Modeling microbial abundances and dysbiosis with beta-binomial regression

DOI10.1214/19-AOAS1283zbMATH Open1439.62223arXiv1902.02776WikidataQ100301050 ScholiaQ100301050MaRDI QIDQ86089FDOQ86089

Authors: Bryan D. Martin, Amy D. Willis, Bryan D. Martin, Amy Willis, Daniela M. Witten 

Publication date: 1 March 2020

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

Abstract: Using a sample from a population to estimate the proportion of the population with a certain category label is a broadly important problem. In the context of microbiome studies, this problem arises when researchers wish to use a sample from a population of microbes to estimate the population proportion of a particular taxon, known as the taxon's relative abundance. In this paper, we propose a beta-binomial model for this task. Like existing models, our model allows for a taxon's relative abundance to be associated with covariates of interest. However, unlike existing models, our proposal also allows for the overdispersion in the taxon's counts to be associated with covariates of interest. We exploit this model in order to propose tests not only for differential relative abundance, but also for differential variability. The latter is particularly valuable in light of speculation that dysbiosis, the perturbation from a normal microbiome that can occur in certain disease conditions, may manifest as a loss of stability, or increase in variability, of the counts associated with each taxon. We demonstrate the performance of our proposed model using a simulation study and an application to soil microbial data.

Full work available at URL: https://arxiv.org/abs/1902.02776

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zbMATH Keywords

overdispersionbeta-binomialcorrelated datahigh throughput sequencingmicrobiomerelative abundance

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Measures of association (correlation, canonical correlation, etc.) (62H20) Applications of statistics to environmental and related topics (62P12)

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• Modeling microbial abundances and dysbiosis with beta-binomial regression

Cited In (11)

• Modeling clustered binary data with nonparametric unobserved heterogeneity: an application to stock crash analysis
• Identification of microbial features in multivariate regression under false discovery rate control
• Title not available (Why is that?)
• Assessing mediating effects of high‐dimensional microbiome measurements in dietary intervention studies
• A multiview model for relative and absolute microbial abundances
• A Flexible Zero-Inflated Poisson-Gamma Model with Application to Microbiome Sequence Count Data
• A Bayesian framework for identifying consistent patterns of microbial abundance between body sites
• A Zero-Inflated Logistic Normal Multinomial Model for Extracting Microbial Compositions
• corncob
• Modeling microbial abundances and dysbiosis with beta-binomial regression
• Log-Contrast Regression with Functional Compositional Predictors: Linking Preterm Infant's Gut Microbiome Trajectories to Neurobehavioral Outcome

Uses Software

• R
• Bioconductor
• VGAM
• edgeR
• trust
• ggplot2
• Phyloseq
• Voom
• brglm2
• USEARCH
• UPARSE
• DivNet
• DESeq2

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