Modeling microbial abundances and dysbiosis with beta-binomial regression
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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.
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Cites work
- scientific article; zbMATH DE number 47310 (Why is no real title available?)
- scientific article; zbMATH DE number 4128217 (Why is no real title available?)
- scientific article; zbMATH DE number 1243473 (Why is no real title available?)
- scientific article; zbMATH DE number 720689 (Why is no real title available?)
- scientific article; zbMATH DE number 1873785 (Why is no real title available?)
- scientific article; zbMATH DE number 3307153 (Why is no real title available?)
- scientific article; zbMATH DE number 3050468 (Why is no real title available?)
- 394: The Analysis of Binary Responses from Toxicological Experiments Involving Reproduction and Teratogenicity
- A logistic normal multinomial regression model for microbiome compositional data analysis
- Binary Regression Using an Extended Beta-Binomial Distribution, With Discussion of Correlation Induced by Covariate Measurement Errors
- Modeling microbial abundances and dysbiosis with beta-binomial regression
- Numerical Optimization
- On the existence of maximum likelihood estimates in logistic regression models
- Smoothing spline ANOVA for exponential families, with application to the Wisconsin epidemiological study of diabetic retinopathy. (The 1994 Neyman Memorial Lecture)
- Space-time smoothing of complex survey data: small area estimation for child mortality
- Variable selection for sparse Dirichlet-multinomial regression with an application to microbiome data analysis
- ggplot2. Elegant graphics for data analysis. With contributions by Carson Sievert
Cited in
(11)- A multiview model for relative and absolute microbial abundances
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- Log-Contrast Regression with Functional Compositional Predictors: Linking Preterm Infant's Gut Microbiome Trajectories to Neurobehavioral Outcome
- Modeling clustered binary data with nonparametric unobserved heterogeneity: an application to stock crash analysis
- Modeling microbial abundances and dysbiosis with beta-binomial regression
- scientific article; zbMATH DE number 2087932 (Why is no real title available?)
- Assessing mediating effects of high‐dimensional microbiome measurements in dietary intervention studies
- corncob
- A Zero-Inflated Logistic Normal Multinomial Model for Extracting Microbial Compositions
- 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
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