In microbial genomics, a single reference genome is often not enough to describe the diversity of a species. Two strains may belong to the same species while carrying different genes, different mobile elements, different metabolic capacities or different technological properties.
The concept of the pangenome was developed to describe this diversity. Instead of looking at one genome as representative of a species, pangenome analysis considers the full set of genes found across several related strains.
A pangenome is the complete collection of genes found within a group of related organisms, usually strains from the same species or closely related species. It includes genes shared by all strains and genes present only in some strains.
The genes found in every strain form the core genome. These genes usually correspond to essential biological functions and are useful for phylogeny and species-level comparison. Genes found only in some strains form the accessory genome. They may be involved in adaptation, metabolism, stress resistance, virulence, plasmid functions or industrial traits.
Pangenome analysis is therefore a powerful way to understand how genomic diversity is distributed within a microbial group.
The core genome represents the stable genetic backbone shared by all strains in the analysis. It is often used to study evolutionary relationships and to compare strains at a conserved genomic level.
The accessory genome contains genes that are not present in all strains. These genes can be carried by plasmids, genomic islands, prophages, transposons or other mobile genetic elements. In industrial microbiology, the accessory genome can be highly informative because it may contain genes linked to technological properties, environmental adaptation or strain-specific behaviour.
Understanding both the core and accessory genome is essential when comparing microbial strains for research, quality control or industrial development.
Pangenome analysis helps answer several practical questions. Which genes are shared by all strains? Which genes are specific to a candidate strain? Are some genes associated with a phenotype of interest? Is a strain genetically close to a known industrial lineage? Does a strain contain unique elements that could explain its performance?
In fermentation, probiotics, food microbiology, environmental microbiology or animal health, these questions can be important for strain selection, documentation, monitoring and R&D strategy.
Pangenome analysis also helps compare proprietary strains with public genomes, identify genomic markers, explore microbial diversity and build a clearer understanding of strain portfolios.
Industrial strains are often selected for specific properties such as robustness, productivity, flavour production, stress tolerance, safety, stability or interaction with other microorganisms. These properties may not be explained by species identification alone.
By comparing the gene content of multiple strains, pangenome analysis can help identify genetic features that distinguish high-value strains from less suitable candidates. It can also support the detection of genes related to metabolic pathways, resistance mechanisms, transport systems or specific functional capacities.
For companies working with microbial resources, the pangenome can therefore become a strategic tool for understanding, organising and valorising strain diversity.
Pangenome analysis is one component of comparative genomics. While comparative genomics can include SNP analysis, synteny analysis, genome rearrangements and structural variation, pangenome analysis focuses mainly on gene presence and absence across strains.
Together, these approaches provide a more complete view of microbial diversity. SNP analysis can distinguish very closely related strains, while pangenome analysis can reveal broader differences in gene content and functional potential.
For a broader introduction, read our article on comparative genomics for industrial strain selection.
Biomanda provides bioinformatics services for microbial genomics, comparative genomics and pangenome analysis. Depending on the project, Biomanda can support genome assembly, annotation, orthologous gene clustering, core genome analysis, accessory genome analysis, strain comparison and biological interpretation.
The objective is not only to produce a list of genes, but to help connect genomic diversity with biological meaning and industrial questions. This interpretation can support strain selection, portfolio analysis, microbial characterisation, R&D decisions and communication with partners or clients.
The pangenome is a key concept for understanding microbial diversity. It shows that a species cannot always be represented by a single genome and that strain-specific genes can have major biological and industrial importance.
For industrial microbiology and applied biotechnology, pangenome analysis provides a useful framework to compare strains, identify relevant genomic traits and support better R&D decisions.