ArticleFrontiers in microbiology2021
Reverse Microbiomics: A New Reverse Dysbiosis Analysis Strategy and Its Usage in Prediction of Autoantigens and Virulent Factors in Dysbiotic Gut Microbiomes From Rheumatoid Arthritis Patients.
Article in Frontiers in microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers, 1 of them a synthesis that pooled it.
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Who cites it
12 citing papers in PubMed, 1 synthesis or guideline pooled it, 12 citations in OpenAlex.
- Profiling of human lung and gut microbiomes in different conditions of chronic obstructive pulmonary disease using ontology-based evidence synthesis and reasoning.Frontiers in cellular and infection microbiology · 2026Pooled it
- Time-Controlled Refrigerated Stem Cell Therapy Mitigates Scleroderma Fibrosis via Modulation of Mitochondrial Autophagy and Gut Metabolism.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Hydrogels Modulating the Microbiome: Therapies for Tissue Regeneration with Infection Control.Gels (Basel, Switzerland) · 2025Review
- Immunomodulatory properties of the gut microbiome: diagnostic and therapeutic potential for rheumatoid arthritis.Clinical and experimental medicine · 2025Review
- Investigating the causal relationship between the gut microbiome and rheumatoid arthritis: mediating effects of immune cells.Journal of translational medicine · 2025Article
- Treatment for Rheumatoid Arthritis Associated With Alterations in the Gastrointestinal Microbiota.ACR open rheumatology · 2024Article
- Microbial Mechanisms of Rheumatoid Arthritis Pathogenesis.Current rheumatology reports · 2024Review
- Relationship between gut microbiota and rheumatoid arthritis: A bibliometric analysis.Frontiers in immunology · 2023Article
- COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning.Briefings in bioinformatics · 2022Article
- Prediction of Pathogenic Factors in Dysbiotic Gut Microbiomes of Colorectal Cancer Patients Using Reverse Microbiomics.Frontiers in oncology · 2022Article
- Characteristics of the Gut Microbiome and Its Relationship With Peripheral CD4Frontiers in microbiology · 2022Article
- EnteropathogenicFrontiers in cellular and infection microbiology · 2021Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alterations in the gut microbiome have been associated with various human diseases. Most existing gut microbiome studies stopped at the stage of identifying microbial alterations between diseased or healthy conditions. As inspired by reverse vaccinology (RV), we developed a new strategy called Reverse Microbiomics (RM) that turns this process around: based on the identified microbial alternations, reverse-predicting the molecular mechanisms underlying the disease and microbial alternations. Our RM methodology starts by identifying significantly altered microbiota profiles, performing bioinformatics analysis on the proteomes of the microbiota identified, and finally predicting potential virulence or protective factors relevant to a microbiome-associated disease. As a use case study, this reverse methodology was applied to study the molecular pathogenesis of rheumatoid arthritis (RA), a common autoimmune and inflammatory disease. Those bacteria differentially associated with RA were first identified and annotated from published data and then modeled and classified using the Ontology of Host-Microbiome Interactions (OHMI). Our study identified 14 species increased and 9 species depleted in the gut microbiota of RA patients. Vaxign was used to comparatively analyze 15 genome sequences of the two pairs of species: Gram-negative
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