S057_LYME_1
Shotgun metagenomic sequencing was conducted at Maintain Biotech (Wuhan, China). Sequencing libraries were prepared according to Illumina's protocol, with 200 g of genomic DNA fragmented by Covaris to an average size of 300-350 bp. The fragments underwent end repair, phosphorylation, and A-tailing, followed by adapter ligation. After size selection and PCR amplification, the prepared libraries were sequenced on an Illumina NovaSeq PE150 System (Illumina Inc., San Diego, CA, USA). Raw paired-end reads were initially trimmed and filtered using FASTP (v0.23.2) 35. Reads containing more than 10 ambiguous or undetermined base calls, having a mean quality score less than 30, or with a length smaller than 90 nt after trimming were removed. The trimmed and quality-controlled reads were then host-filtered using BBSplit from BBMap v38.99 (https://sourceforge.net/projects/bbmap/) to remove human DNA mapped to hg38. Bacterial taxonomic profiling of the preprocessed metagenomes was performed using MetaPhlAn4 (v4.0.6) with the mpa_vOct22_CHOCOPhlAnSGB_202212 database 36.