design: Biofilms from an upflow fixed-film bioreactor were scrapped, and metagenomic DNA was extracted. DNA purity and integrity were evaluated using agarose gel electrophoresis, while concentration was quantified with the Qubit 2.0 fluorometer for accurate measurement. Physical shearing was performed using a Covaris Sonicator. The efficiency and quality of DNA fragmentation were assessed using the Agilent 2100 Bioanalyzer and quantitative PCR (qPCR) to verify adequate target enrichment. Sequencing libraries were prepared using random fragmentation, followed by paired-end sequencing on the Illumina NextSeq 500 platform.