Journal Article

Modeling time-series data from microbial communities

Dearing, M Denise, Williams, Janet E, Ridenhour, Benjamin J, Miller, Aaron W, Brooker, Sarah L, Remien, Christopher H, Van Leuven, James T

2017

Overview

As sequencing technologies have advanced, the amount of information regarding the composition of bacterial communities from various environments (for example, skin or soil) has grown exponentially. To date, most work has focused on cataloging taxa present in samples and determining whether the distribution of taxa shifts with exogenous covariates. However, important questions regarding how taxa interact with each other and their environment remain open thus preventing in-depth ecological understanding of microbiomes. Time-series data from 16S rDNA amplicon sequencing are becoming more common within microbial ecology, but methods to infer ecological interactions from these longitudinal data are limited. We address this gap by presenting a method of analysis using Poisson regression fit with an elastic-net penalty that (1) takes advantage of the fact that the data are time series; (2) constrains estimates to allow for the possibility of many more interactions than data; and (3) is scalable enough to handle data consisting of thousands of taxa. We test the method on gut microbiome data from white-throated woodrats ( Neotoma albigula ) that were fed varying amounts of the plant secondary compound oxalate over a period of 22 days to estimate interactions between OTUs and their environment.

• Publisher: Nature Publishing Group UK,Oxford University Press,Nature Publishing Group
• Subject: 45/23 / 45/47 / 631/158/1745 / 631/158/2451 / 631/158/853/2006 / 631/326/2565/2134 / 631/326/2565/855 / Animals / Arvicolinae - microbiology / Arvicolinae - physiology / Bacteria / Bacteria - classification / Bacteria - genetics / Bacteria - isolation & purification / Biomedical and Life Sciences / Communities / Ecology / Evolutionary Biology / Feeding Behavior / Gastrointestinal Microbiome / Gastrointestinal Tract - microbiology / Intestinal microflora / Kinetics / Life Sciences / Microbial activity / Microbial Ecology / Microbial Genetics and Genomics / Microbiology / Microbiomes / Microorganisms / Models, Biological / Original / original-article / Oxalic acid / Phylogeny / Plants - parasitology / Poisson density functions / Regression analysis / rRNA 16S / Sequences / Skin / Statistical analysis / Test procedures / Time series