Microbial inoculum alters the rumen epithelial transcriptome and associated meta-transcriptome in calves

Authors: FREGULIA, PRISCILA - Oak Ridge Institute For Science And Education (ORISE); PARK, TANSOL - Oak Ridge Institute For Science And Education (ORISE); Li, Wenli; CERSOSIMO, LAURA - Oak Ridge Institute For Science And Education (ORISE); Zanton, Geoffrey

Submitted to: American Dairy Science Association Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: 2/15/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Early-life alteration of the rumen microbial ecosystem may affect ruminal fermentation and enhance the productive performance of dairy cows. Our objective was to evaluate the effects of dosing three different types of microbial inoculum on the rumen epithelial tissue (RET) transcriptome and its associated meta-transcriptome in dairy calves. Fifteen Holstein bull calves were enrolled in the study at birth and randomly assigned to one of three intraruminal inoculum treatments dosed once weekly from 3 to 6 wk of age. Inoculum treatments were prepared from rumen fluid collected from four adult cows and were processed for ARF (autoclaved; the control), BE (bacteria-enriched by centrifugation), or PE (protozoa-enriched by sedimentation). From the start of the study, calves were fed 7.5 L/d pasteurized waste milk through 7 wk along with texturized starter for ad libitum consumption which was continued until euthanasia at 9 wk of age, at which point RET was collected for host transcriptome and microbial meta-transcriptome sequencing analyses (using both rRNA and microbial coding gene transcripts). Compared to ARF, 36 genes were differentially expressed (DE, P<0.01) in BE and 107 in PE. Between BE and PE, 127 genes were DE. We observed a reduction in alpha diversity indices for the RET microbiome in ARF (observed genera and Chao1 [P < 0.05]). At the rRNA transcript level, nine genera showed significant abundance changes among the treatments (P<0.05), while several genera identified were associated with expression changes in RET genes. These included: Roseburia (26 genes), Entamoeba (2 genes), Anaerosinus (1 gene), Lachnospira (1 gene), and Succiniclasticum (1 gene). Analysis using microbial protein coding reads indicated that both BE and PE had a significant impact on the abundance of KEGG (Kyoto Encyclopedia of Genes and Genomes) modules related to acyl-CoA synthesis, type VI secretion, and methanogenesis, while PE alone had a significant impact on the abundance of KEGG modules related to ectoine biosynthesis and D-xylose transport. Our study provides empirical evidence that different microbial dosing regimens elicited changes in the host RET transcriptome. Most importantly, our findings suggest that differential dosing in early life not only altered the microbial community composition, but also the associated microbial functions associated with the RET.