The effects of a probiotic yeast on the bacterial diversity and population structure in the rumen of cattle.. Bacteria

We have been able to link changes in the fermentation pattern of the rumen of cattle to a shift in the microbial population using short read sequencing technology. Using a model of sub-acidosis we have demonstrated that a supplementation of probiotic yeast could restore a healthy fermentation in the rumen of lactating cow (VFAs, pH, Eh and lactate). These improvements were accompanied with a shift in the main fibrolytic group (Fibrobacter and Ruminococcus) and lactate utilising bacteria (Megasphaera and Selenomonas). We have also shown that the analysis of short V1 region of 16s rRNA gene (50-60bp) could give as much phylogenetic information as a longer read (454 pyrosequencing of 250 bp) which suggest that next generation sequencing such as Illumina could replace the more expensive 454 technology for microbiome analysis. This study also highlights the difficulty to draw broad conclusions on composition and diversity of complex microbiota because of the variation caused by the use of different method (sequencing technology or analysis). Therefore this study provides an insight as to how short read sequences can be used to describe the changes in microbial ecology in response to feed additives and suggests some of the pitfalls to avoid.