EBI Metagenomics - enabling the reconstruction of microbial populations

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Microorganisms inhabit practically all environments on Earth. For example, there are more microbes in the ocean than stars in the known universe, with complex communities living in vastly different niches, from the tropics to the polar waters and from well-lit surface waters to the deep abyss. They harvest and transduce solar energy and is estimated that they contribute 50-90% to global primary production, turning light into biomass through photosynthesis, making them vital to the world's food chain. Microbes produce and consume most greenhouse gases (carbon dioxide, nitrous oxide and methane), which is of particular importance in relation to man-made climate change. They are also responsible for over half of all oxygen production on Earth. Within ecosystems, microbes catalyse the key bio-geochemical transformations of nutrients and trace elements that sustain organic productivity. Understanding these processes would bring many potential benefits. For example, working out the mechanisms by which microbes unlock organic phosphate to a soluble form that can be absorbed by plants could reduce the use of fertilizers and increase agricultural yields. Within each environment, the microbial population contains a vast and dynamic reservoir of genetic variability, much of which is yet to be studied. Current biological databases do not represent the vast majority of environmental organisms, as traditional genome sequencing approaches require isolation and culturing. Metagenomics, the sequencing of the entire collection of DNA found within an environmental sample, circumvents this need. As a result, we have begun to answer some of the key questions about which organisms are found in which environments. There has been a huge uptake of the approach across a broad range of disciplines. Nevertheless, the majority of metagenomics projects produced over the past decade have given only a fragmentary picture of underlying micro-organisms genomes, as larger volumes of sequencing are required to improve the level of genomic detail.In the era of data driven science, and with widespread access to sequencing technology and ever diminishing costs, huge volumes of sequence data present an amazing opportunity to understand the microbial world at a more detailed level. However, the field of metagenomics faces the following issues: 1) given the vast data volumes, specialist expert-built pipelines are required for efficient, high-throughput analysis; 2) bioinformatics analysis of results is costly to produce and requires expert knowledge; 3) to extract maximum knowledge from experiments, there is a need to systematically capture the associated experimental data along with the sequence data; 4) there is a lack of consistency between different analysis approaches, affecting comparability. The EBI Metagenomics (EMG) resource solves these issues by offering a free service for the analysis and archiving of all metagenomic data. With advances in algorithms and methods, it is now possible to piece together the fragments that make up an individual organism's genome. In this project, we will not only continue the provision of the EMG, but also develop the analysis, archiving, tools and data presentation frameworks required to generate genomes from metagenomes. Due to the unique position of EMG, we will be also able to combine data across different projects that contain similar microbial communities. This important data reuse will enable us to generate the highest quality genomes, allow us to detect different strains of bacteria and ensure that we capitalize on previous investments. Our genomes will enrich the current tree of life, and we will extend the EMG interfaces to accommodate the new data that we will produce. This will empower research and innovation in the environment, bioindustries, agriculture and medicine (human and livestock). We will work closely with biotechnological industries, to enable them to harness the huge potential for discovery.