Metagenomic taxa of chicken manure and chicken manure wastewater
Total genomic DNA was extracted from chicken manure. Shotgun metagenomic libraries were prepared and sequenced on an Illumina pair-end platform (2  150 bp). Raw reads were quality-filtered using fastp v0.36, and host contamination was removed with Bowtie2 v2.1.0. Clean reads were assembled using megahit v1.2.9 and SPAdes v3.13. Genes (100 bp) were predicted with Prodigal v2.60, and a non-redundant gene catalog was constructed using CD-HIT v2.60 (95% identity, 90% coverage). Gene abundance was quantified by mapping reads to the gene catalog using Bowtie2 and SAMtools v0.1.18. Functional and taxonomic annotation was performed using DIAMOND v0.8.20 against NR, KEGG, COG, CARD, CAZy, GO, SEED, BacMet, VFDB, TCDB, PHI, and ARGS databases.