Bioinformatic processing
Paired-end reads were adapter- and quality-filtered using Trimmomatic v.0.36 (Truong et al., 2015) with the following parameters: PE ILLUMINACLIP:TruSeq3-PE:3:30:10 LEADING:10 MINLEN:30 SLIDINGWINDOW: 4:30; HEADCROP:10. Samples included in the downstream analysis had at least 7.4 million paired-end reads of at least 91 bp in length after quality control. The quality of reads was checked before and after this process using FastQC v.0.11.5.
Using the quality-controlled paired-end reads, taxonomic profiling was performed using the metagenomic phylogenetic analysis (MetaPhlAn) v.2.6 (Franzosa et al., 2018), which uses a database of clade-specific markers to quantify microbiota constituents at the species and higher taxonomic levels. The generation of the abundance of metabolic pathways was performed using HUMAnN2 (Asnicar et al., 2015). Taxonomic and metabolic profiles for both islands were visualized using GraPhlAn v.0.9.7 (Whittaker, 1972). Sequenced metagenomic data were submitted to the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under BioProject ID PRJNA503909. Summary of the quality-controlled fecal microbiome sequencing reads is shown in Supplementary file 1f.