An Overview of Microbial Source Tracking Using Host-Specific Genetic Markers to Identify Origins of Fecal Contamination in Different Water Environments

Paruch, Lisa; Paruch, Adam M.

doi:10.3390/w14111809

Cited by 11 publications

(3 citation statements)

References 102 publications

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“…It has been demonstrated that PMMoV correlates well with other human markers such as Bacteriodes HF183 and PyV, suggesting that it is associated with human waste [173]. PM-MoV has been found at high concentrations in domestic raw and treated fecal wastewater and also in wastewater-polluted environments [54].…”

Section: Human Waste Associationmentioning

confidence: 99%

Application of the Human Viral Surrogate Pepper Mild Mottle Virus for Wastewater Fecal Pollution Management

Maniah

Nour

Hanif

et al. 2022

Water

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Global water scarcity has led to significant dependence on reclaimed or recycled water for potable uses. Effluents arising from human and animal gut microbiomes highly influence water quality. Wastewater pollution is, therefore, frequently monitored using bacterial indicators (BI). However, threats to public health arise from the frequent incidence of wastewater-mediated viral infections–undetected by BI. Moreover, the enteric viromes contaminating wastewater are characterized by high abundance, genetic diversity and persistence in various water environments. Furthermore, humans usually suffer a minimum of a single acute diarrheal episode over their lifetime arising from extraneously acquired enteric microbiomes. A wide range of management methods are employed—in particular, microbial source tracking (MST) approaches to confront infections arising from exposure to contaminated wastewater. This review elaborates the viral contamination of treated wastewater and associated public health issues. Latterly, we discuss the various management strategies of wastewater pollution using conventional fecal indicators, viral indicators and human viral surrogates, with particular interest in the pepper mild mottle virus (PMMoV). Globally, PMMoV has been detected in rivers, aquifers, irrigation systems, and coastal and marine waters at high prevalence rates and concentrations greater than 105 genome copies per liter (gc/L). PMMoV was also found in almost all untreated wastewater environments. PMMoV concentrations in wastewater vary from 103 to 107 gc/L. These values are more than the maximum recorded viral indicator concentrations in wastewater for other proposed indicators. Limited variability in the daily concentrations of PMMoV in fecal wastewater has been studied, with an estimated average concentration of 105 gc/L with insignificant seasonal variability. The information summarized in this article offers fundamental knowledge for decision making in terms of defining the suitability criteria of candidate fecal indicators, risk assessment application and efficient wastewater management.

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Section: Human Waste Associationmentioning

confidence: 99%

Application of the Human Viral Surrogate Pepper Mild Mottle Virus for Wastewater Fecal Pollution Management

Maniah

Nour

Hanif

et al. 2022

Water

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“…More recently, quantitative PCR (qPCR) has been widely used for MST because it is culture-independent. Numerous qPCR markers have been designed, including HF183 and BacHum, which detect human-specific Bacteroides [14,15], Pig2Bac, which detects pig-specific Bacteroidales [16], and GFD, which detects bird-specific Helicobacter spp [17].…”

Section: Introductionmentioning

confidence: 99%

A comprehensive database of human and livestock fecal microbiome for community-wide microbial source tracking: a case study in South Korea

Song,

Unno

2024

Appl Biol Chem

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Fecal waste from livestock farms contains numerous pathogens, and improperly managed waste may flow into water bodies, causing water-borne diseases. Along with the popularization of high-throughput technologies, community-wide microbial source-tracking methods have been actively developed in recent years. This study aimed to construct a comprehensive fecal microbiome database for community-wide microbial source tracking and apply the database to identify contamination sources in the Miho River, South Korea. Total DNA was extracted from the samples, and the 16 S rRNA gene was amplified to characterize the microbial communities. The fecal microbiome database was validated by developing machine-learning models that predict host species based on microbial community structure. All machine learning models developed in this study showed high performance, where the area under the receiver operating characteristic curve was approximately 1. Community-wide microbial source tracking results showed a higher contribution of fecal sources to the contamination of the main streams after heavy rain. In contrast, the contribution of fecal sources remained comparatively stable in tributaries after rainfall. Considering that farms are more concentrated upstream of tributaries compared to the main streams, this result implies that the pathway for manure contaminants to reach the main streams could be groundwater rather than surface runoff. Systematic monitoring of the water quality, which encompasses river water and groundwater, should be conducted in the future. In addition, continuous efforts to identify and plug abandoned wells are necessary to prevent further water contamination.

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“…Historically, MST systems have relied on fecal coliforms and other indicator bacteria, such as E. coli, to follow terrestrial contamination through aquatic and marine systems, as well as determine water quality/safety [13,15]. However, these techniques are labor-intensive and have many limitations in their ability to discern point sources or the interplay between multiple sources, so the use of genetic markers and genetic libraries have been adopted as being more precise in measuring point sources as molecular methodologies continue to advance [16][17][18][19]. With advances in technology, the ability to track multiple taxa in microbial communities through systems has become possible [20][21][22][23].…”

Section: Introductionmentioning

confidence: 99%

Comparative Microbial Community Analysis of Fur Seals and Aquaculture Salmon Gut Microbiomes in Tasmania

D’Agnese

McLaughlin²,

Lea

et al. 2023

Oceans

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In Tasmania, Australian fur seals (Arctocephalus pusillus doriferus) regularly interact with Atlantic salmon (Salmo salmar L.) aquaculture lease operations and opportunistically consume fish. The microbial communities of seals and aquaculture salmon were analyzed for potential indicators of microbial sharing and to determine the potential effects of interactions on wild seal microbiome composition. The high-throughput sequencing of the V1–V3 region of the 16S rRNA genes from the gut microbial communities of 221 fur seals was performed: 41 males caught at farms, 50 adult scats from haul-outs near farms, 24 necropsied seals, and controls from Bass Strait breeding colonies, encompassing 56 adult scats and 50 pup swabs. QIIME2 and R Studio were used for analysis. Foraging at or near salmon farms significantly shifted seal microbiome biodiversity. Taxonomic analysis showed a greater divergence in Bacteroidota representatives in male seals captured at farms compared to all other groups. Pathogens were identified that could be monitoring targets. Potential indicator amplicon sequence variants were found across a variety of taxa and could be used as minimally invasive indicators for interactions at this interface. The diversity and taxonomic shifts in the microbial communities of seals indicate a need to further study this interface for broader ecological implications.

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An Overview of Microbial Source Tracking Using Host-Specific Genetic Markers to Identify Origins of Fecal Contamination in Different Water Environments

Cited by 11 publications

References 102 publications

Application of the Human Viral Surrogate Pepper Mild Mottle Virus for Wastewater Fecal Pollution Management

Application of the Human Viral Surrogate Pepper Mild Mottle Virus for Wastewater Fecal Pollution Management

A comprehensive database of human and livestock fecal microbiome for community-wide microbial source tracking: a case study in South Korea

Comparative Microbial Community Analysis of Fur Seals and Aquaculture Salmon Gut Microbiomes in Tasmania

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