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

微生物ゲノムは遺伝子の増減を通じて時間とともに変化します。種内では、複数の系統がコアゲノムと呼ばれる共通の遺伝子セットを一貫して受け継ぎます。例えば、細菌種Xは解析株全体で共有する約5つのコア遺伝子ファミリーを持つと推定されています。また、一部の株は水平遺伝子移動を通じて追加の遺伝子を得ることもあります。種Xのパンゲノムは、研究された株全体に存在するコア遺伝子ファミリーの全セットと、多くの株にまたがる追加の遺伝子によって形成されます。一部の種では、新しい遺伝子セットが得られるにつれてパンゲノムが継続的に拡大します。これらの獲得遺伝子は中性的または有害であり、微生物ゲノムでよく見られる遺伝子欠失を引き起こす一方で、自然選択は有益な遺伝子を保持します。つまり、基本的な生存のためのすべての遺伝子は、種のコアゲノムの一部です。

微生物ゲノムの進化

微生物ゲノム進化は、種や系統を超えた遺伝子の継続的な増減によって形作られた非常に動的なプロセスです。このゲノムの柔軟性により、微生物は環境圧力や他の生物との相互作用に迅速に適応できます。この多様性を理解する上で中心的なのはコアゲノムとパンゲノムの区別です。コアゲノムは、種のサンプル化されたすべての系統が共有する遺伝子で構成されており、基本的な細胞プロセスに必要な重要な機能を表現しています。例えば、 サルモネラ・エンテリカ は約2,800個のコア遺伝子を含むと推定されていますが、この数は分析される株によって異なります。これに対し、パンゲノムはすべての株にまたがるすべての遺伝子を含み、コア遺伝子と株特異的遺伝子の両方を取り入れています。 S. enterica Typhimuriumのような特定のセロバは、種の全ゲノムを拡大する独自の遺伝子を提供します。水平遺伝子移動(HGT)は遺伝子獲得の主要な推進力であり、微生物が抗生物質に抵抗したり、新たなニッチを占めたり、新しい基質を代謝したりする新しい形質を導入します。しかし、多くの獲得遺伝子は利益をもたらさず、ゲノム欠失や遺伝的ドリフトによって除去されることもあり、多くの微生物系統でゲノムの効率的な維持に役立ちます。同時に、一部の微生物は生態的ニッチがより広範な代謝能力を必要とする際に遺伝子増殖を経験します。比較ゲノミクスにより、すべての細菌ゲノムおよび古細菌ゲノムは約30〜60の普遍に保存された遺伝子ファミリーの小さなセットを共有していることが明らかになりました。これらの遺伝子はDNA複製、転写、翻訳、基本的な代謝経路などのコア機能をコードしており、深い進化的制約を反映しています。遺伝子獲得、喪失、選択的保持は、微生物ゲノムが驚くほど適応力を持ちつつも、本質的な生物学的要件によって根本的に制約されていることを示しています。

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

微生物学

Unit

ユニット

Microbial Evolution

微生物の進化

KEY TERMS AND CONCEPTS

主要用語と概念

Evolution of Microbial Genome

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

origin of cellular life

How Early Cells Got Their Start

Early cellular life began under the harsh conditions of early Earth, where simple chemicals could form more complex organic molecules. Experimental evidence supports the idea that RNA nucleotides, amino acids, and lipids could arise spontaneously in this environment. Volcanic activity, strong UV radiation, and an atmosphere with little or no free oxygen likely helped drive these reactions. Hydrothermal vents on the ocean floor are considered one likely setting for the first life forms. These...

origin of photosynthesis

How Photosynthesis Changed Earth

Photosynthesis changed Earth’s atmosphere and made complex life possible. It began about 3.4 to 3.8 billion years ago, when the first photosynthetic organisms used light energy to build organic compounds. These early organisms were anoxygenic phototrophs, which means they made food from light but did not release oxygen. Early photosynthesis used hydrogen sulfide (H2S) or ferrous iron (Fe2+) as electron donors instead of water. Because of that, it did not produce molecular oxygen (O2) as a...

evolutionary processes in microbes

How Microbes Gain New Traits

Microbes gain new traits through fast genetic change. Their short generation times help evolution happen quickly. Mutation, horizontal gene transfer, recombination, and genetic drift all contribute to this process. Together, these mechanisms help microbial populations adjust to changing environments. Horizontal gene transfer, or HGT, moves genes between different species. It happens in three main ways: conjugation, transformation, and transduction. Conjugation requires direct cell-to-cell...

evolution of new traits in microbes

Microbial Adaptation in Changing Environments

Microbial adaptation in changing environments can happen very quickly. Microorganisms often evolve fast because they have large population sizes and short generation times. In the lab, these changes can sometimes be measured within days. Natural selection acts on standing genetic variation, which is the genetic diversity already present in a population. When conditions change, helpful traits can be kept and increased because they improve fitness. This lets microbes respond to new pressures...

evolution of microbial genome

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...

microbial phylogeny

Reading Microbial Family Trees

Reading microbial family trees helps scientists study how microorganisms are related. These trees are important in microbial ecology and taxonomy. They use molecular sequences such as DNA, RNA, or proteins to compare bacteria and archaea and trace genetic changes over time. A phylogenetic tree has tips, branches, and nodes. The tips are the species that are sampled or still alive. The branches show evolutionary paths, and branch length reflects the number of genetic changes between nodes.

phylogenetic species concept in microbiology

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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