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##Factors Driving the Differences in Microbial Community Composition and Diversity of Individual Meals
There was no effect of diet type on the overall community composition within individual meals (PERMANOVA with compare_categories.py, P=0.591). There was no significant clustering based on any potentially distinguishing feature tested, including whether the meals contained fermented foods, dairy, whether they ware raw or cooked, or the calculated nutritional content (see Table 3 for complete meal metadata.)
Nevertheless, a large amount of variation (53%) is explained by
PC1 (Figure PCo1 (i.e., the eigenvector that explains the most variation)(Figure 2), and our attempts to determine the factors driving this variation led us to look at specific taxonomic groups that may be important. We did this in two ways. First, we sorted the stacked bar charts by the
PC1 loadings (EXPLAIN THIS). (See figure 3) values that each meal had for PCo1 (Figure 3). This made it apparent that the cluster of 4 meals on the right side of
PC1 the PCo1 axis was comprised of samples that were dominated by Lactic Acid
Bacteria (WHAT ARE THESE?), that Bacteria. These are members of the
order Lactobacillales, which are commonly found in association with both food products, especially in fermented milk products (CITATION) and human mucosal surfaces (CITATION). The Vegan Snack #1 was unique in that it is dominated
by Xanthamonadaceae (70.4%)
(WHAT ARE THESE?), and that the by Xanthamonadaceae, a family containing many plant pathogens. The cluster of 7
samples on the left side of
PC1 PCo1 axis was a group of meals with a large percentage (average = 27%) of
Thermus (WHAT ARE THESE). Thermus, a clade containing many heat-resistant organisms. Second, we looked for correlations between the relative abundance of a single taxon and the
PC1 loading PCo1 value for each meal using a simple regression. The bacterial family most tightly correlated with
PC1 PCo1 is Streptococcaceae (r = 0.852).
(Figure 4 - make this figure with abundance of streptococcaceae across all samples)
We also asked whether the relative abundance of a particular taxonomic group was significantly correlated to the nutritional content of the meals, via
pairwise Pearson's correlations. For this, we only looked at organisms that were present in all 15 meals. Due to the exploratory nature of this study, there were no specific hypotheses tested with these correlations, but some taxa frequently abundant in human microbiome studies were found to be significantly correlated with
a nutrient particular nutrients (Table 6). For example, members of the genus Blautia are frequently observed in human fecal samples, and in our study, it was found to be less abundant in meals with a lower sugar content
(Fig. X). (Figure 5). The implications of this finding are unclear, but it does suggest that there could be an interesting relationship between the nutritional content of the foods that we eat and our gut microbiome, not just because we are "feeding" our gut microbes, but because we are eating them as well.