copyrighter

copyrighter corrects gene copy number (GCN) bias in microbial profiles derived from 16S rRNA amplicon sequencing to improve quantitative accuracy of relative abundance estimates.

Key Features:

• Phylogenetic framework: Leverages a phylogenetic framework based on 2,900 sequenced reference genomes to relate GCN to microbial taxonomy and infer GCN across bacterial and archaeal lineages within the Greengenes database.
• Pre-computed GCN estimates: Uses pre-computed GCN estimates for all taxa in the reference taxonomy to parse and correct microbial profiles without recalculating copy numbers on the fly.
• Rapid correction: Applies parsed pre-computed estimates to perform rapid GCN correction of 16S rRNA amplicon-derived relative abundances.
• Validation: Validated by in silico simulations and in vitro mock community experiments demonstrating improved accuracy of relative abundance estimates and increased congruence between metagenomic data and amplicon profiles.
• Impact on interpretation: Can substantially alter biological interpretations, for example changing gut microbiome enterotype classification from two to three in a twin study after GCN correction.
• Effects on quantitative metrics: Alters estimates of qPCR total abundance and α and β diversity metrics in analyzed datasets.

Scientific Applications:

• Human-associated microbiomes: Refines relative abundance estimates and community structure analyses, including enterotype assignment in gut microbiome studies.
• Anaerobic digester microbiomes: Modifies quantitative abundance estimates and diversity metrics used to assess anaerobic digester communities.
• Reconciliation of metagenomic and amplicon datasets: Improves congruence between shotgun metagenomic data and 16S rRNA amplicon profiles by accounting for GCN variation.
• Culture-independent molecular surveys: Provides corrected abundance data for diversity and ecological analyses in culture-independent surveys across diverse ecosystems.
• qPCR-based quantitation: Informs interpretation of qPCR total abundance estimates by adjusting for gene copy number variation.

Methodology:

Uses a phylogenetic framework built from 2,900 sequenced reference genomes and pre-computed GCN estimates for Greengenes to infer and apply GCN corrections to 16S rRNA amplicon profiles; validated with in silico simulations and in vitro mock communities.