{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T04:49:26Z","timestamp":1773118166532,"version":"3.50.1"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2024,5,1]],"date-time":"2024-05-01T00:00:00Z","timestamp":1714521600000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union\u2019s Horizon 2020 Research and Innovation Programme","award":["816303"],"award-info":[{"award-number":["816303"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,5,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Simulating gut microbial dynamics is extremely challenging. Several computational tools, notably the widely used BacArena, enable modeling of dynamic changes in the microbial environment. These methods, however, do not comprehensively account for microbe\u2013microbe stimulant or inhibitory effects or for nutrient\u2013microbe inhibitory effects, typically observed in different compounds present in the daily diet.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present BN-BacArena, an extension of BacArena\u00a0consisting on the incorporation within the native computational framework of a Bayesian network model that accounts for microbe\u2013microbe and nutrient\u2013microbe interactions. Using in vitro experiments, 16S rRNA gene sequencing data and nutritional composition of 55 foods, the output Bayesian network showed 23 significant nutrient\u2013bacteria interactions, suggesting the importance of compounds such as polyols, ascorbic acid, polyphenols and other phytochemicals, and 40 bacteria\u2013bacteria significant relationships. With test data, BN-BacArena demonstrates a statistically significant improvement over BacArena to predict the time-dependent relative abundance of bacterial species involved in the gut microbiota upon different nutritional interventions. As a result, BN-BacArena opens new avenues for the dynamic modeling and simulation of the human gut microbiota metabolism.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>MATLAB and R code are available in https:\/\/github.com\/PlanesLab\/BN-BacArena<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae266","type":"journal-article","created":{"date-parts":[[2024,4,29]],"date-time":"2024-04-29T19:42:12Z","timestamp":1714419732000},"source":"Crossref","is-referenced-by-count":8,"title":["BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7819-8668","authenticated-orcid":false,"given":"Telmo","family":"Blasco","sequence":"first","affiliation":[{"name":"Department of Biomedical Engineering and Sciences, Tecnun School of Engineering, University of Navarra , San Sebasti\u00e1n 20018, Spain"}]},{"given":"Francesco","family":"Balzerani","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering and Sciences, Tecnun School of Engineering, University of Navarra , San Sebasti\u00e1n 20018, Spain"}]},{"given":"Luis V","family":"Valc\u00e1rcel","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering and Sciences, Tecnun School of Engineering, University of Navarra , San Sebasti\u00e1n 20018, Spain"},{"name":"Biomedical Engineering Center, Campus Universitario, University of Navarra , Pamplona, Navarra 31009, Spain"},{"name":"Instituto de Ciencia de los Datos e Inteligencia Artificial (DATAI), Campus Universitario, University of Navarra , Pamplona 31080, Spain"}]},{"given":"Pedro","family":"Larra\u00f1aga","sequence":"additional","affiliation":[{"name":"Departamento de Inteligencia Artificial, Universidad Polit\u00e9cnica de Madrid , Madrid 28660, Spain"}]},{"given":"Concha","family":"Bielza","sequence":"additional","affiliation":[{"name":"Departamento de Inteligencia Artificial, Universidad Polit\u00e9cnica de Madrid , Madrid 28660, Spain"}]},{"given":"Mar\u00eda Pilar","family":"Francino","sequence":"additional","affiliation":[{"name":"Area de Gen\u00f3mica y Salud, Fundaci\u00f3n para el Fomento de la Investigaci\u00f3n Sanitaria y Biom\u00e9dica de la Comunitat Valenciana-Salud P\u00fablica , Valencia 46020, Spain"},{"name":"CIBER en Epidemiolog\u00eda y Salud P\u00fablica, Instituto de Salud Carlos III , Madrid 28029, Spain"}]},{"given":"Jos\u00e9 \u00c1ngel","family":"Rufi\u00e1n-Henares","sequence":"additional","affiliation":[{"name":"Departamento de Nutrici\u00f3n y Bromatolog\u00eda, Centro de Investigaci\u00f3n Biom\u00e9dica, Instituto de Nutrici\u00f3n y Tecnolog\u00eda de los Alimentos, Universidad de Granada , Granada 18016, Spain"},{"name":"Instituto de Investigaci\u00f3n Biosanitaria ibs. GRANADA, Universidad de Granada , Granada 18012, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1155-3105","authenticated-orcid":false,"given":"Francisco J","family":"Planes","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering and Sciences, Tecnun School of Engineering, University of Navarra , San Sebasti\u00e1n 20018, Spain"},{"name":"Biomedical Engineering Center, Campus Universitario, University of Navarra , Pamplona, Navarra 31009, Spain"},{"name":"Instituto de Ciencia de los Datos e Inteligencia Artificial (DATAI), Campus Universitario, University of Navarra , Pamplona 31080, Spain"}]},{"given":"Sergio","family":"P\u00e9rez-Burillo","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering and Sciences, Tecnun School of Engineering, University of Navarra , San Sebasti\u00e1n 20018, 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