Scoring Species for Synthetic Community Design: Network Analyses of Functional Core Microbiomes

Abstract

Constructing biological communities is a major challenge in both basic and applied sciences. Although model synthetic communities with a few species have been constructed, designing systems consisting of tens or hundreds of species remains one of the most difficult goals in ecology and microbiology. By utilizing high-throughput sequencing data of interspecific association networks, we here propose a framework for exploring "functional core" species that have great impacts on whole community processes and functions. The framework allows us to score each species within a large community based on three criteria: namely, topological positions, functional portfolios, and functional balance within a target network. The criteria are measures of each species' roles in maximizing functional benefits at the community or ecosystem level. When species with potentially large contributions to ecosystem-level functions are screened, the framework also helps us design "functional core microbiomes" by focusing on properties of species groups (modules) within a network. When embedded into agroecosystems or human gut, such functional core microbiomes are expected to organize whole microbiome processes and functions. An application to a plantassociated microbiome dataset actually highlighted potential functional core microbes that were known to control rhizosphere microbiomes by suppressing pathogens. Meanwhile, an example of application in mouse gut microbiomes called attention to poorly investigated bacterial species, whose potential roles within gut microbiomes deserve future experimental studies. The framework for gaining "bird's-eye" views of functional cores within networks is applicable not only to agricultural and medical data but also to datasets produced in food processing, brewing, waste water purification, and biofuel production.

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“…In this case, transplantation of the normal microbiota can effectively restore the infected microbiota back to normal (Bakken et al 2011). However, simply implanting a desirable microbiota is not a universal method for its establishment (Rilling et al 2015, Castledine et al 2020, and a more systematic methodology is required (Mueller and Sachs 2015, Sbahi and Di Palma 2016, Toju et al 2020.…”