Work

Integrated microbial and proteomic analysis elucidates quality degradation mechanisms of fresh milk through the industrial processing stage

Year: 2025

Type: article

Abstract: Fresh milk quality deterioration during processing is a major dairy challenge, with microbial-driven protein degradation mechanisms unclear. This study pioneers an integrated microbiome-proteome approach to systematically elucidate the dynamic interplay between microbial succession and protein quality changes during industrial processing. Microbial community analysis revealed oscillatory richness, with 2.3-fold and 1.8-fold increases during pre-treatment (PL) and refrigerated transport (RC), respectively. Pseudomonas (12.4 % → 31.7 %) and Acinetobacter (8.1 % → 19.3 %) dominated key phases, with proteomics showing significant nutrient loss (IgM: −69.8 %; IgG: −54.15 %). Integrating microbial metagenomics with proteolytic pathway analysis identified proteases from Pseudomonas and Acinetobacter as key drivers of protein degradation (68 % activity). Pasteurization cut microbial load by 82 % but paradoxically intensified nutrient loss via protein denaturation. Crucially, our data establish a time-dependent degradation model, revealing that combined microbial enzymatic action and thermal effects account for 76 % of total protein hydrolysis, providing a theoretical framework for developing targeted intervention strategies in dairy processing optimization. • Integrated multi-omics analysis reveals microbial-protein interplay driving fresh milk quality loss. • Dynamic monitoring of microbial and protein changes in fresh milk during processing stages. • Pseudomonas and Acinetobacter dominate critical stages and secrete protease. • Microbial enzymatic action and thermal effects synergistically drive 76 % of total protein hydrolysis. • Time-dependent model quantifies microbial and thermal contributions to degradation for targeted interventions.

Source: Food Chemistry X

DOI: 10.1016/j.fochx.2025.103062