A multiview model for relative and absolute microbial abundances

The absolute abundance of bacterial taxa in human host-associated environments plays a critical role in reproductive and gastrointestinal health. However, obtaining the absolute abundance of many bacterial species is typically prohibitively expensive. In contrast, relative abundance data for many species are comparatively cheap and easy to collect (e.g., with universal primers for the 16S rRNA gene). In this paper, we propose a method to jointly model relative abundance data for many taxa and absolute abundance data for a subset of taxa. Our method provides point and interval estimates for the absolute abundance of all taxa. Crucially, our proposal accounts for differences in the efficiency of taxon detection in the relative and absolute abundance data. We show that modeling taxon-specific efficiencies substantially reduces the estimation error for absolute abundance, and controls the coverage of interval estimators. We demonstrate the performance of our proposed method via a simulation study, a study of the effect of HIV acquisition on microbial abundances, and a sensitivity study where we jackknife the taxa with observed absolute abundances.

Automated summary

The paper proposes a method to jointly model relative abundance data for many taxa and absolute abundance data for a subset of taxa, providing point and interval estimates for all taxa. By modeling taxon-specific efficiencies, the method substantially reduces estimation error for absolute abundance and controls the coverage of interval estimators. The performance of the proposed method is demonstrated through simulation studies, studies on the effect of HIV acquisition on microbial abundances, and sensitivity studies.