mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation

Area of Science:

• Genomics
• Microbiome research
• Bioinformatics

Background:

• Large-scale studies collect host mutational profiles and microbiome data.
• Integrating host genetics and microbial data offers insights into disease development and treatment responses.
• 16S ribosomal RNA (rRNA) sequencing and whole genome sequencing reveal the interplay between human genetics and microbial communities.

Purpose of the Study:

• Introduce mbQTL, the first R package for integrating 16S rRNA sequencing with single-nucleotide variation (SNV) and single-nucleotide polymorphism (SNP) data.
• Facilitate the identification of microbe-SNV pairs and their association with microbial abundance.

Main Methods:

• The mbQTL package implements statistical methods for identifying microbe-SNV associations.
• It includes relevant statistical measures and plotting functionalities for data interpretation.

Main Results:

• The study introduces the mbQTL R package, a novel tool for analyzing host genetic variation and microbial communities.
• The package integrates diverse data types, including 16S rRNA sequencing and SNV/SNP data.

Conclusions:

• The mbQTL package provides a comprehensive framework for exploring microbe-quantitative trait loci (mbQTLs).
• This tool is expected to advance research into the genetic underpinnings of the human microbiome and its impact on health and disease.