Background: The gastrointestinal microbiota of neonatal calves changes rapidly during the first weeks of life. The dam is considered an important source of microbes for the calf; consequently, the development of calf microbiota may vary with farming system due to differences between the contact the calf has with the dam. The objective of this study was to characterise the early maturation of oral and faecal microbiota in beef and dairy calves using high-throughput sequencing of the 16S rRNA gene. The microbiota of calves was compared to selected anatomical niches on their dams which were likely to contribute to the vertical transfer of microbes.
Results: A total of 14,125 amplicon sequence variants (ASVs) were identified and taxonomically assigned. The oral microbiota of calves and their dams became more similar over the first four weeks of life. The faecal microbiota of four-week old calves was most similar to the oral microbiota of calves and adult cows but there was little similarity between the faecal microbiota of calves and cows. ASVs were identified in the oral microbiota of four-week old calves that were also at present cow niches at calving. Very few ASVs were present in the calf faecal microbiota at four-weeks of age that were present in any adult cow niche at calving. These results were observed in both beef and dairy calves. Conclusions: We did not observe any marked differences in the maturation of the oral and faecal microbiota between beef or dairy calves, despite dairy calves having very limited contact with their dam. This suggests the development of gastrointestinal microbiota in calves is not affected by continued vertical transmission of microbes from the dam. The oral microbiota of calves matured more quickly than the faecal microbiota and by four-weeks of age it was similar to the oral microbiota of adult cows. Although the calf faecal microbiota changed over the first four-weeks of life, it bore little resemblance to the faeces of adult cows. Any maternal influence on these changes presumably occurred immediately post-partum as there were few differences between the trends observed in beef and dairy calves.