Kindt R, Legendre P, O’hara RB, Simpson GL, Stevens MHH, Wagner H (2015) Vegan: community ecology package. R package version 2.2−1. Available online: Accessed 12 March 2018
  42. Park KBW, Jo MR, Kwon JY, Son KT, Lee DS, Lee HJ (2010) Evaluation of the bacteriological safety of the shellfish-growing area in Gangjinman, Korea. Korean J Fish Aquat Sci 43(6):614–622Google Scholar
  43. Park K, Jo MR, Kim YK, Lee HJ, Kwon JY, Son KT, Lee TS (2012) Evaluation of the effects of the inland pollution sources after rainfall events on the bacteriological water quality in Narodo area, Korea. Korean J Fish Aquat Sci 45(5):414–422Google Scholar
  44. Presnell MW, Miescier JJ (1971) Coliforms and fecal coliforms in an oyster-growing area. J Water Pollut Control Fed 43(3):407–416Google Scholar
  45. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2012) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41(D1):D590–D596CrossRefGoogle Scholar
  46. Ratkowsky DA, Olley J, McMeekin TA, Ball A (1982) Relationship between temperature and growth rate of bacterial cultures. J Bacteriol 149(1):1–5Google Scholar
  47. Rognes T, Flouri T, Nichols B, Quince C, Mahé F (2016) VSEARCH: a versatile open source tool for metagenomics. PeerJ 4:e2584CrossRefGoogle Scholar
  48. Shannon CE (1948) A mathematical theory of communication. Bell Syst Tech J 27:379–423 623–656CrossRefGoogle Scholar
  49. Shin SB, Ha KS, Lee KJ, Jeong SH, Lee JH, Oh EG, Kim YK, Lee HJ (2017) Assessment of sanitary safety of the oyster (Crassostrea gigas), short neck clam (Ruditapes philippinarum) and small ark shell (Scapharca subcrenata) in Gangjin Bay, Korea. Korean J Malacol 33(4):275–283CrossRefGoogle Scholar
  50. Suzuki R, Shimodaira H (2006) Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 22(12):1540–1542CrossRefGoogle Scholar
  51. Symonds EM, Young S, Verbyla ME, McQuaig-Ulrich SM, Ross E, Jimenez JA, Harwood VJ, Breitbart M (2017) Microbial source tracking in shellfish harvesting waters in the Gulf of Nicoya, Costa Rica. Water Res 111:177–184CrossRefGoogle Scholar
  52. U.S. FDA (Food and Drug Administration) (2015) National Shellfish Sanitation Program (NSSP): guide for the control of molluscan shellfish, 2015 Revision. Available online: (accessed on 20 January 2017)
  53. Warnes GR, Bolker B, Bonebakker L, Gentleman R, Huber W, Liaw A, Lumley T, Maechler M, Magnusson A, Moeller S, Schwartz M, Venables B (2016) gplots: various R programming tools for plotting data. Available online: Accessed on 20 April 2018
  54. Whitford MF, Forster RJ, Beard CE, Gong J, Teather RM (1998) Phylogenetic analysis of rumen bacteria by comparative sequence analysis of cloned 16S rRNA genesß. Anaerobe 4(3):153–163CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Soon Bum Shin
    • 1
  • Ji Hee Lee
    • 1
  • Chi Won Lim
    • 1
  • Kwang Tae Son
    • 2
  • Sang Hyeon Jeong
    • 1
    Email author
  1. 1.South Sea Fisheries Research InstituteNational Institute of Fisheries ScienceYeosuRepublic of Korea
  2. 2.Food Safety and Processing Research DivisionNational Institute of Fisheries ScienceBusanRepublic of Korea

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