16S rRNA-based assays for quantitative detection of universal, human-, cow-, and dog-specific fecal Bacteroidales: A Bayesian approach

Kildare, Beverly J.; Leutenegger, Christian M.; McSwain, Belinda S.; Bambic, Dustin G.; Rajal, Verónica Beatriz; Wuertz, Stefan

doi:10.1016/j.watres.2007.06.037

Cited by 394 publications

(438 citation statements)

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“…Bayes' theorem was used to calculate the conditional probability that detection of the LA35 marker gene was the result of a true positive event rather than detection of nontarget fecal material in the environmental sample. The method used has been previously described (22). Calculation of P(H\T), the probability (P) that there is poultry litter contamination (H) in an environmental sample given the event that the LA35 marker gene is positive (T) for the sample, is shown in equation 1:…”

Section: Vol 77 2011mentioning

confidence: 99%

Correlation of Quantitative PCR for a Poultry-Specific Brevibacterium Marker Gene with Bacterial and Chemical Indicators of Water Pollution in a Watershed Impacted by Land Application of Poultry Litter

Weidhaas¹,

Macbeth²,

Olsen³

et al. 2011

Appl Environ Microbiol

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The impact of fecal contamination from human and agricultural animal waste on water quality is a major public health concern. Identification of the dominant source(s) of fecal pollution in a watershed is necessary for assessing the safety of recreational water and protecting water resources. A field study was conducted using quantitative PCR (qPCR) for the 16S rRNA gene of Brevibacterium sp. LA35 to track feces-contaminated poultry litter in environmental samples. Based on sensitivity and specificity characteristics of the qPCR method, the Bayesian conditional probability that detection of the LA35 marker gene in a water sample represented a true-positive result was 93%. The marker's covariance with fecal indicator bacteria (FIB) and metals associated with poultry litter was also assessed in litter, runoff, surface water, and groundwater samples. LA35 was detected in water and soil samples collected throughout the watershed, and its concentration covaried with concentrations of Escherichia coli, enterococci, As, Cu, P, and Zn. Significantly greater concentrations of FIB, As, Cu, P, and Zn were observed in edge-of-field runoff samples in which LA35 was detected, compared to samples in which it was not detected. Furthermore, As, Cu, P, and Zn concentrations covaried in environmental samples in which LA35 was detected and typically did not in samples in which the marker gene was not detected. The covariance of the poultry-specific LA35 marker gene with these known contaminants from poultry feces provides further evidence that it is a useful tool for assessing the impact of poultry-derived fecal pollution in environmental waters.

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Section: Vol 77 2011mentioning

confidence: 99%

Correlation of Quantitative PCR for a Poultry-Specific Brevibacterium Marker Gene with Bacterial and Chemical Indicators of Water Pollution in a Watershed Impacted by Land Application of Poultry Litter

Weidhaas¹,

Macbeth²,

Olsen³

et al. 2011

Appl Environ Microbiol

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“…Total genomic DNA was extracted from respective filters as described previously in Barrett et al (2013). MST qPCR assay conditions were identical to those described by Kildare et al (2007). (Primers and probes used for these assays are outlined in Supplemental Material #2, namely human-specific (BacHum) and ruminant-specific (BacBov) Bacteroidales markers.)…”

Section: Molecular Analysismentioning

confidence: 99%

“…Sample analysis by library-independent polymerase chain reaction for the detection of host specific 16S RNA gene abundance aimed to distinguish between human and bovine sources of fecal waste, using real time assays designed by Kildare et al(2007). These assays target regions of the Bacteroidales bacteria that are specific to human (BacHum) and cow (BacCow) fecal material.…”

Section: Molecular Analysismentioning

confidence: 99%

“…These assays target regions of the Bacteroidales bacteria that are specific to human (BacHum) and cow (BacCow) fecal material. Total genomic DNA extraction followed the protocol of Barrett et al (2013) with assay conditions for quantitative PCR (qPCR) carried out following the protocol of Kildare et al (2007) …”

Section: Molecular Analysismentioning

confidence: 99%

“…More recently, microbial source tracking (MST) has further assisted in determining the origin of FIOs detected in water supplies (Seurinck et al, 2005). In Ireland a library-independent method, developed by Kildare et al (2007) , has permitted its application to typical environmental settings and has designed host-specific qPCR assays based on the order Bacteroidales. Since this bacterial group are more prevalent in the gastrointestinal tract than the FIOs, and make up approximately one-third of the human faecal microflora (Noble et al, 2006), qPCR assays targeting variable regions of the Bacteroidales 16S rRNA gene allow for the discrimination between human and ruminant sources of faecal pollution.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Using microbiological tracers to assess the impact of winter land use restrictions on the quality of stream headwaters in a small catchment

Flynn

Deakin

Archbold

et al. 2016

Science of The Total Environment

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General rights Copyright for the publications made accessible via the Queen's University Belfast Research Portal is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights.Take down policy The Research Portal is Queen's institutional repository that provides access to Queen's research output. Every effort has been made to ensure that content in the Research Portal does not infringe any person's rights, or applicable UK laws. If you discover content in the Research Portal that you believe breaches copyright or violates any law, please contact openaccess@qub.ac.uk.

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Identification of host‐specific Bacteroidales 16S rDNA sequences from human sewage and ruminant feces

Dorai-Raj

O’Grady

Cormican

et al. 2011

J. Basic Microbiol.

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The need to identify the source of fecal contamination of water has led to the development of various fecal source identification methods, a field known as microbial source tracking (MST). One promising method of MST focuses on fecal members of the order Bacteroidales, some of which exhibit a high degree of host-specificity. In order to identify host-specific Bacteroidales genetic markers, a ~1060 bp section of Bacteroidales 16S rDNA was amplified from human sewage (n = 6), and bovine (n = 6) and ovine fecal (n = 5) samples and used for the generation of three clone libraries. Phylogenetic analysis of sequences from the three clone libraries revealed that the Bacteroidales species found in both human sewage and bovine and ovine feces were a highly diverse group of organisms, many of which were not represented by previously characterised 16S rDNA. Ovine and bovine feces appear to host similar populations of Bacteroidales species and these species were more diverse and less closely related to cultivated species than the Bacteroidales population found in human sewage. Species of Bacteroidales from the ruminant and human feces formed isolated clusters containing putatively host-specific sequences. These sequences were subsequently exploited for the design of host-specific primers which were used in MST studies. Introduction *Water polluted by feces poses a significant risk to human health and can lead to economic losses due to expenditure associated with treatment of patients with waterborne diseases and economic losses due to closure of beaches, lakes and shellfish harvesting areas. Monitoring methods used to detect fecal contamination of water have traditionally been based on the cultivation and enumeration of fecal indicator bacteria (i.e. fecal coliforms, E. coli and fecal enterococci). However, since these indicator bacteria are found in the feces of both animals and humans, these methods provide us with no information on the source of fecal contamination.Correspondence: Siobhán Dorai-Raj, Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland. E-mail: Siobhandorairaj@hotmail.com Phone: +353 91 493864 Fax: +353 91 494598 The need to determine the source of contamination has led to the development of various fecal source identification methods, a field which is often called MST.Recently, a number of studies have been performed on a method of MST based on the detection of hostspecific strains of bacteria from the order Bacteroidales [1][2][3][4]. Members of Bacteroidales are among the most numerous bacterial populations in feces, greatly exceeding the numbers of E. coli [2]. In addition, members of the Bacteroidales order are genetically diverse, with a distribution that is limited to body cavities and, due to their anaerobic nature, are unlikely to survive for long after being released into water [2]. Most importantly, for the purpose of MST, several researchers have concluded that some strains of the microorganisms are of human fecal origin, whereas others are exclusively ...

show abstract

16S rRNA-based assays for quantitative detection of universal, human-, cow-, and dog-specific fecal Bacteroidales: A Bayesian approach

Cited by 394 publications

References 22 publications

Correlation of Quantitative PCR for a Poultry-Specific Brevibacterium Marker Gene with Bacterial and Chemical Indicators of Water Pollution in a Watershed Impacted by Land Application of Poultry Litter

Correlation of Quantitative PCR for a Poultry-Specific Brevibacterium Marker Gene with Bacterial and Chemical Indicators of Water Pollution in a Watershed Impacted by Land Application of Poultry Litter

Using microbiological tracers to assess the impact of winter land use restrictions on the quality of stream headwaters in a small catchment

Identification of host‐specific Bacteroidales 16S rDNA sequences from human sewage and ruminant feces

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