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Development of rumen microbiota in dairy calves: impact of weaning and different weaning strategies
Weaning stress affects the establishment of rumen bacterial community in dairy calves, which is important for rumen development and future rumen physiology. This study examined the effects of different weaning strategies on the microbial composition of rumen in 24 male and 20 female Holstein dairy calves. Calves were blocked according to gender and birth weight, and randomly assigned to a step-down weaning (SW) or an abrupt weaning (AW) treatment. All calves had free access to water and starter intake throughout the experiment and 9 L/d of milk until d 36 of life and weaned on d 49 of life. Calves in SW group were weaned gradually by reducing milk intake from 9 to 4.5 L/d from d 37 to d 48 while the AW calves were abruptly weaned on d 49 by reducing milk intake from 9 to 0 L/d. Rumen fluid was sampled on d 36 (pre-weaning) and on d 54 (post-weaning) of life. DNA was extracted and V4 region of 16S rRNA gene was amplified and subjected to paired-end Illumina sequencing. The output paired-end reads were merged using PANDASeq assembler and analyzed using QIIME. The resulted operational taxonomic units were aligned to Greengenes database. Alpha-diversity of bacterial community was calculated using different richness estimators. Differences in beta-diversity of microbiota across treatments and time points were tested using Permutational ANOVA. Alpha-diversity of microbiota declined post-weaning, indicating a compositional heterogeneity reduction in rumen population. Beta-diversity of microbiota differed (P < 0.05) between pre- and post-weaning. Different weaning strategies did not affect alpha and beta-diversities. Predominant phyla before weaning included Bacteroidetes (66%), Firmicutes (19%) and Proteobacteria (11%). Another 18 phyla were present at low abundance; each below 1% of population. In post-weaned calves, Bacteroidetes was reduced (44%) while Firmicutes and Proteobacteria increased. However, a smaller increase in Firmicutes and a greater increase in Proteobacteria were observed after weaning in SW compared to AW calves (28% vs. 38%, and 22% vs.17%, respectively). Eighty-two out of 348 identified bacterial genera were different between pre- and post-weaned calves across AW and SW treatments, which accounted for 50% of sequences. The impact of weaning strategy was observed on several genera, including but not limited to, several members of Alphaproteobacteria, RF32, Alcaligenaceae, and Helicobacter. Data provided novel information on the profile of rumen microbiota associated with weaning and weaning strategy that can be used as biomarkers in future studies.
Keywords: Calves, weaning, rumen microbiota