Second revision of analyses for Functional plasticity in oyster gut microbiomes along a eutrophication gradient in an urbanized estuary

Analysis repository for for Stevick, R. J., Post, A. F., Gomez-Chiarri, M. (2020) Functional plasticity in oyster gut microbiomes along a eutrophication gradient in an urbanized estuary. This updated release contains the scripts, pre-processed sequencing data, QIIME2 artifacts, and the R script files to reproduce the figures in the manuscript. The raw sequences generated for this study can be found in the NCBI Short Read Archive under BioProject no. PRJNA598635.

New analyses include:

1. The statistical analysis for the beta-diversity calculations in Figure 3B were summarized, added as Table S2.
2. Within site variability of oyster gut samples observed in Figure 3B was quantified and added as Figure 3C.
3. Core microbiomes for each of the 16S rRNA gene amplicon and metatranscriptome datasets were calculated and included as Figure S6 and Table S3.