Does weaning age affect the development of ruminal and fecal microbiomes in dairy calves?

Abstract Text:

Despite the advantages of feeding an elevated plane of nutrition to pre-weaned calves, this feeding strategy may increase a calf’s susceptibility to depressed growth during weaning. We hypothesised that weaning at an earlier age would result in a more rapid shift in gut microbiota and consequently be the cause of this growth depression. Thus, our study examined the effects of weaning age on ruminal and fecal microbiomes in Holstein calves fed an elevated plane of nutrition pre-weaning. Twenty female Holstein calves were randomly assigned at birth to be weaned at 6 (early, EW) or 8 (late, LW) weeks. Milk replacer (150 g powder/L water) was offered at 1.2 kg/calf/day in 2 meals until a 1-week step-down. Rumen fluid and feces were sampled at week 5, 7 and 9, representing EW5, EW7, EW9, LW5, LW7 and LW9. DNA was extracted and the V4 region of the 16S rRNA bacterial gene was amplified and subjected to paired-end Illumina sequencing. The output paired-end reads were merged using the PANDASeq assembler, analysed using QIIME and aligned to the Greengenes database. Alpha-diversity of bacterial communities were calculated using different richness estimators. Differences in beta-diversity of microbiota across treatments and age were tested using PERMANOVA. Alpha diversity indices did not differ (P>0.05) across weaning age x week in feces. However, differences (P<0.05) between EW5 and EW7 calves were observed in the rumen for Shannon and Inverse Simpson indices. Beta-diversity of both rumen and fecal microbiota differed (P≤0.04) between weaning age x week, indicating a more gradual shift in late weaned calves towards a post-weaned state, compared to an abrupt shift in early-weaned calves. Bacteroidetes was the dominant ruminal phyla in pre-weaned calves, decreasing in abundance (P=0.02) post-weaning, regardless of the age of weaning. A corresponding increase (P≤0.09) in Firmicutes at weaning resulted in it becoming the dominant ruminal phyla in post-weaned calves. The opposite shift in dominance, was observed in feces where Firmicutes was dominant pre-weaning and Bacteroidetes dominant in post-weaned calves. These two phyla accounted for an average 86% of total ruminal or fecal sequences regardless of age or treatment. These results indicate that late weaning at 8 wk facilitates a more gradual shift in microbiota towards a post-weaned state compared to early weaning at wk 6. Hence, weaning later could reduce the adverse effects caused by feeding a high-plane of nutrition pre-weaning.  

Keywords: 16S rRNA gene sequencing, microbiome, rumen, feces, calves, weaning