Pre-weaning Ruminal Administration of Differentially-Enriched, Rumen-Derived Inocula Shaped Rumen Bacterial Communities and Co-occurrence Networks of Post-weaned Dairy Calves

Abstract

Adult rumen fluid inoculations have been considered to facilitate the establishment of rumen microbiota of pre-weaned dairy calves. However, the sustained effects of the inoculations remain to be explored. In our previous study, 20 pre-weaned dairy calves had been dosed with four types of adult rumen inoculums [autoclaved rumen fluid, bacterial-enriched rumen fluid (BE), protozoal-enriched (PE), and BE + PE] weekly at 3 to 6 weeks of age. To verify the sustained effect of adult rumen inoculation, the rumen bacterial communities, fermentation characteristics, and animal performance measurements were measured after sacrifice from 20 post-weaned dairy bull calves (9 weeks of age). Ruminal pH tended to be lower in BE treated calves (n = 10). All PE treated calves had rumen ciliates (>10⁴ cells per ml of rumen fluid). PE treated calves had greater VFA concentrations (P = 0.052), lower molar proportions of isobutyrate (P = 0.073), and butyrate (P = 0.019) compared to those of control calves. No treatment differences were found in all animal performance measurements. Both PE and BE inocula increased bacterial species richness, Faith's phylogenetic diversity, and Shannon's index in rumen liquid fractions. However, the relative proportion of those bacterial taxa possibly transferred from the donor's rumen was minor. Microbial network analysis showed different co-occurrence and mutually exclusive interactions between treatments of microbial inoculations. Collectively, adult rumen inoculations in pre-weaned dairy calves slightly altered the rumen bacteriome of post-weaned calves without changing fermentation and animal performance.

Keywords: adult rumen inoculation; dairy calves; microbial network; protozoa; rumen bacterial communities.

FIGURE 1

Principal coordinates analysis (PCoA) plot based on unweighted and weighted UniFrac distance matrices showing overall rumen bacterial microbiota distributions in (A) liquid and (B) solid fraction of dairy calves differed by microbial inoculations with two types of inoculums (BE and PE).

FIGURE 2

Venn Diagram depicting the number of shared and exclusive bacterial (A) phyla or (B) genera by microbial inoculations at either rumen liquid or solid fractions.

FIGURE 3

Exclusive co-occurrence and mutual exclusion microbial network either at (A) rumen liquid and (B) rumen solid. Node color represents exclusive microbial nodes (orange) and keystone taxa (blue) selected based on the betweenness centrality, authority, and eigenvector centrality measurements within each exclusive network. Edge color represents co-occurrence (blue) or mutual exclusive (red) interactions. Edge thickness was adjusted based on the absolute value of the correlation coefficients of each interaction.

FIGURE 4

PCA plot showing the effect of microbial inoculations on the overall functional distribution at rumen liquid and solid fractions. Overall functional distribution was computed based on the relative abundance of KEGG orthologs predicted by PICRUSt2.

FIGURE 5

Correlations between (A) rumen measurements (stomach compartments, fermentation, and protozoal counts) and (B) animal performance measurements with differentially abundant bacterial genera. Only strong significant correlation coefficients (| r| ≥ 0.5, P ≤ 0.05) were shown on the plot.