Abstract The buccal, rumen, and fecal microbiomes within the bovine gastrointestinal tract house many microorganisms that contribute to and explain differences in phenotypic performance and feed efficiency. Most literature focuses only on evaluating the rumen microbial environment of cattle, while samples from the buccal and fecal microbiomes are easier to obtain for producers. The objective of this study was to evaluate the shared core microbiota within the buccal, rumen, and fecal microbiomes of beef cattle consuming forage-based diets varying in type and nutritive value. Commercial Angus heifers (250. 8± 24. 3 kg; n = 48) were weaned at 7-8 months of age and preconditioned for 45 days. Heifers were blocked by body weight (BW) and randomly assigned to one of four forage treatments. Forage treatments used in this study were: alfalfa baleage (diet A), millet baleage (diet M), wheat baleage (diet W), and fescue hay (diet H). Forage bales were offered ad libitum, and a commercial grower feed was provided at 0. 5% BW, three times weekly to maintain nutrient requirements of growing heifers. The feeding trial was a total of 168-days (September 2023 – March 2024), BW was recorded every 28 days, and samples of the buccal environment via sterile swab, rumen environment via esophageal tubing, and fecal environment via sterile rectal palpation, were collected at day 140. DNA was extracted and subsequent 16S rRNA library preparation and sequencing was completed amplifying the V3-V4 hypervariable region. There was a total of 61, 602 amplicon sequence variants (ASV) across the buccal (n = 48), rumen (n = 47), and fecal (n = 47) samples. The fecal and buccal microbiomes had a significantly lower alpha diversity shown by a lower Faith’s PD (P 0. 001), Pielou’s Evenness (P 0. 001), and Shannon Diversity (P 0. 001) indices, than the rumen microbiome. Samples grouped separately by type when comparing beta diversity using a PCoA plot. When comparing the three microbiomes, there were no ASVs or species level taxa shared. However, they did share taxa at the phylum (n = 5), family (n = 6) and genus (n = 2) levels of taxonomy, which were used for further analyses. The rumen and fecal microbiomes shared significantly more taxa (phylum n = 8, family n = 24, and genus n = 25), than the buccal and rumen microbiomes (phylum n = 6, family n = 7, and genus n = 4). Dietary treatment effects and differences in relative abundance of the shared core taxa are summarized in Table 1. The genera Ruminococcus and ChristensenellaceaeR-7group were identified in all buccal, rumen, and fecal samples and should be evaluated further to determine if the relative abundances of these genera within a specific microbiome possess significant relationships with production efficiency phenotypes of beef cattle. This information could promote selective breeding strategies to improve production efficiency and sustainability of beef cattle operations using genomic information.
Cornett et al. (Wed,) studied this question.