Katariina Pärnänen from the University of Turku uses metagenome sequence data that is stored in extensive open databases. She uses supercomputers at CSC – IT Center for Science (the Finnish ELIXIR node) to analyse the data,allowing her to identify different species of bacteria and their resistance genes.
“In some species of bacteria, it is possible to identify genes that appear in its genome only once. By comparing these with genes in the databases of other species, we can identify the species in question. We look for matches with resistance genes stored in databases. Then we can say that the person has ten resistance genes in their stool sample, or that they carry a certain amount of coliform bacteria.”
Katariina Pärnänen would like to extend her research to the world’s entire human population and study the gut microbe samples that have been metagenome sequenced and are openly available in databases.
“It would be interesting to discuss the technical feasibility of such a project with CSC experts.It would also promote open science, because the identified resistance genes and species found in microbiomes could also be stored for use by other researchers.”
CSC – IT Center for Science
is a non-profit, state-owned company administered by the Ministry of Education and Culture. CSC maintains and develops the state-owned, centralised IT infrastructure.
https://research.csc.fi/cloud-computing
ELIXIR
builds infrastructure in support of the biological sector. It brings together the leading organisations of 21 European countries and the EMBL European Molecular Biology Laboratory to form a common infrastructure for biological information. CSC – IT Center for Science is the Finnish centre within this infrastructure.
ELIXIR is partly funded by the European Commission