How sequencing technology shapes our understanding of river water microbiomes and resistomes: a comparative study

Accurate characterization of microbial communities and their functional traits, such as antibiotic resistance, is essential for evaluating water quality and associated public health risks. However, the selection of sequencing methods can substantially influence the detection and interpretation of microbial community composition and functional potential in environmental samples. By directly comparing amplicon, short-read metagenomic, and long-read metagenomic sequencing across 48 freshwater samples collected across different sites and time points, this study builds upon earlier work that typically focused on only two methods or less complex communities. It provides a comparative evaluation of three widely used sequencing approaches, demonstrating how methodological differences affect the resolution and reliability of taxonomic and functional profiling in complex environmental microbiomes. By highlighting the strengths and limitations of each platform, these findings enhance our understanding of how sequencing strategy shapes environmental microbiome analyses and contributes to evidence-based method selection in environmental microbiology and antimicrobial resistance monitoring.