Dataset Information

Microbial diversity and host-specific sequences of Canada goose feces.

ABSTRACT: Methods to assess the impact of goose fecal contamination are needed as the result of the increasing number of Canada geese (Branta canadensis) near North American inland waters. However, there is little information on goose fecal microbial communities, and such data are important for the development of host-specific source-tracking methods. To address this issue, 16S rRNA gene clone libraries for Canada goose fecal samples from Ontario, Canada, and Ohio were analyzed. Analyses of fecal clones from Ontario (447) and Ohio (302) showed that goose fecal communities are dominated by the classes "Clostridia" (represented by 33.7% of clones) and "Bacilli" (38.1% of clones) and the phylum "Bacteroidetes" (10.1% of clones). Sequences not previously found in other avian fecal communities were used to develop host-specific assays. Fecal DNA extracts from sewage plants (10 samples) and different species of birds (11 samples) and mammals (18 samples) were used to test for host specificity. Of all the assays tested, one assay showed specificity for Canada goose fecal DNA. The PCR assay was positive for Canada goose fecal DNA extracts collected from three locations in North America (Ohio, Oregon, and Ontario, Canada). Additionally, of 48 DNA extracts from Lake Ontario waters presumed to be impacted by waterfowl feces, 19 tested positive by the assay, although 10 were positive only after a nested PCR approach was used. Due to the level of host specificity and the presence of signals in environmental waters, the assay is proposed as a part of the toolbox to detect Canada goose contamination in waterfowl-contaminated waters.

SUBMITTER: Lu J

PROVIDER: S-EPMC2747875 | biostudies-literature | 2009 Sep

REPOSITORIES: biostudies-literature

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Microbial diversity and host-specific sequences of Canada goose feces.

Lu Jingrang J Santo Domingo Jorge W JW Hill Stephen S Edge Thomas A TA

Applied and environmental microbiology 20090724 18

Methods to assess the impact of goose fecal contamination are needed as the result of the increasing number of Canada geese (Branta canadensis) near North American inland waters. However, there is little information on goose fecal microbial communities, and such data are important for the development of host-specific source-tracking methods. To address this issue, 16S rRNA gene clone libraries for Canada goose fecal samples from Ontario, Canada, and Ohio were analyzed. Analyses of fecal clones f ...[more]

PMID: 19633110

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Project description:BackgroundClassic goose parvovirus (cGPV) causes high mortality and morbidity in goslings and Muscovy ducklings. Novel GPV (N-GPV) causes short beak and dwarfism syndrome (SBDS) in Cherry Valley ducks, Pekin ducks and Mule ducks. Both cGPV and N-GPV have relatively strict host specificity, with obvious differences in pathogenicity. Specific detection of cGPV and N-GPV may result in false positives due to high nucleotide similarity with Muscovy duck parvovirus (MDPV). The aim of this study was to develop a highly specific, sensitive, and reliable TaqMan real-time PCR (TaqMan qPCR) assay for facilitating the molecular detection of cGPV and N-GPV.ResultsAfter genetic comparison, the specific conserved region (located on the NS gene) of cGPV and N-GPV was selected for primer and probe design. The selected regions were significantly different from MDPV. Through a series of optimization experiments, the limit of detection was 50.2 copies/μl. The assay was highly specific for the detection of cGPV and N-GPV and no cross-reactivity was observed with E. coli., P.M., R.A., S.S., MDPV, N-MDPV, DAdV-A, DEV, GHPV, DHAV-1, DHAV-3, ATmV, AIV, MDRV and N-DRV. The assay was reproducible with an intra-assay and inter-assay variability of less than 2.37%. Combined with host specificity, the developed TaqMan qPCR can be used for cGPV and N-GPV in differential diagnoses. The frequency of cGPV in Muscovy duckling and goslings was determined to be 12 to 44%, while N-GPV frequency in Mule ducks and Cherry Valley ducks was 36 to 56%. Additionally, fluorescence-positive signals can be found in Mule duck embryos and newly hatched Mule ducklings. These findings provide evidence of possible vertical transmission of N-GPV from breeding Mule ducks to ducklings.ConclusionsWe established a quantitative platform for epidemiological investigations and pathogenesis studies of cGPV and N-GPV DNA that was highly sensitive, specific, and reproducible. N-GPV and cGPV infections can be distinguished based on host specificity.

Project description:IntroductionVery little is known about the impact of n-3 long-chain fatty acids (n-3 LCFAs) on the microbiota of sows and their piglets. The aim of this study was to evaluate the effect of n-3 LCFA in sow diets on the microbiota composition of sows' feces, colostrum, and milk as well as that of piglets' feces.MethodsTwenty-two sows were randomly assigned to either a control or an n-3 LCFA diet from service to weaning. Sows' and piglets' performance was monitored. The gestating and lactating sows' microbiomes in feces, colostrum, and milk were characterized by 16s ribosomal RNA gene sequencing. The fecal microbiome from the two lowest (>800 g) and the two highest birth weight piglets per litter was also characterized, and the LPS levels in plasma were analyzed at weaning.Results and discussionn-3 LCFA increased microbiota alpha diversity in suckling piglets' and gestating sows' feces. However, no effects were observed in colostrum, milk, or lactating sows' feces. Dietary n-3 LCFA modified the microbiota composition of gestating sows' feces, milk, and suckling piglets' feces, without affecting lactating sows' feces or colostrum. In gestating sows' feces and milk, the decrease in genus Succinivibrio and the increase of Proteobacteria phylum, due to the increased genera Brenneria and Escherichia, respectively, stand out. In the feces of suckling piglets, the higher abundance of the beneficial genus Akkermansia and Bacteroides, and different species of Lactobacillus are highlighted. In addition, positive correlations for families and genera were found between lactating sows' feces and milk, milk and suckling piglets' feces, and lactating sows' feces and suckling piglets' feces. To conclude, dietary n-3 LCFA had a positive impact on the microbiome of suckling piglet's feces by increasing microbial diversity and some beneficial bacteria populations, had a few minor modifications on the microbiome of milk and gestating sows' feces and did not change the microbiome in lactating sows' feces or colostrum. Therefore, this study shows the effect of dietary n-3 LCFA on the microbiota of sows, colostrum, milk, and suckling piglets during the lactation period providing crucial information on the microbiota status at the early stages of life, which have an impact on the post-weaning.

Dataset Information

Microbial diversity and host-specific sequences of Canada goose feces.

Publications

Microbial diversity and host-specific sequences of Canada goose feces.

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