ReviewmSystems
From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota.
Review in mSystems. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
53 citing papers in PubMed.
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- Computational and multi-omics systems biology for precision microbiome therapeutics.Frontiers in microbiomes · 2026Review
- Nutrition as a systems regulator of brain aging trajectories.Frontiers in molecular neuroscience · 2026Review
- Reframing brain aging: neuroinflammation as an interconnected network process.Frontiers in aging · 2026Review
- Competition and cooperation: The plasticity of bacterial interactions across environments.PLoS computational biology · 2025Article
- Reducing redundancy and enhancing accuracy through a phylogenetically-informed microbial community metabolic modeling approach.Bioinformatics (Oxford, England) · 2025Article
- A novel framework unveiling the importance of heterogeneous selection and drift on the community structure of symbiotic microbial indicator taxa across altitudinal gradients in amphibians.Microbiology spectrum · 2025Article
- Microbes as medicine.Annals of the New York Academy of Sciences · 2024Review
- Progress on network modeling and analysis of gut microecology: a review.Applied and environmental microbiology · 2024Review
- Inflammatory bowel disease biomarkers revealed by the human gut microbiome network.Scientific reports · 2023Article
- Integrating Omics Data in Genome-Scale Metabolic Modeling: A Methodological Perspective for Precision Medicine.Metabolites · 2023Review
- Article
- Small molecule modulation of microbiota: a systems pharmacology perspective.BMC bioinformatics · 2022Article
- Review
- Impact of Contaminants on Microbiota: Linking the Gut-Brain Axis with Neurotoxicity.International journal of environmental research and public health · 2022Review
- A Computational Framework for Studying Gut-Brain Axis in Autism Spectrum Disorder.Frontiers in physiology · 2022Article
- Article
- Metagenome-Scale Metabolic Network Suggests Folate Produced byMicroorganisms · 2021Article
- Building Robust Assemblages of Bacteria in the Human Gut in Early Life.Applied and environmental microbiology · 2021Review
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
An important hallmark of the human gut microbiota is its species diversity and complexity. Various diseases have been associated with a decreased diversity leading to reduced metabolic functionalities. Common approaches to investigate the human microbiota include high-throughput sequencing with subsequent correlative analyses. However, to understand the ecology of the human gut microbiota and consequently design novel treatments for diseases, it is important to represent the different interactions between microbes with their associated metabolites. Computational systems biology approaches can give further mechanistic insights by constructing data- or knowledge-driven networks that represent microbe interactions. In this minireview, we will discuss current approaches in systems biology to analyze the human gut microbiota, with a particular focus on constraint-based modeling. We will discuss various community modeling techniques with their advantages and differences, as well as their application to predict the metabolic mechanisms of intestinal microbial communities. Finally, we will discuss future perspectives and current challenges of simulating realistic and comprehensive models of the human gut microbiota.
Indexed as
Identifiers
What OpenQuestion holds
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.