Co-existence of Network Architectures Supporting the Human Gut Microbiome

Caitlin V Hall; Anton Lord; Richard Betzel; Martha Zakrzewski; Lisa A Simms; Andrew Zalesky; Graham Radford-Smith; Luca Cocchi

doi:10.1016/j.isci.2019.11.032

Co-existence of Network Architectures Supporting the Human Gut Microbiome

iScience. 2019 Dec 20:22:380-391. doi: 10.1016/j.isci.2019.11.032. Epub 2019 Nov 21.

Authors

Caitlin V Hall¹, Anton Lord², Richard Betzel³, Martha Zakrzewski⁴, Lisa A Simms², Andrew Zalesky⁵, Graham Radford-Smith², Luca Cocchi⁶

Affiliations

¹ Clinical Brain Networks Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; School of Biomedical Sciences, University of Queensland, Brisbane, QLD 4006, Australia. Electronic address: [email protected].
² Gut Health Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.
³ Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN 47405, USA.
⁴ Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.
⁵ Melbourne Neuropsychiatry Centre and Department of Biomedical Engineering, The University of Melbourne, Melbourne, VIC 3010, Australia.
⁶ Clinical Brain Networks Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; School of Biomedical Sciences, University of Queensland, Brisbane, QLD 4006, Australia.

Abstract

Microbial organisms of the human gut microbiome do not exist in isolation but form complex and diverse interactions to maintain health and reduce risk of disease development. The organization of the gut microbiome is assumed to be a singular assortative network, where interactions between operational taxonomic units (OTUs) can readily be clustered into segregated and distinct communities. Here, we leverage recent methodological advances in network modeling to assess whether communities in the human microbiome exhibit a single network structure or whether co-existing mesoscale network architectures are present. We found evidence for core-periphery structures in the microbiome, supported by strong, assortative community interactions. This complex architecture, coupled with previously reported functional roles of OTUs, provides a nuanced understanding of how the microbiome simultaneously promotes high microbial diversity and maintains functional redundancy.

Keywords: Association Analysis; Bioinformatics; Microbiology; Microbiome.