BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities

Balzerani, F. (Francesco)|||/items/8b7a4faf-167a-4631-8dd0-676cfce9e04a; Valcárcel-García, L.V. (Luis Vitores)|||/items/2621f70f-28ce-4020-ab9c-93b38096a0ea; Larrañaga, P. (Pedro)|||/items/07ddcb09-5f31-48fb-a64c-25fa67d82e59; Bielza, C. (Concha)|||/items/89bb2f94-17e5-47c4-a6da-abb4bbc11c7e; Francino, M.P. (M. Pilar)|||/items/7da65cad-65d1-4cbc-b71c-b2362bd38f04; Rufián-Henares, J.Á. (Ángel José)|||/items/e6bc3d5e-2e59-491b-8075-528a4288a5cf; Planes-Pedreño, F.J. (Francisco Javier)|||/items/3234f2e5-4407-41e9-9058-1834965f6afa; Pérez-Burillo, S. (Sergio)|||/items/f693a845-e93f-45a7-80a5-d4e63a300f18; Blasco-Aramburu, T. (Telmo)|||/items/d5e49995-9c11-4047-8bbd-748bcf13cb06

BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities

Motivation: 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–microbe stimulant or inhibitory e...

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Detalles Bibliográficos
Autores:	Balzerani, F. (Francesco)\|\|\|/items/8b7a4faf-167a-4631-8dd0-676cfce9e04a, Valcárcel-García, L.V. (Luis Vitores)\|\|\|/items/2621f70f-28ce-4020-ab9c-93b38096a0ea, Larrañaga, P. (Pedro)\|\|\|/items/07ddcb09-5f31-48fb-a64c-25fa67d82e59, Bielza, C. (Concha)\|\|\|/items/89bb2f94-17e5-47c4-a6da-abb4bbc11c7e, Francino, M.P. (M. Pilar)\|\|\|/items/7da65cad-65d1-4cbc-b71c-b2362bd38f04, Rufián-Henares, J.Á. (Ángel José)\|\|\|/items/e6bc3d5e-2e59-491b-8075-528a4288a5cf, Planes-Pedreño, F.J. (Francisco Javier)\|\|\|/items/3234f2e5-4407-41e9-9058-1834965f6afa, Pérez-Burillo, S. (Sergio)\|\|\|/items/f693a845-e93f-45a7-80a5-d4e63a300f18, Blasco-Aramburu, T. (Telmo)\|\|\|/items/d5e49995-9c11-4047-8bbd-748bcf13cb06
Tipo de recurso:	artículo
Fecha de publicación:	2024
País:	España
Institución:	Universidad de Navarra
Repositorio:	Dadun. Depósito Académico Digital de la Universidad de Navarra
Idioma:	inglés
OAI Identifier:	oai:dadun.unav.edu:10171/70158
Acceso en línea:	https://hdl.handle.net/10171/70158
Access Level:	acceso abierto
Palabra clave:	Gut microbial dynamics BacArena Microbe–microbe Nutrient–microbe

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repository_id_str
spelling	BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communitiesBalzerani, F. (Francesco)\|\|\|/items/8b7a4faf-167a-4631-8dd0-676cfce9e04aValcárcel-García, L.V. (Luis Vitores)\|\|\|/items/2621f70f-28ce-4020-ab9c-93b38096a0eaLarrañaga, P. (Pedro)\|\|\|/items/07ddcb09-5f31-48fb-a64c-25fa67d82e59Bielza, C. (Concha)\|\|\|/items/89bb2f94-17e5-47c4-a6da-abb4bbc11c7eFrancino, M.P. (M. Pilar)\|\|\|/items/7da65cad-65d1-4cbc-b71c-b2362bd38f04Rufián-Henares, J.Á. (Ángel José)\|\|\|/items/e6bc3d5e-2e59-491b-8075-528a4288a5cfPlanes-Pedreño, F.J. (Francisco Javier)\|\|\|/items/3234f2e5-4407-41e9-9058-1834965f6afaPérez-Burillo, S. (Sergio)\|\|\|/items/f693a845-e93f-45a7-80a5-d4e63a300f18Blasco-Aramburu, T. (Telmo)\|\|\|/items/d5e49995-9c11-4047-8bbd-748bcf13cb06Gut microbial dynamicsBacArenaMicrobe–microbeNutrient–microbeMotivation: 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–microbe stimulant or inhibitory effects or for nutrient–microbe inhibitory effects, typically observed in different compounds present in the daily diet. Results: Here, we present BN-BacArena, an extension of BacArena consisting on the incorporation within the native computational framework of a Bayesian network model that accounts for microbe–microbe and nutrient–microbe interactions. Using in vitro experiments, 16S rRNA gene sequencing data and nutritional composition of 55 foods, the output Bayesian network showed 23 significant nutrient–bacteria interactions, suggesting the importance of compounds such as polyols, ascorbic acid, polyphenols and other phytochemicals, and 40 bacteria–bacteria 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.Oxford University PressDadun. Depósito Académico Digital Universidad de Navarra20242024-10-1520242024-01-0120242024-01-01journal articlehttp://purl.org/coar/resource_type/c_6501info:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/10171/70158reponame:Dadun. Depósito Académico Digital de la Universidad de Navarrainstname:Universidad de NavarraInglésengopen accesshttp://purl.org/coar/access_right/c_abf2info:eu-repo/semantics/openAccessoai:dadun.unav.edu:10171/701582026-06-21T12:47:57Z
dc.title.none.fl_str_mv	BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities
title	BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities
spellingShingle	BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities Balzerani, F. (Francesco)\|\|\|/items/8b7a4faf-167a-4631-8dd0-676cfce9e04a Gut microbial dynamics BacArena Microbe–microbe Nutrient–microbe
title_short	BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities
title_full	BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities
title_fullStr	BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities
title_full_unstemmed	BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities
title_sort	BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities
dc.creator.none.fl_str_mv	Balzerani, F. (Francesco)\|\|\|/items/8b7a4faf-167a-4631-8dd0-676cfce9e04a Valcárcel-García, L.V. (Luis Vitores)\|\|\|/items/2621f70f-28ce-4020-ab9c-93b38096a0ea Larrañaga, P. (Pedro)\|\|\|/items/07ddcb09-5f31-48fb-a64c-25fa67d82e59 Bielza, C. (Concha)\|\|\|/items/89bb2f94-17e5-47c4-a6da-abb4bbc11c7e Francino, M.P. (M. Pilar)\|\|\|/items/7da65cad-65d1-4cbc-b71c-b2362bd38f04 Rufián-Henares, J.Á. (Ángel José)\|\|\|/items/e6bc3d5e-2e59-491b-8075-528a4288a5cf Planes-Pedreño, F.J. (Francisco Javier)\|\|\|/items/3234f2e5-4407-41e9-9058-1834965f6afa Pérez-Burillo, S. (Sergio)\|\|\|/items/f693a845-e93f-45a7-80a5-d4e63a300f18 Blasco-Aramburu, T. (Telmo)\|\|\|/items/d5e49995-9c11-4047-8bbd-748bcf13cb06
author	Balzerani, F. (Francesco)\|\|\|/items/8b7a4faf-167a-4631-8dd0-676cfce9e04a
author_facet	Balzerani, F. (Francesco)\|\|\|/items/8b7a4faf-167a-4631-8dd0-676cfce9e04a Valcárcel-García, L.V. (Luis Vitores)\|\|\|/items/2621f70f-28ce-4020-ab9c-93b38096a0ea Larrañaga, P. (Pedro)\|\|\|/items/07ddcb09-5f31-48fb-a64c-25fa67d82e59 Bielza, C. (Concha)\|\|\|/items/89bb2f94-17e5-47c4-a6da-abb4bbc11c7e Francino, M.P. (M. Pilar)\|\|\|/items/7da65cad-65d1-4cbc-b71c-b2362bd38f04 Rufián-Henares, J.Á. (Ángel José)\|\|\|/items/e6bc3d5e-2e59-491b-8075-528a4288a5cf Planes-Pedreño, F.J. (Francisco Javier)\|\|\|/items/3234f2e5-4407-41e9-9058-1834965f6afa Pérez-Burillo, S. (Sergio)\|\|\|/items/f693a845-e93f-45a7-80a5-d4e63a300f18 Blasco-Aramburu, T. (Telmo)\|\|\|/items/d5e49995-9c11-4047-8bbd-748bcf13cb06
author_role	author
author2	Valcárcel-García, L.V. (Luis Vitores)\|\|\|/items/2621f70f-28ce-4020-ab9c-93b38096a0ea Larrañaga, P. (Pedro)\|\|\|/items/07ddcb09-5f31-48fb-a64c-25fa67d82e59 Bielza, C. (Concha)\|\|\|/items/89bb2f94-17e5-47c4-a6da-abb4bbc11c7e Francino, M.P. (M. Pilar)\|\|\|/items/7da65cad-65d1-4cbc-b71c-b2362bd38f04 Rufián-Henares, J.Á. (Ángel José)\|\|\|/items/e6bc3d5e-2e59-491b-8075-528a4288a5cf Planes-Pedreño, F.J. (Francisco Javier)\|\|\|/items/3234f2e5-4407-41e9-9058-1834965f6afa Pérez-Burillo, S. (Sergio)\|\|\|/items/f693a845-e93f-45a7-80a5-d4e63a300f18 Blasco-Aramburu, T. (Telmo)\|\|\|/items/d5e49995-9c11-4047-8bbd-748bcf13cb06
author2_role	author author author author author author author author
dc.contributor.none.fl_str_mv	Dadun. Depósito Académico Digital Universidad de Navarra
dc.subject.none.fl_str_mv	Gut microbial dynamics BacArena Microbe–microbe Nutrient–microbe
topic	Gut microbial dynamics BacArena Microbe–microbe Nutrient–microbe
description	Motivation: 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–microbe stimulant or inhibitory effects or for nutrient–microbe inhibitory effects, typically observed in different compounds present in the daily diet. Results: Here, we present BN-BacArena, an extension of BacArena consisting on the incorporation within the native computational framework of a Bayesian network model that accounts for microbe–microbe and nutrient–microbe interactions. Using in vitro experiments, 16S rRNA gene sequencing data and nutritional composition of 55 foods, the output Bayesian network showed 23 significant nutrient–bacteria interactions, suggesting the importance of compounds such as polyols, ascorbic acid, polyphenols and other phytochemicals, and 40 bacteria–bacteria 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.
publishDate	2024
dc.date.none.fl_str_mv	2024 2024-10-15 2024 2024-01-01 2024 2024-01-01
dc.type.none.fl_str_mv	journal article http://purl.org/coar/resource_type/c_6501
dc.type.openaire.fl_str_mv	info:eu-repo/semantics/article
format	article
dc.identifier.none.fl_str_mv	https://hdl.handle.net/10171/70158
url	https://hdl.handle.net/10171/70158
dc.language.none.fl_str_mv	Inglés eng
language_invalid_str_mv	Inglés
language	eng
dc.rights.none.fl_str_mv	open access http://purl.org/coar/access_right/c_abf2
dc.rights.openaire.fl_str_mv	info:eu-repo/semantics/openAccess
rights_invalid_str_mv	open access http://purl.org/coar/access_right/c_abf2
eu_rights_str_mv	openAccess
dc.format.none.fl_str_mv	application/pdf
dc.publisher.none.fl_str_mv	Oxford University Press
publisher.none.fl_str_mv	Oxford University Press
dc.source.none.fl_str_mv	reponame:Dadun. Depósito Académico Digital de la Universidad de Navarra instname:Universidad de Navarra
instname_str	Universidad de Navarra
reponame_str	Dadun. Depósito Académico Digital de la Universidad de Navarra
collection	Dadun. Depósito Académico Digital de la Universidad de Navarra
repository.name.fl_str_mv
repository.mail.fl_str_mv
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BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities

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