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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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Related in: MedlinePlus

Distribution of PhyloChip OTU’s for all 14 samples. Samples (rumen and colon) are arranged in rows and are clustered on the vertical axis (y-axis). OTU’s are arranged vertically and are on the horizontal axis (x-axis). Clustering was done for each using Phylotrac’s heatmap option with Pearson correlations and complete linkage algorithms.
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Figure 6: Distribution of PhyloChip OTU’s for all 14 samples. Samples (rumen and colon) are arranged in rows and are clustered on the vertical axis (y-axis). OTU’s are arranged vertically and are on the horizontal axis (x-axis). Clustering was done for each using Phylotrac’s heatmap option with Pearson correlations and complete linkage algorithms.

Mentions: Data were evaluated down to the taxonomic level of family for most analyses since each OTU represented more than one species[32]. A heatmap (Figure6) showing the presence or absence, and relative intensity of each OTU was created using all 14 samples. Samples were arranged in rows and were clustered on the vertical axis. OTUs were arranged vertically and were clustered on the horizontal axis. Clustering was done using Phylotrac’s heatmap option with Pearson correlation, a measure of the correlation between two variables, and complete linkage algorithms (farthest neighbor), which clusters based on the maximum distance between two variables.


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

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

Distribution of PhyloChip OTU’s for all 14 samples. Samples (rumen and colon) are arranged in rows and are clustered on the vertical axis (y-axis). OTU’s are arranged vertically and are on the horizontal axis (x-axis). Clustering was done for each using Phylotrac’s heatmap option with Pearson correlations and complete linkage algorithms.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Distribution of PhyloChip OTU’s for all 14 samples. Samples (rumen and colon) are arranged in rows and are clustered on the vertical axis (y-axis). OTU’s are arranged vertically and are on the horizontal axis (x-axis). Clustering was done for each using Phylotrac’s heatmap option with Pearson correlations and complete linkage algorithms.
Mentions: Data were evaluated down to the taxonomic level of family for most analyses since each OTU represented more than one species[32]. A heatmap (Figure6) showing the presence or absence, and relative intensity of each OTU was created using all 14 samples. Samples were arranged in rows and were clustered on the vertical axis. OTUs were arranged vertically and were clustered on the horizontal axis. Clustering was done using Phylotrac’s heatmap option with Pearson correlation, a measure of the correlation between two variables, and complete linkage algorithms (farthest neighbor), which clusters based on the maximum distance between two variables.

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
Related in: MedlinePlus