Evolution of rumen and oral microbiota in calves is influenced by age and time of weaning

Background: The rumen bacterial communities are changing dynamically through the first year of calf's life and the weaning period is a stressful event . Rumen microbiome analysis is often limited to invasive rumen sampling procedures. The oral cavity of ruminants is expected to harbour rumen microbes due to regurgitation activity. The present study used buccal swab samples to define the rumen core microbiome and characterize the shifts in rumen and oral microbial communities occurring as result of calf's age as well as time of weaning.Results: Buccal swab samples of 59 calves were collected along the first 140 days of life and compared to stomach tubing sample of the rumen at day 140. Animals were randomly divided into two weaning groups. Microbiota of saliva and rumen content was analysed by 16S rRNA gene amplicon sequencing. Our study showed that most rumen-specific bacterial taxa were equally observed in rumen samples as well as in the buccal swabs, though relative abundance varied. The occurrence of rumen-specific OTUs in buccal swab samples increased approximately 2.8 times from day 42 to day 140, indicating the gradual development of rumen as calf aged. The rumen-specific bacterial taxa diversity increased, and inter-animal variations decreased with age. An age-dependent decrease in the phylum Actinobacteria and an increase in Bacteroidetes and candidatus Saccharibacteria was observed. Early weaning (7 weeks of age) rapidly increased the rumen microbial diversity from pre- to post-weaned state. Rumen microbiota of early-weaned calves seemed to have a suppressed growth of starch and carbohydrate utilizing bacteria and increased fibre degraders. Whereas in late-weaned calves (17 weeks of age) no impact of dietary modifications was observed on rumen microbiota composition after weaning. Oral-specific bacterial community composition was significantly affected by calf's age and time of weaning.Conclusions: The present study showed the significant impact of calf's age and weaning on the establishment of rumen- and oral-specific bacterial communities utilizing buccal swab samples. The results emphasize the possibility of using buccal swab samples as a replacement of complex stomach tube method for large-scale predictive studies on ruminants.