LungMicroHostR: an R package for integrated host-microbiome analysis of bronchoalveolar lavage fluid metagenomic...

Bronchoalveolar lavage fluid metagenomic next-generation sequencing captures microbial profiles and host-derived molecular measurements from the same respiratory specimen, but downstream analysis requires coordinated handling of low-biomass microbial signals, negative-control information and multiple feature tables.

We developed LungMicroHostR, an R package for downstream host-microbiome analysis of bronchoalveolar lavage fluid metagenomic sequencing data. The package brings processed microbial profiles, host-derived molecular measurements, sample metadata and negative-control information into a unified R workflow for feature filtering, comparative model evaluation, visualization and reproducible reporting.

Using the public GSE252118 resource comprising 402 samples from patients with lung cancer or pulmonary infections, LungMicroHostR assembled matched microbial, host and clinical feature tables, estimated prevalence in negative controls and compared host transcriptomic, microbial-profile and combined host-microbial models. In the test set, the 10-feature host transcriptome nearest-centroid model achieved an AUC of 0.772 (95% confidence interval, 0.680-0.860), the five-feature RNA microbial logistic model achieved an AUC of 0.745 (0.655-0.832), and the combined host transcriptome-RNA microbial logistic model achieved an AUC of 0.765 (0.655-0.866) with balanced accuracy of 0.720. An external PRJNA714488 BALF shotgun metagenomic dataset was additionally analysed at the mOTU level; LungMicroHostR matched the resulting feature table with phenotype metadata and generated a 388-feature by 26-sample microbial abundance matrix.

LungMicroHostR provides documented functions for respiratory metagenomic analyses that require joint evaluation of microbial profiles, host-derived measurements, negative-control information and external microbial feature tables.