Optimization of probiotic therapeutics using machine learning in an artificial human gastrointestinal tract

Abstract The gut microbiota’s metabolome is composed of bioactive metabolites that confer disease resilience. Probiotics’ therapeutic potential hinges on their metabolome altering ability; however, characterizing probiotics’ metabolic activity remains a formidable task. In order to solve this proble...

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Autores principales:	Susan Westfall, Francesca Carracci, Molly Estill, Danyue Zhao, Qing-li Wu, Li Shen, James Simon, Giulio Maria Pasinetti
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/58954e4fead346f8a84ebed7d4de5fad
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spelling	oai:doaj.org-article:58954e4fead346f8a84ebed7d4de5fad2021-12-02T14:01:22ZOptimization of probiotic therapeutics using machine learning in an artificial human gastrointestinal tract10.1038/s41598-020-79947-y2045-2322https://doaj.org/article/58954e4fead346f8a84ebed7d4de5fad2021-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-79947-yhttps://doaj.org/toc/2045-2322Abstract The gut microbiota’s metabolome is composed of bioactive metabolites that confer disease resilience. Probiotics’ therapeutic potential hinges on their metabolome altering ability; however, characterizing probiotics’ metabolic activity remains a formidable task. In order to solve this problem, an artificial model of the human gastrointestinal tract is introduced coined the ABIOME (A Bioreactor Imitation of the Microbiota Environment) and used to predict probiotic formulations’ metabolic activity and hence therapeutic potential with machine learning tools. The ABIOME is a modular yet dynamic system with real-time monitoring of gastrointestinal conditions that support complex cultures representative of the human microbiota and its metabolome. The fecal-inoculated ABIOME was supplemented with a polyphenol-rich prebiotic and combinations of novel probiotics that altered the output of bioactive metabolites previously shown to invoke anti-inflammatory effects. To dissect the synergistic interactions between exogenous probiotics and the autochthonous microbiota a multivariate adaptive regression splines (MARS) model was implemented towards the development of optimized probiotic combinations with therapeutic benefits. Using this algorithm, several probiotic combinations were identified that stimulated synergistic production of bioavailable metabolites, each with a different therapeutic capacity. Based on these results, the ABIOME in combination with the MARS algorithm could be used to create probiotic formulations with specific therapeutic applications based on their signature metabolic activity.Susan WestfallFrancesca CarracciMolly EstillDanyue ZhaoQing-li WuLi ShenJames SimonGiulio Maria PasinettiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-15 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Susan Westfall Francesca Carracci Molly Estill Danyue Zhao Qing-li Wu Li Shen James Simon Giulio Maria Pasinetti Optimization of probiotic therapeutics using machine learning in an artificial human gastrointestinal tract
description	Abstract The gut microbiota’s metabolome is composed of bioactive metabolites that confer disease resilience. Probiotics’ therapeutic potential hinges on their metabolome altering ability; however, characterizing probiotics’ metabolic activity remains a formidable task. In order to solve this problem, an artificial model of the human gastrointestinal tract is introduced coined the ABIOME (A Bioreactor Imitation of the Microbiota Environment) and used to predict probiotic formulations’ metabolic activity and hence therapeutic potential with machine learning tools. The ABIOME is a modular yet dynamic system with real-time monitoring of gastrointestinal conditions that support complex cultures representative of the human microbiota and its metabolome. The fecal-inoculated ABIOME was supplemented with a polyphenol-rich prebiotic and combinations of novel probiotics that altered the output of bioactive metabolites previously shown to invoke anti-inflammatory effects. To dissect the synergistic interactions between exogenous probiotics and the autochthonous microbiota a multivariate adaptive regression splines (MARS) model was implemented towards the development of optimized probiotic combinations with therapeutic benefits. Using this algorithm, several probiotic combinations were identified that stimulated synergistic production of bioavailable metabolites, each with a different therapeutic capacity. Based on these results, the ABIOME in combination with the MARS algorithm could be used to create probiotic formulations with specific therapeutic applications based on their signature metabolic activity.
format	article
author	Susan Westfall Francesca Carracci Molly Estill Danyue Zhao Qing-li Wu Li Shen James Simon Giulio Maria Pasinetti
author_facet	Susan Westfall Francesca Carracci Molly Estill Danyue Zhao Qing-li Wu Li Shen James Simon Giulio Maria Pasinetti
author_sort	Susan Westfall
title	Optimization of probiotic therapeutics using machine learning in an artificial human gastrointestinal tract
title_short	Optimization of probiotic therapeutics using machine learning in an artificial human gastrointestinal tract
title_full	Optimization of probiotic therapeutics using machine learning in an artificial human gastrointestinal tract
title_fullStr	Optimization of probiotic therapeutics using machine learning in an artificial human gastrointestinal tract
title_full_unstemmed	Optimization of probiotic therapeutics using machine learning in an artificial human gastrointestinal tract
title_sort	optimization of probiotic therapeutics using machine learning in an artificial human gastrointestinal tract
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/58954e4fead346f8a84ebed7d4de5fad
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Optimization of probiotic therapeutics using machine learning in an artificial human gastrointestinal tract

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