Mice receiving AAV-GFP injection 3
Raw data were processed using fastp (parameters: -l 100 -g -W 6 -5 -q 20 -u 30) to obtain high-quality clean data. Preprocessing steps included: (1) removal of adapter sequences, (2) quality scanning with a sliding window approach (6 bp window size, trimming if average quality < 20), (3) removal of sequences < 100 bp post-trimming, and (4) removal of host sequence contamination. Valid data were assembled using MEGAHIT, employing a multi-kmer size strategy to construct succinct de Bruijn graphs iteratively, resulting in contigs. Contigs > 500 bp were retained for clustering analysis. Metaprodigal was used to predict coding regions (CDS) from contigs, filtering out sequences < 100 nt. MMseqs2 software was used for redundancy reduction, yielding a non-redundant set of unigenes. Bowtie2 aligned clean data to unigene sequences, calculating read counts for each unigene. Unigenes with read counts 2 across all samples were filtered out, leaving the final set for subsequent analysis. Low abundance OTUs (<0.001%) were removed. The relative abundance at phylum, family, genus, and species levels was further analyzed.