Metabolome and microbiome associations after a grain and sugar challenge

Abstract Text: Holstein heifers (n = 40) were allocated to 5 groups: (1) control (no additives); (2) virginiamycin (10 g/head.d:VM); (3) monensin (2.2 g/head.d d) + tylosin (0.44 g/head.d:MT); (4) monensin (2.5 g/head.d) + yeast (Levucell SC Direct 25 g/head.d:MY); (5) sodium bicarbonate (200 g/head.d) + magnesium oxide (30 g/head.d:BUF). Heifers were fed twice daily a 62% forage:38% concentrate total mixed ration at 1.25% of bodyweight (BW) dry matter (DM)/d for a 20-d adaptation period with their additive(s). Fructose (0.1% of BW/d) was added to the ration for the last 10 d of adaptation. On d-21 heifers were challenged with a ration consisting of 1.0% of BW DM wheat and 0.2% of BW fructose plus their additive(s). Stomach tube rumen samples were collected 3.6 hrs after consumption of the challenge ration and analyzed for pH, and ammonia, D- and L-lactate, and volatile fatty acids (VFA), and histamine concentrations and total bacteria. The 16S rRNA gene spanning the V4 region was PCR amplified and sequenced using an Illumina MiSeq platform. Sequence data was analyzed using the Quantitative Insights Into Microbial Ecology software package (QIIME). Co-inertia analysis, including monte-carlo estimations (Ade4 package, R software) was conducted using operational taxonomic units (OTU) and rumen fermentation data from each group. A linear model was fitted to the OTU data and pairwise comparisons were performed to examine the significantly different OTU between groups (q < 0.1). Co-inertial analysis explained 31.9% of the total variation in the associations among rumen fermentation products, bacterial community composition, and groups. Histamine and valerate concentrations explained the most variation in the microbiome. Contrasts between the control vs. BUF and control vs. MT groups showed these groups had the lowest number of significantly different OTU (14 and 23 OTU, respectively), indicating they may have similar microbiomes. The MLY vs. BUF had the highest number of significantly different OTU (826 OTU), suggesting their microbiomes had the greatest difference. New Reference OTU14997 from the Streptococcus genus was more abundant in the control vs. MLY, VM vs. MLY, and BUF vs. MLY groups. New Reference OTU20477 from the Lactobacillus genus was more abundant in the control vs. VM, MLY vs. VM, BUF vs. VM groups. Lactobacillus ruminis was also more abundant in the MLY vs. VM and BUF vs. VM groups. Lactobacillus muscosae was more abundant in the BUF vs. VM group. The feed additives appeared to influence different microbial populations after the challenge.

Keywords: co-inertia, feed additives, ruminal acidosis