Skip to main content

Advanced toolbox for rapid and cost-effective functional metagenomic screening - microbiology meets microfluidics.

Periodic Reporting for period 2 - METAFLUIDICS (Advanced toolbox for rapid and cost-effective functional metagenomic screening - microbiology meets microfluidics.)

Reporting period: 2017-12-01 to 2019-05-31

Enzyme discovery is the first step towards a more sustainable and greener bioeconomy, in which traditional energy intensive and waste generating processes are replaced by milder, enzyme-catalyzed alternatives or even completely redesigned versions. The natural diversity provides a wealthy source of biocatalysts for industry, most of which are of microbial origin. However, the vast majority of the enzyme diversity resides in unculturable microbes that conform “the microbial dark matter”. Consequently, culture independent, high-throughput methods are required if rare enzymes are to be found in the vast libraries of environmental DNA. For this reason, successful screening of metagenomes has often relied on the use of costly robotic equipment, not accessible to the vast majority of researchers.

Although some success stories in terms of metagenomic screening for industrial enzymes have been possible, the potential of metagenomics is highly underrealized due to a certain intrinsically diverse nature of its methods, which is usually sample- and context- dependent. Therefore, and to help solve these issues, MetaFluidics places emphasis on the development of new, synergic, “broad-range” and affordable discovery tools as well as “easy to use” bioinformatic analysis spanning into a platform designed to beat the odds of discovering relevant gene candidates rapidly and more efficiently by any laboratory.
The first 18 months of MetaFluidics have focused on sample acquisition and the development of cutting edge tools towards the screening stage of the project, which will begin officially in month 24.
In that regard, environments have been sampled (always with utmost care of environmental and ABS issues) a) that complement and do not overlap with previous samplings and b) where we have deemed it most likely to find organisms and their enzymes useful in the applications targeted by the MetaFluidics partners. Some of the most relevant enzymes in industry require resistance to drastic conditions, such as those found in the extreme environments sampled, such as arctic soil, hot springs, salterns among others. Other coveted industrial enzymes, those that degrade complex polysaccharides, are found in biotopes such as ruminants and eutrophicated water bodies, which we have also sampled. Finally, we have also sampled the marine invertebrate diversity in the hope of finding relevant bioactive molecules with pharmacological application.

The expression of environmental DNA into functional enzymes that can be assayed is far from universal, as it needs to overcome the lack of congruence between the biology and physicochemical conditions of the organism of origin and those of the expression host. Consequently, the expression of DNA from extreme environments requires the development of new molecular biology tools, which MetaFluidics partners have devised in order to access the diversity of hot, cold and high salinity environments and increase the odds of successful screening operations for these relevant industrial enzymes.

In parallel, conventional screening assays have been reduced to a microfluidic format, that is, the size of the test tube reduced to a microscopic droplet, with a concomitant increase in throughput and reduction in costs. Hydrolytic enzyme assays have already been tested, allowing us to screen millions of samples in a day and yielding tens of hits per screening. These “frontrunners” help us optimize the experimental setups for more demanding assays currently being developed, including assaying enzymes under the “unusual” temperature or salinity conditions found in extreme environments

Congruently with the philosophy of democratization of metagenomics, besides developing easy to implement biological and microfluidic tools, in MetaFluidics we are also developing the next generation of bioinformatics tools, to help process the vast amount of sequence data obtained typically in metagenomics. To that end, the opinion and experience of users has been collected through various initiatives and implemented in test and beta versions of the CLC genomics Microbial Genomics Module, the most used software tool in the market.
In MetaFluidics, progress beyond the state of the art is taking place in these three areas: development of biological, microfluidic and bioinformatics tools. Thus, the first 18 months of this project have seen the development of new vectors, hosts and other tools for recombinant expression of environmental DNA, regardless of biotope of origin. We have also seen the first ever metagenomic screening of some hydrolytic activities in microfluidic format, with unprecedented hit numbers. Building on these breakthroughs, in the next period, we will expand the range of enzymes that can be screened in this innovative miniaturized format as well as the conditions of temperature and salinity of these assays and further modifications, all directed towards one goal: increasing the amount of found candidate hits. The new bioinformatics tools continue to collect feedback from users and develop towards the final version of the software to be released by the end of the project.

The potential impact of these tools is being illustrated using significant case studies which have been deemed extremely relevant for the European bioeconomy strategy as well as for the welfare of Europeans, such as food safety and functional foods, enzymes for biofuels, for biocatalysis, for bioremediation, but also the discovery of new active pharmaceutical ingredients in nature. In order to improve the chances to valorize these discoveries, a careful contouring of IP landscapes and opportunities is continuously ongoing in MetaFluidics, as well as a careful survey of potential marketable outputs, including not only enzymes but also technologies and services. In this first periodic report, we have already begun to prove the unparalleled hit rate of our screening methods, obtaining on average tens of hits from a single screen. This results in more candidates for industrial applications and therefore an increased probability that one of them will reach production.

Last but not least, in MetaFluidics we are very aware of the right of European citizens to science and its benefits. Therefore, we keep a very active dissemination and communication strategy, addressed at specialized audiences, but also at the general public to maximize the impact of our work and to promote biotechnology as the path to a greener and more sustainable Europe.
"The ""extended"" workflow of metagenomics according to MetaFluidics"