NITMETFUN

Food systems are responsible for approximately one third of global anthropogenic greenhouse gas emissions, making them a major driver of climate change. Europe’s agri-food system is characterized by inefficient utilization of dietary protein (i.e. nitrogenous feedstuff), with substantial nitrogen losses to the environment, estimated at around 77% of total nitrogen input and resulting in soil, water, and air pollution. Protein is not only the most expensive feed component, but its inefficient use also reduces farm profitability. Moreover, high-grain diets promote rumen dysbiosis, negatively affecting animal health and performance.

The rumen, the largest compartment of the ruminant gastrointestinal tract, hosts a complex and diverse microbiome comprising bacteria, archaea, protists, and anaerobic fungi. Rumen microbial activity is almost entirely responsible for nutrient conversion and supply to the host animal. Among these microorganisms, anaerobic fungi remain the least well characterized, despite constituting up to ~20% of the microbial biomass and being increasingly recognized as “hidden champions” of efficient nitrogen and carbon metabolism in ruminants.

In NITMETFUN, we propose to investigate how farming practices, feedstuff composition, and host genetics influence the abundance and metabolic activity of anaerobic fungi in the rumen. Our specific objective is to generate new knowledge on the contribution of anaerobic fungi to improved nitrogen (i.e. protein) use efficiency and reduced methane emissions in dairy cattle.

By linking anaerobic fungal community dynamics to host genetics and infrared-based estimates of nitrogen and carbon metabolism, the project will enable the identification of cow–microbiome combinations that maximize feed efficiency while reducing environmental losses. Beyond improved dietary management, NITMETFUN will support the active selection of dairy cows hosting optimally adapted rumen fungal communities, offering a cumulative and permanent mitigation strategy with long-term benefits for greenhouse gas reduction and nutrient retention at the farm level.

The project will directly benefit the farming community in Luxembourg and across North-Western Europe by delivering rapid, non-invasive tools for monitoring anaerobic fungi through faecal molecular analyses and enhanced infrared prediction models based on milk and faeces. These innovations will enable scalable, cost-effective assessment of feed nitrogen utilization efficiency and methane emissions, strengthening the sustainability, competitiveness, and climate resilience of the regional dairy sector.