Details zur Publikation

Kategorie Textpublikation
Referenztyp Zeitschriften
DOI 10.26508/lsa.202101167
Lizenz creative commons licence
Titel (primär) OrtSuite: from genomes to prediction of microbial interactions within targeted ecosystem processes
Autor 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.
Quelle Life Science Alliance
Erscheinungsjahr 2021
Department ISOBIO; UMB
Band/Volume 4
Heft 12
Seite von e202101167
Sprache englisch
Topic T7 Bioeconomy
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
dauerhafte UFZ-Verlinkung
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 10.26508/lsa.202101167