ReviewComputational and structural biotechnology journal2022
Modeling approaches for probing cross-feeding interactions in the human gut microbiome.
Review in Computational and structural biotechnology journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 40 citations in OpenAlex.
- Optimization and application of probiotics complex for grouper based on dynamic model.World journal of microbiology & biotechnology · 2026Article
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- Dietary and water probiotics enhance immunity, modulate microbiota, and increase survival of Penaeus vannamei challenged with V. parahaemolyticus.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- Article
- Mapping the Gut Microbiota Composition in the Context of Raltegravir, Dolutegravir, and Bictegravir-A Scoping Review.International journal of molecular sciences · 2025Article
- RBI: a novel algorithm for regulatory-metabolic network model in designing the optimal mutant strain.PeerJ. Computer science · 2025Article
- Article
- Screening Microbial Interactions During Inulin Utilization Reveals Strong Competition and Proteomic Changes in Lacticaseibacillus paracasei M38.Probiotics and antimicrobial proteins · 2024Article
- Using metabolic networks to predict cross-feeding and competition interactions between microorganisms.Microbiology spectrum · 2024Article
- PyCoMo: a python package for community metabolic model creation and analysis.Bioinformatics (Oxford, England) · 2024Article
- Article
- Effect of a multi-strain probiotic mixture consumption on anxiety and depression symptoms induced in adult mice by postnatal maternal separation.Microbiome · 2024Article
- Gut microbiome-metabolome interactions predict host condition.Microbiome · 2024Article
- ScyNet: Visualizing interactions in community metabolic models.Bioinformatics advances · 2024Article
- Evolution of a cross-feeding interaction following a key innovation in a long-term evolution experiment withMicrobiology (Reading, England) · 2023Article
- Pharmacomicrobiomics and type 2 diabetes mellitus: A novel perspective towards possible treatment.Frontiers in endocrinology · 2023Review
- Multi-omics in Crohn's disease: New insights from inside.Computational and structural biotechnology journal · 2023Review
- Microbial interactions and the homeostasis of the gut microbiome: the role ofMicrobiome research reports · 2023Review
- Article
- Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microbial communities perform emergent activities that are essentially different from those carried by their individual members. The gut microbiome and its metabolites have a significant impact on the host, contributing to homeostasis or disease. Food molecules shape this community, being fermented through cross-feeding interactions of metabolites such as lactate, acetate, and amino acids, or products derived from macromolecule degradation. Mathematical and experimental approaches have been applied to understand and predict the interactions between microorganisms in complex communities such as the gut microbiota. Rational and mechanistic understanding of microbial interactions is essential to exploit their metabolic activities and identify keystone taxa and metabolites. The latter could be used in turn to modulate or replicate the metabolic behavior of the community in different contexts. This review aims to highlight recent experimental and modeling approaches for studying cross-feeding interactions within the gut microbiome. We focus on short-chain fatty acid production and fiber fermentation, which are fundamental processes in human health and disease. Special attention is paid to modeling approaches, particularly kinetic and genome-scale stoichiometric models of metabolism, to integrate experimental data under different diet and health conditions. Finally, we discuss limitations and challenges for the broad application of these modeling approaches and their experimental verification for improving our understanding of the mechanisms of microbial interactions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.