deletions | additions       diff --git a/Results Taxonomic Diversity Across Dietary Patterns.md b/Results Taxonomic Diversity Across Dietary Patterns.md  index 818bc1d..a9a5407 100644  --- a/Results Taxonomic Diversity Across Dietary Patterns.md  +++ b/Results Taxonomic Diversity Across Dietary Patterns.md 
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The number of high-quality sequences per sample (i.e. meal) ranged from 168,669 to 318,956. Sequences were clustered and clusters were assigned to a taxonomic group (when possible) using the pick\_open\_reference\_otus.py script with a 97% similarity cutoff and the gg\_13\_8\_otus reference taxonomy provided by the Greengenes Database Consortium (http://greengenes.secondgenome.com.) After OTU assignment, mitochondrial and chloroplast sequences were filtered out, sequences that were observed only once across all samples were removed, and sequences that were Unassigned at the Domain taxonomic level were removed (these Unassigned sequences were verified via a manual BLAST search to be chloroplast sequences.) After this filtration, the range of sequences per sample decreased to 771-244,597. All subsequent diversity analyses were performed on samples that were rarefied to 771 sequences per sample.  ##Taxonomic Composition and Diversity of the Different Dietary Patterns  In terms of taxonomic richness (both measured by number of OTUs and phylogenetic diversity,) there was no significant difference between diet types dietary patterns  (Figure 1) (non-parametric Kruskal-Wallis test with compare\_alpha\_diversity.py, P>0.6). We also tested for the significant variation in frequency of individual OTUs between diet types using the Kruskal-Wallis test, as implemented in the group_significance.py script. This test is appropriate for comparing independent groups, with unequal samples sizes, that may not be normally distributed. None of the OTUs were significantly different between the three diet types. The most abundant 50 OTUs (clustered at 97% similarity) belong to 25 different bacterial families, including many that are commonly found in association with plants and animals (see Figure 7). (I FEEL LIKE HERE WE SHOULD EXPLAIN WHAT THE 3 DIFFERENT DIVERSITY INDECES BEING SHOWN IN THE FIGURE ARE)