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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.

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Rarefaction analysis for the assessment of OTU coverage.(A) Sample-based rarefaction curve showing the increase in OTU numbers as a function of the number of individuals sampled. Each added sample adds OTUs to the plot which has not yet been seen in previous samples. The curve becomes asymptotic as the OTU number saturates, and each sample adds an increasingly smaller number of new OTUs, indicating adequate coverage for the environment being tested. (B) Individual rarefaction curves for each rumen sample taken.
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pone-0033306-g001: Rarefaction analysis for the assessment of OTU coverage.(A) Sample-based rarefaction curve showing the increase in OTU numbers as a function of the number of individuals sampled. Each added sample adds OTUs to the plot which has not yet been seen in previous samples. The curve becomes asymptotic as the OTU number saturates, and each sample adds an increasingly smaller number of new OTUs, indicating adequate coverage for the environment being tested. (B) Individual rarefaction curves for each rumen sample taken.

Mentions: We sampled the ruminal contents of 16 Holstein Friesian lactating cows fed the same diet ad libitum for several months and held under the same experimental conditions for 6 weeks. Samples were taken 1 h after feeding as described by Brulc et al. [3]. Microbial cells were separated from the rumen samples and their DNA was extracted using a protocol described by Stevenson and Weimer [6]. We then identified and characterized the overall ruminal bacterial composition as well as the taxa shared by all cows, by using bacterial tag-encoded amplicon pyrosequencing generated from the V2 and V3 regions of the 16 S rRNA gene. In total, 162,000 reads were generated with an average of 9587±2059 reads per sample. We used the QIIME pipeline [12] to filter the reads and for quality control, as well as for some of the data analyses. After filtering, quality control and chimera removal (see materials and methods), the total number of operational taxonomic units (OTUs) detected by the analysis reached 4986, with an average 1800±324 OTUs per rumen sample (an OTU was defined as a read sharing ≥97% nucleotide sequence identity) (Tables S1, S2). We performed a sample-based rarefaction test to assess whether our sampling and sequencing efforts provided efficient OTU coverage. After the tenth sample, the number of OTUs was saturated, as revealed by the asymptotic nature of the sample rarefaction curve (Figure 1A). Taxonomic assignment showed that the dominant ruminal bacterial phyla, summing to 93% of total bacterial reads, were Firmicutes and Bacteroidetes, representing 42% and 51% of total OTUs, respectively; 5.21% of the reads were attributed to the phylum Proteobacteria, 0.87% to Actinobacteria, and 0.68% to Tenericutes. Other phyla were also present but at lower percentages (Figure 2A). Examining each sample composition at the phylum level, we observed noticeable differences between individual cows reflected by changes in the abundance of Firmicutes, Bacteroidetes and Proteobacteria (Figure 2B).


Composition and similarity of bovine rumen microbiota across individual animals.

Jami E, Mizrahi I - PLoS ONE (2012)

Rarefaction analysis for the assessment of OTU coverage.(A) Sample-based rarefaction curve showing the increase in OTU numbers as a function of the number of individuals sampled. Each added sample adds OTUs to the plot which has not yet been seen in previous samples. The curve becomes asymptotic as the OTU number saturates, and each sample adds an increasingly smaller number of new OTUs, indicating adequate coverage for the environment being tested. (B) Individual rarefaction curves for each rumen sample taken.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3303817&req=5

pone-0033306-g001: Rarefaction analysis for the assessment of OTU coverage.(A) Sample-based rarefaction curve showing the increase in OTU numbers as a function of the number of individuals sampled. Each added sample adds OTUs to the plot which has not yet been seen in previous samples. The curve becomes asymptotic as the OTU number saturates, and each sample adds an increasingly smaller number of new OTUs, indicating adequate coverage for the environment being tested. (B) Individual rarefaction curves for each rumen sample taken.
Mentions: We sampled the ruminal contents of 16 Holstein Friesian lactating cows fed the same diet ad libitum for several months and held under the same experimental conditions for 6 weeks. Samples were taken 1 h after feeding as described by Brulc et al. [3]. Microbial cells were separated from the rumen samples and their DNA was extracted using a protocol described by Stevenson and Weimer [6]. We then identified and characterized the overall ruminal bacterial composition as well as the taxa shared by all cows, by using bacterial tag-encoded amplicon pyrosequencing generated from the V2 and V3 regions of the 16 S rRNA gene. In total, 162,000 reads were generated with an average of 9587±2059 reads per sample. We used the QIIME pipeline [12] to filter the reads and for quality control, as well as for some of the data analyses. After filtering, quality control and chimera removal (see materials and methods), the total number of operational taxonomic units (OTUs) detected by the analysis reached 4986, with an average 1800±324 OTUs per rumen sample (an OTU was defined as a read sharing ≥97% nucleotide sequence identity) (Tables S1, S2). We performed a sample-based rarefaction test to assess whether our sampling and sequencing efforts provided efficient OTU coverage. After the tenth sample, the number of OTUs was saturated, as revealed by the asymptotic nature of the sample rarefaction curve (Figure 1A). Taxonomic assignment showed that the dominant ruminal bacterial phyla, summing to 93% of total bacterial reads, were Firmicutes and Bacteroidetes, representing 42% and 51% of total OTUs, respectively; 5.21% of the reads were attributed to the phylum Proteobacteria, 0.87% to Actinobacteria, and 0.68% to Tenericutes. Other phyla were also present but at lower percentages (Figure 2A). Examining each sample composition at the phylum level, we observed noticeable differences between individual cows reflected by changes in the abundance of Firmicutes, Bacteroidetes and Proteobacteria (Figure 2B).

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