Genetics and Genomics in Host-Pathogen Interactions

Topic Information

Dear Colleagues,

Over long evolutionary timescales, a relationship between a parasite and its host tends towards equilibrium, ensuring the survival of both. However, this is not always the case because of the genetic variability of both pathogens and humans. Moreover, these interactions are also influenced by environmental conditions (microbiota, immune status, comorbidities, and more). As a result, many pathogens (viruses, bacteria, parasites, and fungi) alter human homeostasis and remain as one cause of an enormous disease burden.

In this context, this Topic is aimed to compile cutting-edge research regarding molecular aspects of pathogens and humans that will contribute to a better understanding of the host–pathogen interactions as a foundation for new approaches to combat those pathogens that continue threatening humans and other animals.

We welcome submissions of research articles, letters, short communications, and timely reviews covering topics including, but not limited to, the following:

• Virulent factors
• Pathogenic agents (virus, bacteria, parasites and fungi)
• Molecular mechanisms of antimicrobial resistance
• New drugs against well-defined molecular targets
• Genetic traits and disease associations
• Molecular evolution of pathogens
• Application of genomics, transcriptomics, proteomics and metabolomics to study the host-pathogen interactions
• Immune response molecular aspects in the host–pathogen interaction

Dr. Jose María Requena
Dr. Silvia Turroni
Topic Editors

Keywords

Participating Journals

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Genes genes	3.1	5.9	2010	13.3 Days	CHF 2600	Submit
International Journal of Molecular Sciences ijms	5.6	10.0	2000	17.5 Days	CHF 2900	Submit
Microbiology Research microbiolres	2.5	3.5	2010	18.8 Days	CHF 1800	Submit
Microorganisms microorganisms	4.7	8.2	2013	16.5 Days	CHF 2700	Submit
Pathogens pathogens	3.8	6.7	2012	12.5 Days	CHF 2400	Submit

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Published Papers (1 paper)

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All Genes IJMS Microbiology Research Microorganisms Pathogens

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35 pages, 7662 KB  

Open AccessReview

From Multi-Omics to Molecular Causality: A Five-Tier Evidence Framework for the Single-Bacterium–Metabolite Axis in IBD

by Xingyue Song, Wanting Wang, Jingjing Yang, Xinning Liang and Wanli Ji

Microorganisms 2026, 14(8), 1744; https://doi.org/10.3390/microorganisms14081744 - 8 Aug 2026

Viewed by 1182

Abstract

Gut microbiota research in inflammatory bowel disease (IBD) is transitioning from holistic community-level associations toward causal validation of individual bacteria and their metabolites. However, existing causal evidence is dispersed across diverse pathways and experimental models, lacking systematic integration and comparative assessment of evidence [...] Read more.

Gut microbiota research in inflammatory bowel disease (IBD) is transitioning from holistic community-level associations toward causal validation of individual bacteria and their metabolites. However, existing causal evidence is dispersed across diverse pathways and experimental models, lacking systematic integration and comparative assessment of evidence strength. Building on the concept of grading causal evidence in microbiome studies, we extend this approach into a five-tier progressive validation framework that covers the entire causal chain—from initial association discovery to the identification of specific effector metabolites. Using this framework, we systematically collate the single-bacterium–metabolite–host target axes that have been validated by high-level experimental methods. Focusing on four major pathways—AhR/tryptophan metabolism, bile acid/nuclear receptor signaling, short-chain fatty acid/vitamin/energy metabolism, and cell death-related pathogenic mechanisms—we integrate the molecular mechanisms through which specific bacteria and their causally linked metabolites regulate intestinal barrier integrity, immune responses, and inflammation resolution. We further discuss the modulatory influences of host genetics, diet, and medications on these axes, as well as therapeutic strategies such as live bacterial preparations, engineered probiotics, and postbiotics. Causal studies on individual bacteria and metabolites in IBD have progressed from isolated mechanistic discoveries towards systematic consolidation. It should be acknowledged, however, that most of the high-level evidence summarized in this review derives from animal models and preclinical studies, whereas robust human validation remains limited. In addition, protective mechanisms appear to considerably outnumber pathogenic ones, suggesting a marked imbalance in the current evidence base. To bridge the gap between mechanistic validation and clinical application, future research should focus on validating causal chains from animal models in well-designed human cohorts, exploring pathogenic mechanisms that drive disease onset, and clarifying interactions among different metabolites. By synthesizing available evidence, identifying key research gaps, and acknowledging translational limitations, this review aims to provide a foundational reference for researchers, while recognizing that further translational efforts are needed to move these preclinical findings toward clinical application. Full article

(This article belongs to the Topic Genetics and Genomics in Host-Pathogen Interactions)

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