Innovations in DNA sequencing technologies allowed for rapid development of new biological science disciplines, in particular metagenomics (DNA sequencing of environmental samples). As a result, a plethora of new uncultivated microorganisms has been discovered, including methane-producing (methanogenic) archaea. Methanogens are widespread in nature, often found in extreme environments; actually some of them might even be capable of surviving on Mars. They show growing potential for biotechnological uses, including biogas production, but studies on newly discovered species are hindered by the long and expensive process of establishing their cultures.
PhyMet2 (Phylogeny and Metabolism of Metthanogens) is the second iteration of the database Methanogens first published in 2015 (http://metanogen.biotech.uni.wroc.pl/). It is the largest database providing information on culturing conditions of methanogenic archaea with a user-friendly interface and a set of tools (e.g. homology search and phylogeny programs) for interactive data browsing, searching, sorting, comparing and downloading. At present, PhyMet2 contains 153 manually curated, high quality records. MethanoGram, an N-gram analyzer implemented in the database, will reduce the cost of searching for culturing conditions of newly discovered methanogenic species. Our database also aims at setting standards for other data-sharing platforms by combining species description and culturing conditions with genetic information.
PhyMet2 has been a collaborative effort of the Department of Genomics
at the Faculty of Biotechnology, University of Wroclaw.
PhyMet2 is supported by Leading National Research Center (KNOW) and a National Science Centre (grants 2015/17/N/NZ2/01845 and 2017/24/T/NZ2/00003) to Michał Burdukiewicz.
Technical support: Al-Yawir Rashad (email@example.com)
CitationsBurdukiewicz M., Gagat P., Jabłoński S., Chilimoniuk J., Gaworski M., Mackiewicz P., Łukaszewicz M. (2018) PhyMet2: a database and toolkit for phylogenetic and metabolic analyses of methanogens. 10:378-382.