Abstract
Exploring the mechanisms of maintaining microbial community structure is important to understand biofilm development or microbiota dysbiosis. In this paper, we propose a functional gene-based composition prediction (FCP) model to predict the population structure composition within a microbial community. The model predicts the community composition well in both a low-complexity community as acid mine drainage (AMD) microbiota, and a complex community as human gut microbiota. Furthermore, we define community structure shaping (CSS) genes as functional genes crucial for shaping the microbial community. We have identified CSS genes in AMD and human gut microbiota samples with FCP model and find that CSS genes change with the conditions. Compared to essential genes for microbes, CSS genes are significantly enriched in the genes involved in mobile genetic elements, cell motility, and defense mechanisms, indicating that the functions of CSS genes are focused on communication and strategies in response to the environment factors. We further find that it is the minority, rather than the majority, which contributes to maintaining community structure. Compared to health control samples, we find that some functional genes associated with metabolism of amino acids, nucleotides, and lipopolysaccharide are more likely to be CSS genes in the disease group. CSS genes may help us to understand critical cellular processes and be useful in seeking addable gene circuitries to maintain artificial self-sustainable communities. Our study suggests that functional genes are important to the assembly of microbial communities.
Highlights
There has never been a better time to investigate microbial communities [1]
With the application of the functional gene-based composition prediction (FCP) model, we identified community structure shaping (CSS) genes and investigated which parts of functional genes were critical for shaping the community structure
Our model provides a viewpoint of the relationships between functional genes and microbial community structure, and our study suggests that functional genes are key to the assembly of microbial communities
Summary
There has never been a better time to investigate microbial communities [1]. is the influence of microbial communities on biogeochemical cycles, Earth’s climate, and human health beginning to be understood, and cultivation-independent omics techniques as well as highthroughput sequencing technologies are driving a rapid revolution of our knowledge on the diversity and complexity of microbial communities in natural environments [2]. Microorganisms are probably the most diverse organisms and microbial community structures are very important to understand ecosystem functions [3]. Many issues remain elusive, such as the mechanisms underlying microbiota development and maintenance [4]. Maintaining the structure of microbial communities is critical to ecosystem and human health. There are great differences in the microbial community structure between lowly and highly metal contaminated samples [5]. Gut microbial dysbiosis is associated with various diseases, including irritable bowel syndrome (IBS) [6,7,8] and depression [9]. Understanding the development and maintenance of microbiota may be helpful in providing feasible strategies for bioremediation and disease therapy
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
