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Alpha diversity based on 16S rDNA V1–V3 sequence data.

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posted on 22.01.2013, 19:12 authored by Audrie Lin, Elisabeth M. Bik, Elizabeth K. Costello, Les Dethlefsen, Rashidul Haque, David A. Relman, Upinder Singh

(A) Rank abundance curves. The vertical axis displays OTU relative abundance on a logarithmic scale. The horizontal axis lists the OTUs in rank order of descending abundance. (B) Alpha diversity statistics. Phylogenetic Diversity (PD) is the minimum total branch length of the phylogenetic tree that incorporates all OTUs in a sample. The number of observed species was calculated at a similarity threshold of 97%. Shannon Diversity index (H) characterizes species diversity and accounts for abundance and evenness of the species. Shannon equitability index (EH) is a measure of evenness. If S is the number of observed species, then EH = H/ln (S). Due to the unequal number of measurements in the time series for each child (5 for Bangladeshi children and 6 for U.S. children), all 5 monthly measurements from each of 4 Bangladeshi children and the first 5 monthly measurements from each of 4 U.S. children were averaged. Only samples from the children (BC and UC participants) were included in this alpha diversity analysis (Table 1). Error bars represent the standard error of the mean (SEM).