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. 2020 Sep 11;10:14977. doi: 10.1038/s41598-020-71939-2

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© The Author(s) 2020

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Simulation results of the genome-scale metabolic models of all Bacteroides and Bifidobacterium species detected in biopsy samples, plus the most highly enriched species at one biopsy location only in at least two patients (Supplementary Fig. 10; Supplementary Table 1). Results are reported by biopsy location: terminal ileum plus caecum (TI*), transverse colon (TC), and rectum (RE). (A) Jaccard index for each modelled species. (B) Biopsy location-based summation of the secretion of the main bacterial metabolites. (C) Uptake and secretion of the metabolites showing a variation across the modelled species. (D–F) Growth rate plots of the modelled species as a function of environmental oxygen level for TI (D), TC (E), and RE (F). The most enriched Bacteroides of the three biopsy locations are highlighted in red (C–F).