Characterisation and optimisation of the rumen microbiome

瘤胃微生物群可以说是地球上最重要的经济微生物群之一。全球有超过10亿头牛和其他生产食物的反刍动物，它们对粮食安全至关重要，为数十亿人提供肉类和乳制品。然而，目前的全球粮食体系无法养活地球上70亿人口中的10%，2050年人口将超过90亿，2100年将超过110亿。因此，粮农组织估计，到2050年，肉类产量将需要增加76%，乳制品产量需要增加63%。同时，我们必须减少粮食系统对环境的影响。简而言之，我们必须用更少的资源生产更多的食物。因此，了解反刍动物如何将食物转化为能量，进而转化为牛奶和肌肉蛋白质，显然是重要的。如果我们能够提高反刍动物对食物的消化效率，我们可能能够在使用更少资源的情况下生产更多的食物，这是改善全球粮食安全的关键目标。奶牛瘤胃适应于将植物材料分解为能量和营养物质，这一任务主要由瘤胃微生物群编码的酶执行。瘤胃包含一个微生物生态系统，其中细菌、古菌、原生动物和真菌的密集和复杂的混合物将碳水化合物转化为短链挥发性脂肪酸(VFAS)。我们在牛的瘤胃中发现了数千种新的细菌和古菌物种，我们能够使用计算技术来预测它们的代谢潜力。然而，充分了解它们在瘤胃微生物生态系统中的作用和行为将需要将这些新物种引入培养，并在体外和在体内进行研究。在本博士学位中，您将(I)将重要的瘤胃微生物物种引入培养，重点关注当前目录中的空白(大约有2,300个物种缺失)；(Ii)在实验室研究这些新微生物的代谢潜力，以及它们在各种底物上的生长和行为；(Iii)建立模拟有益行为的微生物群落，并使用多组学技术研究这些群落；(Iv)在动物试验中测试其中一些群落，以研究它们对重要反刍动物表型的影响

The rumen microbiome is arguably one of the most economically important microbiomes on the planet. Globally, there are over 1 billion cattle and other food-producing ruminants and they are of vital importance for food security, providing meat and dairy products to billions of humans. However, the current global food system fails to feed 10% of the 7 billion humans on the planet, and the population is set to exceed 9 billion in 2050 and 11 billion in 2100. As such, the FAO estimates that by 2050 meat production will need to increase by 76% and dairy production by 63%. At the same time we must reduce the impact of the food system on the environment. In short, we must produce more food using fewer resources.Understanding how ruminants convert their food into energy, and subsequently milk and muscle protein, is therefore of obvious importance. If we can improve the efficiency of food digestion by ruminants, we may be able to produce more food while using fewer resources, a key aim of improving global food security. The cow rumen is adapted for the breakdown of plant material into energy and nutrients, a task largely performed by enzymes encoded by the rumen microbiome. The rumen contains a microbial ecosystem in which a dense and complex mixture of bacteria, archaea, protozoa and fungi convert carbohydrates to short-chain, volatile fatty acids (VFAs).We have discovered thousands of novel Bacterial and Archaeal species in the cattle rumen, and we are able to predict their metabolic potential using computational techniques. However, full understanding of their role and behaviour in the rumen microbial ecosystem will require bringing these novel species into culture, and studying them in vitro and in vivo.In this PhD, you will (i) bring into culture important rumen microbial species, focusing on gaps in the current catalogue (there are an approximately 2,300 missing species; (ii) study these novel microbes in the lab in terms of their metabolic potential, and growth and behaviour on various substrates; (iii) build beneficial communities of microbes that mimic beneficial behaviour and study these communities using multi-omics techniques; (iv) test some of these communities in an animal trial to study their effect on important ruminant phenotypes