Our aim was to simultaneously investigate the gut bacteria typical characteristic and conduct rumen metabolites profiling of high production dairy cows when compared to low‐production dairy cows. The bacterial differences in rumen fluid and feces were identified by 16S rDNA gene sequencing. The metabolite differences were identified by metabolomics profiling with liquid chromatography mass spectrometry ( LC ‐ MS ). The results indicated that the high‐production dairy cows presented a lower rumen bacterial richness and species evenness when compared to low‐production dairy cows. At the phylum level, the high‐production cows increased the abundance of Proteobacteria and decreased the abundance of Bacteroidetes, SR 1, Verrucomicrobia, Euryarchaeota, Planctomycetes, Synergistetes, and Chloroflexi significantly ( p < 0.05). At the genus level, the rumen fluid of the high‐production group was significantly enriched for Butyrivibrio , Lachnospira , and Dialister ( p < 0.05). Meanwhile, rumen fluid of high‐production group was depleted for Prevotella, Succiniclasticum, Ruminococcu, Coprococcus, YRC 22, CF 231, 02d06, Anaeroplasma, Selenomonas , and Ruminobacter significantly ( p < 0.05). A total of 92 discriminant metabolites were identified between high‐production cows and low‐production cows. Compared to rumen fluid of low‐production dairy cows, 10 differential metabolites were found up‐regulated in rumen fluid of high‐production dairy cows, including 6alpha‐Fluoropregn‐4‐ene‐3,20‐dione, 3‐Octaprenyl‐4‐hydroxybenzoate, disopyramide, compound III (S), 1,2‐Dimyristyl‐sn‐glycerol, 7,10,13,16‐Docosatetraenoic acid, ferrous lactate, 6‐Deoxyerythronolide B, vitamin D2, L‐Olivosyl‐oleandolide. The remaining differential metabolites were found down‐regulated obviously in high‐production cows. Metabolic pathway analyses indicated that most increased abundances of rumen fluid metabolites of high‐yield cows were related to metabolic pathways involving biosynthesis of unsaturated fatty acids, steroid biosynthesis, ubiquinone and other terpenoid‐quinone biosynthesis. Most down‐regulated metabolic pathways were relevant to nucleotide metabolism, energy metabolism, lipid metabolism and biosynthesis of some antibiotics.

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Dairy cows are economically important livestock animals that supply milk for humans. The cow’s rumen is a complex and symbiotic ecosystem composed of diverse microorganisms, which has evolved to digest high-fiber diets.

Subacute ruminal acidosis (SARA) represents one of the most important digestive disorders in intensive dairy farms, and dairy cows are individually different in the severity of SARA risk. The objectives of the current study were to investigate differences in the ruminal bacterial community and metabolome in dairy cattle with different susceptibility to SARA. In the present study, 12 cows were initially enrolled in the experiment. Based on average ruminal pH, 4 cows with the lowest ruminal pH were assigned to the susceptible group (SUS, pH = 5.76, n = 4) and 4 cows with the highest ruminal pH assigned to the tolerant group (TOL, pH = 6.10, n = 4). Rumen contents from susceptible (SUS, n = 4) and tolerant (TOL, n = 4) dairy cows were collected through rumen fistula to systematically reveal the rumen microbial and metabolic alterations of dairy cows with different susceptibility to SARA using multi-omics approaches (16S and 18S rRNA gene sequencing and metabolome). The results showed that despite being fed the same diet, SUS cows had lower ruminal pH and higher concentrations of total volatile fatty acids (VFA) and propionate than TOL cows ( P < 0.05). No significant differences were observed in dry matter intake, milk yield, and other milk compositions between the SUS and TOL groups ( P > 0.05). The principal coordinates analysis based on the analysis of molecular variance indicated a significant difference in bacterial composition between the two groups ( P = 0.01). More specifically, the relative abundance of starch-degrading bacteria ( Prevotella spp.) was greater ( P < 0.05), while the proportion of fiber-degrading bacteria (unclassified Ruminococcaceae spp., Ruminococcus spp., Papillibacter , and unclassified Family_XIII) was lower in the rumen of SUS cows compared with TOL cows ( P < 0.05). Community analysis of protozoa showed that there were no significant differences in the diversity, richness, and community structure ( P > 0.05). Metabolomics analysis revealed that the concentrations of organic acids (such as lactic acid), biogenic amines (such as histamine), and bacterial degradation products (such as hypoxanthine) were significantly higher in the SUS group compared to the TOL group ( P < 0.05). These findings revealed that the higher proportion of starch-degrading bacteria/lower fiber-degrading bacteria in the rumen of SUS cows resulted in higher VFA-producing capacity, in particular propionate. This caused a disruption in metabolic homeostasis in the rumen which might be the reason for the higher susceptibility to SARA. Overall, these findings enhanced our understanding of the ruminal microbiome and metabolic changes in cows susceptible to SARA.

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