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Hagedorn, Charles; Harwood, Valerie J.; Blanch, Anicet R.

doi:10.1007/978-1-4419-9386-1_1

Cited by 13 publications

(22 citation statements)

References 25 publications

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“… 6 The field of microbial source tracking (MST) seeks to develop methods allowing for the discrimination between different animal sources of fecal pollution to improve water quality management. 7 …”

Section: Introductionmentioning

confidence: 99%

Global Distribution of Human-Associated Fecal Genetic Markers in Reference Samples from Six Continents

Mayer

Reischer

Ixenmaier

et al. 2018

Environ. Sci. Technol.

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Numerous bacterial genetic markers are available for the molecular detection of human sources of fecal pollution in environmental waters. However, widespread application is hindered by a lack of knowledge regarding geographical stability, limiting implementation to a small number of well-characterized regions. This study investigates the geographic distribution of five human-associated genetic markers (HF183/BFDrev, HF183/BacR287, BacHum-UCD, BacH, and Lachno2) in municipal wastewaters (raw and treated) from 29 urban and rural wastewater treatment plants (750–4 400 000 population equivalents) from 13 countries spanning six continents. In addition, genetic markers were tested against 280 human and nonhuman fecal samples from domesticated, agricultural and wild animal sources. Findings revealed that all genetic markers are present in consistently high concentrations in raw (median log10 7.2–8.0 marker equivalents (ME) 100 mL–1) and biologically treated wastewater samples (median log10 4.6–6.0 ME 100 mL–1) regardless of location and population. The false positive rates of the various markers in nonhuman fecal samples ranged from 5% to 47%. Results suggest that several genetic markers have considerable potential for measuring human-associated contamination in polluted environmental waters. This will be helpful in water quality monitoring, pollution modeling and health risk assessment (as demonstrated by QMRAcatch) to guide target-oriented water safety management across the globe.

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Section: Introductionmentioning

confidence: 99%

Global Distribution of Human-Associated Fecal Genetic Markers in Reference Samples from Six Continents

Mayer

Reischer

Ixenmaier

et al. 2018

Environ. Sci. Technol.

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“…1 This has led to the development of a plethora of microbial source tracking (MST) methods, many of which have been recently reviewed. 2 During recent years library-independent MST methods such as those involving genetic markers targeting host-associated and abundant populations of fecal anaerobic bacteria, e.g. from the phylum Bacteroidetes , have become increasingly prominent.…”

Section: Introductionmentioning

confidence: 99%

Performance Characteristics of qPCR Assays Targeting Human- and Ruminant-AssociatedBacteroidetesfor Microbial Source Tracking across Sixteen Countries on Six Continents

Reischer¹,

Ebdon²,

Bauer³

et al. 2013

Environ. Sci. Technol.

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Numerous quantitative PCR assays for microbial fecal source tracking (MST) have been developed and evaluated in recent years. Widespread application has been hindered by a lack of knowledge regarding the geographical stability and hence applicability of such methods beyond the regional level. This study assessed the performance of five previously reported quantitative PCR assays targeting human-, cattle-, or ruminant-associated Bacteroidetes populations on 280 human and animal fecal samples from 16 countries across six continents. The tested cattle-associated markers were shown to be ruminant-associated. The quantitative distributions of marker concentrations in target and nontarget samples proved to be essential for the assessment of assay performance and were used to establish a new metric for quantitative source-specificity. In general, this study demonstrates that stable target populations required for marker-based MST occur around the globe. Ruminant-associated marker concentrations were strongly correlated with total intestinal Bacteroidetes populations and with each other, indicating that the detected ruminant-associated populations seem to be part of the intestinal core microbiome of ruminants worldwide. Consequently tested ruminant-targeted assays appear to be suitable quantitative MST tools beyond the regional level while the targeted human-associated populations seem to be less prevalent and stable, suggesting potential for improvements in human-targeted methods.

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“…In this approach, the relative abundance for the sink is modeled: where α i is the mixture proportion for source i ∈{1… K } ( K is the number of known sources) and γ ij is the relative abundance of each source for each OTU j ∈{1… N }. The parameters are updated using the EM algorithm proposed by Shenhav et al [ 5 ]. The application of expectation-maximization with RAD source reduction is referred to as RAD-FEAST.…”

Section: Methodsologymentioning

confidence: 99%

“…Microbial source-tracking refers to statistical methods which aim to identify sources of (contaminant) microbes (referred as source in this research) in an observed microbial population, i.e., sink [ 4 , 5 ]. With a variety of massively parallel sequencing technologies, source-tracking methods have been employed by constructing microbial profiles using nucleotides, k-mers, or Operational Taxonomic Unit (OTU) counts as features.…”

Section: Introductionmentioning

confidence: 99%

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Microbial community dissimilarity for source tracking with application in forensic studies

et al. 2020

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Microbial source-tracking is a useful tool for trace evidence analysis in Forensics. Community-wide massively parallel sequencing profiles can bypass the need for satellite microbes or marker sets, which are unreliable when handling unstable samples. We propose a novel method utilizing Aitchison distance to select important suspects/sources, and then integrate it with existing algorithms in source tracking to estimate the proportions of microbial sample coming from important suspects/sources. A series of comprehensive simulation studies show that the proposed method is capable of accurate selection and therefore improves the performance of current methods such as Bayesian SourceTracker and FEAST in the presence of noise microbial sources.

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Overview

Cited by 13 publications

References 25 publications

Global Distribution of Human-Associated Fecal Genetic Markers in Reference Samples from Six Continents

Global Distribution of Human-Associated Fecal Genetic Markers in Reference Samples from Six Continents

Performance Characteristics of qPCR Assays Targeting Human- and Ruminant-AssociatedBacteroidetesfor Microbial Source Tracking across Sixteen Countries on Six Continents

Microbial community dissimilarity for source tracking with application in forensic studies

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