Abstract
Purpose: The purpose of this research is to represent the complex system of the rumen microbiome through a multi-layer network, to explore the main biological functions related to methane metabolism.
Methods: A three-layer heterogeneous network has been constructed based on rumen metabolites, rumen microbial genes and rumen microbial communities. Node association is calculated based on linear and non-linear association p-value voting combined with the permutation test. This research proposed a method to generate key hubs based on the topological properties of nodes in a multilayer network.
Results: 1) A total of 59 individuals (including metabolites, microbial genera, and microbial genes) were found in the topological hubs. Among them, 23 indi-viduals appeared in more than one topologically ranked hub. 2) The metabolite with the highest topological centrality is methane, which is the top one in the 9 topological property rankings. Among the top 10 topologically central 35 micro-bial genes, based on the reconstruction of the metabolic network, the most in-volved metabolic pathway is methane metabolism which included 14 microbial genes. 3) There are 3 genera of microbes (including Aeropyrum, Desulfurococcus and Thermosphaera) from the same family and are ranked top 10 in at least 2 topological characteristics. In the topological hub of the Bottleneck, we found that from Aeropyrum and Desulfurococcus of the same family, their indirect paths are associated with methane. And SufD (K09015), a protein related to the family in the same hub, was also found to be positively associated with methane.
Conclusion: The nodes with important topological properties at the metabolite level and the microbial level are associated with methane functions, indicating the consistency of the biological functions of the topological properties between the layers. This method provided a solution for extracting related hubs of highly central nodes and shows potential in the understanding of biological functions. The topological property-Bottleneck showed the most potential by identified hub nodes were found as exhibiting the consistent sulfur reduction functions through-out multilayer networks.
Methods: A three-layer heterogeneous network has been constructed based on rumen metabolites, rumen microbial genes and rumen microbial communities. Node association is calculated based on linear and non-linear association p-value voting combined with the permutation test. This research proposed a method to generate key hubs based on the topological properties of nodes in a multilayer network.
Results: 1) A total of 59 individuals (including metabolites, microbial genera, and microbial genes) were found in the topological hubs. Among them, 23 indi-viduals appeared in more than one topologically ranked hub. 2) The metabolite with the highest topological centrality is methane, which is the top one in the 9 topological property rankings. Among the top 10 topologically central 35 micro-bial genes, based on the reconstruction of the metabolic network, the most in-volved metabolic pathway is methane metabolism which included 14 microbial genes. 3) There are 3 genera of microbes (including Aeropyrum, Desulfurococcus and Thermosphaera) from the same family and are ranked top 10 in at least 2 topological characteristics. In the topological hub of the Bottleneck, we found that from Aeropyrum and Desulfurococcus of the same family, their indirect paths are associated with methane. And SufD (K09015), a protein related to the family in the same hub, was also found to be positively associated with methane.
Conclusion: The nodes with important topological properties at the metabolite level and the microbial level are associated with methane functions, indicating the consistency of the biological functions of the topological properties between the layers. This method provided a solution for extracting related hubs of highly central nodes and shows potential in the understanding of biological functions. The topological property-Bottleneck showed the most potential by identified hub nodes were found as exhibiting the consistent sulfur reduction functions through-out multilayer networks.
| Original language | English |
|---|---|
| Title of host publication | Advanced Computing - 11th International Conference, IACC 2021 |
| Editors | Deepak Garg, Sarangapani Jagannathan, Ankur Gupta, Lalit Garg, Suneet Gupta |
| Place of Publication | Cham |
| Publisher | Springer Cham |
| Chapter | 13 |
| Pages | 165–175 |
| Number of pages | 11 |
| Volume | 1528 |
| ISBN (Electronic) | 978-3-030-95502-1 |
| ISBN (Print) | 978-3-030-95501-4 |
| DOIs | |
| Publication status | Published (in print/issue) - 8 Feb 2022 |
| Event | 11th International Advanced Computing Conference : Special session: “Integrative Data Analysis in Computational Biology - University of Malta, Malta, Malta Duration: 18 Dec 2021 → 19 Jan 2022 Conference number: 11th https://www.computingconf.com/index.php |
Publication series
| Name | Communications in Computer and Information Science |
|---|---|
| Volume | 1528 CCIS |
| ISSN (Print) | 1865-0929 |
| ISSN (Electronic) | 1865-0937 |
Conference
| Conference | 11th International Advanced Computing Conference |
|---|---|
| Abbreviated title | IDACB-2021 |
| Country/Territory | Malta |
| City | Malta |
| Period | 18/12/21 → 19/01/22 |
| Internet address |
Bibliographical note
Publisher Copyright:© 2022, Springer Nature Switzerland AG.
Keywords
- Rumen microbe
- Metabolites
- Metagenomics
- Multilayer network
- Topological properties
