Abstract
BackgroundThe rumen bacterial communities are changing dynamically throughout the first year of calf’s life including the weaning period as a critical event. Rumen microbiome analysis is often limited to invasive rumen sampling procedures but 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.ResultsBuccal 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 1.7 times from day 70 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. 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 on rumen microbiota composition was observed after weaning. Oral-specific bacterial community composition was significantly affected by calf’s age and time of weaning.ConclusionsThe 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. For in-depth rumen microbiome studies, the time of sampling should be carefully considered using an active phase of regurgitation.
Highlights
The rumen bacterial communities are changing dynamically throughout the first year of calf’s life including the weaning period as a critical event
The pattern of milk replacer (MR) and C intake was similar for both weaning groups until day 28 when weaning was initiated for early-weaned group and there were no significant differences in intake amounts (122–133 g DM/day)
While the late-weaned group was maintained at a constant MR level of approximately 1300 g DM/day and continued to increase C intake until 2 kg was reached at day ~ 70, the MR intake of the earlyC group was gradually reduced until day 42
Summary
The rumen bacterial communities are changing dynamically throughout the first year of calf’s life including the weaning period as a critical event. 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. The rumen proportions are relatively smaller than in adult cows and lack some major functional components (i.e., rumen wall villi), which are essential for nutrient absorption [1]. The increase in fermentation products and microbial biomass result in structural and physiological modifications of rumen characteristics [2, 3], with subsequent establishment of a fully functional rumen and adult-like microbiota near weaning [4]
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