Comparison of rumen bacteria distribution in original rumen digesta, rumen liquid and solid fractions in lactating Holstein cows

BACKGROUND: Original rumen digesta, rumen liquid and solid fractions have been frequently used to assess the rumen bacterial community. However, bacterial profiles in rumen original digesta, liquid and solid fractions vary from each other and need to be better established. METHODS: To compare bacterial profiles in each fraction, samples of rumen digesta from six cows fed either a high fiber diet (HFD) or a high energy diet (HED) were collected via rumen fistulas. Rumen digesta was then squeezed through four layers of cheesecloth to separate liquid and solid fractions. The bacterial profiles of rumen original digesta, liquid and solid fractions were analyzed with High-throughput sequencing technique. RESULTS: Rumen bacterial diversity was mainly affected by diet and individual cow (P > 0.05) rather than rumen fraction. Bias distributed bacteria were observed in solid and liquid fractions of rumen content using Venn diagram and LEfSe analysis. Fifteen out of 16 detected biomarkers (using LEfSe analysis) were found in liquid fraction, and these 15 biomarkers contributed the most to the bacterial differences among rumen content fractions. CONCLUSIONS: Similar results were found when using samples of original rumen digesta, rumen liquid or solid fractions to assess diversity of rumen bacteria; however, more attention should be draw onto bias distributed bacteria in different ruminal fractions, especially when liquid fraction has been used as a representative sample for rumen bacterial study. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s40104-017-0142-z) contains supplementary material, which is available to authorized users.