Identifying hub nodes and sub-networks from cattle rumen microbiome multilayer networks

Mengyuan Wang, Huiru Zheng, Haiying Wang, Richard J. Dewhurst, Rainer Roeheb

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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.
Original languageEnglish
Title of host publicationAdvanced Computing - 11th International Conference, IACC 2021
EditorsDeepak Garg, Sarangapani Jagannathan, Ankur Gupta, Lalit Garg, Suneet Gupta
Place of PublicationCham
PublisherSpringer Cham
Chapter13
Pages165–175
Number of pages11
Volume1528
ISBN (Electronic)978-3-030-95502-1
ISBN (Print)978-3-030-95501-4
DOIs
Publication statusPublished - 8 Feb 2022
Event11th International Advanced Computing Conference : Special session: “Integrative Data Analysis in Computational Biology - University of Malta, Malta, Malta
Duration: 18 Dec 202119 Jan 2022
Conference number: 11th
https://www.computingconf.com/index.php

Publication series

NameCommunications in Computer and Information Science
Volume1528 CCIS
ISSN (Print)1865-0929
ISSN (Electronic)1865-0937

Conference

Conference11th International Advanced Computing Conference
Abbreviated title IDACB-2021
Country/TerritoryMalta
CityMalta
Period18/12/2119/01/22
Internet address

Bibliographical note

Publisher Copyright:
© 2022, Springer Nature Switzerland AG.

Keywords

  • Rumen microbe
  • Metabolites
  • Metagenomics
  • Multilayer network
  • Topological properties

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