Temporal establishment of the colon microbiota in Angus calves from birth to post-weaning

During the peri- and early post-partum period, the gastrointestinal tract (GIT) of the calf is colonised by a combination of commensal and pathogenic microbes. Current understanding of the temporal microbial establishment of neonatal colon is, however, limited. This study focused on the ontogeny of colon microbiota establishment in Angus Beef calves from birth through weaning. Colon digesta contents were collected from Aberdeen Angus calves reared on two farms. Calves were euthanized at birth (n=7), day (D) 7 (n=7), D14 (n=6), D21 (n=7), D28 (n=6), and D96 (n=7) of life. Microbial DNA was extracted from colon samples and subjected to 16S rRNA amplicon sequencing. The effect of time on alpha (GLM procedure of SAS; 9.4) and beta (PERMANOVA) diversity of the colon microbiota was assessed with age and farm included as fixed effects. Differential abundance (Maaslin2) analyses were conducted with the same fixed effects. The alpha-diversity of the bacterial community progressed from birth onwards (D0 H’ mean = 0.59 and D96 H’ mean = 5.33) with apparent stabilisation between D14 v D21 (P=0.21). Weaning had a further statistically significant effect on the diversity of the colon microbiota (D28 v D96; P <0.001). Similarly, PERMANOVA analysis indicated stabilised colonisation of the colon microbiota from D14 to D21 (P=0.22), albeit weaning altered the colon microbiota (D28 v D96; P <0.001). This study is amongst the first to describe the ontogeny of colonisation of the colon microbiota, from birth to weaning in beef calves and provides fundamental information to support the establishment of beneficial microbes in the lower GIT of ruminants.