ArticlePLoS computational biology2018
Interactions between species introduce spurious associations in microbiome studies.
Article in PLoS computational biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
23 citing papers in PubMed, 1 synthesis or guideline pooled it, 33 citations in OpenAlex.
- Meta-analysis of microbiome association networks reveal patterns of dysbiosis in diseased microbiomes.Scientific reports · 2022Pooled it
- Molecular basis of precision nutrition: Food components, microbiome-derived metabolites, and multi-omics modeling.Food chemistry. Molecular sciences · 2026Review
- Spatial Multi-Omics Analysis of the Qianqiu Goat Gut Microbiome and Metabolome.International journal of molecular sciences · 2025Article
- Probiotics Attenuate Food Allergy via Short-Chain Fatty Acids-Mediated Immune Modulation and Gut Barrier Restoration.Foods (Basel, Switzerland) · 2025Article
- Article
- Screening Microbial Interactions During Inulin Utilization Reveals Strong Competition and Proteomic Changes in Lacticaseibacillus paracasei M38.Probiotics and antimicrobial proteins · 2024Article
- Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation.mSystems · 2023Article
- Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities.Bioinformatics (Oxford, England) · 2023Article
- Landscapes and bacterial signatures of mucosa-associated intestinal microbiota in Chilean and Spanish patients with inflammatory bowel disease.Microbial cell (Graz, Austria) · 2021Article
- The Multifaceted Role of Serotonin in Intestinal Homeostasis.International journal of molecular sciences · 2021Review
- Effects of lipid emulsions on the formation of Escherichia coli-Candida albicans mixed-species biofilms on PVC.Scientific reports · 2021Article
- Analysis of Human Gut Microbiota Composition Associated to the Presence of Commensal and Pathogen Microorganisms in Côte d'Ivoire.Microorganisms · 2021Article
- SiGMoiD: A super-statistical generative model for binary data.PLoS computational biology · 2021Article
- Vaccination against the brown stomach worm, Teladorsagia circumcincta, followed by parasite challenge, induces inconsistent modifications in gut microbiota composition of lambs.Parasites & vectors · 2021Article
- Mechanistic insights into the attenuation of intestinal inflammation and modulation of the gut microbiome by krill oil using in vitro and in vivo models.Microbiome · 2020Article
- Infection with the sheep gastrointestinal nematode Teladorsagia circumcincta increases luminal pathobionts.Microbiome · 2020Article
- An Integrated Multi-Disciplinary Perspectivefor Addressing Challenges of the Human Gut Microbiome.Metabolites · 2020Review
- The Pathobiome in Animal and Plant Diseases.Trends in ecology & evolution · 2019Review
- Use and abuse of correlation analyses in microbial ecology.The ISME journal · 2019Review
- Microbiome analysis as a platform R&D tool for parasitic nematode disease management.The ISME journal · 2019Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microbiota contribute to many dimensions of host phenotype, including disease. To link specific microbes to specific phenotypes, microbiome-wide association studies compare microbial abundances between two groups of samples. Abundance differences, however, reflect not only direct associations with the phenotype, but also indirect effects due to microbial interactions. We found that microbial interactions could easily generate a large number of spurious associations that provide no mechanistic insight. Using techniques from statistical physics, we developed a method to remove indirect associations and applied it to the largest dataset on pediatric inflammatory bowel disease. Our method corrected the inflation of p-values in standard association tests and showed that only a small subset of associations is directly linked to the disease. Direct associations had a much higher accuracy in separating cases from controls and pointed to immunomodulation, butyrate production, and the brain-gut axis as important factors in the inflammatory bowel disease.
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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.