Have genetic targets for faecal pollution diagnostics and source tracking revolutionized water quality analysis yet?

Demeter, Katalin; Linke, Rita; Reischer, Georg H.; Mayer, René; Vierheilig, Julia; Kolm, Claudia; Stevenson, Margaret E.; Derx, Julia; Kirschner, Alexander K. T.; Sommer, Regina; Shanks, Orin C.; Blanch, Anicet R.; Rose, Joan B.; Ahmed, Warish; Farnleitner, Andreas H.

doi:10.1093/femsre/fuad028

Cited by 18 publications

(6 citation statements)

References 270 publications

(344 reference statements)

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“…The collective findings underscore the significance of MST in pinpointing the specific hosts responsible for potential impacts on river water quality. This importance of MST has also been emphasized in previous studies [44][45][46][47].…”

Section: Plos Watersupporting

confidence: 55%

Performance evaluation and application of host-specific Bacteroidales and mitochondrial DNA markers to identify sources of fecal contamination in river water in Japan

Malla,

Yamamoto,

Furukawa

et al. 2024

PLOS Water

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Microbial source tracking (MST) using host-specific Bacteroidales and mitochondrial DNA (mtDNA) markers is an efficient tool to identify the sources of fecal contamination in environmental water. This study evaluated and updated the previously reported performances of seven host-specific Bacteroidales markers (three human-, two cattle-, and two pig-specific). Additionally, the performance of a cattle-specific Bovine mtDNA and a pig-specific Swine mtDNA marker were evaluated and then applied to MST of river water samples collected in Yamanashi Prefecture, Japan. We collected 48 fecal-source samples, including raw sewage, secondary-treated sewage, an effluent of a domestic wastewater treatment tank, pig feces, pig wastewater, and cattle feces, which were quantitatively analyzed using host-specific Bacteroidales and mtDNA markers. BacHum and gyrB markers (human-specific), BacR and Bovine mtDNA markers (cattle-specific), and Pig2Bac and Swine mtDNA markers (pig-specific) were judged the best-performing markers. Then, these selected markers were applied to MST to identify the sources of fecal contamination in 59 river water samples collected at 21 sites. Of them, 20 (95%), 21 (100%), and 16 (76%) sites were positive for at least one human, cattle, and pig marker, respectively, indicating the need for immediate action and monitoring to control fecal pollution.

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Section: Plos Watersupporting

confidence: 55%

Performance evaluation and application of host-specific Bacteroidales and mitochondrial DNA markers to identify sources of fecal contamination in river water in Japan

Malla,

Yamamoto,

Furukawa

et al. 2024

PLOS Water

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“…Box 4. Use of Microbial Source Tracking Genetic Targets for Water Quality [13] The impact on faecal pollution analysis in health-related water quality research by nucleic acid-based methods, such as PCR analysis and sequencing, was assessed by rigorous literature analysis. A wide range of application areas and study designs was identified, since the first application more than 30 years ago (>1,000 publications).…”

Section: Use Of Innovative Molecular Methodsmentioning

confidence: 99%

Global microbial water quality data and predictive analytics: Key to health and meeting SDG 6

Rose,

Hofstra,

Hollmann

et al. 2023

PLOS Water

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Microbial water quality is an integral to water security and is directly linked to human health, food safety, and ecosystem services. However, specifically pathogen data and even faecal indicator data (e.g., E. coli), are sparse and scattered, and their availability in different water bodies (e.g., groundwater) and in different socio-economic contexts (e.g., low- and middle-income countries) are inequitable. There is an urgent need to assess and collate microbial data across the world to evaluate the global state of ambient water quality, water treatment, and health risk, as time is running out to meet Sustainable Development Goal (SDG) 6 by 2030. The overall goal of this paper is to illustrate the need and advocate for building a robust and useful microbial water quality database and consortium worldwide that will help achieve SDG 6. We summarize available data and existing databases on microbial water quality, discuss methods for producing new data on microbial water quality, and identify models and analytical tools that utilize microbial data to support decision making. This review identified global datasets (7 databases), and regional datasets for Africa (3 databases), Australia/New Zealand (6 databases), Asia (3 databases), Europe (7 databases), North America (12 databases) and South America (1 database). Data are missing for low- and middle-income countries. Increased laboratory capacity (due to COVID-19 pandemic) and molecular tools can identify potential pollution sources and monitor directly for pathogens. Models and analytical tools can support microbial water quality assessment by making geospatial and temporal inferences where data are lacking. A genomics, information technology (IT), and data revolution is upon us and presents unprecedented opportunities to develop software and devices for real-time logging, automated analysis, standardization, and modelling of microbial data to strengthen knowledge of global water quality. These opportunities should be leveraged for achieving SDG 6 around the world.

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“…This fact can be partly explained by the association of Bacteroides with the diet of urban populations [ 14 ]. Due to the high prevalence of crAssphages in the human intestine, it is currently proposed to monitor their levels in treated wastewater to detect contamination with human feces [ 15 , 16 , 17 ].…”

Section: Introductionmentioning

confidence: 99%

Genome Analysis of Epsilon CrAss-like Phages

Babkin,

Tikunov,

Baykov

et al. 2024

Viruses

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CrAss-like phages play an important role in maintaining ecological balance in the human intestinal microbiome. However, their genetic diversity and lifestyle are still insufficiently studied. In this study, a novel CrAssE-Sib phage genome belonging to the epsilon crAss-like phage genomes was found. Comparative analysis indicated that epsilon crAss-like phages are divided into two putative genera, which were proposed to be named Epsilonunovirus and Epsilonduovirus; CrAssE-Sib belongs to the former. The crAssE-Sib genome contains a diversity-generating retroelement (DGR) cassette with all essential elements, including the reverse transcriptase (RT) and receptor binding protein (RBP) genes. However, this RT contains the GxxxSP motif in its fourth domain instead of the usual GxxxSQ motif found in all known phage and bacterial DGRs. RBP encoded by CrAssE-Sib and other Epsilonunoviruses has an unusual structure, and no similar phage proteins were found. In addition, crAssE-Sib and other Epsilonunoviruses encode conserved prophage repressor and anti-repressors that could be involved in lysogenic-to-lytic cycle switches. Notably, DNA primase sequences of epsilon crAss-like phages are not included in the monophyletic group formed by the DNA primases of all other crAss-like phages. Therefore, epsilon crAss-like phage substantially differ from other crAss-like phages, indicating the need to classify these phages into a separate family.

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Have genetic targets for faecal pollution diagnostics and source tracking revolutionized water quality analysis yet?

Cited by 18 publications

References 270 publications

Performance evaluation and application of host-specific Bacteroidales and mitochondrial DNA markers to identify sources of fecal contamination in river water in Japan

Performance evaluation and application of host-specific Bacteroidales and mitochondrial DNA markers to identify sources of fecal contamination in river water in Japan

Global microbial water quality data and predictive analytics: Key to health and meeting SDG 6

Genome Analysis of Epsilon CrAss-like Phages

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