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Alexandria B. Boehm - One of the best experts on this subject based on the ideXlab platform.
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New Performance Metrics for Quantitative Polymerase Chain Reaction-Based Microbial Source Tracking Methods
Environmental Science & Technology Letters, 2013Co-Authors: Dan Wang, Hyatt C. Green, Orin C. Shanks, Alexandria B. BoehmAbstract:The ability to select the best quantitative Microbial Source Tracking method for a particular application is paramount. Binary sensitivity and specificity metrics are not adequate to describe the performance of the quantitative methods because the estimates depend on the amount of material tested and the limit of detection. We introduce a new framework for comparing the performance of quantitative fecal Source identification methods.
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Recommendations following a multi-laboratory comparison of Microbial Source Tracking methods.
Water research, 2013Co-Authors: Jill R. Stewart, Orin C. Shanks, Alexandria B. Boehm, Kelly D. Goodwin, John F. Griffith, Rachel T. Noble, Eric A. Dubinsky, Theng Theng Fong, Kannappan Vijayavel, Stephen B. WeisbergAbstract:Microbial Source Tracking (MST) methods were evaluated in the Source Identification Protocol Project (SIPP), in which 27 laboratories compared methods to identify host Sources of fecal pollution from blinded water samples containing either one or two different fecal types collected from California. This paper details lessons learned from the SIPP study and makes recommendations to further advance the field of MST. Overall, results from the SIPP study demonstrated that methods are available that can correctly identify whether particular host Sources including humans, cows and birds have contributed to contamination in a body of water. However, differences between laboratory protocols and data processing affected results and complicated interpretation of MST method performance in some cases. This was an issue particularly for samples that tested positive (non-zero Ct values) but below the limits of quantification or detection of a PCR assay. Although false positives were observed, such samples in the SIPP study often contained the fecal pollution Source that was being targeted, i.e., the samples were true positives. Given these results, and the fact that MST often requires detection of targets present in low concentrations, we propose that such samples be reported and identified in a unique category to facilitate data analysis and method comparisons. Important data can be lost when such samples are simply reported as positive or negative. Actionable thresholds were not derived in the SIPP study due to limitations that included geographic scope, age of samples, and difficulties interpreting low concentrations of target in environmental samples. Nevertheless, the results of the study support the use of MST for water management, especially to prioritize impaired waters in need of remediation. Future integration of MST data into quantitative Microbial risk assessments and other models could allow managers to more efficiently protect public health based on site conditions.
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Evaluation of the repeatability and reproducibility of a suite of qPCR-based Microbial Source Tracking methods
Water research, 2013Co-Authors: Darcy L. Ebentier, Yiping Cao, Alexandria B. Boehm, Kaitlyn T. Hanley, Brian D. Badgley, Jared S. Ervin, Kelly D. Goodwin, Michèle Gourmelon, John F. Griffith, Patricia A. HoldenAbstract:Many PCR-based methods for Microbial Source Tracking (MST) have been developed and validated within individual research laboratories. Inter-laboratory validation of these methods, however, has been minimal, and the effects of protocol standardization regimes
Michael J. Sadowsky - One of the best experts on this subject based on the ideXlab platform.
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Microbial Source Tracking using metagenomics and other new technologies
Journal of Microbiology, 2021Co-Authors: Shahbaz Raza, Michael J. Sadowsky, Jungman Kim, Tatsuya UnnoAbstract:The environment is under siege from a variety of pollution Sources. Fecal pollution is especially harmful as it disperses pathogenic bacteria into waterways. Unraveling origins of mixed Sources of fecal bacteria is difficult and Microbial Source Tracking (MST) in complex environments is still a daunting task. Despite the challenges, the need for answers far outweighs the difficulties experienced. Advancements in qPCR and next generation sequencing (NGS) technologies have shifted the traditional culture-based MST approaches towards culture independent technologies, where community-based MST is becoming a method of choice. Metagenomic tools may be useful to overcome some of the limitations of community-based MST methods as they can give deep insight into identifying host specific fecal markers and their association with different environments. Adoption of machine learning (ML) algorithms, along with the metagenomic based MST approaches, will also provide a statistically robust and automated platform. To compliment that, ML-based approaches provide accurate optimization of reSources. With the successful application of ML based models in disease prediction, outbreak investigation and medicine prescription, it would be possible that these methods would serve as a better surrogate of traditional MST approaches in future.
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Influence of Library Composition on SourceTracker Predictions for Community-Based Microbial Source Tracking.
Environmental science & technology, 2018Co-Authors: Clairessa M. Brown, P. Mathai, Tina Loesekann, Christopher Staley, Michael J. SadowskyAbstract:Community-based Microbial Source Tracking (MST) utilizes high-throughput DNA sequencing to profile and compare the Microbial communities in different fecal Sources and environmental samples. Source...
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the evolving science of Microbial Source Tracking
2016Co-Authors: Valerie J Harwood, Charles Hagedorn, Michael J. SadowskyAbstract:Section X of the Manual of Environmental Microbiology addresses the burgeoning area of Microbial Source Tracking (MST), a collection of methodologies and approaches whose aim is to determine the dominant Source(s) of fecal contamination of water bodies. Many health- and management-related areas can benefit from MST analyses, including total maximum daily load (TMDL) determinations, beach and water reSource management, quantitative Microbial risk assessment (QMRA), and epidemiology. This chapter provides a brief overview of the rationale for and theory of MST, followed by chapters that detail MST methodologies and practice. This chapter also suggests future directions for a field that has changed considerably over the last two decades - as it has evolved from an emphasis on building large databases of bacterial phenotypes or genotypes toward the use of culture-independent methods that focus on single genetic targets or Microbial community structure. The field is in the process of adopting high-throughput DNA sequencing methods that allow consideration of genomic and metagenomic data to identify host-associated microorganisms and/or patterns in communities that may contribute to accurate identification of fecal pollution Sources in the environment.
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Manual of Environmental Microbiology - The Evolving Science of Microbial Source Tracking
Manual of Environmental Microbiology, 2015Co-Authors: Valerie J Harwood, Charles Hagedorn, Michael J. SadowskyAbstract:Section X of the Manual of Environmental Microbiology addresses the burgeoning area of Microbial Source Tracking (MST), a collection of methodologies and approaches whose aim is to determine the dominant Source(s) of fecal contamination of water bodies. Many health- and management-related areas can benefit from MST analyses, including total maximum daily load (TMDL) determinations, beach and water reSource management, quantitative Microbial risk assessment (QMRA), and epidemiology. This chapter provides a brief overview of the rationale for and theory of MST, followed by chapters that detail MST methodologies and practice. This chapter also suggests future directions for a field that has changed considerably over the last two decades - as it has evolved from an emphasis on building large databases of bacterial phenotypes or genotypes toward the use of culture-independent methods that focus on single genetic targets or Microbial community structure. The field is in the process of adopting high-throughput DNA sequencing methods that allow consideration of genomic and metagenomic data to identify host-associated microorganisms and/or patterns in communities that may contribute to accurate identification of fecal pollution Sources in the environment.
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Microbial Source Tracking - The Future of Microbial Source Tracking Studies
Microbial Source Tracking, 2014Co-Authors: Michael J. Sadowsky, Douglas R. Call, Jorge W. Santo DomingoAbstract:This chapter summarizes some of the challenges that people interested in Source identification are currently facing, provides information on the Microbial ecology of the gut and potential microorganisms to use in Source-Tracking studies, discusses research tools that will likely improve marker discovery, and offers some suggestions on the future needs for determining Sources of microorganisms impacting waterways. There is considerable debate as to the choice of organism(s) to be used as an indicator of fecal contamination of waterways and for Microbial Source Tracking (MST) studies. There are four basic types of digestive systems in animals: simple stomach or monogastric (man, pig), equine-modified simple stomach (horse), ruminant or polygastric (sheep, cow, goat, deer), and avian (chicken, turkey). Genome sequence analyses, as well as the emergence of other ‘’omic ‘’ based technologies including metagenomics, proteomics, and transcriptomics, will enhance one’s understanding of the molecular and biochemical diversity of the animal GI tract. While genome sequence information for protozoa is not as wide ranging as that for bacteria and viruses, sequence analyses have shown strong host dependence due to the lack of biosynthetic pathways. The study of the gut metagenome has clear implications to human health. In this study, sequencing analysis of cloned transcripts showed the presence of transcripts linked to sulfur, carbon, and nitrogen biogeochemical processes. Results from the Microbial characterization of animal intestinal tracts have suggested that anatomical and physiological differences found in different digestive systems may lead to conditions that affect the structure of gut Microbial communities.
Valerie J Harwood - One of the best experts on this subject based on the ideXlab platform.
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Environmental Microbial Forensics - Toward Forensic Uses of Microbial Source Tracking
Microbiology spectrum, 2018Co-Authors: Christopher M Teaf, David Flores, Michele M Garber, Valerie J HarwoodAbstract:The science of Microbial Source Tracking has allowed researchers and watershed managers to go beyond general indicators of fecal pollution in water such as coliforms and enterococci, and to move toward an understanding of specific contributors to water quality issues. The premise of Microbial Source Tracking is that characteristics of microorganisms that are strongly associated with particular host species can be used to trace fecal pollution to particular animal species (including humans) or groups, e.g., ruminants or birds. Microbial Source Tracking methods are practiced largely in the realm of research, and none are approved for regulatory uses on a federal level. Their application in the conventional sense of forensics, i.e., to investigate a crime, has been limited, but as some of these methods become standardized and recognized in a regulatory context, they will doubtless play a larger role in applications such as total maximum daily load assessment, investigations of sewage spills, and contamination from agricultural practices.
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toward forensic uses of Microbial Source Tracking
Microbiology spectrum, 2018Co-Authors: Christopher M Teaf, David Flores, Michele M Garber, Valerie J HarwoodAbstract:The science of Microbial Source Tracking has allowed researchers and watershed managers to go beyond general indicators of fecal pollution in water such as coliforms and enterococci, and to move toward an understanding of specific contributors to water quality issues. The premise of Microbial Source Tracking is that characteristics of microorganisms that are strongly associated with particular host species can be used to trace fecal pollution to particular animal species (including humans) or groups, e.g., ruminants or birds. Microbial Source Tracking methods are practiced largely in the realm of research, and none are approved for regulatory uses on a federal level. Their application in the conventional sense of forensics, i.e., to investigate a crime, has been limited, but as some of these methods become standardized and recognized in a regulatory context, they will doubtless play a larger role in applications such as total maximum daily load assessment, investigations of sewage spills, and contamination from agricultural practices.
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the evolving science of Microbial Source Tracking
2016Co-Authors: Valerie J Harwood, Charles Hagedorn, Michael J. SadowskyAbstract:Section X of the Manual of Environmental Microbiology addresses the burgeoning area of Microbial Source Tracking (MST), a collection of methodologies and approaches whose aim is to determine the dominant Source(s) of fecal contamination of water bodies. Many health- and management-related areas can benefit from MST analyses, including total maximum daily load (TMDL) determinations, beach and water reSource management, quantitative Microbial risk assessment (QMRA), and epidemiology. This chapter provides a brief overview of the rationale for and theory of MST, followed by chapters that detail MST methodologies and practice. This chapter also suggests future directions for a field that has changed considerably over the last two decades - as it has evolved from an emphasis on building large databases of bacterial phenotypes or genotypes toward the use of culture-independent methods that focus on single genetic targets or Microbial community structure. The field is in the process of adopting high-throughput DNA sequencing methods that allow consideration of genomic and metagenomic data to identify host-associated microorganisms and/or patterns in communities that may contribute to accurate identification of fecal pollution Sources in the environment.
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Manual of Environmental Microbiology - The Evolving Science of Microbial Source Tracking
Manual of Environmental Microbiology, 2015Co-Authors: Valerie J Harwood, Charles Hagedorn, Michael J. SadowskyAbstract:Section X of the Manual of Environmental Microbiology addresses the burgeoning area of Microbial Source Tracking (MST), a collection of methodologies and approaches whose aim is to determine the dominant Source(s) of fecal contamination of water bodies. Many health- and management-related areas can benefit from MST analyses, including total maximum daily load (TMDL) determinations, beach and water reSource management, quantitative Microbial risk assessment (QMRA), and epidemiology. This chapter provides a brief overview of the rationale for and theory of MST, followed by chapters that detail MST methodologies and practice. This chapter also suggests future directions for a field that has changed considerably over the last two decades - as it has evolved from an emphasis on building large databases of bacterial phenotypes or genotypes toward the use of culture-independent methods that focus on single genetic targets or Microbial community structure. The field is in the process of adopting high-throughput DNA sequencing methods that allow consideration of genomic and metagenomic data to identify host-associated microorganisms and/or patterns in communities that may contribute to accurate identification of fecal pollution Sources in the environment.
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Assumptions and limitations associated with Microbial Source Tracking methods.
Microbial Source Tracking, 2014Co-Authors: Valerie J HarwoodAbstract:This chapter provides a critical evaluation of Microbial Source Tracking (MST) methods, including an analysis of the current expectations of MST tools. The ultimate goal of all Microbial Source Tracking studies is to link fecal contamination with its host Source, whether contamination is a concern in water or food. Characteristics considered desirable for an “ideal” MST tool are presented in the chapter, followed by a discussion of the assumptions made about tools currently used, research studies that have addressed these assumptions, and known limitations of the tools. Host specificity of commensal and mutualistic microflora of the gastrointestinal (GI) tract may, however, be the exception rather than the rule, particularly among the culturable fraction of the inhabitants of the GI tract. MST methods as related to food are also concerned with direct detection and Tracking of the Source of food-borne pathogens, some of which are zoonotic and are easily transmitted from animal hosts to humans. An MST tool that is adopted for beach water quality monitoring, total maximum daily load (TMDL) assessment, and food quality programs throughout the United States should meet the assumptions listed in the chapter. Several studies on the distribution of Escherichia coli species/pattern/markers (SPMs) in primary versus secondary habitats noted distinct differences in the populations.
Hor-gil Hur - One of the best experts on this subject based on the ideXlab platform.
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integrated online system for a pyrosequencing based Microbial Source Tracking method that targets bacteroidetes 16s rdna
Environmental Science & Technology, 2012Co-Authors: Tatsuya Unno, Michael J. Sadowsky, Jeonghwan Jang, Yae Seul Suh, Hor-gil HurAbstract:Genotypic Microbial Source Tracking (MST) methods are now routinely used to determine Sources of fecal contamination impacting waterways. We previously reported the development of a pyrosequencing-based MST method that assigns contamination Sources based on shared operational taxonomic units (OTUs) between fecal and environmental bacterial communities. Despite decreasing sequencing costs, pyrosequencing-based MST approaches are not used in routine water quality monitoring studies due in large part to difficulties in handling massive data sets and difficulties in determining Sources of fecal contamination. In the studies presented here we describe the development of an online MST tool, PyroMiST ( http://env1.gist.ac.kr/∼aeml/MST.html) that uses total bacterial or Bacteroidetes 16S rDNA pyrosequencing reads to determine fecal contamination of waterways. The program cd-hit was used for OTU assignment and a Perl script was used to calculate the number of shared OTUs. The analyses require only a small number of pyrosequencing reads from environmental samples. Our results indicate that PyroMiST provides a user-friendly web interface for pyrosequence data that significantly reduces analysis time required to determine potential Sources of fecal contamination in the environment.
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f rna coliphage based Microbial Source Tracking in water reSources of south korea
Science of The Total Environment, 2011Co-Authors: Jung Eun Lee, Heetae Lee, Youhee Cho, Hor-gil HurAbstract:We previously demonstrated that genotyping followed by proper statistical analyses of F plus (F+)-specific RNA coliphages can effectively represent fecal origins of either humans or animals. Here, we performed Microbial Source Tracking (MST) using F+ RNA coliphages as a target MST microorganism for identifying fecal Sources contaminating ground and surface water in metropolitan Seoul and Gyeonggi Province in South Korea. In total, 71 groundwater and 5 surface water samples were collected and screened for the presence of F+ RNA coliphages. More than 124 F+ coliphages were isolated from six groundwater and five surface water samples by the single agar layer method. F+ RNA coliphages were predominant in both waters (100% and 91%, respectively). Genotyping of 118 F+ RNA coliphages revealed that most (51/60) of the groundwater F+ RNA coliphages belonged to group I, whereas both groups I (25/58) and IV (31/58) were predominantly observed in surface water. Further comparison of phage isolates from human and animal (pig, cow, goose, and chicken) fecal Sources using nucleic acid sequencing and principal coordinate analysis showed that groundwater samples formed clusters associated with cow feces, whereas surface waters formed clusters related to chicken and human feces. These results indicate the potential of the F+ RNA coliphage-based MST for identifying fecal contamination Sources, which may be further exploited and validated in different geographical regions of the world.
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Molecular Characterization of Bacteriophages for Microbial Source Tracking in Korea
Applied and environmental microbiology, 2009Co-Authors: Jung Eun Lee, Sunghee Lee, Mi Young Lim, Sei Yoon Kim, Heetae Lee, Hor-gil HurAbstract:We investigated coliphages from various fecal Sources, including humans and animals, for Microbial Source Tracking in South Korea. Both somatic and F + -specific coliphages were isolated from 43 fecal samples from farms, wild animal habitats, and human wastewater plants. Somatic coliphages were more prevalent and abundant than F + coliphages in all of the tested fecal samples. We further characterized 311 F + coliphage isolates using RNase sensitivity assays, PCR and reverse transcription-PCR, and nucleic acid sequencing. Phylogenetic analyses were performed based on the partial nucleic acid sequences of 311 F + coliphages from various Sources. F + RNA coliphages were most prevalent among geese (95%) and were least prevalent in cows (5%). Among the genogroups of F + RNA coliphages, most F + coliphages isolated from animal fecal Sources belonged to either group I or group IV, and most from human wastewater Sources were in group II or III. Some of the group I coliphages were present in both human and animal Source samples. F + RNA coliphages isolated from various Sources were divided into two main clusters. All F + RNA coliphages isolated from human wastewater were grouped with Qβ-like phages, while phages isolated from most animal Sources were grouped with MS2-like phages. UniFrac significance statistical analyses revealed significant differences between human and animal bacteriophages. In the principal coordinate analysis (PCoA), F + RNA coliphages isolated from human waste were distinctively separate from those isolated from other animal Sources. However, F + DNA coliphages were not significantly different or separate in the PCoA. These results demonstrate that proper analysis of F + RNA coliphages can effectively distinguish fecal Sources.
Kwanrawee Sirikanchana - One of the best experts on this subject based on the ideXlab platform.
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Effect of Quantitative Polymerase Chain Reaction Data Analysis Using Sample Amplification Efficiency on Microbial Source Tracking Assay Performance and Source Attribution.
Environmental science & technology, 2020Co-Authors: Akechai Kongprajug, Natcha Chyerochana, Skorn Mongkolsuk, Kwanrawee SirikanchanaAbstract:The widely used Microbial Source Tracking (MST) technique, quantitative polymerase chain reaction (qPCR), quantifies host-specific gene abundance in polluted water to identify and prioritize contam...
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CrAssphage as a Potential Human Sewage Marker for Microbial Source Tracking in Southeast Asia
Environmental Science & Technology Letters, 2019Co-Authors: Akechai Kongprajug, Skorn Mongkolsuk, Kwanrawee SirikanchanaAbstract:The human gut bacteriophage crAssphage has been proposed as a human-specific Microbial Source Tracking (MST) marker for impacted water bodies. However, its global use as a human-specific MST marker requires validation in a tropical region. In this study, a crAssphage qPCR marker (CPQ_056) was detected in 21 sewage samples in Thailand with 100% sensitivity. The marker was detected in sewage from hospitals and residential buildings at 5.28–7.38 log10 copies/100 mL and in four influent and four effluent samples of municipal wastewater treatment plants at 4.23–6.19 and 3.78–4.89 log10 copies/100 mL, respectively. Furthermore, a 99.2% specificity (n = 127) was observed using feces from swine, cattle, chicken, duck, goat, sheep, buffalo, and fish, with cross-detection only occurring for one composite swine sample. The crAssphage marker was present in 56.25% (27 out of 48) of river samples at 3.20–7.29 log10 copies/100 mL. The concentrations of the crAssphage marker and a prevalidated human-specific Bacteroidale...
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CrAssphage as a Potential Human Sewage Marker for Microbial Source Tracking in Southeast Asia
2019Co-Authors: Akechai Kongprajug, Skorn Mongkolsuk, Kwanrawee SirikanchanaAbstract:The human gut bacteriophage crAssphage has been proposed as a human-specific Microbial Source Tracking (MST) marker for impacted water bodies. However, its global use as a human-specific MST marker requires validation in a tropical region. In this study, a crAssphage qPCR marker (CPQ_056) was detected in 21 sewage samples in Thailand with 100% sensitivity. The marker was detected in sewage from hospitals and residential buildings at 5.28–7.38 log10 copies/100 mL and in four influent and four effluent samples of municipal wastewater treatment plants at 4.23–6.19 and 3.78–4.89 log10 copies/100 mL, respectively. Furthermore, a 99.2% specificity (n = 127) was observed using feces from swine, cattle, chicken, duck, goat, sheep, buffalo, and fish, with cross-detection only occurring for one composite swine sample. The crAssphage marker was present in 56.25% (27 out of 48) of river samples at 3.20–7.29 log10 copies/100 mL. The concentrations of the crAssphage marker and a prevalidated human-specific Bacteroidales marker (HF183/BFDrev) did not differ significantly in any of the sewage or wastewater samples, whereas the crAssphage marker abundance was higher in river samples. This initial validation of the crAssphage gene as a human-specific MST marker in Southeast Asia will promote its inclusion in an MST toolbox
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PCR data and comparative performance of Bacteroidales Microbial Source Tracking genetic markers.
Data in brief, 2018Co-Authors: Pornjira Somnark, Akechai Kongprajug, Natcha Chyerochana, Skorn Mongkolsuk, Kwanrawee SirikanchanaAbstract:Abstract We reported modified endpoint PCR results analyzed by universal and human-, swine-, and cattle-specific Bacteroidales gene markers with human sewage and animal fecal samples (i.e., swine, cattle, chicken, goat, sheep, buffalo, and duck) from Tha Chin and Chao Phraya watersheds. Annealing locations of PCR primers were illustrated by maps of 16s rRNA Bacteroidales genes. We also summarized previously published work on the performance of the PCR assays. For further discussion of the data presented here, please refer to Somnark et al., Performance evaluation of Bacteroidales genetic markers for human and animal Microbial Source Tracking in tropical agricultural watersheds, Environ. Pollut. 236 (2018) 100–110.