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Testing hypotheses about the microbiome using the linear decomposition model (LDM).

Yi-Juan Hu1, Glen A Satten2

  • 1Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322.

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|April 22, 2020
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Summary
This summary is machine-generated.

This study introduces the linear decomposition model (LDM) for microbiome data analysis, offering unified global and individual operational taxonomic unit (OTU) tests while controlling the false discovery rate (FDR). The LDM provides a flexible approach for diverse microbiome studies.

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Area of Science:

  • Microbiome analysis
  • Statistical modeling
  • Bioinformatics

Background:

  • Current microbiome analysis methods are fragmented, with separate tests for global effects and individual operational taxonomic units (OTUs).
  • Existing methods often fail to provide a unified approach, making it difficult to reconcile global and individual OTU findings.
  • Many individual OTU tests do not adequately control the false discovery rate (FDR).

Purpose of the Study:

  • To introduce a unified statistical framework for microbiome data analysis.
  • To develop a method that integrates global microbiome effect testing with individual OTU analysis.
  • To ensure control of the false discovery rate (FDR) in microbiome studies.

Main Methods:

  • Introduction of the linear decomposition model (LDM) for integrated microbiome analysis.
  • The LDM accommodates continuous and discrete variables, interaction terms, and confounding covariates.
  • Utilizes permutation-based P-values for sample correlation and offers an 'omnibus' test for combined results across transformations.

Main Results:

  • The LDM provides correct Type I error for global testing and comparable power to existing distance-based methods.
  • The LDM effectively controlled FDR for individual OTU testing, outperforming DESeq2 and MetagenomeSeq in simulations.
  • The LDM demonstrated flexibility in analyzing diverse microbiome data, with an enhanced PERMANOVA implementation.

Conclusions:

  • The linear decomposition model (LDM) offers a unified and robust approach to microbiome data analysis.
  • LDM effectively controls FDR and integrates global and individual OTU testing.
  • The LDM provides a flexible and powerful tool for various microbiome research applications.