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Evolution of Microbial Genome

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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.

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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.

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The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
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Related Experiment Video

Updated: Jun 14, 2026

Characterization of a Pathogenic Escherichia coli Strain Derived from Oreochromis spp. Farms Using Whole-Genome Sequencing

Characterization of a Pathogenic Escherichia coli Strain Derived from Oreochromis spp. Farms Using Whole-Genome Sequencing

Published on: December 23, 2022

Genome-based insights into the evolution of enterococci.

Willem van Schaik¹, Rob J L Willems

¹Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands.

Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases

|March 30, 2010

Summary

Genomic analysis reveals significant diversity within Enterococcus faecalis and Enterococcus faecium strains, driven by mobile genetic elements. Next-generation sequencing enhances our understanding of these important bacterial pathogens.

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Area of Science:

Microbiology
Genomics
Molecular Biology

Background:

The sequencing of the first free-living organism's genome 15 years ago marked a revolution in microbiology.
Enterococcus faecalis and Enterococcus faecium are major causes of nosocomial infections.
Genomic data has become crucial for understanding microbial pathogens.

Purpose of the Study:

To review recent advancements in the genomics of Enterococcus faecalis and Enterococcus faecium.
To focus on genome-based analyses of enterococcal diversity and phylogeny.
To highlight the impact of next-generation sequencing on characterizing these species.

Main Methods:

Comparative genome hybridization (CGH) was used to assess inter-strain genomic diversity.
Analysis of mobile genetic elements such as phages, plasmids, and pathogenicity islands.
Application of next-generation sequencing (NGS) technologies for comprehensive gene repertoire characterization.

Main Results:

Both Enterococcus faecalis and Enterococcus faecium exhibit substantial genomic diversity among strains.
Genomic variation is primarily attributed to the presence or absence of phages, plasmids, pathogenicity islands, and conjugative elements.
NGS enables robust population structure and diversity analyses across multiple isolates.

Conclusions:

Genomic diversity is a key feature of Enterococcus faecalis and Enterococcus faecium.
Mobile genetic elements play a significant role in shaping the genomes of these enterococci.
Advanced sequencing technologies provide powerful tools for studying bacterial population genetics and evolution.