Comparative Genomics of Lactic Acid Bacteria and Probiotic Species
Summary
Comparative genomics of lactic acid bacteria investigates the genetic architecture that underpins their metabolic diversity, adaptation to ecological niches and probiotic functionalities. By analysing the complete and draft genomes of multiple strains and species, researchers discern the core genome – genes shared across a taxon – and the accessory genome comprising niche-specific traits. This approach resolves phylogenetic relationships, reveals genetic determinants of host interactions, and identifies enzymatic and immunomodulatory factors relevant to food fermentation and human health. Insights into carbohydrate utilisation cassettes, bacteriocin biosynthesis, stress-response pathways and CRISPR–Cas immune systems inform strain selection for industrial and therapeutic applications. Together, these studies illuminate global biodiversity among lactobacilli and related genera, providing a blueprint for rational design of next-generation probiotics and improving the safety and efficacy of fermented foods.
Research from Nature Portfolio
Recent studies have established a robust phylogenomic framework of lactobacilli by sequencing over two hundred strains across the genus and associated lactic acid bacteria. This work mapped genetic repertoires for carbohydrate and protein biotransformations, uncovered novel CRISPR–Cas immune systems for potential genome editing, and characterised host-interaction factors such as bacteriocins and stress-tolerance genes. The resulting classification refines species boundaries and guides discovery of unique metabolic pathways, opening avenues for biotechnology, from tailored probiotics to enhanced fermentation processes.
Comparative Genomics of Lactic Acid Bacteria and Probiotic Species publication trend
The graph below shows the total number of articles in comparative genomics of lactic acid bacteria and probiotic species across all publications each year (not limited to Nature Index journals).
Technical terms
Pan-genome: The full complement of genes present across all strains of a species, encompassing core and accessory genes.
Core genome: The set of genes shared by all strains within a given species or group, reflecting essential functions.
Accessory genome: Genes present in some but not all strains, often associated with niche adaptation, antimicrobial production or stress resistance.
Phylogenomics: The application of genome-wide data to infer evolutionary relationships and taxonomic classification among organisms.
CRISPR–Cas system: An adaptive immune mechanism in bacteria that provides resistance against phages and mobile genetic elements, and can be repurposed for genome editing.
References
- Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera. Nature Communications (2015).
- Comparative Genomic and Functional Analysis of 100 Lactobacillus rhamnosus Strains and Their Comparison with Strain GG. PLOS Genetics (2013).
- Lactobacillus paracasei Comparative Genomics: Towards Species Pan-Genome Definition and Exploitation of Diversity. PLOS ONE (2013).
- Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features. mSystems (2017).
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