RT Journal Article
SR Electronic
T1 OrtSuite: from genomes to prediction of microbial interactions within targeted ecosystem processes
JF Life Science Alliance
JO Life Sci. Alliance
FD Life Science Alliance LLC
SP e202101167
DO 10.26508/lsa.202101167
VO 4
IS 12
A1 Saraiva, João Pedro
A1 Bartholomäus, Alexandre
A1 Kallies, René
A1 Gomes, Marta
A1 Bicalho, Marcos
A1 Coelho Kasmanas, Jonas
A1 Vogt, Carsten
A1 Chatzinotas, Antonis
A1 Stadler, Peter
A1 Dias, Oscar
A1 Nunes da Rocha, Ulisses
YR 2021
UL http://www.life-science-alliance.org/content/4/12/e202101167.abstract
AB 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.