Quantifying Shared and Unique Gene Content across 17 Microbial Ecosystems.

Area of Science:

• Microbial ecology
• Metagenomics
• Bioinformatics

Background:

• Traditional microbial diversity assessment relies on taxonomy.
• Previous microbial gene catalogs are incomplete and inaccurately clustered.
• Quantifying shared genetic elements across diverse microbiomes is lacking.

Purpose of the Study:

• To quantify gene content heterogeneity across 17 distinct ecological niches.
• To compare microbial gene catalogs from human-associated and other environments.
• To identify environmentally differentiating genes and assess shared genetic elements.

Main Methods:

• Analysis of 117,629,181 nonredundant genes from 14,183 metagenomic samples.
• Categorization of samples into human-associated, nonhuman host-associated, and other environments.
• Identification of singleton genes, universally shared genes, and ecology-associated genes.

Main Results:

• 66% of identified genes were singletons, appearing in only one sample.
• Only 1,864 genes (0.001%) were present in all 17 metagenomes analyzed.
• Prior gene catalogs were found to be incomplete and inaccurately clustered.
• Shared species between human gut and environmental microbiomes are often pathogens.

Conclusions:

• Microbial gene content exhibits significant heterogeneity across diverse ecosystems.
• A vast majority of microbial genes are rare, highlighting extensive genetic diversity.
• The study identifies a rare class of universally shared genes and refutes the completeness of existing gene catalogs.