Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis

Abstract Inflammatory bowel diseases, such as Crohn’s Disease, are characterised by an altered blood and faecal metabolome, and changes in gut microbiome composition. Here, we present an efficient, scalable, tractable systems biology framework to mechanistically link microbial strains and faecal met...

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Autores principales:	Almut Heinken, Johannes Hertel, Ines Thiele
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/e6e483ee5d984df2971eaa7426fe3994
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spelling	oai:doaj.org-article:e6e483ee5d984df2971eaa7426fe39942021-12-02T15:37:59ZMetabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis10.1038/s41540-021-00178-62056-7189https://doaj.org/article/e6e483ee5d984df2971eaa7426fe39942021-05-01T00:00:00Zhttps://doi.org/10.1038/s41540-021-00178-6https://doaj.org/toc/2056-7189Abstract Inflammatory bowel diseases, such as Crohn’s Disease, are characterised by an altered blood and faecal metabolome, and changes in gut microbiome composition. Here, we present an efficient, scalable, tractable systems biology framework to mechanistically link microbial strains and faecal metabolites. We retrieve strain-level relative abundances from metagenomics data from a cohort of paediatric Crohn’s Disease patients with and without dysbiosis and healthy control children and construct and interrogate a personalised microbiome model for each sample. Predicted faecal secretion profiles and strain-level contributions to each metabolite vary broadly between healthy, dysbiotic, and non-dysbiotic microbiomes. The reduced microbial diversity in IBD results in reduced numbers of secreted metabolites, especially in sulfur metabolism. We demonstrate that increased potential to synthesise amino acids is linked to Proteobacteria contributions, in agreement with experimental observations. The established modelling framework yields testable hypotheses that may result in novel therapeutic and dietary interventions targeting the host-gut microbiome-diet axis.Almut HeinkenJohannes HertelInes ThieleNature PortfolioarticleBiology (General)QH301-705.5ENnpj Systems Biology and Applications, Vol 7, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Almut Heinken Johannes Hertel Ines Thiele Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis
description	Abstract Inflammatory bowel diseases, such as Crohn’s Disease, are characterised by an altered blood and faecal metabolome, and changes in gut microbiome composition. Here, we present an efficient, scalable, tractable systems biology framework to mechanistically link microbial strains and faecal metabolites. We retrieve strain-level relative abundances from metagenomics data from a cohort of paediatric Crohn’s Disease patients with and without dysbiosis and healthy control children and construct and interrogate a personalised microbiome model for each sample. Predicted faecal secretion profiles and strain-level contributions to each metabolite vary broadly between healthy, dysbiotic, and non-dysbiotic microbiomes. The reduced microbial diversity in IBD results in reduced numbers of secreted metabolites, especially in sulfur metabolism. We demonstrate that increased potential to synthesise amino acids is linked to Proteobacteria contributions, in agreement with experimental observations. The established modelling framework yields testable hypotheses that may result in novel therapeutic and dietary interventions targeting the host-gut microbiome-diet axis.
format	article
author	Almut Heinken Johannes Hertel Ines Thiele
author_facet	Almut Heinken Johannes Hertel Ines Thiele
author_sort	Almut Heinken
title	Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis
title_short	Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis
title_full	Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis
title_fullStr	Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis
title_full_unstemmed	Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis
title_sort	metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/e6e483ee5d984df2971eaa7426fe3994
work_keys_str_mv	AT almutheinken metabolicmodellingrevealsbroadchangesingutmicrobialmetabolismininflammatoryboweldiseasepatientswithdysbiosis AT johanneshertel metabolicmodellingrevealsbroadchangesingutmicrobialmetabolismininflammatoryboweldiseasepatientswithdysbiosis AT inesthiele metabolicmodellingrevealsbroadchangesingutmicrobialmetabolismininflammatoryboweldiseasepatientswithdysbiosis
_version_	1718386206644895744

Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis

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