The transfer of DNA and thereby virulence factors is either accomplished by transduction through phages, conjugation through pili, or by uptake of naked, environmental DNA . In particular environmental microbiomes such as wastewater treatment plants are reservoirs for clinically relevant virulence genes, and are important drivers for the exchange and transmission of genes . Therefore, monitoring the presence of virulence factors in risky environments poses a crucial task in the One Health concept. The identification and quantification of virulence factors from microbial communities can be tentatively assessed using metagenomics and qPCR , but the synthesis and secretion of virulence factors is prone to environmental influence, e.g., nutrient concentration or temperature . Therefore, proteomics and metaproteomics methods are more suitable to explore their actual synthesis and secretion. In practice, Graf et al. identified several virulence factors, including staphylococcal leukocidin, in sputum samples of cystic fibrosis patients, and Messer et al. observed protein virulence factors at marine plastic surfaces. Thereby, metaproteomics is able to contribute to human health research and risk assessment, when dealing with environmental matrices.