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Assisted Selection of Biomarkers by Linear Discriminant Analysis Effect Size LEfSe in Microbiome Data

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EMBED: Essential MicroBiomE Dynamics, a dimensionality reduction approach for longitudinal microbiome studies.

Mayar Shahin¹, Brian Ji², Purushottam D Dixit^3,4,5,6

¹Department of Physics, University of Florida, Gainesville, FL, 32611, USA. mayar.shahin@ufl.edu.

NPJ Systems Biology and Applications

|June 20, 2023

Summary

This summary is machine-generated.

We developed EMBED, a new method for microbiome analysis. EMBED simplifies complex microbial community data, revealing essential dynamics at both community and individual bacteria levels.

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Area of Science:

Microbiome research
Computational biology
Systems ecology

Background:

High-dimensional microbiome data present challenges for understanding ecological dynamics.
Existing methods lack the ability to represent microbiome dynamics at both community and individual taxa levels simultaneously.

Purpose of the Study:

To introduce EMBED (Essential MicroBiomE Dynamics), a novel probabilistic nonlinear tensor factorization approach.
To provide a method for dimensionality reduction of microbiome data that captures collective behaviors and individual taxa dynamics.

Main Methods:

EMBED infers ecological normal modes (ECNs) analogous to normal mode analysis in structural biophysics.
The approach utilizes probabilistic nonlinear tensor factorization to model microbiome dynamics.
Multi-subject treatment is incorporated to identify subject-specific and universal dynamics.

Main Results:

A small number of ECNs accurately approximate complex microbiome dynamics across various datasets.
Inferred ECNs serve as templates for partitioning individual bacterial dynamics.
EMBED successfully identifies subject-specific and universal abundance patterns missed by traditional methods.

Conclusions:

EMBED is a versatile tool for dimensionality reduction in microbiome studies.
The method offers novel insights into collective and individual microbial behaviors.
EMBED advances the analysis of complex ecological interactions within microbial communities.