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Additional file 5.

Additional file 4. Supplementary Tables.

Additional file 1.

Additional file 3. Supplementary Figures.

Additional file 2.

Additional file 10: Figure S10. Heatmap of differential KOs associated with each sampling timepoint of collection. Only KOs that are significantly different at p

Additional file 5: Figure S5. Distribution of opportunistic pathogens Moraxella spp. and Mycoplasma spp. across the 4 sampling time points. Moraxella spp. and Mycoplasma spp. are considered as opportunistic pathogens that predispose animals to IBK infection.

Additional file 4: Figure S4. Differential ASVs found among time sampling comparison. (Key- * denotes taxa at family level, ** denotes taxa at order level, and *** denotes taxa at class level.).

Additional file 8: Figure S8. Observed ASVs (A) and Chao1 estimates (B) indicating alpha-diversity differences between sampling time points. Significant differences in predicted functional gene alpha-diversity was identified between all sampling periods. After initial swabbing for baseline community, the diversity significantly decreased and recovered over time in subsequent samplings. The initial swabbing, would be deemed as the first perturbation or disruption to the ocular microbiota.

Additional file 3: Figure S3. Distribution of “Core” ASVs across sampling time-points demonstrating predominance of opportunistic pathogens in the bovine ocular microbiota. Perturbations, or disruptions, to the ocular microbiota occurred by taking ocular swabs. Core bacterial ASVs were identified based on the presence of an ASV in at least 80% of all samples. Only 3 core ASVs were identified that fell into this criteria. The core ASVs include; Pasteurellaceae spp. (Blue), Mycoplasma spp. (Orange) and Weeksellacea spp. (Grey).

Additional file 7: Figure S7. Prevalence of Moraxella spp. in total (7a), as well as individually for Moraxella bovis (7b) and Moraxella bovoculi (7c) obtained from the eyes of calves at different time points. Letters denote statistically different groups (p

Additional file 11: Figure S11. List of CMM ASV with relative abundance at each time sampling. (Key- * denotes taxa at family level, ** denotes taxa at order level, and *** denotes taxa at class level.).

Additional file 9: Figure S9. Principal Coordinate analysis (PCoA) demonstrating between sample variations in predicted functional genes. PCoA plot was generated using a Bray-Curtis distance matrix. Day 0 and day 139 demonstrated similar gene structure that was different from 21 days and 41 days. Color scheme; Red – time point 1, Green - time point 2, Teal – time point 3, and Purple – time point 4.

Additional file 2: Figure S2. Principal Coordinate analysis (PCoA) demonstrating between individual cohort sample variations in beta-diversity. PCoA plot was generated using a weighted UniFrac distance matrix. A) Cohort A B) Cohort B and C) Cohort C. PERMANOVA revealed there was no significant difference between the eyes sampled at day 17 (p = 0.37, p = 0.245, and p = 0.659; respectively).

Additional file 13: Table S1. Scores of ulcers from cattle infected with IBK during the study.

Additional file 12: Figure S12. Distribution of the calves age throughout the duration of the trial.