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Bioinformatics in Microbiota

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Front. Microbiol. | doi: 10.3389/fmicb.2019.01205

Metabolic Dependencies Underlie Interaction Patterns of Gut Microbiota during Enteropathogenesis

Die Dai1, Teng Wang1, Sicheng Wu1,  Na L. Gao1 and  Wei-Hua Chen1*
  • 1Huazhong University of Science and Technology, China

In recent decades, increasing evidence has strongly suggested that gut microbiota play an important role in many intestinal diseases including inflammatory bowel disease (IBD) and colorectal cancer (CRC). The composition of gut microbiota is thought to be largely shaped by interspecies competition for available resources and also by cooperative interactions. However, to what extent the changes could be attributed to external factors such as diet of choice and internal factors including mutual relationships among gut microbiota respectively are yet to be elucidated. Due to the advances of high-throughput sequencing technologies, flood of (meta)-genome sequence information and high-throughput biological data are available for gut microbiota and their association with intestinal diseases, making it easier to gain understanding of microbial physiology at the systems level. In addition, the newly developed genome-scale metabolic models that cover significant proportion of known gut microbes enable researchers to analyze and simulate the system-level metabolic response in response to different stimuli in the gut, providing deeper biological insights. Using metabolic interaction network based on pair-wise metabolic dependencies, we found the same interaction pattern in two IBD datasets and one CRC datasets. We report here for the first time that the growth of significantly enriched bacteria in IBD and CRC patients could be boosted by other bacteria including other significantly increased ones. Conversely, the growth of probiotics could be strongly inhibited from other species, including other probiotics. Therefore, it is very important to take the mutual interaction of probiotics into consideration when developing probiotics or ‘microbial based therapies’. Together, our metabolic interaction network analysis can predict majority of the changes in terms of the changed directions in the gut microbiota during enteropathogenesis. Our results thus revealed unappreciated interaction patterns between species could underlie alterations in gut microbiota during enterophathogenesis, and between probiotics and other microbes. Our methods provided a new framework for studying interactions in gut microbiome and their roles in health and disease.

Keywords: bacterial interaction patterns, Metabolic interaction network, gut microbiota community, Intestinal microbial ecology, enteropathogenesis, Probiotics

Received: 07 Dec 2018; Accepted: 13 May 2019.

Edited by:

Qi Zhao, Shenyang Aerospace University, China

Reviewed by:

Ravinder Nagpal, Wake Forest School of Medicine, United States
Josef Neu, University of Florida, United States  

Copyright: © 2019 Dai, Wang, Wu, Gao and Chen. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Prof. Wei-Hua Chen, Huazhong University of Science and Technology, Wuhan, 430074, Hubei Province, China, weihuachen@hust.edu.cn