The UK’s Microbiology Society, one of Europe’s largest microbiology membership charities for scientists, released a policy report on 15 November summarising the challenges in microbiome research and recommendations for overcoming them.
One such challenge is organising and sharing the data needed to progress research in metagenomics — the study of genetic material in a microbe’s genome. The report states that a single metagenomic project might involve sequencing thousands of microbiome samples, producing huge volumes of data at a faster rate than scientists can gain insights for research. To take advantage of these big datasets, they must be properly standardised and stored — especially capturing information about how both the wet laboratory and sequence information was generated.
The report pointed out ELIXIR’s contribution in developing resources vital to handling the large volume of data generated from sequencing microbiome samples. Scientists involved in ELIXIR have also proposed ways to address the lack of standards in metagenomics research. Ultimately, metagenomics helps scientists better understand the role microbes play in human, animal and environmental health. The ELIXIR Marine Metagenomics Use Case is developing services that facilitate this process.
Increasing usability of marine metagenomics data
Scientists can map out more of a metagenome when other research groups working to accomplish the same goal have consistent, reproducible and portable pipelines, and access to high quality reference datasets.
Work conducted under the ELIXIR umbrella has enabled the EBI Metagenomics to completely overhaul the taxonomic profiling section of their pipeline, updating the underlying reference databases and tools. The result is more, higher-resolution taxonomic assignments that help classify a microbiome.
ELIXIR’s Marine Metagenomics Portal also provides the research community with improved pipelines, such as the META-pipe pipeline, and reference datasets that enhance the precision and accuracy of biodiversity and function analysis.
Research in marine metagenomics requires training for how to use the appropriate data resources and pipelines — a gap that the ELIXIR Training Platform has been working to fill.
- Microbiology Society. Unlocking the Microbiome: Opportunities and challenges of microbiome research for health, agriculture, environment and biotechnology. 15 Nov. 2017.
- Hoppen P, Finn R, Bongo L, et al. The metagenomic data life-cycle: Standards and best practices. GigaScience 2017, 6:8. doi: https://doi.org/10.1093/gigascience/gix047