Speaker: Dr Rob Finn, European Bioinformatics Institute (EBI), will present a seminar entitled : Do we know the composition of the human gut microbiome?
Host: John Walshaw
Metagenomics, the analysis of the sum of genetic material from a sample, has started to shed light on the huge diversity of micro-organisms that occupy environments such as the human body, soil and the world’s oceans. The EBI metagenomics platform provides both a free to use service for all types of metagenomics data and access to one of the largest collection of consistently analysed metagenomics datasets, regardless of source biome. We have recently introduced metagenomics assembly into the repertoire of services provide by EBI metagenomics.
Assembled contigs enable the identification of full length protein sequences and the production of databases containing millions of unique proteins, the majority of which have never been seen before. Ultimately, such sequences need to be linked to a taxonomic identifier. But how much can we trust de novo assembly and binning techniques to provide draft genomes? Partly to answer this question we have undertaken a large-scale analysis of public human gut microbiome datasets, performing de novo assembly on thousands of samples containing adequate read depth. We have compared computed genomics bins (metagenome assembled genomes, MAGs) with isolate genomes and used the latter to assess the quality of the MAGs, the tools for assessing MAG quality and provide an estimate of how many species are yet to be represented in genomic reference catalogues for studying the human microbiome. As we build a more complete picture of the human microbiome constituents, we can start developing and testing better mechanistic models.
Dr Rob Finn leads EMBL-EBI’s Sequence Families team, which is responsible for the InterPro, Pfam, Rfam and RNAcentral data resources. The team also looks after EMBL-EBI’s fast-growing Metagenomics data service.
Rob joined EMBL-EBI from the Janelia Research Campus in the US, where he led a group that designed fast, web-based, interactive protein-sequence searches and annotations. Between 2001 and 2010, he was the project leader for Pfam at the Wellcome Trust Sanger Institute in the UK.
Rob’s academic background is in microbiology and he holds a PhD in biochemistry from Imperial College, London.
All staff from organisations on the Research Park are welcome to attend.