EMBED: Essential MicroBiomE Dynamics, a dimensionality reduction approach for longitudinal microbiome studies.
NPJ Syst Biol Appl
; 9(1): 26, 2023 06 20.
Article
en En
| MEDLINE
| ID: mdl-37339950
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: Essential MicroBiomE Dynamics, 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.
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Microbiota
Tipo de estudio:
Prognostic_studies
Idioma:
En
Revista:
NPJ Syst Biol Appl
Año:
2023
Tipo del documento:
Article
País de afiliación:
Estados Unidos
Pais de publicación:
Reino Unido