Microbiome modeling: a beginner's guide
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Abstract
Microbiomes, comprised of diverse microbial species and viruses, play pivotal roles in human health, environmental processes, and biotechnological applications and interact with each other, their environment, and hosts via ecological interactions. Our understanding of microbiomes is still limited and hampered by their complexity. A concept improving this understanding is systems biology, which focuses on the holistic description of biological systems utilizing experimental and computational methods. An important set of such experimental methods are metaomics methods which analyze microbiomes and output lists of molecular features. These lists of data are integrated, interpreted, and compiled into computational microbiome models, to predict, optimize, and control microbiome behavior. There exists a gap in understanding between microbiologists and modelers/bioinformaticians, stemming from a lack of interdisciplinary knowledge. This knowledge gap hinders the establishment of computational models in microbiome analysis. This review aims to bridge this gap and is tailored for microbiologists, researchers new to microbiome modeling, and bioinformaticians. To achieve this goal, it provides an interdisciplinary overview of microbiome modeling, starting with fundamental knowledge of microbiomes, metaomics methods, common modeling formalisms, and how models facilitate microbiome control. It concludes with guidelines and repositories for modeling. Each section provides entry-level information, example applications, and important references, serving as a valuable resource for comprehending and navigating the complex landscape of microbiome research and modeling.
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Flagged first, then by citations
- Authors
- Lange, E., Kranert, L., Krüger, J., Benndorf, D., & Heyer, R.
- Affiliations
- Bielefeld University (DE)
- Eindhoven University of Technology (NL)
- Anhalt University of Applied Sciences (DE)
- Corresponding author
- Lange, Emanuel
- Heyer, Robert
- Venue
- Frontiers in Microbiology
- Publisher
- Frontiers Media SA
- Published
- 2024-06-19
- Volume
- 15
- Pages
- 1368377-1368377
- ISSN
- 1664-302X (ISSN-L)
- PMC
- PMC11220171
- OpenAlex
- W4399818955
- Cited by
- 21
- References
- 17
- Citations by year
- 2026: 10 · 2025: 10 · 2024: 1
- FWCI
- 0.85
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Frontiers in Microbiology (publishedVersion, cc-by)
- Preprints.org (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- TU/e Research Portal (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Publikationen an der Universität Bielefeld (Universität Bielefeld) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Keywords
- systems biology, modeling formalisms, interdisciplinary collaboration, microbial interactions, host-microbe interactions
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