Wastewater metaproteomics: tracking microbial and human protein biomarkers
peer-reviewed · ISME Communications · 2025
| Date | 2025-12-18 |
| Type | peer-reviewed |
| Venue | ISME Communications |
| Publisher | Oxford University Press |
| Contribution | downstream-application |
| DOI | 10.1093/ismeco/ycaf243 |
| Citations (OpenAlex) | 2 |
Abstract
Wastewater-based surveillance has become a powerful tool for monitoring the spread of pathogens, antibiotic resistance genes, and measuring population-level exposure to pharmaceuticals and chemicals. While surveillance methods commonly target small molecules, DNA, or RNA, wastewater also contains a vast spectrum of proteins. However, despite recent advances in environmental proteomics, large-scale monitoring of protein biomarkers in wastewater is still far from routine. Analyzing raw wastewater presents a challenge due to its heterogeneous mixture of organic and inorganic substances, microorganisms, cellular debris, and various chemical pollutants. To overcome these obstacles, we developed a wastewater metaproteomics approach including efficient protein extraction and an optimized data-processing pipeline. The pipeline utilizes de novo sequencing to customize large public sequence databases to enable comprehensive metaproteomic coverage. Using this approach, we analyzed wastewater samples collected over approximately three months from two urban locations. This revealed a core microbiome comprising a broad spectrum of microbes, gut bacteria and potential opportunistic pathogens. Additionally, we identified nearly 200 human proteins, including promising population-level health indicators, such as immunoglobulins, uromodulin, and cancer-associated proteins.
Methods and tools
- Wastewater microbial + human biomarker metaproteomics: Delft (Pabst / van Loosdrecht) metaproteomics workflow for raw wastewater: efficient protein extraction plus a de novo-sequencing step that customises large public sequence databases so search coverage stays high in the presence of a heterogeneous, chemically noisy matrix. Applied to two urban WWTPs over ~3 months to profile a core microbiome (gut bacteria, opportunistic pathogens) alongside ~200 human proteins as population-level health indicators (immunoglobulins, uromodulin, cancer-associated proteins).