Peer-reviewed article

Immune Cell-Mediated Causal Link Between Gut Microbiota Traits and Childhood Asthma: Evidence From Mendelian Randomization and Metagenomic Sequencing.

Shi R, Yang Z, Zhou X, Xu D, Xue W et al. · 1 Aug 2026

Abstract

Background The gut microbiota may be involved in childhood asthma. However, the causal relationship between the gut microbiota and childhood asthma remains obscure. Whether immune cells mediate the pathway from gut microbiota to childhood asthma has not been elucidated. Methods Genetic data of 196 gut microbiota taxa, 731 immune cell phenotypes, and childhood asthma were retrieved from the MiBioGen consortium and the MRC-IEU OpenGWAS database. Bidirectional Mendelian randomization (MR) analysis was first performed to verify the causal association between gut microbiota and childhood asthma, with reverse MR analysis conducted to rule out reverse causality. Mediation analysis was subsequently applied to identify the immune cell-mediated regulatory pathways. Additionally, a clinical validation cohort including childhood asthma patients and healthy controls was enrolled. Fecal samples from all subjects were subjected to metagenomic sequencing for microbial species identification and functional annotation. Linear discriminant analysis effect size (LEfSe) was used to screen differential gut microbiota taxa, whereas alpha diversity analysis was performed to evaluate microbial community richness. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was utilized for microbial functional pathway annotation, and Python-based bioinformatics analysis was adopted to quantify the abundance of microbial virulence factors based on Virulence Factor Database (VFDB) annotation results. Results MR analysis confirmed significant causal associations between seven gut microbiota taxa and childhood asthma, among which four taxa exhibited robust causal effects, and no reverse causal relationship was detected. A total of 25 immune cell types showed statistically significant effects on childhood asthma risk. Mediation analysis further validated two key immune cell-mediated pathways: the CD64 phenotype on CD14-CD16 immune cells mediated the causal effect of s_Paraprevotella_unclassified on childhood asthma, and the CD45 phenotype on HLA-DR T cells mediated the association of s_Bacteroides_thetaiotaomicron with childhood asthma. Clinical metagenomic sequencing revealed distinct gut microbial signatures between the two groups: The asthma group was characterized by enriched Bacteroides, whereas healthy controls had predominant Akkermansia and Lachnospiraceae, which was consistent with the MR findings. Alpha diversity analysis showed a trend of higher microbial species abundance in children with asthma without statistical significance. KEGG functional analysis indicated that differential microbial pathways between groups were primarily enriched in glucose metabolism, genetic information processing, and immune regulation. Moreover, the abundance of virulence factors including mrkl, mrkJ, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, impF, and hcp/tssD was significantly elevated in the childhood asthma group. Conclusions Specific gut microbiota taxa exert definitive causal effects on childhood asthma. Two immune cell phenotypes serve as crucial intermediate mediators linking gut microbiota dysbiosis to childhood asthma development. These novel findings elucidate the microbiota-immune regulatory mechanism underlying childhood asthma, providing a solid theoretical basis for the development of gut microbiota-targeted intervention strategies for childhood asthma prevention and treatment.