Remaining sequences were grouped into operational
taxonomic units (OTUs) based on a 97% similarity criterion. Rarefaction was performed on each sample to assess sampling adequacy, using a 50 sequence increment. Random subsamples (1000) of OTUs from each sample corresponding to the number of sequences in the lowest sample (i.e. smallest sample size) were then used for further analysis. The same subsampling approach was used to examine variation in community structure between samples (beta diversity) using the Selleck Imatinib theta similarity index of Yue and Clayton, an index that accounts for proportional abundances of both shared and non-shared OTUs [51]. Similarity between samples was visualized by ordination of samples by non-metric multidimensional scaling (NMDS) as well
as dendrogram construction. Spatial separation of Autophagy inhibitors library samples in NMDS was tested through analysis of molecular variance (AMOVA), while clustering of samples within the dendrogram was tested using the UniFrac distance metric [52]. Availability of supporting data All sequences used in this study are available in the NCBI Sequence Read Archive under study accession SRP032750 (http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP032750). Funding Partial funding for this work was provided by the Honor’s College of the University of Mississippi. Electronic supplementary material Additional file 1: Rarefaction of pyrosequencing data. Rarefaction analysis of the 454 pyrosequencing data for each sample as performed in mothur using the “rarefaction” command, with a 50 read increment. (XLSX 37 KB) References 1. Ryan RP, Germaine K, Franks A, Ryan DJ, Dowling DN: Bacterial endophytes: recent developments
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