Landscapes and bacterial signatures of mucosa-associated intestinal microbiota in Chilean and Spanish patients with inflammatory bowel disease
Authors:Nayaret Chamorro1,#, David A. Montero1,2,#, Pablo Gallardo3, Mauricio Farfán3, Mauricio Contreras4, Marjorie De la Fuente2, Karen Dubois2, Marcela A. Hermoso2, Rodrigo Quera5,6, Marjorie Pizarro-Guajardo7,8,9, Daniel Paredes-Sabja7,8,9, Daniel Ginard10, Ramon Rosselló-Móra11 and Roberto Vidal1,8,12
doi: 10.15698/mic2021.09.760
Volume 8, pp. 223 to 238, published 18/06/2021.
1 Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Chile.
2 Programa de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Chile.
3 Facultad de Medicina, Departamento de Pediatría y Cirugía Infantil, Campus Oriente-Hospital Dr. Luis Calvo Mackenna, Universidad de Chile, Chile.
4 Facultad de Ciencias Básicas, Departamento de Física, Universidad Metropolitana de Ciencias de la Educación, Santiago, Chile.
5 Programa Enfermedad Inflamatoria Intestinal. Servicio de Gastroenterología, Clínica Las Condes, Santiago, Chile.
6 Gastroenterología, Clínica Universidad de Los Andes, Santiago, Chile.
7 Microbiota-Host Interactions and Clostridia Research Group, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.
8 ANID – Millennium Science Initiative Program – Millennium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile.
9 Department of Biology, Texas A&M University, College Station, TX, 77843, USA.
10 Department of Gastroenterology and Palma Health Research Institute, Hospital Universitario Son Espases, Palma de Mallorca, Spain.
11 Marine Microbiology Group, Department of Animal and Microbial Diversity, IMEDEA (CSIC-UIB), 07190 Esporles, Illes Balears, Spain.
12 Instituto Milenio de Inmunología e Inmunoterapia, Facultad de Medicina, Universidad de Chile, Chile.
# These authors contributed equally.
Keywords:
Mucosa-associated intestinal microbiota, inflammatory bowel disease, ulcerative Colitis, Crohn's Disease, microbiome, bacterial biomarkers, dysbiosis
Corresponding Author(s):
Conflict of interest statement:
Funding institutions did not influence the study design or interpretation of the result. Moreover, the authors de-clare that they have no competing interests.
Please cite this article as:
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 and Roberto Vidal (2021). Landscapes and bacterial signa-tures of mucosa-associated intestinal microbiota in Chilean and Spanish patients with inflammatory bowel disease. Microbial Cell 8(9): 223-238. doi: 10.15698/mic2021.09.760
© 2021 Chamorro et al. This is an open-access article released under the terms of the Creative Commons Attribution (CC BY) license, which allows the unrestricted use, distribution, and reproduc-tion in any medium, provided the original author and source are acknowledged.
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.