Using an intervening sequence of Faecalibacterium 16S rDNA to identify poultry feces

Shen, Zhenyu; Duan, Chaojun; Zhang, Chao; Carson, A. W.; Xu, Dong; Zheng, Guoan

doi:10.1016/j.watres.2013.08.013

Cited by 18 publications

(20 citation statements)

References 48 publications

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“…However, other genes such as ( Yampara-Iquise et al, 2008 ) the thetaiotaomicron -specific α-1-6, mannanase, and ( Shanks et al, 2009 ) Bacteroidales -like cell surface-associated genes have also been reported. Avian MST markers developed thus far, identify bacteria of various taxonomic groups, including ( Shen et al, 2013 ) Faecalibacterium , ( Green et al, 2012 ; Ryu et al, 2012 ) C. marimammalium , and ( Weidhaas and Lipscomb, 2013 ; Ryu et al, 2014 ) Brevibacterium sp. 16S rRNA gene clone libraries ( Lu et al, 2009 ) from geese droppings were used to explore microbial communities from these sources to design host-specific assays.…”

Section: Introductionmentioning

confidence: 99%

The Development of a Novel qPCR Assay-Set for Identifying Fecal Contamination Originating from Domestic Fowls and Waterfowl in Israel

et al. 2016

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The emerging microbial source tracking (MST) methodologies aim to identify fecal contamination originating from domestic and wild animals, and from humans. Avian MST is especially challenging, primarily because the Aves class includes both domesticated and wild species with highly diverse habitats and dietary characteristics. The quest for specific fecal bacterial MST markers can be difficult with respect to attaining sufficient assay sensitivity and specificity. The present study utilizes high throughput sequencing (HTS) to screen bacterial 16S rRNA genes from fecal samples collected from both domestic and wild avian species. Operational taxonomic unit (OTU) analysis was then performed, from which sequences were retained for downstream quantitative polymerase chain reaction (qPCR) marker development. Identification of unique avian host DNA sequences, absent in non-avian hosts, was then carried out using a dedicated database of bacterial 16S rRNA gene taken from the Ribosomal Database Project. Six qPCR assays were developed targeting the 16S rRNA gene of Lactobacillus, Gallibacterium, Firmicutes, Fusobacteriaceae, and other bacteria. Two assays (Av4143 and Av163) identified most of the avian fecal samples and demonstrated sensitivity values of 91 and 70%, respectively. The Av43 assay only identified droppings from battery hens and poultry, whereas each of the other three assays (Av24, Av13, and Av216) identified waterfowl species with lower sensitivities values. The development of an MST assay-panel, which includes both domestic and wild avian species, expands the currently known MST analysis capabilities for decoding fecal contamination.

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Section: Introductionmentioning

confidence: 99%

The Development of a Novel qPCR Assay-Set for Identifying Fecal Contamination Originating from Domestic Fowls and Waterfowl in Israel

et al. 2016

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“…Host-specific microbial genetic markers have also become a common strategy for determining the source of fecal contamination (Field and Samadpour, 2007). However, many species of wildlife and domestic animals lack specific microbial markers; therefore, the application of these methods is limited (Chase et al, 2012;Mieszkin et al, 2009b;Shen et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Persistence of mitochondrial DNA markers as fecal indicators in water environments

Shi

Cui

et al. 2015

Science of The Total Environment

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“…Microbial source tracking (MST) methodology offers tools to diagnose and identify fecal contamination sources in the environment (1,2). Although it is not a standard environmental monitoring method used for routine regulatory purposes, it has been extensively studied and applied worldwide, especially for deciphering fecal pollution in surface and recreational waters (3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14).…”

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confidence: 99%

Microbial Source Tracking in Adjacent Karst Springs

Ohad

Vaizel-Ohayon

Rom

et al. 2015

Appl Environ Microbiol

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cModern man-made environments, including urban, agricultural, and industrial environments, have complex ecological interactions among themselves and with the natural surroundings. Microbial source tracking (MST) offers advanced tools to resolve the host source of fecal contamination beyond indicator monitoring. This study was intended to assess karst spring susceptibilities to different fecal sources using MST quantitative PCR (qPCR) assays targeting human, bovine, and swine markers. It involved a dual-time monitoring frame: (i) monthly throughout the calendar year and (ii) daily during a rainfall event. Data integration was taken from both monthly and daily MST profile monitoring and improved identification of spring susceptibility to host fecal contamination; three springs located in close geographic proximity revealed different MST profiles. The Giach spring showed moderate fluctuations of MST marker quantities amid wet and dry samplings, while the Zuf spring had the highest rise of the GenBac3 marker during the wet event, which was mirrored in other markers as well. The revelation of human fecal contamination during the dry season not connected to incidents of raining leachates suggests a continuous and direct exposure to septic systems. Pigpens were identified in the watersheds of Zuf, Shefa, and Giach springs and on the border of the Gaaton spring watershed. Their impact was correlated with partial detection of the Pig-2-Bac marker in Gaaton spring, which was lower than detection levels in all three of the other springs. Ruminant and swine markers were detected intermittently, and their contamination potential during the wet samplings was exposed. These results emphasized the importance of sampling design to utilize the MST approach to delineate subtleties of fecal contamination in the environment.

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Using an intervening sequence of Faecalibacterium 16S rDNA to identify poultry feces

Cited by 18 publications

References 48 publications

The Development of a Novel qPCR Assay-Set for Identifying Fecal Contamination Originating from Domestic Fowls and Waterfowl in Israel

The Development of a Novel qPCR Assay-Set for Identifying Fecal Contamination Originating from Domestic Fowls and Waterfowl in Israel

Persistence of mitochondrial DNA markers as fecal indicators in water environments

Microbial Source Tracking in Adjacent Karst Springs

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