Composition and in Situ Gene Expression of Rumen Wall Microbial Communities

The rumen wall is the interface between the ruminant host animal the site of metabolite absorption and exchange and it has long been known to be covered by microorganisms. A number of recent studies have analyzed the composition of rumen wall microbial communities under different feeding and management strategies and in different ruminant species. However, our knowledge about the function of rumen wall microbes is still highly limited. This lack of knowledge is surprising as the rumen wall microbes occupy a niche which is central for rumen function with respect to nutrient exchange and also as barrier against pathogens. The exploration of function of rumen wall microbiota is thus relevant for basic and applied research for a better understanding of the effects of different nutrition, metabolic disorders such as subacute ruminal acidosis (SARA), and host-microbe interactions at the rumen wall. In this talk, I will provide an overview on our research on rumen wall microbial community composition and function in dairy cattle. I will focus on changes of microbial community composition under different feeding and during SARA conditions and I will be presenting functional insights into rumen wall tissue and microbiota gene expression based on metatranscriptome sequencing under forage-diet and SARA conditions. Our results reveal high levels of transcription of genes involved in central metabolism and general housekeeping genes. In addition, we show that urease activity, oxygen scavenging, degradation of starch and amino acids are important functions of the rumen wall microbial communities, based on their high levels of gene expression. Furthermore, we provide evidence for nitrogen fixation and sulfate reduction at the rumen wall and show the presence and metabolic activity of archaea and fungi on the rumen wall. We found only few statistically significant differences in gene expression patterns between a forage-based diet and a four-week SARA challenge. Analysis of rumen wall microbial community composition revealed significant changes during the adaptation from a forage-based diet to a high-grain based diet. Furthermore, I will present first insights into an ongoing project analyzing the stratification of rumen wall microbial communities in dairy cattle. A stratification of rumen content in dairy cattle has been known for a long time. We hypothesize that the stratification of the rumen content is mirrored by the rumen wall microbial communities. Our results from 16S rRNA gene amplicon sequencing suggest that rumen wall microbial communities do indeed show a stratification.