Microbiome compositional data analysis for survival studies

• Published in: NAR genomics and bioinformatics Vol. 6; no. 2; p. lqae038
• Main Authors: Pujolassos, Meritxell, Susín, Antoni, Calle, M Luz
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.06.2024
• Subjects: Methods
• ISSN: 2631-9268; 2631-9268
• DOI: 10.1093/nargab/lqae038

The growing interest in studying the relationship between the human microbiome and our health has also extended to time-to-event studies where researchers explore the connection between the microbiome and the occurrence of a specific event of interest. The analysis of microbiome obtained through high throughput sequencing techniques requires the use of specialized Compositional Data Analysis (CoDA) methods designed to accommodate its compositional nature. There is a limited availability of statistical tools for microbiome analysis that incorporate CoDA, and this is even more pronounced in the context of survival analysis. To fill this methodological gap, we present for survival studies, a new methodology for the identification of microbial signatures in time-to-event studies. The algorithm implements an elastic-net penalized Cox regression model adapted to compositional covariates. We illustrate algorithm for survival studies with a case study about the time to develop type 1 diabetes for non-obese diabetic mice. Our algorithm identified a bacterial signature composed of 21 genera associated with diabetes development. for survival studies is integrated in the R package as an extension of the existing functions for cross-sectional and longitudinal studies.