Diversity within species: interpreting strains in microbiomes.

Area of Science:

• Microbiology
• Genetics
• Bioinformatics

Background:

• Traditional methods for studying within-species microbial variation relied on culturable isolates and low-resolution techniques.
• Advances in metagenomic sequencing offer culture-free, high-resolution analysis of strain and subspecies diversity.
• The proliferation of methods and terminology for infraspecific variation analysis presents a challenge for researchers.

Purpose of the Study:

• To clarify advances in studying within-species bacterial and archaeal diversity using metagenomics.
• To provide a comprehensive overview of microevolutionary concepts relevant to microbial population genetics.
• To guide researchers in selecting appropriate terms and analytical approaches for high-resolution microbiome data.

Main Methods:

• Review of microevolutionary concepts and population genetics principles.
• Summary of metagenomic approaches for analyzing within-species variation.
• Description of common applications of metagenomic data for studying infraspecific diversity.

Main Results:

• Metagenomics enables high-throughput, culture-free, high-resolution analysis of microbial infraspecific variation.
• Established foundational microevolutionary concepts applicable to microbial communities.
• Detailed how within-species variation can be studied and stratified within complex microbiomes.

Conclusions:

• Metagenomic sequencing is a powerful tool for dissecting microbial strain and subspecies diversity.
• Standardized terminology and analytical approaches are crucial for advancing microbiome research.
• This review facilitates the effective utilization of large-scale, high-resolution microbiome sequencing data.