@misc{10481/93218,
year = {2024},
month = {4},
url = {https://hdl.handle.net/10481/93218},
abstract = {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.},
organization = {European Union’s Horizon 2020 Research and Innovation Programme through the Stance4Health Project [816303]},
organization = {Plan propio de Investigación y Transferencia of the University of Granada under the program ‘Intensificación de la Investigación, modalidad B’.},
organization = {Spanish Ministry of Science and Innovation [Ref.: FJC2020- 046252 I].},
publisher = {Bioinformatics},
title = {BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities},
doi = {10.1093/bioinformatics/btae266},
author = {Blasco, Telmo and Balzerani, Francesco and Valcárcel, Luis V. and Larrañaga, Pedro and Bielza, Concha and Francino, María Pilar and Rufián Henares, José Ángel and Planes, Francisco J. and Pérez Burrillo, Sergio},
}