2.3. Sequence analysis

Raw Illumina paired-end reads were uploaded as FASTQ files and analysed using the MG-RAST server v 4.0.3 [1], [2], [3] High-quality reads were subjected to analysis to predict, identify, and assign biological functions (gene annotations) to proteins and rRNA and then designate the functional categories using the COG ontology [4], NOG ontology, KEGG orthologs ontology, and Subsystems ontology. Taxonomic analysis was accomplished using data from the M5NR database [5]. Finally, the MG-RAST pipeline produced the sequence coverage by rarefaction analysis and the alpha diversity of species.