abgs2025LOW20251124
At the end of the operation period, 20 mL of ABGS was collected from each reactor for total DNA extraction and subsequent metagenomic sequencing analysis. Sequencing was performed using the Illumina NovaSeq 6000 platform (Illumina, USA). Raw sequencing reads were subjected to quality control to remove low-quality reads, resulting in high-quality sequences for downstream analysis. De novo assembly was conducted using MEGAHIT (https://github.com/voutcn/megahit), and the assembled sequences were used for open reading frame (ORF) prediction. Specifically, ORFs were predicted from assembled contigs using Prodigal v2.6.3 (https://github.com/hyattpd/Prodigal), and gene sequences of at least 100 bp were retained and translated into corresponding amino acid sequences. Predicted gene sequences from all samples were clustered using CD-HIT (http://www.bioinformatics.org/cd-hit/), and the longest sequence from each cluster was selected as the representative to construct a non-redundant gene catalog. Finally, high-quality reads from each sample were aligned to the non-redundant gene catalog using SOAPaligner, and the abundance of each gene was quantified for functional annotation and comparative analysis. Subsequently, species annotation was performed using the nr database, functional annotation was conducted with KEGG, and ARGs and MGEs were annotated using the CARD and MGEs90 databases.
SUB15791118
abgs2025LOW20251124