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Inflammatory bowel disease biomarkers revealed by the human gut microbiome network
Inflammatory bowel diseases (IBDs) are complex medical conditions in which the gut microbiota is attacked by the immune system of genetically predisposed subjects when exposed to yet unclear environmental factors. The complexity of this class of diseases makes them suitable to be represented and stu...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10632483/ https://www.ncbi.nlm.nih.gov/pubmed/37940667 http://dx.doi.org/10.1038/s41598-023-46184-y |
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author | Hu, Mirko Caldarelli, Guido Gili, Tommaso |
author_facet | Hu, Mirko Caldarelli, Guido Gili, Tommaso |
author_sort | Hu, Mirko |
collection | PubMed |
description | Inflammatory bowel diseases (IBDs) are complex medical conditions in which the gut microbiota is attacked by the immune system of genetically predisposed subjects when exposed to yet unclear environmental factors. The complexity of this class of diseases makes them suitable to be represented and studied with network science. In this paper, the metagenomic data of control, Crohn’s disease, and ulcerative colitis subjects’ gut microbiota were investigated by representing this data as correlation networks and co-expression networks. We obtained correlation networks by calculating Pearson’s correlation between gene expression across subjects. A percolation-based procedure was used to threshold and binarize the adjacency matrices. In contrast, co-expression networks involved the construction of the bipartite subjects-genes networks and the monopartite genes-genes projection after binarization of the biadjacency matrix. Centrality measures and community detection were used on the so-built networks to mine data complexity and highlight possible biomarkers of the diseases. The main results were about the modules of Bacteroides, which were connected in the control subjects’ correlation network, Faecalibacterium prausnitzii, where co-enzyme A became central in IBD correlation networks and Escherichia coli, whose module has different patterns of integration within the whole network in the different diagnoses. |
format | Online Article Text |
id | pubmed-10632483 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-106324832023-11-10 Inflammatory bowel disease biomarkers revealed by the human gut microbiome network Hu, Mirko Caldarelli, Guido Gili, Tommaso Sci Rep Article Inflammatory bowel diseases (IBDs) are complex medical conditions in which the gut microbiota is attacked by the immune system of genetically predisposed subjects when exposed to yet unclear environmental factors. The complexity of this class of diseases makes them suitable to be represented and studied with network science. In this paper, the metagenomic data of control, Crohn’s disease, and ulcerative colitis subjects’ gut microbiota were investigated by representing this data as correlation networks and co-expression networks. We obtained correlation networks by calculating Pearson’s correlation between gene expression across subjects. A percolation-based procedure was used to threshold and binarize the adjacency matrices. In contrast, co-expression networks involved the construction of the bipartite subjects-genes networks and the monopartite genes-genes projection after binarization of the biadjacency matrix. Centrality measures and community detection were used on the so-built networks to mine data complexity and highlight possible biomarkers of the diseases. The main results were about the modules of Bacteroides, which were connected in the control subjects’ correlation network, Faecalibacterium prausnitzii, where co-enzyme A became central in IBD correlation networks and Escherichia coli, whose module has different patterns of integration within the whole network in the different diagnoses. Nature Publishing Group UK 2023-11-08 /pmc/articles/PMC10632483/ /pubmed/37940667 http://dx.doi.org/10.1038/s41598-023-46184-y Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/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/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Hu, Mirko Caldarelli, Guido Gili, Tommaso Inflammatory bowel disease biomarkers revealed by the human gut microbiome network |
title | Inflammatory bowel disease biomarkers revealed by the human gut microbiome network |
title_full | Inflammatory bowel disease biomarkers revealed by the human gut microbiome network |
title_fullStr | Inflammatory bowel disease biomarkers revealed by the human gut microbiome network |
title_full_unstemmed | Inflammatory bowel disease biomarkers revealed by the human gut microbiome network |
title_short | Inflammatory bowel disease biomarkers revealed by the human gut microbiome network |
title_sort | inflammatory bowel disease biomarkers revealed by the human gut microbiome network |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10632483/ https://www.ncbi.nlm.nih.gov/pubmed/37940667 http://dx.doi.org/10.1038/s41598-023-46184-y |
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