Human population growth is driving a rise in cattle production for food, which necessitates more efficient and sustainable practices. One promising route to achieve this, is to unravel the connection between the feed cows eat, their bodily function and the microbes in their gut, not only to optimize nutrition but also to reduce the emission of greenhouse gases (methane). Our new strategy to collectively study the animal, its diet and all its microbes as one unit (the holobiont), is known as holo-omics. This strategy, enabled by recent biotechnological developments, can improve our understanding of how animals digest their feed and sustain their growth. This project combines novel methane-inhibiting feed ingredients, animal experiments and holo-omics to jointly analyze cows, their feed and their microbes. The outcome will be optimization of feeding strategies tailored to specific types of cows, to ultimately improve their growth and production whilst reducing their carbon footprint.

As the human population surges towards 10 billion, the production and consumption of aquaculture products such as fish is expanding. Therefore, efficient and environmentally sustainable practices are required to ensure long-term food security. To solve these challenges, attractive solutions include developing new feed ingredients and better broodstock genetics to improve fish production and welfare. Intriguingly, it has been shown that both feed and host genetics can modulate the gut microbiome of animals and thus influence its integral connection to host phenotype. The ambitious aim of ImprovAFish is to decipher the intimate functional coupling along the feed-microbiome-host axis in an applied context, with the emphasis on a promising ‘next generation’ functional feed ingredient (beta-mannan) that is known to promote beneficial microbiota in livestock and has shown promising preliminary results in fish.

Our approach is to jointly analyze how diet affects the metabolic function of the host and its microbiome as a single unit of action, using a novel and powerful framework called “holo-omics”. This entails monitoring how changes in enzymes and metabolites produced by microbiota correlates with uptake and metabolism of nutrients in the gut and liver of the fish. By doing this across life stages, different feeds and with recordings of key performance indices, we aim to identify exploitable interactions between specific feed components and microbiome functions that can be used to improve fish phenotype. In addition, associations between broodstock genetic variation, microbiome composition and diet will be determined, which will facilitate selection for fish with preferred gut microbiota. Ultimately ImprovAFish will facilitate optimization of improved and sustainable feeding strategies that are specifically tailored to host genetics (or vice versa), with an emphasis on socially responsible outcomes facilitated by a dedicated Responsible Research and Innovation process.

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According to UN forecasts, there will 10 billion people to feed by 2050, which is a major challenge. To securely meet this challenge, society must produce more food whilst using fewer resources and reducing its carbon footprint. Agriculture is the world's single largest provider of food, yet it is also accountable for a significant part of our anthropogenic carbon emissions, including production of methane gas by cows. Nutritional manipulation of methane production is considered a feasible strategy that, however, still is relatively unexplored and where rationalization is still far off. Notably, feeding seaweed to cows has recently emerged as a promising strategy for reducing methane production. Understanding of this effect requires a holistic insight into the maze of metabolic routes that constitutes the rumen microbiome, an elaborate community comprised of bacteria, archaea, viruses and eukaryotes. Despite the rumen microbiome being key in solving the cow-methane problem, definitive links between what the cows eat, their microbiome, their methane emissions and their productivity remain largely unknown.

SeaCow's main objectives are to characterize the microbiome-host interactions that underlie the metabolic transformation during inhibition of enteric methane production in cows using novel seaweed-based nutritional manipulation strategies. Animal feeding trials will elucidate the real effect of seaweed additives on Norwegian Red cattle, whereas a unique state-of-the-art characterization of the rumen microbiome will model metabolic routes and keystone microbial populations that drive host performance and methane emissions. Importantly, this approach entails focus on emerging less studied members of the rumen microbiota (such as eukaryotes). Ultimately, the outcome of the SeaCow project will enhance our understanding of the feed-microbiome-host axis that is crucial to optimize feeding regimes in agriculture to promote an efficient and low methane emitting livestock.

Communities of microorganisms (microbiomes) are increasingly known to play a critical role in health and disease in human hosts, and also as part of environmental ecosystems. Sequencing the genetic material (DNA) from these microbial communities catalogs the different organisms making up these complex systems, and how this composition may change under different conditions (e.g. health versus disease in humans, introduction of pollutants within an environmental ecosystem etc.). However, DNA sequencing alone only provides a limited picture of the system. Consequently, researchers lack knowledge of how, at a detailed molecular level, microbiomes interact and respond to their surroundings. This knowledge could lead to new breakthroughs for engineering microbiomes to help fight disease, clean‐up toxins in the environment, or produce environmentally friendly biofuels. To gain such knowledge, measurement of additional molecules encoded by the microbial DNA (e.g. RNA, proteins) is necessary. Fortunately, large‐scale data on the identify and abundance of RNA and protein can now be readily generated, but there is a lack of effective software that can analyze the data in an integrated fashion and help researchers make new discoveries. To address this current bottleneck, we will establish a new trans‐Atlantic partnership between two highly complementary Minnesota and NMBU research teams. We will develop and optimize integrative analysis of large‐scale DNA, RNA and protein data within the Galaxy framework. We will disseminate the software, putting it in the hands of researchers who will use it to advance knowledge of microbiomes and how these complex communities may be used to improve human and environmental health.