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.