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The metagenomic analysis identified 22 new population genomes and revealed that the microbial compositions between the two configurations were remarkably different, demonstrating a higher methanogenic biodiversity in the two-stage configuration.
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Unweighted UniFrac and PCA were performed to assess differences in microbial composition between the samples.
The differences in microbial composition between two studies were explained by an increased capacity of the obesity-associated microbiome to harvest energy from the diet.
It has, however, been shown that high variation occurs in microbial composition between individual chickens and flocks of genetically closely related animals [ 20].
This supports the results of our study, which shows no apparent differences in gut microbial composition between cohoused Nod2 −/− and WT littermates.
Analysis of the module for glycolysis clearly differentiated the gut microbial composition between adults and infants as well as among infants.
Nevertheless, including healthy subjects as additional controls would have allowed for more comparisons and a broader view of differences in microbial composition between periodontal health and disease.
*Genes involved in the specific GO-category Differences in ileal mucosa-adherent microbial composition between the IR group and the OUT group were associated with large host-specific transcriptional differences in the ileum.
All clone libraries were constructed under identical conditions in order to minimize sample-to-sample variation, thus the relative differences in microbial composition between the samples truly reflect animal treatment differences.
Specifically, for each data set, we used the vegdist function in the R package vegan (Oksanen et al., 2013) to calculate a 48 × 48 Bray Curtis dissimilarity matrix, which describes the global dissimilarity in gut microbial composition between each pair of individuals in the data set.
Further resolution at the class level revealed that the microbial compositions overlapped between the bioreactor samples.
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