ArticleCell reports methods2023
Causal inference on microbiome-metabolome relations in observational host-microbiome data via in silico in vivo association pattern analyses.
Article in Cell reports methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 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
13 citing papers in PubMed, 14 citations in OpenAlex.
- From association to causality: mechanistic pathways linking the gut microbiome to psychiatric disorders.Translational psychiatry · 2026Review
- Integrating host-microbiome multi-omics with machine learning: methods, benchmarks, and translational applications.Science China. Life sciences · 2026Review
- Article
- From association to causation: a decision-aware framework for reproducible biomarker discovery and precision intervention design in the human gut microbiome.Briefings in bioinformatics · 2026Article
- Biohacking the human gut microbiome for precision health and therapeutic innovation.Frontiers in microbiology · 2026Review
- Toward the Next Generation of In Silico Modeling of Dynamic Host-Microbiota Interactions in the Skin.JID innovations : skin science from molecules to population health · 2025Review
- Deciphering dynamic antibiotics-microbiome-metabolome interactions in preterm infants using systems biology.iScience · 2025Article
- How is the human microbiome linked to kidney stones?Frontiers in cellular and infection microbiology · 2025Review
- Characterising functional redundancy in microbiome communities via relative entropy.Computational and structural biotechnology journal · 2025Article
- Coupling metabolomics and exome sequencing reveals graded effects of rare damaging heterozygous variants on gene function and human traits.Nature genetics · 2025Article
- In silico metabolic modelling links microbiome-derived metabolites to risk factors of Alzheimer's disease.Gut microbes reports · 2025Article
- Integrating multi-omics to unravel host-microbiome interactions in inflammatory bowel disease.Cell reports. Medicine · 2024Review
- Progress on network modeling and analysis of gut microecology: a review.Applied and environmental microbiology · 2024Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 3 institutions in 3 countries.
Funding
Abstract
Understanding the effects of the microbiome on the host's metabolism is core to enlightening the role of the microbiome in health and disease. Herein, we develop the paradigm of in silico in vivo association pattern analyses, combining microbiome metabolome association studies with in silico constraint-based community modeling. Via theoretical dissection of confounding and causal paths, we show that in silico in vivo association pattern analyses allow for causal inference on microbiome-metabolome relations in observational data. We justify the corresponding theoretical criterion by structural equation modeling of host-microbiome systems, integrating deterministic microbiome community modeling into population statistics approaches. We show the feasibility of our approach on a published multi-omics dataset (n = 347), demonstrating causal microbiome-metabolite relations for 26 out of 54 fecal metabolites. In summary, we generate a promising approach for causal inference in metabolic host-microbiome interactions by integrating hypothesis-free screening association studies with knowledge-based in silico modeling.
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.