New approaches to resolving community metaproteomes: ComProt

了解生态系统中生物之间的相互作用是生态学研究的关键部分，有助于我们了解生态系统是如何运行的，这对微生物和微型节肢动物尤其重要，因为它们往往很难实时原位研究。目前自然环境面临许多挑战，我们需要能够衡量气候变化、污染物水平、集约化农业和低成本系统发展的影响，以了解群落的适应能力以及碳、氮和磷循环受到的影响。微生物在我们的环境中扮演着至关重要的角色，它们占据着从我们的肠道和身体表面到海底热喷口的广泛栖息地，它们在土壤中对养分循环和植物健康至关重要，并负责从草中消化纤维素，这些纤维素在奶牛特殊的胃中被分解，称为瘤胃，以及海洋中碳的全球循环，因为许多细菌可以进行光合作用，从而获得光能来固定二氧化碳。我们研究这些微生物的生理和整体活动的能力存在一个主要问题，因为我们不能在实验室中分离和培养(至今)绝大多数微生物(可能超过98%)。我们之所以知道它们的存在，是因为我们使用了类似于DNA法医方法的方法，仅根据它们的DNA使用特征基因来检测它们，从而使我们能够对它们进行识别和分组。这种多样性大多是细菌的，但也有几类真菌。正在开发新的方法来研究这些微生物种群，这被称为元基因组学，我们在这个项目中专注于产生的蛋白质被称为元蛋白质组。蛋白质等同于活性，因为所有的酶都是蛋白质，是反应的催化剂。因此，我们可以使用元基因组来帮助识别哪些蛋白质存在，因为蛋白质中的DAN代码和多肽序列之间存在关系。建立这种联系是具有挑战性的，所以我们的目标是提高对如何将一系列肽序列翻译成功能蛋白质的理解，并认识到它们的起源和可能的功能。这样，我们就可以将微生物群落作为一个由许多基因组组成的种群来研究，而不是试图分离和研究一个基因组。我们可以在我们的肠道或土壤中研究这个种群，方法是提取和分析DNA以进行多样性分析，提取和分析RNA以进行基因表达，提取和分析蛋白质以确认活动，并通过代谢产物来确定生理。此外，我们还可以提取DNA并在其他可培养的细菌中表达。这使我们能够捕获DNA并对其进行表达，从而深入了解某些功能，如具有特殊性质的特定酶或色素。拟议工作的目的是建立一个学术伙伴网络，以建设这一重要科学领域的能力，以确保我们能够研究和利用细菌种群的所有有趣和令人兴奋的属性，并利用它们创造一个可持续的未来。

Understanding interactions between organisms in an ecosystem is a critical part of ecological research and facilitates our understanding of how ecosystems function and this is particularly important for microorganisms and microarthropods as they are often difficult to study in situ in real time. Currently the natural environment faces many challenges and we need to be able to measure the impacts of changes in climate, pollutant levels, intensive farming and development of ley systems to understand how resilient communities are and how Carbon, nitrogen and phosphorous cycles are affected.Microrganisms play a vital role in our environment they occupy a wide range of habitats from our gut and body surfaces all the way to hot vents under the sea, they are critical in the soil for recycling of nutrients and plant health and responsible for the essential digestion of cellulose from grass being broken down in the specialised stomach of the cow termed the rumen to the global cycling of carbon in the oceans via harvesting of sunlight as many bacteria can photosynthesize and thus harvest light energy to fix carbon dioxide. A major problem exists in our ability to study the physiology and overall activities of these microbes due to the fact that we cannot isolate and cultivate (yet) the vast majority (probably over 98%) of them in the laboratory. We know they exist because we have used methods similar to DNA forensic approaches to detect them solely based on their DNA using signature genes which allow us to identify and group them. Most of this diversity is bacterial but there are also several groups of fungi. New methods are being developed for the study of these microbial populations and this is called metagenomics and we are focused in this projects on the proteins produced termed metaproteomic. Proteins equate with activity as all enzymes are proteins and act as catalysts for reactions. Therefore, we can use the metagenomes to help in identifying which proteins are present because there is a relationship between the DAN code and the sequence of peptides in a protein. Making this link is challenging so we aim to improve the understanding of how to translate a series of peptide sequences into functioning proteins and recognise both their origins and putative function.so that we study the microbial community as a population of many genomes rather than trying to isolate and study one. We can study this population in our guts or in the soil by extracting and analysing DNA for diversity analysis, RNA for gene expression and protein for confirmation of activities and metabolites to determine physiology. In addition we can extract DNA and express it in other bacteria which are culturable. This allows us to capture the DNA and express it thus gaining an insight into some functions such as specific enzymes or pigments with special properties. The imof the proposed work is to establish a network of academic partners to build capacity in this important area of science to ensure that we are able to study and exploit all the interesting and exciting attributes of bacterial populations and harness them for a sustainable future.