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Insight into the bacterial gut microbiome of the North American moose (Alces alces).

Ishaq SL, Wright AD - BMC Microbiol. (2012)

Bottom Line: Second generation (G2) PhyloChips were used to determine the presence of hundreds of operational taxonomic units (OTUs), representing multiple closely related species/strains (>97% identity), found in the rumen and colon of the moose.There were 73 OTUs, representing 21 bacterial families, which were found exclusively in the rumen samples: Lachnospiraceae, Prevotellaceae and several unclassified families, whereas there were 71 OTUs, representing 22 bacterial families, which were found exclusively in the colon samples: Clostridiaceae, Enterobacteriaceae and several unclassified families.Overall, there were 164 OTUs that were found in 100% of the samples.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Animal Science, College of Agriculture and Life Sciences, University of Vermont, 203 Terrill Building, 570 Main Street, Burlington, VT 05405, USA. slpelleg@uvm.edu

ABSTRACT

Background: The work presented here provides the first intensive insight into the bacterial populations in the digestive tract of the North American moose (Alces alces). Eight free-range moose on natural pasture were sampled, producing eight rumen samples and six colon samples. Second generation (G2) PhyloChips were used to determine the presence of hundreds of operational taxonomic units (OTUs), representing multiple closely related species/strains (>97% identity), found in the rumen and colon of the moose.

Results: A total of 789 unique OTUs were used for analysis, which passed the fluorescence and the positive fraction thresholds. There were 73 OTUs, representing 21 bacterial families, which were found exclusively in the rumen samples: Lachnospiraceae, Prevotellaceae and several unclassified families, whereas there were 71 OTUs, representing 22 bacterial families, which were found exclusively in the colon samples: Clostridiaceae, Enterobacteriaceae and several unclassified families. Overall, there were 164 OTUs that were found in 100% of the samples. The Firmicutes were the most dominant bacteria phylum in both the rumen and the colon. Microarray data available at ArrayExpress, accession number E-MEXP-3721.

Conclusions: Using PhyloTrac and UniFrac computer software, samples clustered into two distinct groups: rumen and colon, confirming that the rumen and colon are distinct environments. There was an apparent correlation of age to cluster, which will be validated by a larger sample size in future studies, but there were no detectable trends based upon gender.

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Jackknife environment clustering in UniFrac, by sample. (a) An unweighted UniFrac algorithm and (b) a weighted UniFrac algorithm were used, and were not normalized as different evolutionary rates of gene did not need to be accounted for. Jackknife counts for each are provided for each node. The weighted UniFrac algorithm takes into account abundance of sequences, and is better suited to analysis of mixed bacterial samples. Samples are labeled by individual moose (1–8) and sample type (rumen, R or colon, C), and gender, weight and age information is provided in the legend.
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Figure 4: Jackknife environment clustering in UniFrac, by sample. (a) An unweighted UniFrac algorithm and (b) a weighted UniFrac algorithm were used, and were not normalized as different evolutionary rates of gene did not need to be accounted for. Jackknife counts for each are provided for each node. The weighted UniFrac algorithm takes into account abundance of sequences, and is better suited to analysis of mixed bacterial samples. Samples are labeled by individual moose (1–8) and sample type (rumen, R or colon, C), and gender, weight and age information is provided in the legend.

Mentions: P-test significance was run using all 14 samples together and 100 permutations, resulting in a corrected p-value of < 0.01, designating that each sample was significantly different from each other. Environment clusters and jackknife values are provided (Figure4), showing a statistical measurement of the correctness of the tree created. The weighted algorithm accounted for the relative abundance of sequences in a sample, which is typical for environmental samples. UniFrac and PhyloTrac both clustered the rumen and colon samples into two distinct groups: the first node was present 100% of the time in the unweighted and weighted UniFrac clusters. The branching pattern for the rumen group is different between UniFrac algorithm (Figure4) and between programs (Figure5). However, the branching pattern for the colon group is identical between PhyloTrac, and the unweighted and weighted UniFrac outputs. A principal component analysis (PCA) scatterplot (Figure5) was also created using the weighted algorithm, which grouped the rumen and colon samples separately.


Insight into the bacterial gut microbiome of the North American moose (Alces alces).

Ishaq SL, Wright AD - BMC Microbiol. (2012)

Jackknife environment clustering in UniFrac, by sample. (a) An unweighted UniFrac algorithm and (b) a weighted UniFrac algorithm were used, and were not normalized as different evolutionary rates of gene did not need to be accounted for. Jackknife counts for each are provided for each node. The weighted UniFrac algorithm takes into account abundance of sequences, and is better suited to analysis of mixed bacterial samples. Samples are labeled by individual moose (1–8) and sample type (rumen, R or colon, C), and gender, weight and age information is provided in the legend.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3585231&req=5

Figure 4: Jackknife environment clustering in UniFrac, by sample. (a) An unweighted UniFrac algorithm and (b) a weighted UniFrac algorithm were used, and were not normalized as different evolutionary rates of gene did not need to be accounted for. Jackknife counts for each are provided for each node. The weighted UniFrac algorithm takes into account abundance of sequences, and is better suited to analysis of mixed bacterial samples. Samples are labeled by individual moose (1–8) and sample type (rumen, R or colon, C), and gender, weight and age information is provided in the legend.
Mentions: P-test significance was run using all 14 samples together and 100 permutations, resulting in a corrected p-value of < 0.01, designating that each sample was significantly different from each other. Environment clusters and jackknife values are provided (Figure4), showing a statistical measurement of the correctness of the tree created. The weighted algorithm accounted for the relative abundance of sequences in a sample, which is typical for environmental samples. UniFrac and PhyloTrac both clustered the rumen and colon samples into two distinct groups: the first node was present 100% of the time in the unweighted and weighted UniFrac clusters. The branching pattern for the rumen group is different between UniFrac algorithm (Figure4) and between programs (Figure5). However, the branching pattern for the colon group is identical between PhyloTrac, and the unweighted and weighted UniFrac outputs. A principal component analysis (PCA) scatterplot (Figure5) was also created using the weighted algorithm, which grouped the rumen and colon samples separately.

Bottom Line: Second generation (G2) PhyloChips were used to determine the presence of hundreds of operational taxonomic units (OTUs), representing multiple closely related species/strains (>97% identity), found in the rumen and colon of the moose.There were 73 OTUs, representing 21 bacterial families, which were found exclusively in the rumen samples: Lachnospiraceae, Prevotellaceae and several unclassified families, whereas there were 71 OTUs, representing 22 bacterial families, which were found exclusively in the colon samples: Clostridiaceae, Enterobacteriaceae and several unclassified families.Overall, there were 164 OTUs that were found in 100% of the samples.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Animal Science, College of Agriculture and Life Sciences, University of Vermont, 203 Terrill Building, 570 Main Street, Burlington, VT 05405, USA. slpelleg@uvm.edu

ABSTRACT

Background: The work presented here provides the first intensive insight into the bacterial populations in the digestive tract of the North American moose (Alces alces). Eight free-range moose on natural pasture were sampled, producing eight rumen samples and six colon samples. Second generation (G2) PhyloChips were used to determine the presence of hundreds of operational taxonomic units (OTUs), representing multiple closely related species/strains (>97% identity), found in the rumen and colon of the moose.

Results: A total of 789 unique OTUs were used for analysis, which passed the fluorescence and the positive fraction thresholds. There were 73 OTUs, representing 21 bacterial families, which were found exclusively in the rumen samples: Lachnospiraceae, Prevotellaceae and several unclassified families, whereas there were 71 OTUs, representing 22 bacterial families, which were found exclusively in the colon samples: Clostridiaceae, Enterobacteriaceae and several unclassified families. Overall, there were 164 OTUs that were found in 100% of the samples. The Firmicutes were the most dominant bacteria phylum in both the rumen and the colon. Microarray data available at ArrayExpress, accession number E-MEXP-3721.

Conclusions: Using PhyloTrac and UniFrac computer software, samples clustered into two distinct groups: rumen and colon, confirming that the rumen and colon are distinct environments. There was an apparent correlation of age to cluster, which will be validated by a larger sample size in future studies, but there were no detectable trends based upon gender.

Show MeSH