Temporal changes in the fecal bacterial community in Holstein dairy calves from birth through the transition to a solid diet

Abstract

The development of a robust microbiome is critical to the health of dairy calves, but relatively little is known about the progression of the microbiome through the weaning transition. In this study, fecal samples were obtained from ten female Holstein calves at 6 timepoints between 2-13 weeks of age. Calves were fed acidified milk until weaning at 8 weeks old and had access to starter grain throughout the study. Fecal samples were extracted for genomic DNA, PCR-amplified for the V1-V2 region of the 16S rRNA bacterial gene, sequenced on the Illumina MiSeq platform, and analyzed using the QIIME2 pipeline. Bacterial richness, estimated by number of observed species, and bacterial diversity, estimated by Shannon diversity index, both differed significantly between timepoints and both increased over time (P <0.05), with the largest increases occurring during weaning. Weighted and unweighted UniFrac analysis showed significant differences (P <0.05) between bacterial communities across timepoints; betadisper analysis revealed that the microbiomes of individual calves became more similar with time. Throughout the study, Firmicutes was the dominant phylum, followed by Bacteroidetes. Thirteen bacterial genera were found to be significantly influenced by time, including Faecalibacterium, Clostridium, unclassified S24-7, Collinsella, Sharpea, and Treponema. Unclassified Ruminococcaceae was the most prevalent genus at timepoints 1, 3, 5, and 6, but different amplicon sequence variants were detected at each timepoint suggesting the presence of different species of Ruminococcaceae at different times. Bacteroides was the most prevalent genus at timepoint 2, and Prevotella was most prevalent at timepoint 4. Our results indicate that there is considerable variation in the calf microbiome pre-weaning, but the microbial community stabilizes and becomes similar to the adult microbiome at weaning. Further studies to describe the phylogeny and functionality of core microbiota through the weaning transition are needed to improve health and reduce diarrhea in the neonatal period.

Analysis of Cow-Calf Microbiome Transfer Routes and Microbiome Diversity in the Newborn Holstein Dairy Calf Hindgut

“…Available studies in humans, lambs, and foals have focused on understanding the hindgut microbiome when microbial colonization starts (4)(5)(6). However, few studies have focused on the calf microbiome (7)(8)(9).…”

Does algae β-glucan affect the fecal bacteriome in dairy calves?

“…The starter concentrate intake, besides being essential for nutrient supply and rumen development, was shown to correlate positively with the bacterial genera Blautia , Alloprevotella , and Faecalibacterium . Hennessy et al [ 41 ] also observed an increased abundance of Blautia as animals made the transition from liquid to a solid diet. In addition, these authors have noted that the genus Faecalibacterium has a positive correlation with Blautia .…”

Enrofloxacin Alters Fecal Microbiota and Resistome Irrespective of Its Dose in Calves

“…Gut microbiota highly fluctuate in the early life of calves until weaning, after which adult-like microbiota is established [ 2 ]. The age of calves at enrollment in this study was between 12 and 16 weeks; thus, significant microbial variation related to early life was not expected.…”

“…Gut microbiota, consisting of bacteria, archaea, viruses, protozoa, and fungi, play vital roles in animals by conferring colonization resistance against pathogens, modulating immunity, and increasing food-conversion efficiency [ 1 , 2 ]. However, these beneficial commensal organisms are vulnerable to external aggressions, such as antibiotic exposure [ 3 , 4 , 5 ].…”