Abstract
Better characterization of changes in the rumen microbiota in dairy cows over the lactation period is crucial for understanding how microbial factors may potentially be interacting with host phenotypes. In the present study, we characterized the rumen bacterial and archaeal community composition of 60 lactating Holstein dairy cows (33 multiparous and 27 primiparous), sampled twice within the same lactation with a 122 days interval. Firmicutes and Bacteroidetes dominated the rumen bacterial community and showed no difference in relative abundance between samplings. Two less abundant bacterial phyla (SR1 and Proteobacteria) and an archaeal order (Methanosarcinales), on the other hand, decreased significantly from the mid-lactation to the late-lactation period. Moreover, between-sampling stability assessment of individual operational taxonomic units (OTUs), evaluated by concordance correlation coefficient (C-value) analysis, revealed the majority of the bacterial OTUs (6,187 out of 6,363) and all the 79 archaeal OTUs to be unstable over the investigated lactation period. The remaining 176 stable bacterial OTUs were mainly assigned to Prevotella, unclassified Prevotellaceae, and unclassified Bacteroidales. Milk phenotype-based screening analysis detected 32 bacterial OTUs, mainly assigned to unclassified Bacteroidetes and Lachnospiraceae, associated with milk fat percentage, and 6 OTUs, assigned to Ruminococcus and unclassified Ruminococcaceae, associated with milk protein percentage. These OTUs were only observed in the multiparous cows. None of the archaeal OTUs was observed to be associated with the investigated phenotypic parameters, including methane production. Co-occurrence analysis of the rumen bacterial and archaeal communities revealed Fibrobacter to be positively correlated with the archaeal genus vadinCA11 (Pearson r = 0.76) and unclassified Methanomassiliicoccaceae (Pearson r = 0.64); vadinCA11, on the other hand, was negatively correlated with Methanobrevibacter (Pearson r = –0.56). In conclusion, the rumen bacterial and archaeal communities of dairy cows displayed distinct stability at different taxonomic levels. Moreover, specific members of the rumen bacterial community were observed to be associated with milk phenotype parameters, however, only in multiparous cows, indicating that dairy cow parity could be one of the driving factors for host–microbe interactions.
Highlights
Ruminants live in a symbiotic relationship with a complex consortium of microorganisms residing in the rumen, responsible for the breakdown of feed ingredients, especially plant material rich in oligo- and polysaccharides (Flint et al, 2008)
The rumen bacterial community was dominated by Bacteroidetes (74.9%), Firmicutes (14.5%) and Fibrobacteres (1.5%), accounting for more than 90% of the analyzed amplicons (Figure 1) and the relative abundances of these dominant phyla did not yijkl = μ + bi dim + bj (OTU) + Pk + al + eijkl (1)
Lactation stage has been considered as an important factor responsible for shifts in the rumen bacterial communities of lactating dairy cows (Jewell et al, 2015; Bainbridge et al, 2016) and transition cows (Pitta et al, 2014a; Lima et al, 2015; Dieho et al, 2017; Zhu et al, 2018), and likewise for parity (Pitta et al, 2014a; Jewell et al, 2015; Lima et al, 2015)
Summary
Ruminants live in a symbiotic relationship with a complex consortium of microorganisms residing in the rumen, responsible for the breakdown of feed ingredients, especially plant material rich in oligo- and polysaccharides (Flint et al, 2008) This functional feature results in the production of a wide range of microbial metabolites in the rumen, including shortchain fatty acids (SCFA), amino acids, vitamins, and methane. Recent studies on large dairy cow and beef cattle cohorts have, identified heritable taxa of the rumen microbiota, suggesting that host genetics is a determinant factor for rumen microbiota composition (Difford et al, 2018; John Wallace et al, 2019; Li et al, 2019) Findings like this have been a driver for hypothesizing the rumen microbiota to be composed of two key components; (i) a stable “core microbiota,” with conserved house-keeping features, crucial for functional stability of the rumen microbial community as well as the host and (ii) a “dynamic microbiota,” with an inherent plasticity allowing for adaption to swift changes in environmental stimuli, provided e.g., via the diet
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