Stage-associated enrichment of Dietzia in the conjunctival microbiome of calves with infectious bovine keratoconjunctivitis: a cross-sectional microbiome and genomic characterization study.

BACKGROUND

Infectious bovine keratoconjunctivitis (IBK) is a major ocular disease of cattle. Although the bovine conjunctival microbiome has been studied in IBK-affected and healthy animals, microbiome patterns across clinically defined lesion stages remain poorly understood, and the occurrence of Dietzia on the diseased bovine ocular surface has not been systematically investigated.

METHODS

This cross-sectional study enrolled 57 calves from two commercial farms in Kazakhstan, stratified across six clinical stages of IBK severity (0-5). Conjunctival swabs were analyzed by culture-based Dietzia recovery and 16S rRNA gene amplicon sequencing. Alpha and beta diversity were assessed using standard ecological metrics, and stage-associated Dietzia abundance was evaluated using Kruskal-Wallis testing and quadratic regression. Two representative Dietzia isolates were subjected to whole-genome sequencing, phylogenomic placement and homology-based screening against resistance and virulence-factor databases.

RESULTS

IBK stage was not associated with significant global restructuring of the conjunctival microbiome. Alpha-diversity indices did not differ significantly across stages, and PERMANOVA showed no stage-specific beta-diversity separation (R 2 = 0.098, p = 0.323). In contrast, Dietzia showed a non-linear stage-associated abundance pattern in a quadratic model, with the highest reads-per-million (RPM) abundance in samples classified at stages 2-3, which are clinically characterized by active corneal ulceration. Culture-based recovery of Dietzia was frequent overall (42/57 samples; 73.7%) but showed no monotonic relationship with lesion severity. Whole-genome analysis of two isolates revealed phylogenomic heterogeneity: one isolate clustered within phylogenomic Group A, whereas the second was positioned outside the four major Dietzia groups, adjacent to the divergent animal isolate Dietzia sp. B32. Both genomes contained conserved stress-response, regulatory and metabolic homologues, without clear evidence of specialized virulence systems.

CONCLUSION

IBK lesion stage was not associated with major alpha- or beta-diversity restructuring, but Dietzia displayed stage-associated enrichment during the active ulcerative phase. These findings support interpretation of bovine ocular Dietzia as a surface-accessible opportunistic colonizer rather than a confirmed primary aetiological agent of IBK.