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The development of the fecal microbiome in Holstein dairy calves throughout the weaning transition.

M. Hennessy




The development of the fecal microbiome in Holstein dairy calves throughout the weaning transition.
M. Hennessy*1, B. Vecchiarelli1, N. Indugu1, J. Bender1, C. Pappalardo1, M. Leibstein2, J. Toth1, A. Katepalli3, S. Garapati4, D. Pitta1. 1University of Pennsylvania School of Veterinary Medicine New Bolton Center Kennett Square, PA, 2Oceanside High School Oceanside, NY, 3Northwest High School Germantown, MD, 4Drexel University Philadelphia, PA.

Calf diarrhea is the leading cause of death in pre-weaned calves and causes major economic losses to producers. A better understanding of the development of the microbiome throughout the weaning transition could lead to better treatment and prevention strategies. In this study, fecal samples were obtained from 10 cohabiting female Holstein dairy calves at 6 time points between age 2—4 weeks and age 12—14 weeks. Calves were fed on acidified milk until weaning at about 8 weeks of age and had access to starter grain throughout the course of the study. Fecal samples were extracted for genomic DNA, PCR-amplified for the V1-V2 region of the 16S rDNA bacteria 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 time points and both increased over time (P < 0.05), with the largest increases occurring during the weaning transition. Both weighted and unweighted Unifrac analysis showed significant differences (P < 0.05) between bacterial communities across time points. Throughout the course of the study, Firmicutes was the dominant phylum, followed by Bacteroidetes. Seven bacterial genera were found to be significantly influenced by time: Fecalibacterium, Ruminococcaceae, Prevotella, Clostridiales, Sutterella, Lachnospiraceae, and Coriobacteriaceae. Ruminococcaceae was the most prevalent genus at TP1, 3, 5, and 6, Bacteroides was the most prevalent genus at TP2, and Prevotella was the most prevalent genus at TP4. Considerable variation was seen in the proportions of abundant genera between calves as well as between time points; however variations in phylogenetic makeup between individual calves decreased as the calves aged, indicating that cohabitation led the microbiota of individual calves to become more similar with time. Our results indicate that there is considerable flux in the calf microbiome throughout the weaning transition and add to our understanding of the progression of the microbiome during calf development.

Keywords: acidified milk, calf diarrhea, calf weaning.