Although microbial strains may belong to the same species, they do not necessarily possess identical genomes. Modern comparative genomics has shown that microbial diversity can be divided into two complementary components: the core genome and the accessory genome. Understanding these concepts has become essential for microbial research, industrial biotechnology and strain selection.
The core genome corresponds to the set of genes shared by every strain included in a comparative analysis. These genes are generally involved in essential cellular functions such as DNA replication, protein synthesis, central metabolism and cell division.
Because the core genome evolves relatively slowly, it provides an excellent framework for studying evolutionary relationships, reconstructing phylogenies and identifying conserved biological functions.
The accessory genome contains genes that are present in only a subset of strains. These genes may be carried by plasmids, genomic islands, prophages, transposons or other mobile genetic elements acquired during evolution.
Accessory genes often provide adaptive advantages. They may encode antimicrobial resistance, specialised metabolic pathways, stress tolerance, virulence factors or functions that improve survival in particular ecological or industrial environments.
For industrial microbiology, the accessory genome is frequently responsible for the characteristics that distinguish one production strain from another. Two strains classified within the same species may exhibit different fermentation performances, flavour production, enzymatic activities or resistance to industrial stresses because of differences in their accessory genome.
Studying these differences helps researchers identify valuable strains and better understand the genetic basis of industrial phenotypes.
Core and accessory genome analyses are routinely combined with SNP analysis, pangenome analysis and synteny analysis to obtain a comprehensive view of microbial diversity. Together, these approaches allow researchers to compare strains, monitor genomic evolution and identify genetic markers associated with specific biological properties.
These analyses are widely used in industrial fermentation, food biotechnology, environmental microbiology, veterinary microbiology and microbial ecology.
Numerous industrial microorganisms illustrate the importance of the accessory genome. Different strains of lactic acid bacteria, yeasts or Bacillus species may possess unique metabolic pathways or plasmids responsible for flavour production, stress resistance or probiotic properties.
Understanding which genes belong to the core genome and which belong to the accessory genome enables companies to better select, characterise and protect their microbial strains.
Biomanda provides bioinformatics services dedicated to microbial comparative genomics. Depending on the project, analyses may include genome assembly, annotation, pangenome construction, core genome extraction, accessory genome comparison, SNP analysis and biological interpretation.
These analyses support industrial R&D, strain selection and genomic characterisation across food biotechnology, fermentation, environmental microbiology and animal health.
The distinction between the core genome and the accessory genome has transformed our understanding of microbial diversity. Rather than viewing a species as a single genome, comparative genomics reveals a dynamic genetic landscape that explains adaptation, evolution and industrial performance.
Combined with pangenome analysis and comparative genomics, these concepts have become essential tools for modern microbial research.