The rumen liquid meta-transcriptome of post-weaned dairy calves differed by pre-weaning ruminal administration of differentially-enriched, rumen-derived inocula

Authors: PARK, TANSOL - Orise Fellow; CERSOSIMO, LAURA - University Of Florida; Radloff, Wendy; Zanton, Geoffrey; Li, Wenli

Submitted to: Animal Microbiome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/28/2021
Publication Date: 1/5/2022
Citation: Park, T., Cersosimo, L.M., Radloff, W.J., Zanton, G.I., Li, W. 2022. The rumen liquid meta-transcriptome of post-weaned dairy calves differed by pre-weaning ruminal administration of differentially-enriched, rumen-derived inocula. Animal Microbiome. 4. Article 4. https://doi.org/10.1186/s42523-021-00142-z.
DOI: https://doi.org/10.1186/s42523-021-00142-z

Interpretive Summary: Artificial dosing of rumen content as a means to manipulate rumen microbiota of dairy calves has attracted considerable interest from scientific and management perspectives. We have previously reported on the impacts of pre-weaning inoculation of adult-rumen derived microbial inocula in young calves during the post-weaning period. The sustained effects of pre-weaning inoculations were confirmed in post-weaned calves (9 weeks of age). However, our previous microbial methods did not allow us to distinguish among inactive, dead or lysed microbial cells. In this report we use an approach giving us the ability to study the structure and potential function of the active microbial community (metatranscriptomics). The overall microbial functions were affected quantitatively by inoculation with bacterial-enriched inoculum and qualitatively by protozoa-enriched inoculum treatments. We also observed that differentially abundant prokaryotic species significantly correlated to various fermentation and animal measurements, including butyrate proportion, protozoa log-counts, and rumen tissue papillae length and counts. From this work we conclude that using metatranscriptomics has the potential to better elucidate undetermined biological factors affected by microbial inoculations in dairy calves and cattle gene expression profiles.

Technical Abstract: Targeted modification of the dairy calf ruminal microbiome has been attempted through rumen fluid inoculation to alter productive phenotypes later in life. However, sustainable effects of the early life interventions have not been well studied, particularly on the metabolically active rumen microbiota and its functions. This study investigated the sustained effects of adult-derived rumen fluid inoculations in pre-weaning dairy calves on the active ruminal microbiome of post-weaned dairy calves analyzed via RNA-sequencing. Two different adult-derived microbial inocula (bacterial- or protozoal-enriched rumen fluid; BE or PE, respectively) were administered in pre-weaned calves (3-6 weeks) followed by analyzing active rumen microbiome of post-weaned calves (9 weeks of age). The shared bacterial community at the genus level of 16S amplicon-seq and RNA-seq datasets tended to be different (P = 0.078), 23 out of 25 shared major bacterial genera differed in their relative abundance between two analytic pipelines. No significant differences were found in any of the prokaryotic alpha- and beta-diversity measurements (P > 0.05), except the archaeal microbiota was different for BE based on the Bray-Curtis dissimilarity matrix (P = 0.048). Even though the relative abundances of potentially transferred microbial and functional features from the inocula were minor, differentially abundant prokaryotic species significantly correlated to various fermentation and animal measurements including butyrate proportion, protozoa log-counts, and papillae length and counts. The overall microbial functions were affected quantitatively by BE and qualitatively by PE treatments (P < 0.05), and this might be further supported by the individual KEGG module and CAZymes profile differences. Exclusive co-occurrence and mutually exclusive interactions between major microbial (bacterial and archaeal species) and functional features (KEGG modules) were determined to differ by microbial inoculations. This study demonstrated that actively transcribed microbial and functional features showed reliable connections with different fermentation and animal development responses through adult rumen fluid inoculations compared to our previous 16S amplicon sequencing results. Exclusive microbial and functional networks of the active rumen microbiome of dairy calves created by BE and PE might also be responsible for the different ruminal and animal characteristics. Further understanding of the other gastrointestinal tracts using the metatranscriptomics will be necessary to elucidate undetermined biological factors affected by microbial inoculations.