ArticleMicrobiome2013
From meta-omics to causality: experimental models for human microbiome research.
Article in Microbiome, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers, 1 of them a synthesis that pooled it.
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
78 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The gut microbiome-metabolome dataset collection: a curated resource for integrative meta-analysis.NPJ biofilms and microbiomes · 2022Pooled it
- DietaryFood science & nutrition · 2026Article
- Metagenomic sequencing reveals high reproducibility of human donor microbiota transplanted into germ-free mice via lower gut route.Journal of Zhejiang University. Science. B · 2026Article
- Towards standardization in pig microbiome research based on a comprehensive twenty-year review.Animal microbiome · 2026Review
- Gut-microbiota-mediated host immune modulation: mechanisms, pathological dysbiosis, and therapeutic frontiers.Frontiers in cellular and infection microbiology · 2026Review
- Leveraging beneficial microbiome-immune interactions via probiotic use in cancer immunotherapy.Frontiers in immunology · 2025Review
- Phages indirectly maintain tomato plant pathogen defense through regulation of the commensal microbiome.ISME communications · 2025Article
- The Future Exploring of Gut Microbiome-Immunity Interactions: From In Vivo/Vitro Models to In Silico Innovations.Microorganisms · 2024Review
- Infant microbiome cultivation and metagenomic analysis reveal Bifidobacterium 2'-fucosyllactose utilization can be facilitated by coexisting species.Nature communications · 2023Article
- Illuminating the oral microbiome and its host interactions: animal models of disease.FEMS microbiology reviews · 2023Review
- Paradoxical Reactions to Anti-TNFα and Anti-IL-17 Treatment in Psoriasis Patients: Are Skin and/or Gut Microbiota Involved?Dermatology and therapy · 2023Review
- microBiomeGSM: the identification of taxonomic biomarkers from metagenomic data using grouping, scoring and modeling (G-S-M) approach.Frontiers in microbiology · 2023Article
- Comparative analysis of the intestinal microbiome inFrontiers in microbiology · 2023Article
- Review
- Induction of mastitis by cow-to-mouse fecal and milk microbiota transplantation causes microbiome dysbiosis and genomic functional perturbation in mice.Animal microbiome · 2022Article
- Cancer-Associated Microbiota: From Mechanisms of Disease Causation to Microbiota-Centric Anti-Cancer Approaches.Biology · 2022Review
- HDHL-INTIMIC: A European Knowledge Platform on Food, Diet, Intestinal Microbiomics, and Human Health.Nutrients · 2022Article
- Material Engineering in Gut Microbiome and Human Health.Research (Washington, D.C.) · 2022Review
- Evolutionary Relationships Between Dysregulated Genes in Oral Squamous Cell Carcinoma and Oral Microbiota.Frontiers in cellular and infection microbiology · 2022Article
- Skin microbiota dynamics following B. subtilis formulation challenge: an in vivo study in mice.BMC microbiology · 2021Article
18 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Large-scale 'meta-omic' projects are greatly advancing our knowledge of the human microbiome and its specific role in governing health and disease states. A myriad of ongoing studies aim at identifying links between microbial community disequilibria (dysbiosis) and human diseases. However, due to the inherent complexity and heterogeneity of the human microbiome, cross-sectional, case-control and longitudinal studies may not have enough statistical power to allow causation to be deduced from patterns of association between variables in high-resolution omic datasets. Therefore, to move beyond reliance on the empirical method, experiments are critical. For these, robust experimental models are required that allow the systematic manipulation of variables to test the multitude of hypotheses, which arise from high-throughput molecular studies. Particularly promising in this respect are microfluidics-based in vitro co-culture systems, which allow high-throughput first-pass experiments aimed at proving cause-and-effect relationships prior to testing of hypotheses in animal models. This review focuses on widely used in vivo, in vitro, ex vivo and in silico approaches to study host-microbial community interactions. Such systems, either used in isolation or in a combinatory experimental approach, will allow systematic investigations of the impact of microbes on the health and disease of the human host. All the currently available models present pros and cons, which are described and discussed. Moreover, suggestions are made on how to develop future experimental models that not only allow the study of host-microbiota interactions but are also amenable to high-throughput experimentation.
Identifiers
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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.