Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows microorganisms to adapt rapidly to environmental pressures and interactions with other organisms. Central to understanding this diversity is the distinction between the core and pan genomes.
The core genome comprises the genes shared by all sampled strains of a species, representing essential functions needed for fundamental cellular processes. For example, Salmonella enterica is estimated to contain roughly 2,800 core genes, though this number varies with the strains analyzed. In contrast, the pan-genome includes every gene found across all strains, incorporating both core and strain-specific genes. Certain serovars, such as S. enterica Typhimurium, contribute unique genes that expand the species’ pan-genome.
Horizontal gene transfer (HGT) is a major driver of gene acquisition, introducing new traits that enable microbes to resist antibiotics, occupy new niches, or metabolize novel substrates. However, many acquired genes offer no benefit and may be removed through genomic deletions or genetic drift, helping maintain streamlined genomes in many microbial lineages. At the same time, some microbes experience gene expansion when their ecological niches demand broader metabolic capabilities.
Comparative genomics has revealed that all bacterial and archaeal genomes share a small set of approximately 30–60 universally conserved gene families. These genes encode core functions such as DNA replication, transcription, translation, and basic metabolic pathways, reflecting deep evolutionary constraints.
Together, gene acquisition, loss, and selective retention illustrate how microbial genomes remain both remarkably adaptable and fundamentally constrained by essential biological requirements.
Microbial genomes change over time through the gain and loss of genes.
Within a species, multiple strains consistently inherit a shared set of genes known as the core genome.
For example, the bacterial species X has been estimated to possess around 5 core gene families shared across the analysed strains.
Also, some strains can gain extra genes, often through horizontal gene transfer.
The pangenome of species X is formed by the full set of core gene families present across the strains studied, plus the extra genes found across many strains.
In some species, the pan-genome continuously expands as new sets of genes are gained.
These acquired genes can be neutral or even harmful, leading to gene deletions that are common in microbial genomes, while natural selection retains beneficial genes.
So, all the genes for basic survival are part of the core genome of a species.
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