Amplicon 16S for feces diet diabetic control
Libraries were sequenced on the MiSeq system (Illumina Inc, San Diego, CA, USA) considering a minimum of 100,000 reads (2x300 pb) per sample. The MiSeq Reporter (MSR) software for 16S (Reference Guide - Part # 15042317) was used for organismal classification based on the 16S rRNA database  Greengenes (http:// greengenes.lbl.gov/). Raw reads were submitted to quality control using FastQC program v0.11.8 (Babraham Bioinformatics) and low-quality raw reads were trimmed out (Phred Q score <30) using Trimmomatic v0.38 (25). Taxonomic identification was carried out with the OmicsBox (BioBam Bioinformatics S.L., Valencia, Spain) using the taxonomic classification system Kraken2 v2.1.2, which compared our sequences to a curated database (RefSeq 2023.04: archaea, bacteria, fungi, protozoa, viral). OmicsBox were used to generate the rarefaction curves represented as the number of expected bacterial genera (Y-axis) per number of reads (X-axis). Bacterial alpha diversity indices were estimated for each sample on the same platform.