Evaluation method for the potential functionome harbored in the genome and metagenome

Area of Science:

• Genomics and Metagenomics
• Microbial Ecology
• Systems Biology

Background:

• Genomic analysis aims to understand organismal and community functions (functionome).
• A standardized method for evaluating functional potential in genomes and metagenomes is lacking.
• Kyoto Encyclopedia of Genes and Genomes (KEGG) functional modules offer a framework for such evaluation.

Purpose of the Study:

• To develop and validate a novel evaluation method for potential functionomes.
• To assess the utility of this method for analyzing prokaryotic species and human gut microbiomes.
• To characterize functional profiles and identify microbial nutritional strategies.

Main Methods:

• Developed a method based on the completion ratio of KEGG functional modules.
• Analyzed 768 prokaryotic species to categorize module distribution patterns.
• Examined 8 phenotypically distinct bacilli and metagenomes from 13 healthy individuals' gut microbiomes.

Main Results:

• KEGG module completion ratios varied significantly across prokaryotic species, falling into universal, restricted, diversified, and non-prokaryotic patterns.
• Analysis of bacilli revealed module sharing patterns correlated with phenotypic similarity.
• Human gut microbiome analysis uncovered microbial nutritional preferences, suggesting a strategy to avoid host competition.

Conclusions:

• The developed method effectively characterizes functionomes in genomes and metagenomes.
• The method simplifies interpretation by providing taxonomic and host information.
• This approach serves as a powerful tool for comparative functional analysis, applicable to diverse and uncultivable microbial communities.