Department of Genomics, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland.
Department of Biotransformation, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland.
Environ Microbiol Rep. 2018 Jun;10(3):378-382. doi: 10.1111/1758-2229.12648.
The vast biodiversity of the microbial world and how little is known about it, has already been revealed by extensive metagenomics analyses. Our rudimentary knowledge of microbes stems from difficulties concerning their isolation and culture in laboratory conditions, which is necessary for describing their phenotype, among other things, for biotechnological purposes. An important component of the understudied ecosystems is methanogens, archaea producing a potent greenhouse-effect gas methane. Therefore, we created PhyMet , the first database that combines descriptions of methanogens and their culturing conditions with genetic information. The database contains a set of utilities that facilitate interactive data browsing, data comparison, phylogeny exploration and searching for sequence homologues. The most unique feature of the database is the web server MethanoGram, which can be used to significantly reduce the time and cost of searching for the optimal culturing conditions of methanogens by predicting them based on 16S RNA sequences. The database will aid many researchers in exploring the world of methanogens and their applications in biotechnological processes. PhyMet with the MethanoGram predictor is available at http://metanogen.biotech.uni.wroc.pl.
微生物世界的巨大生物多样性及其鲜为人知的特性已经通过广泛的宏基因组学分析得到了揭示。由于在实验室条件下难以分离和培养微生物，我们对微生物的了解还很初步，这对于描述它们的表型等生物技术目的是必要的。在研究较少的生态系统中，产甲烷菌是一个重要组成部分，它们是产生强效温室气体甲烷的古菌。因此，我们创建了 PhyMet，这是第一个将产甲烷菌的描述及其培养条件与遗传信息相结合的数据库。该数据库包含了一组实用程序，可方便地进行交互式数据浏览、数据比较、系统发育探索和序列同源搜索。该数据库的最独特之处在于其网络服务器 MethanoGram，它可以通过基于 16S RNA 序列进行预测，显著减少寻找产甲烷菌最佳培养条件的时间和成本。该数据库将帮助许多研究人员探索产甲烷菌的世界及其在生物技术过程中的应用。PhyMet 及其 MethanoGram 预测器可在 http://metanogen.biotech.uni.wroc.pl 上获得。
