Landscapes and bacterial signatures of mucosa-associated intestinal microbiota in Chilean and Spanish patients with inflammatory bowel disease

Nayaret Chamorro, David A. Montero, Pablo Gallardo, Mauricio Farfán, Mauricio Contreras, Marjorie De La Fuente, Karen Dubois, Marcela A. Hermoso, Rodrigo Quera, Marjorie Pizarro-Guajardo, Daniel Paredes-Sabja, Daniel Ginard, Ramon Rosselló-Móra, Roberto Vidal*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Inflammatory bowel diseases (IBDs), which include ulcerative colitis (UC) and Crohn’s disease (CD), cause chronic inflammation of the gut, affecting millions of people worldwide. IBDs have been frequently associated with an alteration of the gut microbiota, termed dysbiosis, which is generally characterized by an increase in abundance of Proteobacteria such as Escherichia coli, and a decrease in abundance of Firmicutes such as Faecalibacterium prausnitzii (an indicator of a healthy colonic microbiota). The mechanisms behind the development of IBDs and dysbiosis are incompletely understood. Using samples from colonic biopsies, we studied the mucosa-associated intestinal microbiota in Chilean and Spanish patients with IBD. In agreement with previous studies, microbiome comparison between IBD patients and non-IBD controls indicated that dysbiosis in these patients is characterized by an increase of pro-inflammatory bacteria (mostly Proteobacteria) and a decrease of commensal beneficial bacteria (mostly Firmicutes). Notably, bacteria typically residing on the mucosa of healthy individuals were mostly obligate anaerobes, whereas in the inflamed mucosa an increase of facultative anaerobe and aerobic bacteria was observed. We also identify potential co-occurring and mutually exclusive interactions between bacteria associated with the healthy and inflamed mucosa, which appear to be determined by the oxygen availability and the type of respiration. Finally, we identified a panel of bacterial biomarkers that allow the discrimination between eubiosis from dysbiosis with a high diagnostic performance (96% accurately), which could be used for the development of non-invasive diagnostic methods. Thus, this study is a step forward towards understanding the landscapes and alterations of mucosa-associated intestinal microbiota in patients with IBDs.

Original languageEnglish
Pages (from-to)223-238
Number of pages16
JournalMicrobial Cell
Volume8
Issue number9
DOIs
StatePublished - Sep 2021

Bibliographical note

Funding Information:
We thank the National Laboratory for High Performance Computing, NLHPC (ECM-02), for sharing their server facilities, and Mauricio Cerda from the Center of Medical Informatics and Telemedicine (CIMT) at the University of Chile for his technical assistance. We thank Dr. Helen Lowry for her careful review of the manuscript and helpful discussions. This study was supported by Fondo Nacional De Desarrollo Cient?fico y Tecnol?gico FONDECYT grant 1161161 to R. Vidal, CONICYT-PCHA/2014-21140975 fellowship to N. Chamorro, FONDECYT 1120577 and 1170648 to Hermoso MA and the Spanish Ministry of Economy projects CLG2015 66686-C3-1-P to Rossell?-Mora R., as well as funds from the European Regional Development Fund (FEDER) and NSF Dimensions in Biodiversity grant OCE-1342694. Support was also provided by a Millennium Science Initiative grant from the Ministry of Economy, Development and Tourism to Paredes-Sabja D.

Publisher Copyright:
© 2021 Chamorro et al.

Keywords

  • Bacterial biomarkers
  • Crohn's disease
  • Dysbiosis
  • Inflammatory bowel disease
  • Microbiome
  • Mucosa-associated intestinal microbiota
  • Ulcerative Colitis

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