📘 This repository contains data and code for the study titled:

“Stony coral tissue loss disease results in persistent microbial-level disturbances on coral reef ecosystems”

Specifically, we (1) analyzed diversity and co-occurrence patterns over time, (2) predicted functional shifts in microbial communities in response to SCTLD, and (3) evaluated the persistence of SCTLD-associated bacterial biomarkers (Rosales et al. 2023) across sites and disease stages.

📂 The Data/ directory includes the associated metadata for:

1. The sequence data (meta_EPA2.csv)
2. Benthic habitat data (CREMP_percentcover_taxagroups.csv, CREMP_LTA.csv, CREMP_Counts.csv, and DRM.T1T2data.LK.csv)
3. Compressed taxonomy (tax_EPA2.qza)
4. Compressed Amplicon Sequence Variant counts (merged_tables_BacArc_fill_EPA2.qza).

🐍 The analysis code is provided as Python notebooks, allowing outputs to be viewed alongside the code.

🧾 If notebooks do not render properly on GitHub, you can view them using nbviewer.