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Related Concept Videos

Evolution of Microbial Genome01:08

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.
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
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Phylogenetic Species Concept in Microbiology

The phylogenetic species concept (PSC) is a framework used to delineate species based on evolutionary relationships, emphasizing shared ancestry and diagnosable genetic traits. Unlike morphological or biological species concepts, the PSC is particularly advantageous for microbial taxonomy, where traditional reproductive or phenotypic criteria often fall short due to the prevalence of asexual reproduction, minimal morphological differentiation, and widespread horizontal gene transfer among...
Evolutionary Processes in Microbes01:26

Evolutionary Processes in Microbes

Microbial evolution occurs rapidly due to short generation times and a variety of genetic processes, including horizontal gene transfer, mutation, recombination, and genetic drift. These mechanisms collectively enable microbes to adapt swiftly to changing environments.Horizontal gene transfer (HGT) allows genes to move between different species and occurs through three main mechanisms: conjugation, transformation, and transduction. Conjugation involves direct cell-to-cell contact for DNA...
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Genomics

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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
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Explaining microbial phenotypes on a genomic scale: GWAS for microbes.

Bas E Dutilh1, Lennart Backus, Robert A Edwards

  • 1CMBI, NCMLS, Radboud University Medical Centre. Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands. dutilh@cmbi.ru.nl

Briefings in Functional Genomics
|April 30, 2013
PubMed
Summary
This summary is machine-generated.

Microbial genome sequencing offers valuable genotype-phenotype insights. This review details a protocol for microbial functional genomics, enabling gene-trait matching and broader data analysis for biological discovery.

Keywords:
functional genomicsgenome-wide association studiesgenotype–phenotype associationmicrobial genomicsrandom forest

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Area of Science:

  • Microbial genomics
  • Functional genomics
  • Bioinformatics

Background:

  • Increasing availability of microbial genome sequences.
  • Need for consistent phenotype annotation for genotype-phenotype association.
  • Genomic data as a resource for gene function prediction.

Purpose of the Study:

  • To address requirements for successful gene-trait matching in microbial genomics.
  • To outline a protocol for microbial functional genomics.
  • To explore broader applications of association methodologies.

Main Methods:

  • Genome assembly and annotation (including SNPs, orthologous groups, prophages).
  • Data pre-processing and genotype-phenotype association.
  • Visualization and interpretation of results.

Main Results:

  • A comprehensive protocol for microbial functional genomics is presented.
  • Methodologies are adaptable for other data types like transcriptomics and metagenomics.
  • Enables correlation of microbial traits with genomic variations.

Conclusions:

  • Successful gene-trait matching requires standardized annotation.
  • The outlined protocol facilitates microbial functional genomics.
  • The described methods support diverse biological data analysis and discovery.