Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities.

Molecular microbial ecology techniques are widely used to study the composition of the rumen microbiota and to increase understanding of the roles they play. Therefore, sampling and DNA extraction methods that result in adequate yields of microbial DNA that also accurately represents the microbial community are crucial. Fifteen different methods were used to extract DNA from cow and sheep rumen samples. The DNA yield and quality, and its suitability for downstream PCR amplifications varied considerably, depending on the DNA extraction method used. DNA extracts from nine extraction methods that passed these first quality criteria were evaluated further by quantitative PCR enumeration of microbial marker loci. Absolute microbial numbers, determined on the same rumen samples, differed by more than 100-fold, depending on the DNA extraction method used. The apparent compositions of the archaeal, bacterial, ciliate protozoal, and fungal communities in identical rumen samples were assessed using 454 Titanium pyrosequencing. Significant differences in microbial community composition were observed between extraction methods, for example in the relative abundances of members of the phyla Bacteroidetes and Firmicutes. Microbial communities in parallel samples collected from cows by oral stomach-tubing or through a rumen fistula, and in liquid and solid rumen digesta fractions, were compared using one of the DNA extraction methods. Community representations were generally similar, regardless of the rumen sampling technique used, but significant differences in the abundances of some microbial taxa such as the Clostridiales and the Methanobrevibacter ruminantium clade were observed. The apparent microbial community composition differed between rumen sample fractions, and Prevotellaceae were most abundant in the liquid fraction. DNA extraction methods that involved phenol-chloroform extraction and mechanical lysis steps tended to be more comparable. However, comparison of data from studies in which different sampling techniques, different rumen sample fractions or different DNA extraction methods were used should be avoided.

Evaluation of complementary effects of 9,10-anthraquinone and fumaric acid on methanogenesis and ruminal fermentation in vitro.

The objective of the present study was to investigate the hypothesis that 9,10-anthraquinone (AQ) in combination with fumaric acid (FMA) may provide complementary effects to inhibit methanogens and enhance rumen's capacity for better utilisation of FMA towards propionate production. Three levels of AQ and four levels of FMA were tested in a 3 x 4 factorial design using in vitro gas production technique. AQ reduced the total gas and methane production significantly. The combination of 4 ppm AQ with FMA had additive effect on concentration of propionate. Supplementation of AQ alone resulted in hydrogen accumulation (p < 0.001), whereas presence of FMA (up to 6.5 mM) along with AQ declined hydrogen concentration (p < 0.001). The level of 4 ppm AQ did not affect in vitro digestibility, however, a reduction of organic matter digestibility was caused by 8 ppm AQ (p < 0.001), which was partially compensated by the addition of FMA (p = 0.06). The optimum FMA level depended on the AQ concentration. At 4 ppm AQ, a FMA level of 3.5 mM had best possible effect on partitioning factor and microbial biomass production (p < 0.001), though, at 8 ppm AQ the higher level of FMA (6.5 mM) responded better. Overall, FMA in combination with AQ provided an alternative hydrogen sink and might be introduced as a novel strategy for mitigation of enteric methane emission. Nevertheless, the result should be proved by in vivo experiments.