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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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A comparison of the OTUs exclusive to the rumen or the colon. A comparison of the 73 OTUs exclusive in the rumen (n = 8) or 71 OTUs exclusive in the colon (n = 6), by family. Families with three or more associated OTUs are labeled in the chart; all other families with two or fewer OTUs are labeled via the legend. The Unclassified sections are broken down by phyla in Figure2b, and2c, respectively.
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Figure 3: A comparison of the OTUs exclusive to the rumen or the colon. A comparison of the 73 OTUs exclusive in the rumen (n = 8) or 71 OTUs exclusive in the colon (n = 6), by family. Families with three or more associated OTUs are labeled in the chart; all other families with two or fewer OTUs are labeled via the legend. The Unclassified sections are broken down by phyla in Figure2b, and2c, respectively.

Mentions: The rumen samples contained 575 total OTUs; 192 Firmicutes, 142 Proteobacteria, and 66 Bacteroidetes being the dominant phyla. In the rumen samples, there was a range of 308 to 465 OTUs/sample, and an average of 350 OTUs/sample (Table2). There were 237 OTUs found across all eight rumen samples and, of these, 73 OTUs were exclusive to the rumen, representing 21 families (Figure3). The OTUs with unclassified families were assigned by phyla (Figure2b), with the dominant phyla being Bacteroidetes, 27%; Proteobacteria, 19%; and Chloroflexi and NC10 with 11% each. NC10 is a candidate phylum consisting of uncultivated and uncharacterized bacteria that is currently named after the location where the bacteria were sampled, Nullarbor Caves, Australia. All other phyla represented 10% or less of OTUs with unclassified families (Figure2b). Of the unclassified sequences found exclusively in the rumen, there were 51 termite gut clones, 36 marine, wetland, or waterway sediment clones, 13 fecal or colon clones, 11 rumen clones, nine soil clones, and seven sludge clones.


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

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

A comparison of the OTUs exclusive to the rumen or the colon. A comparison of the 73 OTUs exclusive in the rumen (n = 8) or 71 OTUs exclusive in the colon (n = 6), by family. Families with three or more associated OTUs are labeled in the chart; all other families with two or fewer OTUs are labeled via the legend. The Unclassified sections are broken down by phyla in Figure2b, and2c, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: A comparison of the OTUs exclusive to the rumen or the colon. A comparison of the 73 OTUs exclusive in the rumen (n = 8) or 71 OTUs exclusive in the colon (n = 6), by family. Families with three or more associated OTUs are labeled in the chart; all other families with two or fewer OTUs are labeled via the legend. The Unclassified sections are broken down by phyla in Figure2b, and2c, respectively.
Mentions: The rumen samples contained 575 total OTUs; 192 Firmicutes, 142 Proteobacteria, and 66 Bacteroidetes being the dominant phyla. In the rumen samples, there was a range of 308 to 465 OTUs/sample, and an average of 350 OTUs/sample (Table2). There were 237 OTUs found across all eight rumen samples and, of these, 73 OTUs were exclusive to the rumen, representing 21 families (Figure3). The OTUs with unclassified families were assigned by phyla (Figure2b), with the dominant phyla being Bacteroidetes, 27%; Proteobacteria, 19%; and Chloroflexi and NC10 with 11% each. NC10 is a candidate phylum consisting of uncultivated and uncharacterized bacteria that is currently named after the location where the bacteria were sampled, Nullarbor Caves, Australia. All other phyla represented 10% or less of OTUs with unclassified families (Figure2b). Of the unclassified sequences found exclusively in the rumen, there were 51 termite gut clones, 36 marine, wetland, or waterway sediment clones, 13 fecal or colon clones, 11 rumen clones, nine soil clones, and seven sludge clones.

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