ArticleNature microbiology2022
Identification of shared and disease-specific host gene-microbiome associations across human diseases using multi-omic integration.
Article in Nature microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 98 papers, 4 of them syntheses 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
98 citing papers in PubMed, 4 syntheses or guidelines pooled it, 163 citations in OpenAlex.
- A host of issues: pseudoreplication in host-microbiota studies.Applied and environmental microbiology · 2024Pooled it
- Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases.mSystems · 2024Pooled it
- Identification of host gene-microbiome associations in colorectal cancer patients using mendelian randomization.Journal of translational medicine · 2023Pooled it
- Oxidative stress gene expression, DNA methylation, and gut microbiota interaction trigger Crohn's disease: a multi-omics Mendelian randomization study.BMC medicine · 2023Pooled it
- Advancing the Deciphering of Host-Microbe Crosstalk with Spatial Omics: A Mini-Review.Current microbiology · 2026Review
- Prevotella melaninogenica Alleviate Mycoplasma pneumoniae Infection Through the Butyrate Based on Multi-Omic Analysis and Experimental Validation.Chemical biology & drug design · 2026Article
- Effects of L-threonine supplementation on growth performance, intestinal histology, gut microbiota and gene expression related to gut barrier function in broiler chickens.Poultry science · 2026Article
- Observational
- Omics-based decoding of molecular and metabolic crosstalk in the skin barrier ecosystem.Cell death and differentiation · 2026Review
- Integrating host-microbiome multi-omics with machine learning: methods, benchmarks, and translational applications.Science China. Life sciences · 2026Review
- Sex-biased intratumoral microbiome influences tumor molecular and immune landscape and disease outcomes.Cell reports. Medicine · 2026Article
- Integrative host transcriptomic and mucosal microbiome profiling reveals region-specific host-microbiome associations across the human intestine.bioRxiv : the preprint server for biology · 2026Article
- Navigating multi-omic integration methods for human microbiome research.Nature microbiology · 2026Review
- Fecal microbiota transplantation combined with anti-PD-1 therapy in refractory microsatellite-stable gastric cancer: a phase I feasibility and safety study.Journal for immunotherapy of cancer · 2026Article
- An adaptive weight self-distillation deep learning framework for phenotype prediction from longitudinal gut microbiome data.BMC microbiology · 2026Article
- Article
- Comparative urinary metabolomics reveals unique and shared pathways in COVID-19 and liver diseases.Metabolomics : Official journal of the Metabolomic Society · 2026Article
- Microbiota-host interaction in colorectal cancer: emerging computational technology, multi-omics integration, and mechanisms.Cancer biology & medicine · 2026Review
- Host genotypes interact with microbial communities to modulate gene expression in the human intestine.medRxiv : the preprint server for health sciences · 2026Article
- Metabolic modeling and functional genomics reveal taxa and host gene interactions in colorectal cancer.bioRxiv : the preprint server for biology · 2026Article
38 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
9 authors at 3 institutions in 1 country.
Funding
Abstract
While gut microbiome and host gene regulation independently contribute to gastrointestinal disorders, it is unclear how the two may interact to influence host pathophysiology. Here we developed a machine learning-based framework to jointly analyse paired host transcriptomic (n = 208) and gut microbiome (n = 208) profiles from colonic mucosal samples of patients with colorectal cancer, inflammatory bowel disease and irritable bowel syndrome. We identified associations between gut microbes and host genes that depict shared as well as disease-specific patterns. We found that a common set of host genes and pathways implicated in gastrointestinal inflammation, gut barrier protection and energy metabolism are associated with disease-specific gut microbes. Additionally, we also found that mucosal gut microbes that have been implicated in all three diseases, such as Streptococcus, are associated with different host pathways in each disease, suggesting that similar microbes can affect host pathophysiology in a disease-specific manner through regulation of different host genes. Our framework can be applied to other diseases for the identification of host gene-microbiome associations that may influence disease outcomes.
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.