Wendy Li1,2, Yang Sun3, Lin Dai4, Hongju Chen1,2,5, Bin Yi5, Junkun Niu3, Lan Wang3, Fengrui Zhang3, Juan Luo3, Kunhua Wang6, Rui Guo3, Lianwei Li1,2, Quan Zou7, Zhanshan Sam Ma8,9,10, Yinglei Miao11. 1. Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. 2. Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, China. 3. Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming, Yunnan, China. 4. Faculty of Science, Kunming University of Science and Technology, Kunming, China. 5. College of Mathematics, Honghe University, Mengzi, Yunnan Province, China. 6. Department of General Surgery, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming, Yunnan, China. 7. Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China. 8. Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. ma@vandals.uidaho.edu. 9. Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, China. ma@vandals.uidaho.edu. 10. Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China. ma@vandals.uidaho.edu. 11. Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming, Yunnan, China. miaoyinglei@yeah.net.
Abstract
BACKGROUND: Ulcerative colitis (UC) is one of the primary types of inflammatory bowel disease (IBD), the occurrence of which has been increasing worldwide. Although IBD is an intensively studied human microbiome-associated disease, research on Chinese populations remains relatively limited, particularly on the mucosal microbiome. The present study aimed to analyze the changes in the mucosal microbiome associated with UC from the perspectives of medical ecology and complex network analysis. RESULTS: In total, 56 mucosal microbiome samples were collected from 28 Chinese UC patients and their healthy family partners, followed by amplicon sequencing. Based on sequencing data, we analyzed species diversity, shared species, and inter-species interactions at the whole community, main phyla, and core/periphery species levels. We identified four opportunistic "pathogens" (i.e., Clostridium tertium, Odoribacter splanchnicus, Ruminococcus gnavus, and Flavonifractor plautii) with potential significance for the diagnosis and treatment of UC, which were inhibited in healthy individuals, but unrestricted in the UC patients. In addition, we also discovered in this study: (i) The positive-to-negative links (P/N) ratio, which measures the balance of species interactions or inhibition effects in microbiome networks, was significantly higher in UC patients, indicating loss of inhibition against potentially opportunistic "pathogens" associated with dysbiosis. (ii) Previous studies have reported conflicting evidence regarding species diversity and composition between UC patients and healthy controls. Here, significant differences were found at the major phylum and core/periphery scales, but not at the whole community level. Thus, we argue that the paradoxical results found in existing studies are due to the scale effect. CONCLUSIONS: Our results reveal changes in the ecology and network structure of the gut mucosal microbiome that might be associated with UC, and these changes might provide potential therapeutic mechanisms of UC. The four opportunistic pathogens that were identified in the present study deserve further investigation in future studies.
BACKGROUND:Ulcerative colitis (UC) is one of the primary types of inflammatory bowel disease (IBD), the occurrence of which has been increasing worldwide. Although IBD is an intensively studied human microbiome-associated disease, research on Chinese populations remains relatively limited, particularly on the mucosal microbiome. The present study aimed to analyze the changes in the mucosal microbiome associated with UC from the perspectives of medical ecology and complex network analysis. RESULTS: In total, 56 mucosal microbiome samples were collected from 28 Chinese UC patients and their healthy family partners, followed by amplicon sequencing. Based on sequencing data, we analyzed species diversity, shared species, and inter-species interactions at the whole community, main phyla, and core/periphery species levels. We identified four opportunistic "pathogens" (i.e., Clostridium tertium, Odoribacter splanchnicus, Ruminococcus gnavus, and Flavonifractor plautii) with potential significance for the diagnosis and treatment of UC, which were inhibited in healthy individuals, but unrestricted in the UC patients. In addition, we also discovered in this study: (i) The positive-to-negative links (P/N) ratio, which measures the balance of species interactions or inhibition effects in microbiome networks, was significantly higher in UC patients, indicating loss of inhibition against potentially opportunistic "pathogens" associated with dysbiosis. (ii) Previous studies have reported conflicting evidence regarding species diversity and composition between UC patients and healthy controls. Here, significant differences were found at the major phylum and core/periphery scales, but not at the whole community level. Thus, we argue that the paradoxical results found in existing studies are due to the scale effect. CONCLUSIONS: Our results reveal changes in the ecology and network structure of the gut mucosal microbiome that might be associated with UC, and these changes might provide potential therapeutic mechanisms of UC. The four opportunistic pathogens that were identified in the present study deserve further investigation in future studies.
Entities:
Keywords:
Core/periphery network; Inflammatory bowel disease; Mucosal microbiome; Species co-occurrence network; Species diversity; Ulcerative colitis
Authors: Rodrigo Bibiloni; Marco Mangold; Karen L Madsen; Richard N Fedorak; Gerald W Tannock Journal: J Med Microbiol Date: 2006-08 Impact factor: 2.472
Authors: J Alfredo Blakeley-Ruiz; Alison R Erickson; Brandi L Cantarel; Weili Xiong; Rachel Adams; Janet K Jansson; Claire M Fraser; Robert L Hettich Journal: Microbiome Date: 2019-02-11 Impact factor: 14.650