Characterization of the fecal bacteria communities of forage-fed horses by pyrosequencing of 16S rRNA V4 gene amplicons

Shepherd, Megan; Swecker, William S.; Jensen, Roderick V.; Ponder, Monica A.

doi:10.1111/j.1574-6968.2011.02434.x

Cited by 146 publications

(163 citation statements)

References 51 publications

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“…The higher-diversity indices for human wastewater samples could be attributed to wastewaterassociated bacterial communities as well as human fecal bacteria from a large population releasing wastewater into the WWTP stream (57). The Shannon diversity index for horse fecal samples was similar to the value reported in previous studies that investigated the 16S rRNA gene in horse fecal samples using pyrosequencing (61)(62)(63). Diversity indices can vary greatly among studies, which can be attributed to factors such as variable numbers of reads used in the analyses, different OTU similarity cutoff values, the target regions sequenced, and the methods used, in addition to variations due to the DNA extraction kits used in the studies (64).…”

Section: Discussionsupporting

confidence: 69%

Toolbox Approaches Using Molecular Markers and 16S rRNA Gene Amplicon Data Sets for Identification of Fecal Pollution in Surface Water

Ahmed

Staley

Sadowsky

et al. 2015

Appl Environ Microbiol

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dIn this study, host-associated molecular markers and bacterial 16S rRNA gene community analysis using high-throughput sequencing were used to identify the sources of fecal pollution in environmental waters in Brisbane, Australia. A total of 92 fecal and composite wastewater samples were collected from different host groups (cat, cattle, dog, horse, human, and kangaroo), and 18 water samples were collected from six sites (BR1 to BR6) along the Brisbane River in Queensland, Australia. Bacterial communities in the fecal, wastewater, and river water samples were sequenced. Water samples were also tested for the presence of bird-associated (GFD), cattle-associated (CowM3), horse-associated, and human-associated (HF183) molecular markers, to provide multiple lines of evidence regarding the possible presence of fecal pollution associated with specific hosts. Among the 18 water samples tested, 83%, 33%, 17%, and 17% were real-time PCR positive for the GFD, HF183, CowM3, and horse markers, respectively. Among the potential sources of fecal pollution in water samples from the river, DNA sequencing tended to show relatively small contributions from wastewater treatment plants (up to 13% of sequence reads). Contributions from other animal sources were rarely detected and were very small (<3% of sequence reads). Source contributions determined via sequence analysis versus detection of molecular markers showed variable agreement. A lack of relationships among fecal indicator bacteria, host-associated molecular markers, and 16S rRNA gene community analysis data was also observed. Nonetheless, we show that bacterial community and host-associated molecular marker analyses can be combined to identify potential sources of fecal pollution in an urban river. This study is a proof of concept, and based on the results, we recommend using bacterial community analysis (where possible) along with PCR detection or quantification of host-associated molecular markers to provide information on the sources of fecal pollution in waterways. Fecal indicator bacteria (FIB), such as Escherichia coli and Enterococcus spp., have long been used as indirect measures of public health risks associated with environmental waters (1, 2). However, the use of FIB to identify the health risks associated with enteric viruses and protozoa has been questioned because of their poor cooccurrence or correlation (3-5). Some strains of FIB have been reported to have the ability to adapt in the environment and to persist in sediment and vegetation (6, 7). The major limitation of FIB is that they cannot be assigned to a specific original source due to their cosmopolitan nature (being frequently found in different warm-blooded and some cold-blooded animals) (8, 9). When environmental waters are polluted with FIB from multiple sources, it becomes extremely difficult to implement a robust management plan without identifying the potential sources of this pollution.Over the past 2 decades, library-dependent and library-independent microbial source tracking (MST) methods ha...

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Section: Discussionsupporting

confidence: 69%

Toolbox Approaches Using Molecular Markers and 16S rRNA Gene Amplicon Data Sets for Identification of Fecal Pollution in Surface Water

Ahmed

Staley

Sadowsky

et al. 2015

Appl Environ Microbiol

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“…The first report of pyrosequencing to characterise faecal bacterial communities in two horses was published recently [15], and the method has since been used to identify differences in microbial communities between normal horses and those with colitis [16].…”

Section: Introductionmentioning

confidence: 99%

Characterisation of the faecal metabolome and microbiome of Thoroughbred racehorses

Proudman

Hunter

Darby

et al. 2014

Equine Veterinary Journal

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SummaryReasons for performing study: The intestinal bacterial community of the horse is a key determinant of intestinal and whole-body health. Understanding the bacterial community structure and function is an important foundation for studies of intestinal health and disease.Objectives: To describe the faecal bacterial community and the volatile organic compounds (VOCs) of the faecal metabolome of healthy Thoroughbred (Tb) racehorses, and to characterise responses to dietary supplementation with amylase-rich malt extract.Study Design: This was an intervention study performed with eight privately-owned Thoroughbred racehorses in active race training. Faecal samples were collected noninvasively before and six weeks after supplementation.Methods: Faecal metabolome was characterised using thermal desorption-gas chromatography-mass spectrometry (TD-GC-MS), with spectral analysis performed using AMDIS and compared against the NIST database. Taxonomic description of the faecal microbiota was achieved using error-corrected 454 pyrosequencing data from 16S rRNA gene amplicons. Results:The faecal metabolome of our study population was dominated by organic acids, alcohols and ketones. We identified 81 different VOCs only 28 of which were present in >50% of samples indicating functional diversity. Faecal VOC profiles differed between first and second sampling point, some VOCs being significantly reduced post-supplementation, consistent with a marked response to dietary amylase-rich malt extract. Faecal microbiota was characterised as highly diverse; samples demonstrated verifiable diversity in the range 1200-3000 operational taxonomic units (OTUs) per individual. The methods used also 3 describe high levels of infrequent, low abundance OTUs. Faecal microbial community structure was found to be different following dietary supplementation. Differences in several low-abundance bacterial taxa were detected and also some evidence of inter-horse variation in response. Conclusions:The volatile faecal metabolome of Tb racehorses is dominated by organic acids, alcohols and ketones; this study demonstrates that dietary supplementation with amylase-rich malt extract may significantly alter the profile of VOCs. The faecal microbiome is highly diverse, dominated by Firmicutes and Bacteroidetes. Small but significant changes in microbial community structure were detected following dietary supplementation.Potential relevance: This study describes the faecal metabolome and microbiome of healthy Tb racehorses against which future studies of disease and dietary intervention can be benchmarked.4

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“…Bacterial DNA was extracted from 0.25g of the fecal pellet using two commercial DNA extraction kits, the MoBio Ultra Clean® Fecal and the Zymo Research Soil Microbe DNA MiniPrep™ kit [29].…”

Section: Methodsmentioning

confidence: 99%

Effect of Two Different Commercial DNA Extraction Kits on the Bacterial 16S Ribosomal RNA Gene Denaturing Gradient Gel Electrophoresis Profile of Arabian Gelding Feces

Shepherd

Swecker

Ponder

2015

Journal of Equine Veterinary Science

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Characterization of the fecal bacteria communities of forage-fed horses by pyrosequencing of 16S rRNA V4 gene amplicons

Cited by 146 publications

References 51 publications

Toolbox Approaches Using Molecular Markers and 16S rRNA Gene Amplicon Data Sets for Identification of Fecal Pollution in Surface Water

Toolbox Approaches Using Molecular Markers and 16S rRNA Gene Amplicon Data Sets for Identification of Fecal Pollution in Surface Water

Characterisation of the faecal metabolome and microbiome of Thoroughbred racehorses

Effect of Two Different Commercial DNA Extraction Kits on the Bacterial 16S Ribosomal RNA Gene Denaturing Gradient Gel Electrophoresis Profile of Arabian Gelding Feces

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