Transcriptomics analysis of host liver and meta-transcriptome analysis of rumen epimural microbial community in young calves treated with artificial dosing of rumen content from adult donor cow

Abstract

In mammals, microbial colonization of the digestive tract (GIT) occurs right after birth by several bacterial phyla. Numerous human and mouse studies have reported the importance of early gut microbial inhabitants on host health. However, few attempts have been undertaken to directly interrogate the role of early gut/rumen microbial colonization on GIT development or host health in neonatal ruminants through artificial manipulation of the rumen microbiome. Thus, the molecular changes associated with bacterial colonization are largely unknown in cattle. In this study, we dosed young calves with exogenous rumen fluid obtained from an adult donor cow, starting at birth, and repeated every other week until six weeks of age. Eight Holstein bull calves were included in this study and were separated into two groups of four: the first group was treated with rumen content freshly extracted from an adult cow, and the second group was treated with sterilized rumen content. Using whole-transcriptome RNA-sequencing, we investigated the transcriptional changes in the host liver, which is a major metabolic organ and vital to the calf’s growth performance. Additionally, the comparison of rumen epimural microbial communities between the treatment groups was performed using the rRNA reads generated by sequencing. Liver transcriptome changes were enriched with genes involved in cell signaling and protein phosphorylation. Specifically, up-regulation of SGPL1 suggests a potential increase in the metabolism of sphingolipids, an essential molecular signal for bacterial survival in digestive tracts. Notably, eight genera, belonging to four phyla, had significant increases in abundance in treated calves. Our study provides insight into host liver transcriptome changes associated with early colonization of the microbial communities in neonatal calves. Such knowledge provides a foundation for future probiotics-based research in microbial organism mediated rumen development and nutrition in ruminants.

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

“…In contrast, the period of early ruminal development shows potential to be a favorable time to manipulate and direct the rumen environment (Yáñez-Ruiz et al, 2015). Directfed microbials, early nutrition, and artificial dosing with ruminal contents from adults have been utilized as strategies to direct the microbial ecology of the gastrointestinal tract of young ruminants and subsequent production performance (Schönhusen et al, 2003;Ishaq et al, 2015;Fouladgar et al, 2016;Zhang et al, 2017;Li et al, 2019). Li and co-authors found that separate ruminal wall microbial communities formed between dairy calves dosed with and without adult-derived rumen fluid (Li et al, 2019).…”

The Effects of Artificially Dosed Adult Rumen Contents on Abomasum Transcriptome and Associated Microbial Community Structure in Calves

“…Secondly, 8 young bull calves were randomly assigned into two groups: (1) control group (Con; supplemented with autoclaved rumen content, n = 4) and (2) treatment group (HE; supplemented with inocula from the HE donor cow, n = 4). As mentioned in the paper of Li et al [ 23 ], the control inocula were prepared by autoclaving the combined inocula (50% from each) from the HE donor cow and the LE donor cow. Experiment was carried out from birth to 56 days.…”

“…Experiment was carried out from birth to 56 days. The inocula was administered within 3 days after birth, then at 2, 4, and 6 weeks following the initial dosing [ 23 ]. Until 8 weeks of age, the 4 calves in each group were sacrificed and the abomasum tissues were collected immediately after euthanization.…”

“…This section followed the protocols described in our publications [ 23 ]. For RNA extraction, 30–50 mg raw tissue was grinded using Precellys lysing kit (Bertin Technologies SAS, Montigny-le-Bretonneux, France).…”

“…Numerous human and mouse studies have reported the importance of early establishment of gut microbiota on host health, energy intake and storage [ 22 ]. In our previous study, in the young calves artificially dosed with rumen content from adult cow, we observed that the dosing can not only affect the rumen epithelium microbial community, but also the host liver transcriptome in young calves [ 23 ], indicating the potentially profound impact of early dosing of adult rumen content on the GIT tract in young calves. The abomasum is the ‘true stomach’ in ruminants and known for its vital role in hydrochloric acid secretion, protein digestion, and nutrient transfer.…”