Objective To elucidate the underlying mechanisms by which the traditional Chinese medicinal formula Skullcap Decoction (SCD) enhances intestinal barrier function in chicks challenged with avian pathogenic Escherichia coli (APEC).

Method An APEC infection model was established using Isa Brown chicks. Birds were orally administered 0.05% (ω) SCD granules or modified formulations lacking a single herbal component: Scutellaria baicalensis (HQ), Paeonia alba (SY), Ziziphus jujuba (DZ) or Glycyrrhiza uralensis (GC). Serum diamine oxidase (DAO), jejunal secretory immunoglobulin A (sIgA), and the tight junction proteins ZO-1 and Occludin were measured using ELISA. The mRNA expression levels of ZO-1 and Occludin in the jejunal mucosa were quantified by RT-qPCR. Gut microbial composition was analyzed through 16S rDNA sequencing, and the correlations between intestinal barrier function and microbial taxa were evaluated using Spearman correlation analysis.

Result SCD administration significantly reduced serum DAO and jejunal sIgA levels (P < 0.05) while upregulating ZO-1 and Occludin expression (P < 0.05) in APEC-challenged chicks, indicating enhanced intestinal barrier function and maintenance of gut microbial composition in APEC-challenged chicks. HQ exhibited multi-target regulatory activity on DAO, sIgA, and tight junction proteins, which was closely associated with gut microbiota modulation. DZ and SY exerted positive regulatory effects on DAO and tight junction proteins, potentially mediated via jejunal microbial interactions. GC showed a certain downregulatory effect on Occludin, which may likewise be microbiota-dependent.

Conclusion SCD enhances intestinal barrier function and maintain gut microbial homeostasis in APEC-challenged chicks. Among its constituents, HQ serves as the core active component, while DZ, SY, and GC play synergistic auxiliary roles.