Abstract
SummaryMicrobial 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.
Highlights
The human intestinal microbiome is a complex biological system, whose functions and metabolic processes are the product of multiple interactions between microbial operational taxonomic units (OTUs) (Zelezniak et al, 2015)
Perturbations to microbial interactions may manifest as microbial dysbiosis and have been implicated in a number of pathologies including inflammatory bowel disease (Halfvarson et al, 2017), metabolic dysregulation (Sanz et al, 2014), and neuropsychiatric disorders (Jiang et al, 2015)
We studied the mesoscale architectures underpinning the human gut microbiome by applying the weighted stochastic block model (WSBM), a flexible generative algorithm for detecting community structure (Aicher et al, 2014)
Summary
The human intestinal (gut) microbiome is a complex biological system, whose functions and metabolic processes are the product of multiple interactions between microbial operational taxonomic units (OTUs) (Zelezniak et al, 2015). These diverse interactions can arise from direct or passive mechanisms and may result in beneficial (commensal or mutualistic), neutral, or detrimental (competitive or parasitic) effects to all OTUs involved (Faust and Raes, 2012). An emerging approach to study the structure and function of the microbiome is to define and characterize co-occurrence interactions at the mesoscale (community level). Evidence for a singular assortative structure in the microbiome has been observed in both empirical (Jackson et al, 2018) and computational modeling work
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