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

Dimensionality reduction offers unique insights into high-dimensional microbiome dynamics by leveraging collective abundance fluctuations of multiple bacteria driven by similar ecological perturbations. However, methods providing lower-dimensional representations of microbiome dynamics both at the c...

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Bibliographic Details
Published inNPJ systems biology and applications Vol. 9; no. 1; pp. 26 - 11
Main Authors Shahin, Mayar, Ji, Brian, Dixit, Purushottam D.
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 20.06.2023
Nature Publishing Group
Nature Portfolio
Subjects
631/158
631/57
Antibiotics
Bacteria
Bacteria - genetics
Behavior
Bioinformatics
Biomedical and Life Sciences
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Ecosystem biology
Ecosystems
Life Sciences
Longitudinal studies
Microbiomes
Microbiota - genetics
Systems Biology
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Summary:Dimensionality reduction offers unique insights into high-dimensional microbiome dynamics by leveraging collective abundance fluctuations of multiple bacteria driven by similar ecological perturbations. However, methods providing lower-dimensional representations of microbiome dynamics both at the community and individual taxa levels are not currently available. To that end, we present EMBED: E ssential M icro B iom E D ynamics, a probabilistic nonlinear tensor factorization approach. Like normal mode analysis in structural biophysics, EMBED infers ecological normal modes (ECNs), which represent the unique orthogonal modes capturing the collective behavior of microbial communities. Using multiple real and synthetic datasets, we show that a very small number of ECNs can accurately approximate microbiome dynamics. Inferred ECNs reflect specific ecological behaviors, providing natural templates along which the dynamics of individual bacteria may be partitioned. Moreover, the multi-subject treatment in EMBED systematically identifies subject-specific and universal abundance dynamics that are not detected by traditional approaches. Collectively, these results highlight the utility of EMBED as a versatile dimensionality reduction tool for studies of microbiome dynamics.
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ISSN:2056-7189
2056-7189
DOI:10.1038/s41540-023-00285-6