PT  - JOURNAL ARTICLE
AU  - João Pedro Saraiva
AU  - Alexandre Bartholomäus
AU  - René Kallies
AU  - Marta Gomes
AU  - Marcos Bicalho
AU  - Jonas Coelho Kasmanas
AU  - Carsten Vogt
AU  - Antonis Chatzinotas
AU  - Peter Stadler
AU  - Oscar Dias
AU  - Ulisses Nunes da Rocha
TI  - OrtSuite: from genomes to prediction of microbial interactions within targeted ecosystem processes
AID  - 10.26508/lsa.202101167
DP  - 2021 Dec 01
TA  - Life Science Alliance
PG  - e202101167
VI  - 4
IP  - 12
4099  - https://www.life-science-alliance.org/content/4/12/e202101167.short
4100  - https://www.life-science-alliance.org/content/4/12/e202101167.full
SO  - Life Sci. Alliance2021 Dec 01; 4
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.