A better understanding of global ruminal microbiota and metabolites under extensive feeding conditions is a prerequisite for optimizing rumen function and improving ruminant feed efficiency. Furthermore, the gap between the information on the ruminal microbiota and metabolites needs to be bridged. The aim of this study was to investigate the effects of a wide range of forage to concentrate ratios (F:C) on changes and interactions of ruminal microbiota and metabolites. Four diets with different F:C (80:20, 60:40, 40:60, and 20:80) were limit-fed to 24 Holstein heifers, and Illumina MiSeq sequencing and gas chromatography time-of-flight/mass spectrometry were used to investigate the profile changes of the ruminal microbes and metabolites, and the interaction between them. The predominant bacterial phyla in the rumen were Bacteroidetes (57.2 ± 2.6%) and Firmicutes (26.8 ± 1.6%), and the predominant anaerobic fungi were Neocallimastigomycota (64.3 ± 3.8%) and Ascomycota (22.6 ± 2.4%). In total, 44, 9, 25, and 2 genera, respectively, were identified as the core rumen bacteria, ciliate protozoa, anaerobic fungi, and archaea communities across all samples. An increased concentrate level linearly decreased the relative abundance of cellulolytic bacteria and ciliates, namely Fibrobacter, Succinimonas, Polyplastron, and Ostracodinium (q < 0.05), and linearly increased the relative abundance of Entodinium (q = 0.04), which is a non-fibrous carbohydrate degrader. Dietary F:C had no effect on the communities of anaerobic fungi and archaea. Rumen metabolomics analysis revealed that ruminal amino acids, lipids, organic acids, and carbohydrates were altered significantly by altering the dietary F:C. With increasing dietary concentrate levels, the proportions of propionate and butyrate linearly increased in the rumen (P ≤ 0.01). Correlation analysis revealed that there was some utilization relationship or productive association between candidate metabolites and affected microbe groups. This study provides a better understanding of ruminal microbiota and metabolites under a wide range of dietary F:C, which could further reveal integrative information of rumen function and lead to an improvement in ruminant production.

The community structure of colonised bacteria in the gastrointestinal tracts (GITs) of pre-weaned calves is affected by extrinsic factors, such as the genetics and diet of the calves; however, the dietary impact is not fully understood and warrants further research. Our study revealed that a total of 6, 5, 2 and 10 bacterial genera showed biologically significant differences in the GITs of pre-weaned calves fed four waste-milk diets: acidified waste milk, pasteurised waste milk, untreated bulk milk, and untreated waste milk, respectively. Specifically, generic biomarkers were observed in the rumen (e.g., Bifidobacterium, Parabacteroides, Fibrobacter, Clostridium, etc.), caecum (e.g., Faecalibacterium, Oxalobacter, Odoribacter, etc.) and colon (e.g., Megamonas, Comamonas, Stenotrophomonas, etc.) but not in the faeces. In addition, the predicted metabolic pathways showed that the expression of genes related to metabolic diseases was increased in the calves fed untreated waste milk, which indicated that untreated waste milk is not a suitable liquid diet for pre-weaned calves. This is the first study to demonstrate how different types of waste milk fed to pre-weaned calves affect the community structure of colonised bacteria, and the results may provide insights for the intentional adjustment of diets and gastrointestinal bacterial communities.

BackgroundOriginal 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.MethodsTo 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.ResultsRumen 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.ConclusionsSimilar 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 materialThe online version of this article (doi:10.1186/s40104-017-0142-z) contains supplementary material, which is available to authorized users.

No abstract