Name: microbial core and pan-genome changes
Uploaded: 2026-03-12T13:57:40.000Z
Duration: 1 min 8 s
Channel: JoVE

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.

evolution of microbial genome

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&#8217; 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&#8211;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.

Evolution of Microbial Genome

Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows ...

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Education

JoVE Core

Microbiology

Unit

Microbial Evolution

KEY TERMS AND CONCEPTS

microbial core and pan-genome changes

Microbial genomes change through gene gain and gene loss. These changes help microbes adapt to new environments and to other organisms they live with. In many species, genome evolution is fast and ongoing.

A key idea is the difference between the core genome and the pan-genome. The core genome is the set of genes shared by all sampled strains of a species. These genes support basic cell functions. For example, Salmonella enterica has about 2,800 core genes, although the exact number can change with the strains studied.

The pan-genome includes every gene found across all strains of a species. It contains both the core genes and genes found only in certain strains. In Salmonella enterica, strains such as S. enterica Typhimurium add unique genes that expand the pan-genome.

Horizontal gene transfer, or HGT, is a major way microbes gain new genes. It can give them traits that help them resist antibiotics, use new nutrients, or live in new habitats. Some acquired genes are not useful and may later be removed by genome deletions or genetic drift, which helps keep many microbial genomes streamlined. In some niches, however, microbes expand their gene sets when they need wider metabolic abilities.

Comparative genomics has also shown that bacterial and archaeal genomes share a small group of about 30 to 60 gene families. These conserved genes carry out DNA replication, transcription, translation, and core metabolism. Together, gene acquisition, gene loss, and selective retention show how microbial genomes stay flexible while still keeping essential biological functions.

Microbial Core and Pan-Genome Changes

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How Microbes Gain New Traits

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Microbial genomes change through gene gain and gene loss. These changes help microbes adapt to new environments and to other organisms they live with. In many species, genome evolution is fast and ongoing. A key idea is the difference between the core genome and the pan-genome. The core genome is the set of genes shared by all sampled strains of a species. These genes support basic cell functions. For example, Salmonella enterica has about 2,800 core genes, although the exact number can change...

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Reading Microbial Family Trees

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phylogenetic-species-concept-in-microbiology

How DNA Defines Microbial Species

The phylogenetic species concept helps define microbial species by looking at DNA and evolutionary relatedness. It focuses on shared ancestry and genetic traits that can be diagnosed in different organisms. This approach is especially useful in microbiology, where other species concepts often do not work well. Traditional morphological and biological species concepts rely on body form or reproduction. Those methods can fall short for microbes because many reproduce asexually, show little...

key terms and concepts

Learn how microbial genomes change through gene gain, gene loss, HGT, core genes, and pan-genomes using Salmonella enterica as an example.

Microbial Core and Pan-Genome Changes | JoVE K12

JoVE Core Microbiology provides an engaging introduction to the microbial world and its influence on health, industry, and the environment. This comprehensive collection covers key concepts such as microbial structure, metabolism, genetics, and ecology. It introduces essential laboratory techniques and microscopy methods through visually engaging animations. Corresponding scientist-in-action videos bridge classroom concepts with real-world research and applications.

microbiology

Microbial Core and Pan-Genome Changes

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