Genomic Plasticity and Functional Reweighting Facilitate Microbial Adaptation During the Ripening of Artisanal Goat Cheese

TL;DR

This study explores how microbial genomes change during the ripening of artisanal goat cheese, revealing strain-level diversity and functional shifts that support adaptation.

Contribution

The paper introduces a genome-resolved metagenomic analysis of artisanal goat cheese, revealing strain-level heterogeneity and functional reweighting during ripening.

Findings

Genome reconstruction revealed 37 MAGs in early ripening and 141 in mature cheese, showing increased strain-level diversity.

Functional analysis showed coordinated metabolic reweighting in carbohydrate metabolism, with stability in amino acid and lipid metabolism.

Resistance genes and bacteriophages were identified, indicating the role of mobile genetic elements in microbial adaptation.

Abstract

This study presents a genome-resolved shotgun metagenomic analysis of artisanal raw-milk goat cheese from the Masurian region of Poland, addressing the limited understanding of strain-level diversification and functional restructuring during traditional cheese ripening. While microbial succession in cheese has been widely described, comprehensive genome-resolved analyses integrating strain-level genomic heterogeneity, pathway reweighting, and mobile genetic elements in artisanal goat cheese remain scarce. By combining taxonomic profiling with metagenome-assembled genome (MAG) reconstruction and pathway-level functional analysis, we characterised microbial succession and genome plasticity across ripening stages. Genome reconstruction yielded 37 MAGs during early ripening and 141 MAGs in mature cheese, revealing increased genome recoverability and pronounced strain-level heterogeneity within dominant taxa, including Lactiplantibacillus plantarum, Lacticaseibacillus paracasei, and Lactococcus lactis. Alpha diversity increased in mature samples, consistent with progressive community restructuring. Functional profiling demonstrated coordinated metabolic reweighting, particularly within carbohydrate metabolism, while amino acid and lipid metabolism remained proportionally stable. Genome-resolved analyses further identified tetracycline- and sulfonamide-associated resistance determinants and diverse bacteriophages targeting lactic acid bacteria, highlighting the role of mobile genetic elements in horizontal gene transfer and microevolutionary adaptation during ripening.

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