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Composition and similarity of bovine rumen microbiota across individual animals.

Jami E, Mizrahi I - PLoS ONE (2012)

Bottom Line: Taken together, our results suggest a core microbiome in the bovine rumen.Furthermore, although the bacterial taxa may vary considerably between cow rumens, they appear to be phylogenetically related.This suggests that the functional requirement imposed by the rumen ecological niche selects taxa that potentially share similar genetic features.

View Article: PubMed Central - PubMed

Affiliation: Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, Bet Dagan, Israel.

ABSTRACT
The bovine rumen houses a complex microbiota which is responsible for cattle's remarkable ability to convert indigestible plant mass into food products. Despite this ecosystem's enormous significance for humans, the composition and similarity of bacterial communities across different animals and the possible presence of some bacterial taxa in all animals' rumens have yet to be determined. We characterized the rumen bacterial populations of 16 individual lactating cows using tag amplicon pyrosequencing. Our data showed 51% similarity in bacterial taxa across samples when abundance and occurrence were analyzed using the Bray-Curtis metric. By adding taxon phylogeny to the analysis using a weighted UniFrac metric, the similarity increased to 82%. We also counted 32 genera that are shared by all samples, exhibiting high variability in abundance across samples. Taken together, our results suggest a core microbiome in the bovine rumen. Furthermore, although the bacterial taxa may vary considerably between cow rumens, they appear to be phylogenetically related. This suggests that the functional requirement imposed by the rumen ecological niche selects taxa that potentially share similar genetic features.

Show MeSH
Pairwise similarity calculation.The average of pairwise comparisons of each sample to all others was calculated. The QIIME pipeline was used to compute the Bray-Curtis metric (gray bars) and the weighted UniFrac metric (black bars). The X-axis denotes the serial number of the cow from which the rumen sample was taken, and the Y-axis represents the degree of similarity: the closer the similarity to 1, the more similar the samples. At the bottom, average and standard deviation of each similarity metric calculated across all cow pairs are shown.
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pone-0033306-g005: Pairwise similarity calculation.The average of pairwise comparisons of each sample to all others was calculated. The QIIME pipeline was used to compute the Bray-Curtis metric (gray bars) and the weighted UniFrac metric (black bars). The X-axis denotes the serial number of the cow from which the rumen sample was taken, and the Y-axis represents the degree of similarity: the closer the similarity to 1, the more similar the samples. At the bottom, average and standard deviation of each similarity metric calculated across all cow pairs are shown.

Mentions: To assess the degree of similarity between the samples, we performed a pairwise similarity analysis in which the distances of each sample were paired and then averaged, giving the similarity of a specific sample to all others. To this end, we used the Bray-Curtis metric, as well as the weighted UniFrac metric which also measures the distance between communities based on their phylogenetic lineages (using the pyNAST QIIME implementation for sequence alignment and tree building [13]). Figure 5 shows the pairwise metric values for each individual cow and the average of each of the metrics for all possible cow pairs.


Composition and similarity of bovine rumen microbiota across individual animals.

Jami E, Mizrahi I - PLoS ONE (2012)

Pairwise similarity calculation.The average of pairwise comparisons of each sample to all others was calculated. The QIIME pipeline was used to compute the Bray-Curtis metric (gray bars) and the weighted UniFrac metric (black bars). The X-axis denotes the serial number of the cow from which the rumen sample was taken, and the Y-axis represents the degree of similarity: the closer the similarity to 1, the more similar the samples. At the bottom, average and standard deviation of each similarity metric calculated across all cow pairs are shown.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3303817&req=5

pone-0033306-g005: Pairwise similarity calculation.The average of pairwise comparisons of each sample to all others was calculated. The QIIME pipeline was used to compute the Bray-Curtis metric (gray bars) and the weighted UniFrac metric (black bars). The X-axis denotes the serial number of the cow from which the rumen sample was taken, and the Y-axis represents the degree of similarity: the closer the similarity to 1, the more similar the samples. At the bottom, average and standard deviation of each similarity metric calculated across all cow pairs are shown.
Mentions: To assess the degree of similarity between the samples, we performed a pairwise similarity analysis in which the distances of each sample were paired and then averaged, giving the similarity of a specific sample to all others. To this end, we used the Bray-Curtis metric, as well as the weighted UniFrac metric which also measures the distance between communities based on their phylogenetic lineages (using the pyNAST QIIME implementation for sequence alignment and tree building [13]). Figure 5 shows the pairwise metric values for each individual cow and the average of each of the metrics for all possible cow pairs.

Bottom Line: Taken together, our results suggest a core microbiome in the bovine rumen.Furthermore, although the bacterial taxa may vary considerably between cow rumens, they appear to be phylogenetically related.This suggests that the functional requirement imposed by the rumen ecological niche selects taxa that potentially share similar genetic features.

View Article: PubMed Central - PubMed

Affiliation: Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, Bet Dagan, Israel.

ABSTRACT
The bovine rumen houses a complex microbiota which is responsible for cattle's remarkable ability to convert indigestible plant mass into food products. Despite this ecosystem's enormous significance for humans, the composition and similarity of bacterial communities across different animals and the possible presence of some bacterial taxa in all animals' rumens have yet to be determined. We characterized the rumen bacterial populations of 16 individual lactating cows using tag amplicon pyrosequencing. Our data showed 51% similarity in bacterial taxa across samples when abundance and occurrence were analyzed using the Bray-Curtis metric. By adding taxon phylogeny to the analysis using a weighted UniFrac metric, the similarity increased to 82%. We also counted 32 genera that are shared by all samples, exhibiting high variability in abundance across samples. Taken together, our results suggest a core microbiome in the bovine rumen. Furthermore, although the bacterial taxa may vary considerably between cow rumens, they appear to be phylogenetically related. This suggests that the functional requirement imposed by the rumen ecological niche selects taxa that potentially share similar genetic features.

Show MeSH