Metacontam: A Negative Control-Free Decontamination Method for Metagenomic Analysis

Shotgun metagenomic sequencing enables high-resolution profiling of host-associated microbial communities. However, contaminant DNA can substantially distort biological interpretations, especially in low-biomass samples. Here, we introduce Metacontam, a control-free method for species-level decontamination of shotgun metagenomic data. Metacontam integrates blacklist-guided community detection within a species correlation network with average nucleotide identity (ANI) to identify contaminants arising from shared sources. Across diverse low-biomass and mixed-biomass datasets, Metacontam outperformed existing approaches, improving the detection of low-abundance and low-prevalence contaminants while retaining biologically plausible taxa. It also reduces kit-specific biases in skin metagenomes and improves downstream analyses of tissue microbiome data. Together, these results demonstrate that Metacontam enables accurate identification of contaminant taxa across diverse metagenomic datasets, even in the absence of negative controls.