Understanding the cross-talk between feed, host and the microbiome. 

The mammalian gastrointestinal tract (GIT) represents one of the most complex ecosystems on this planet, harboring eukaryotes, bacteria, archaea and viruses. The bacterial fraction is estimated to harbor 10- 100 trillion bacteria. As for nearly all natural ecosystems, the whole extent of biodiversity has not been fully uncovered yet. The GIT of farm animals is shaped by an intimate coexistence of the host and its microbial colonizers. These colonizers are in homeostatic balance, driven by dynamics in selection, competition and competitive exclusion of microbes. The knowledge of this microbiome and its function is of utmost importance for applied research in livestock. The microbiome is central in food digestion, the development of immunity of the host, maintenance of intestinal homeostasis, and ultimately contribute to the systemic health of the host. Our research addresses the diversity and community profile of microbes and aims to understand the function of these microbes in relation to dietary changes, and physiological host responses. Key approaches are the use of ‘Omics technologies (metagenomics, transcriptomics, metabolomics), which enable to study the uncultured majority of microbes, as well as finding biomarker metabolites that underlie the communication between microbe and host in all stages of livestock production.

Identification of metabolically active rumen microbes in cattle undergoing subacute ruminal dysbiosis. 

Ruminants have evolved as herbivores through a symbiotic relationship with a highly complex rumen microbial community consisting of bacteria, archaea, fungi, protozoa, and viruses. This essential microbial ecosystem enables ruminants to convert feedstuffs that are indigestible to monogastrics such as humans into volatile fatty acids (VFA), essential vitamins, and microbial proteins. Within the rumen microbiome, bacteria are the most diverse and predominant domain, and make the greatest contribution to the digestion and conversion of feeds. Disturbances to the microbial ecosystem result in negative consequences for the ruminant including decreased feed efficiency and in some cases inflammation. One of the most common production problems is subacute ruminal acidosis (SARA), which is defined as bouts of ruminal pH below physiological levels for extended periods in the day. These bouts are usually associated with feeding events, and the rapid fermentation of starches to VFAs. Despite being the focus of extensive research, the aetiology of SARA is poorly understood. This is partially due to the complexity of the rumen microbiome. Our research focuses on understanding the events that precede SARA and the associated changes in the microbial populations and the production of inflammation inducing endotoxins.    

Feed and feed additive impacts on rumen fermentation and microbial diversity.

The production efficiency of ruminant livestock is directly impacted by the efficiency of feed digestion and the stability of the rumen microbial population. Our group is interested in how feedstuffs (beetpulp, sunflower oil, processing cakes) and feed additives impact the fermentation and microbial community of ruminants in production systems.