Exploring colostrum microbiota and its influence on early calf gut microbiota development using full-length 16S rRNA gene metabarcoding

The early gut microbiota of calves is seeded by colostrum and shaped by diet, environment, disease, and antibiotic treatments. This study analyzed the colostrum microbiota of 42 cows and tracked their calves' gut microbiota during early life (days d1, d16, and d57), assessing the impact of antimicrobial dry cow therapy and infection treatments. The full-length 16S rRNA gene was sequenced using Oxford Nanopore, enabling taxonomic classification down to species level. Microbial richness and diversity were lowest at d1 and increased afterwards. Beta diversity analysis showed that d16 samples had microbial profiles intermediate to those of d1 and d57. The most abundant phyla (Pseudomonadota, Bacillota, and Bacteroidota) were common to all sample categories, while genus-level composition showed greater variability. Colostrum was dominated by Paraclostridium, Romboutsia, and Staphylococcus, while Escherichia/Shigella and Clostridium were more abundant in d1 feces, later replaced by Succinivibrio and Faecalibacterium at d16 and d57. Notably, 56.2% of species in d1 feces were also present in colostrum, and 37.4% of colostrum species persisted in feces at d57, highlighting colostrum´s role in bacterial gut colonization. Interindividual variability in gut microbiota decreased over time as richness and diversity increased. Antimicrobial treatments did not significantly alter microbiota diversity or composition, suggesting a limited long-term impact.