Microbial colonisation of the neonatal beef calf gastrointestinal tract: limited influence of birth delivery method across five anatomical regions.

The microbiome assembly of the neonatal gastrointestinal tract is critical for immune and metabolic development, and birth delivery method can influence initial microbial colonisation. Using 16S rRNA gene amplicon sequencing, we investigated the effect of transvaginal and elective caesarean section delivery on microbial composition across five gastrointestinal regions (colon, ileum, jejunum, meconium, and rumen) in Aberdeen Angus calves (transvaginal, TV; n = 12; caesarean section, CS; n = 10) across two research farms. Absolute microbial quantities were measured using 16S rRNA qPCR. Alpha diversity (Observed, Shannon, Simpson) was compared between delivery methods within each region using Wilcoxon rank-sum tests, whereas beta diversity (Bray-Curtis PERMANOVA) and differential abundance (MaAsLin2) analyses were conducted with sex and farm as fixed effects. Alpha diversity varied among gastrointestinal regions (p < 0.05) but did not differ between delivery methods within any region (all BH-adjusted q ≥ 0.74). Gastrointestinal region was the primary determinant of microbial community composition (R2 = 0.24, p < 0.001), with delivery method explaining minimal additional variance. A statistically significant but weak Region × Delivery interaction was observed (R2 = 0.06, p = 0.02), indicating that any influence of delivery method was site-dependent rather than uniform across the gastrointestinal tract. Farm explained negligible variation (R2 = 0.01, p = 0.17) and no overall delivery method effect was detected. Per-region analyses found no statistically significant treatment effects within individual regions (all p ≥ 0.06), suggesting the interaction reflected modest region-specific trends rather than strong site-specific shifts. Microbial load and community composition were comparable between CS and TV calves at birth. Early microbial establishment was therefore primarily driven by anatomical site, with postnatal environmental exposure and host-microbe interactions likely playing a greater role than delivery method in shaping early gastrointestinal microbial assembly in neonatal beef calves.