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Title: Scoring Species for Synthetic Community Design: Network Analyses of Functional Core Microbiomes
Authors: Toju, Hirokazu
Abe, Masato S.
Ishii, Chiharu
Hori, Yoshie
Fujita, Hiroaki
Fukuda, Shinji
Author's alias: 東樹, 宏和
阿部, 真人
石井, 千晴
堀, 淑恵
藤田, 博昭
福田, 真嗣
Keywords: biodiversity
biospheres
metagenomes
keystone species
hub species
network theory
synthetic biology
species interactions
Issue Date: 25-Jun-2020
Publisher: Frontiers Media SA
Journal title: Frontiers in Microbiology
Volume: 11
Thesis number: 1361
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 plant-associated 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.
Description: 微生物の生態系を設計する基幹技術を開発 --生態系レベルの機能を農業・医療・工業に--. 京都大学プレスリリース. 2020-06-26.
Rights: © 2020 Toju, Abe, Ishii, Hori, Fujita and Fukuda. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
URI: http://hdl.handle.net/2433/252359
DOI(Published Version): 10.3389/fmicb.2020.01361
Related Link: http://www.kyoto-u.ac.jp/ja/research/research_results/2020/200625_1.html
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