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MODELING MICROBIAL ABUNDANCES AND DYSBIOSIS WITH BETA-BINOMIAL REGRESSION.

作者信息

Martin Bryan D, Witten Daniela, Willis Amy D

机构信息

Department of Statistics, University of Washington.

Departments of Statistics and Biostatistics, University of Washington.

出版信息

Ann Appl Stat. 2020 Mar;14(1):94-115. doi: 10.1214/19-aoas1283. Epub 2020 Apr 16.


DOI:10.1214/19-aoas1283
PMID:32983313
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7514055/
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 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 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.

摘要

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本文引用的文献

[1]
Estimating diversity in networked ecological communities.

Biostatistics. 2022-1-13

[2]
Conditional Regression Based on a Multivariate Zero-Inflated Logistic-Normal Model for Microbiome Relative Abundance Data.

Stat Biosci. 2018-12

[3]
A marginalized two-part Beta regression model for microbiome compositional data.

PLoS Comput Biol. 2018-7-23

[4]
Interrogating the microbiome: experimental and computational considerations in support of study reproducibility.

Drug Discov Today. 2018-6-8

[5]
Latent variable modeling for the microbiome.

Biostatistics. 2019-10-1

[6]
Niche Separation Increases With Genetic Distance Among Bloom-Forming Cyanobacteria.

Front Microbiol. 2018-3-27

[7]
GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data.

PeerJ. 2018-4-2

[8]
Dysbiosis and Its Discontents.

mBio. 2017-10-10

[9]
Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women.

Proc Natl Acad Sci U S A. 2017-8-28

[10]
Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome.

Mov Disord. 2017-5

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