Comparative genomics reveals population structure and functional differentiation in Limosilactobacillus fermentum

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Limosilactobacillus fermentum is a widespread lactic acid bacterium found in fermented foods and host microbiota.
• Its global genomic diversity and functional variability are not well understood.

Purpose of the Study:

• To characterize the population genomic diversity and functional potential of Limosilactobacillus fermentum.
• To establish a genomic framework for understanding L. fermentum diversity.

Main Methods:

• Comparative genomic analysis of 336 L. fermentum genomes.
• Average Nucleotide Identity (ANI) for species validation and population structure analysis.
• Pangenome reconstruction and Heap's law modeling.

Main Results:

• 15 genomic clusters and four dominant lineages were identified within L. fermentum.
• A weakly open pangenome with a large accessory gene component was observed.
• Functional annotation highlighted variations in carbohydrate metabolism, membrane functions, and defense systems across lineages.

Conclusions:

• Genomic lineage, rather than isolation source, is the primary driver of gene-content variation in L. fermentum.
• Strain-level functional diversity exists, particularly in carbohydrate metabolism and stress response.
• This study provides a population genomic framework for L. fermentum research.