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Microbiome Toolbox: methodological approaches to derive and visualize microbiome trajectories.

Jelena Banjac1, Norbert Sprenger2, Shaillay Kumar Dogra2

  • 1Data Science, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne 1015, Switzerland.

Bioinformatics (Oxford, England)
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Summary

The Microbiome Toolbox offers interactive visualizations and analysis methods for understanding dynamic gut microbiome changes. This open-source Python package aids in exploring microbial data, predicting trajectories, and detecting anomalies over time.

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Area of Science:

  • Microbiome research
  • Computational biology
  • Data science

Background:

  • The gut microbiome is highly dynamic, influenced by factors like age, diet, and medication.
  • Analyzing longitudinal microbiome data presents challenges due to its complexity and rapid changes.

Purpose of the Study:

  • To introduce the Microbiome Toolbox, a software solution for analyzing and visualizing longitudinal microbiome data.
  • To provide researchers with tools for comprehensive exploration, analysis, and reporting of microbiome dynamics.

Main Methods:

  • The Microbiome Toolbox integrates methods for data preparation, feature selection, and statistical analysis.
  • Includes techniques for microbiome trajectory prediction, anomaly detection, and simulated interventions.
  • Utilizes interactive visualizations for enhanced comprehension and reporting of microbiome data.

Main Results:

  • The toolbox facilitates analysis of microbiome features (taxa, functional modules) and associated metadata.
  • Enables two-group analysis, longitudinal anomaly detection, and trajectory differentiation.
  • Offers prediction of microbiome trajectories with feature importance and statistical analysis for universality testing.

Conclusions:

  • The Microbiome Toolbox is an open-source, modular Python package designed for researchers studying gut microbiome changes.
  • It provides a comprehensive suite of tools for in-depth analysis and interactive exploration of longitudinal microbiome data.
  • The software is available on GitHub, promoting accessibility and further development.