Publication Details

Reference Category Journals
DOI / URL link
Creative Commons Licence creative commons licence
Title (Primary) OrtSuite: from genomes to prediction of microbial interactions within targeted ecosystem processes
Author Saraiva, J.P.; Bartholomäus, A.; Kallies, R.; Gomes, M.; Bicalho, M.; Kasmanas, J.C.; Vogt, C.; Chatzinotas, A.; Stadler, P.; Dias, O.; Nunes da Rocha, U.;
Journal Life Science Alliance
Year 2021
Department ISOBIO; UMB;
Volume 4
Issue 12
Language englisch;
Abstract The high complexity found in microbial communities makes the identification of microbial interactions challenging. To address this challenge, we present OrtSuite, a flexible workflow to predict putative microbial interactions based on genomic content of microbial communities and targeted to specific ecosystem processes. The pipeline is composed of three user-friendly bash commands. OrtSuite combines ortholog clustering with genome annotation strategies limited to user-defined sets of functions allowing for hypothesis-driven data analysis such as assessing microbial interactions in specific ecosystems. OrtSuite matched, on average, 96% of experimentally verified KEGG orthologs involved in benzoate degradation in a known group of benzoate degraders. We evaluated the identification of putative synergistic species interactions using the sequenced genomes of an independent study that had previously proposed potential species interactions in benzoate degradation. OrtSuite is an easy-to-use workflow that allows for rapid functional annotation based on a user-curated database and can easily be extended to ecosystem processes where connections between genes and reactions are known. OrtSuite is an open-source software available at https://github.com/mdsufz/OrtSuite.
ID 25187
Persistent UFZ Identifier https://www.ufz.de/index.php?en=20939&ufzPublicationIdentifier=25187
Saraiva, J.P., Bartholomäus, A., Kallies, R., Gomes, M., Bicalho, M., Kasmanas, J.C., Vogt, C., Chatzinotas, A., Stadler, P., Dias, O., Nunes da Rocha, U. (2021):
OrtSuite: from genomes to prediction of microbial interactions within targeted ecosystem processes
Life Sci. Alliance 4 (12), e202101167