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The Cultivation, Growth, and Viability of Lactic Acid Bacteria: A Quality Control Perspective

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Ecological diversification and isolate-specific acidification in Lactococcus lactis.

Yuexin Sun¹, Weicheng Li¹, Lai-Yu Kwok¹

¹Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China; Collaborative Innovative Center for Lactic Acid Bacteria and Fermented Dairy Products, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China.

Journal of Dairy Science

|June 23, 2026

Summary

Genomic diversity in Lactococcus lactis reflects ecological origins, with dairy strains showing specialized traits. However, key fermentation performance like acidification is linked to specific gene variations, not broad lineage differences.

Keywords:

Bacteriocin Carbohydrate Metabolism Comparative genomics Domestication Genome-Wide Association Study Niche Adaptation Protein Structure

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Establishment of an Extracellular Acidic pH Culture System

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Published on: November 19, 2017

Area of Science:

Microbiology
Genomics
Food Science

Background:

Lactococcus lactis is crucial for dairy fermentation, but its genomic diversity, ecological origins, and technological functions are not fully understood.
Understanding these links is vital for optimizing fermentation processes and selecting effective starter cultures.

Purpose of the Study:

To investigate if adaptation to different ecological niches drives specific fermentation traits in L. lactis.
To explore the relationship between genomic variation, ecological source, and technological performance in L. lactis isolates.

Main Methods:

Whole-genome sequencing, functional annotation, and phenotyping of 147 globally sourced L. lactis isolates.
Phylogenomic analysis to identify clades based on isolation source (dairy vs. plant/environmental).
Genome-wide association analysis and structural modeling (AlphaFold2) to link genetic loci to acidification kinetics.

Main Results:

Phylogenetic analysis revealed 5 clades structured by isolation source, with distinct genomic features (size, enzyme repertoires, bacteriocin potential).
Dairy-associated clades exhibited lineage-specific genomic architectures and functional specialization; plant-derived clades had broader carbohydrate utilization.
Acidification kinetics were isolate-specific, not clade-level; key loci (kdgA, oppC, recF, gpr, xseB) and localized protein structural flexibility were associated with acidity.

Conclusions:

L. lactis diversification is influenced by ecological niche, but core technological traits like acidification depend on fine-scale genetic variation.
Findings support precision starter selection based on specific genetic markers for improved fermentation.
This study enhances understanding of bacterial domestication within food ecosystems.