Ruminal microbiota is associated with feed-efficiency phenotype of fattening bulls fed high-concentrate diets

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Abstract
Context: Improving feed efficiency in livestock production is of great importance to reduce feeding costs. Aims: To examine the relationship between ruminal microbiota and variation in feed efficiency in beef cattle fed concentrate-based diets. Methods: Residual feed intake of 389 fattening bulls, supplied with corn-based concentrate and forage ad libitum, was used to estimate animals’ feed efficiency. Faeces and ruminal fluid samples, from 48 bulls chosen at random, were collected to estimate their forage intake and to determine their apparent digestibility, ruminal fermentation and microbiota. Those animals with extreme values of feed efficiency (high-efficiency (HE, n = 12) and low-efficiency (LE, n = 13)) were subjected to further comparisons. Alpha biodiversity was calculated on the basis of the normalised sequence data. Beta diversity was approached through performing a canonical correspondence analysis based on log-transformed sequence data. Genera differential abundance was tested with an ANOVA-like differential expression analysis and genera interactions were determined applying the sparse correlations for compositional data technique. Key results: No differences in dry matter intake were found between the two categories of feed efficiency (P = 0.699); however, HE animals had higher apparent digestibility of dry matter (P = 0.002), organic matter (P = 0.003) and crude protein (P = 0.043). The concentration of volatile fatty acids was unaffected by feed efficiency (P = 0.676) but butyrate proportion increased with time in LE animals (P = 0.047). Ruminal microbiota was different between HE and LE animals (P = 0.022); both α biodiversity and genera network connectance increased with time in LE bulls (P = 0.005 for Shannon index and P = 0.020 for Simpson index), which suggests that LE animals hosted a more robust ruminal microbiota. Certain genera usually related to high energy loss through methane production were found to establish more connections with other genera in LE animals’ rumen than in HE ones. Microbiota function capability suggested that methane metabolism was decreased in HE finishing bulls. Conclusions: Rumen microbiota was associated with feed efficiency phenotypes in fattening bulls fed concentrate-based diets. Implications: The possible trade-off between feed efficiency and robustness of ruminal microbiota should be taken into account for the optimisation of cattle production, especially in systems with intrinsic characteristics that may constitute a disturbance to rumen microbial community.

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