Determination of CrAssphage in Water Samples and Applicability for Tracking Human Faecal Pollution

Overview

Journal Microb Biotechnol

Specialties Biotechnology
Microbiology

Date 2017 Sep 20

PMID 28925595

Citations 49

Authors

Cristina Garcia-Aljaro

Elisenda Balleste

Maite Muniesa

Juan Jofre

Affiliations

Soon will be listed here.

Abstract

In recent decades, considerable effort has been devoted to finding microbial source-tracking (MST) markers that are suitable to assess the health risks of faecally polluted waters, with no universal marker reported so far. In this study, the abundance and prevalence of a crAssphage-derived DNA marker in wastewaters of human and animal origins were studied by a new qPCR assay with the ultimate aim of assessing its potential as an MST marker. crAssphage showed up to 10 GC/ml in the sewage samples of human origin, in both the total DNA and the viral DNA fraction. In wastewaters containing animal faecal remains, 39% of the samples were negative for the presence of the crAssphage sequence, while those showing positive results (41% of the samples) were at least 1 log unit lower than the samples of human origin. Noteworthy, the log values of the ratio (R) crAssphage (GC/ml)/Escherichia coli (CFU/ml) varied significantly depending on the human or animal origin (R > 1.5 for human samples and R < -1.5 for animal wastewater samples. This study opens the way for further research to explore if different specific animal variants of crAssphage exist and whether other zones of the crAssphage genome are better suited to source discrimination.

Citing Articles

Development of a quantitative metagenomic approach to establish quantitative limits and its application to viruses.

Langenfeld K, Hegarty B, Vidaurri S, Crossette E, Duhaime M, Wigginton K Nucleic Acids Res. 2025; 53(5).

PMID: 40036505 PMC: 11878531. DOI: 10.1093/nar/gkaf118.

Recruitment of complete crAss-like phage genomes reveals their presence in chicken viromes, few human-specific phages, and lack of universal detection.

Ramos-Barbero M, Gomez-Gomez C, Vique G, Sala-Comorera L, Rodriguez-Rubio L, Muniesa M ISME J. 2024; 18(1).

PMID: 39361891 PMC: 11475920. DOI: 10.1093/ismejo/wrae192.

Role of bacteriophages in shaping gut microbial community.

Mahmud M, Tamanna S, Akter S, Mazumder L, Akter S, Rakibul Hasan M Gut Microbes. 2024; 16(1):2390720.

PMID: 39167701 PMC: 11340752. DOI: 10.1080/19490976.2024.2390720.

CrAss-Like Phages: From Discovery in Human Fecal Metagenome to Application as a Microbial Source Tracking Marker.

Remesh A, Viswanathan R Food Environ Virol. 2024; 16(2):121-135.

PMID: 38413544 DOI: 10.1007/s12560-024-09584-5.

Detection and Quantification of Bacteriophages in Wastewater Samples by Culture and Molecular Methods.

Sala-Comorera L, Muniesa M, Rodriguez-Rubio L Methods Mol Biol. 2023; 2738:155-173.

PMID: 37966598 DOI: 10.1007/978-1-0716-3549-0_10.

References

Ley R, Lozupone C, Hamady M, Knight R, Gordon J . Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol. 2008; 6(10):776-88. PMC: 2664199. DOI: 10.1038/nrmicro1978. View

Tartera C, Jofre J . Bacteriophages active against Bacteroides fragilis in sewage-polluted waters. Appl Environ Microbiol. 1987; 53(7):1632-7. PMC: 203922. DOI: 10.1128/aem.53.7.1632-1637.1987. View

Payan A, Ebdon J, Taylor H, Gantzer C, Ottoson J, Papageorgiou G . Method for isolation of Bacteroides bacteriophage host strains suitable for tracking sources of fecal pollution in water. Appl Environ Microbiol. 2005; 71(9):5659-62. PMC: 1214671. DOI: 10.1128/AEM.71.9.5659-5662.2005. View

Matsuki T, Watanabe K, Fujimoto J, Miyamoto Y, Takada T, Matsumoto K . Development of 16S rRNA-gene-targeted group-specific primers for the detection and identification of predominant bacteria in human feces. Appl Environ Microbiol. 2002; 68(11):5445-51. PMC: 129894. DOI: 10.1128/AEM.68.11.5445-5451.2002. View

Ramsak A, Peterka M, Tajima K, Martin J, Wood J, Johnston M . Unravelling the genetic diversity of ruminal bacteria belonging to the CFB phylum. FEMS Microbiol Ecol. 2000; 33(1):69-79. DOI: 10.1111/j.1574-6941.2000.tb00728.x. View

Dutilh B, Cassman N, McNair K, Sanchez S, Silva G, Boling L . A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat Commun. 2014; 5:4498. PMC: 4111155. DOI: 10.1038/ncomms5498. View

Ishikawa E, Matsuki T, Kubota H, Makino H, Sakai T, Oishi K . Ethnic diversity of gut microbiota: species characterization of Bacteroides fragilis group and genus Bifidobacterium in healthy Belgian adults, and comparison with data from Japanese subjects. J Biosci Bioeng. 2013; 116(2):265-70. DOI: 10.1016/j.jbiosc.2013.02.010. View

Muniesa M, Lucena F, Blanch A, Payan A, Jofre J . Use of abundance ratios of somatic coliphages and bacteriophages of Bacteroides thetaiotaomicron GA17 for microbial source identification. Water Res. 2012; 46(19):6410-8. DOI: 10.1016/j.watres.2012.09.015. View

Gill S, Pop M, DeBoy R, Eckburg P, Turnbaugh P, Samuel B . Metagenomic analysis of the human distal gut microbiome. Science. 2006; 312(5778):1355-9. PMC: 3027896. DOI: 10.1126/science.1124234. View

10.

Reischer G, Ebdon J, Bauer J, Schuster N, Ahmed W, Astrom J . Performance characteristics of qPCR assays targeting human- and ruminant-associated bacteroidetes for microbial source tracking across sixteen countries on six continents. Environ Sci Technol. 2013; 47(15):8548-56. PMC: 3737603. DOI: 10.1021/es304367t. View

11.

Bernhard A, Field K . 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. 2000; 66(4):1587-94. PMC: 92027. DOI: 10.1128/AEM.66.4.1587-1594.2000. View

12.

Ogilvie L, Caplin J, Dedi C, Diston D, Cheek E, Bowler L . Comparative (meta)genomic analysis and ecological profiling of human gut-specific bacteriophage φB124-14. PLoS One. 2012; 7(4):e35053. PMC: 3338817. DOI: 10.1371/journal.pone.0035053. View

13.

Newton R, Vandewalle J, Borchardt M, Gorelick M, McLellan S . Lachnospiraceae and Bacteroidales alternative fecal indicators reveal chronic human sewage contamination in an urban harbor. Appl Environ Microbiol. 2011; 77(19):6972-81. PMC: 3187108. DOI: 10.1128/AEM.05480-11. View

14.

da Silva A, Le Saux J, Parnaudeau S, Pommepuy M, Elimelech M, Le Guyader F . Evaluation of removal of noroviruses during wastewater treatment, using real-time reverse transcription-PCR: different behaviors of genogroups I and II. Appl Environ Microbiol. 2007; 73(24):7891-7. PMC: 2168159. DOI: 10.1128/AEM.01428-07. View

15.

Gomez-Donate M, Payan A, Cortes I, Blanch A, Lucena F, Jofre J . Isolation of bacteriophage host strains of Bacteroides species suitable for tracking sources of animal faecal pollution in water. Environ Microbiol. 2011; 13(6):1622-31. DOI: 10.1111/j.1462-2920.2011.02474.x. View

16.

Geldreich E, KENNER B . Concepts of fecal streptococci in stream pollution. J Water Pollut Control Fed. 1969; 41(8):Suppl:R336+. View

17.

Gomez-Donate M, Balleste E, Muniesa M, Blanch A . New molecular quantitative PCR assay for detection of host-specific Bifidobacteriaceae suitable for microbial source tracking. Appl Environ Microbiol. 2012; 78(16):5788-95. PMC: 3406134. DOI: 10.1128/AEM.00895-12. View

18.

Blanch A, Belanche-Munoz L, Bonjoch X, Ebdon J, Gantzer C, Lucena F . Tracking the origin of faecal pollution in surface water: an ongoing project within the European Union research programme. J Water Health. 2005; 2(4):249-60. View

19.

Haugland R, Varma M, Sivaganesan M, Kelty C, Peed L, Shanks O . 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. Syst Appl Microbiol. 2010; 33(6):348-57. DOI: 10.1016/j.syapm.2010.06.001. View

20.

McMinn B, Korajkic A, Ashbolt N . Evaluation of Bacteroides fragilis GB-124 bacteriophages as novel human-associated faecal indicators in the United States. Lett Appl Microbiol. 2014; 59(1):115-21. DOI: 10.1111/lam.12252. View