Metagenomic operational taxonomic units (mOTUs)

Metagenomic operational taxonomic units (mOTUs) enable high-resolution taxonomic and strain-level profiling of microbial communities from shotgun metagenomic and metatranscriptomic sequencing by defining species-level units based on single-copy phylogenetic marker genes.

Key Features:

• Species-Level Resolution: mOTUs identify known and previously unknown microorganisms at species-level resolution using marker genes.
• Reference-Independent Profiling: mOTUs rely on single-copy phylogenetic marker genes to profile communities without requiring complete reference genomes.
• Enhanced Coverage and Precision: In a study of 252 human fecal samples, mOTUs captured on average 43% of species abundance and 58% of richness that genome-based methods missed.
• Broad Taxonomic Profiling: mOTUs can profile over 7,700 microbial species, including taxa lacking reference genomes.
• Quantification of Basal Transcriptional Activity: mOTUs enable quantification of basal transcriptional activity in microbial communities by leveraging essential housekeeping marker genes in metatranscriptomic data.
• Strain-Level Insights: mOTUs produce single-nucleotide variation profiles that facilitate comparison of microbial strain populations and align closely with whole-genome data.

Scientific Applications:

• Human microbiome profiling: Quantifying species abundance, richness, and strain variation in human-associated microbiomes using metagenomic and metatranscriptomic data.
• Environmental microbiology surveys: Characterizing microbial diversity and detecting taxa lacking reference genomes across environmental samples.
• Comparative genomics and population genetics: Comparing strain populations across hosts or environments using single-nucleotide variation profiles derived from mOTUs.
• Microbial transcriptional activity analysis: Assessing basal transcriptional activity of microbial communities via housekeeping marker genes in metatranscriptomes.

Methodology:

mOTUs cluster single-copy phylogenetic marker genes extracted from shotgun metagenomic and metatranscriptomic sequencing to define metagenomic operational taxonomic units and derive single-nucleotide variation profiles for strain-level comparisons.