Interrogation of Internal Workings in Microbial Community Assembly: Play a Game through a Behavioral Network? Qian Wang, a Xinjuan Liu, b Libo Jiang, a Yige Cao, a Xiang Zhan, c Christopher H. Griffin, d Rongling Wu a,c a Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China b Department of Gastroenterology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China c Department of Public Health Sciences, Penn State Hershey College of Medicine, Hershey, Pennsylvania, USA d Applied Research Laboratory, The Pennsylvania State University, University Park, Pennsylvania, USA ABSTRACT Increasing evidence shows that the influence of microbiota on biogeo- chemical cycling, plant development, and human health is executed through a com- plex network of microbe-microbe interactions. However, characterizing how mi- crobes interact and work together within closely packed and highly heterogeneous microbial ecosystems is extremely challenging. Here, we describe a rule-of-thumb framework for visualizing polymicrobial interactions and extracting general principles that underlie microbial communities. We integrate elements of metabolic ecology, behavioral ecology, and game theory to quantify the interactive strategies by which microbes at any taxonomic level compete for resources and cooperate symbiotically with each other to form and stabilize ecological communities. We show how the frame- work can chart an omnidirectional landscape of microbial cooperation and competition that may drive various natural processes. This framework can be implemented into genome-wide association studies to unravel the genetic mechanisms underlying micro- bial interaction networks and their evolutionary consequences along spatiotemporal gra- dients. IMPORTANCE Identifying general biological rules that underlie the complexity and heterogeneity of microbial communities has proven to be highly challenging. We pres- ent a rule-of-thumb framework for studying and characterizing how microbes interact with each other across different taxa to determine community behavior and dynamics. This framework is computationally simple but conceptually meaningful, and it can pro- vide a starting point to generate novel biological hypotheses about microbial interac- tions and explore internal workings of microbial community assembly in depth. KEYWORDS game theory, competition, cooperation, microbial interaction network M icrobial communities affect a wide range of natural processes, from biogeochemi- cal cycling to plant development and animal and human health (1, 2). Surveys of microbiome composition across various ecological settings from the soil to the human body have consistently revealed that microbes are organized into functional and stable communities through fundamental ecological principles (3, 4). However, the manner in which the structural-functional relationship of polymicrobial communities is estab- lished remains poorly understood, largely because we know little about the ways in which microbes interact with each other. Different microbes in the same community would compete for resources and space but also cooperate through metabolic exchange or quorum sensing to reach the community’s equilibrium (5, 6). This process proceeds like a game. Game theory, originally developed in economic research (7), enables the formulation of an individual strategy that maximizes payoff by incorporating the strategies of other members (8). Several authors have used pairwise game theory to study the structure of microbial Citation Wang Q, Liu X, Jiang L, Cao Y, Zhan X, Griffin CH, Wu R. 2019. Interrogation of internal workings in microbial community assembly: play a game through a behavioral network? mSystems 4:e00550-19. https://doi.org/10 .1128/mSystems.00550-19. Editor Jack A. Gilbert, University of California San Diego Copyright © 2019 Wang et al. This is an open- access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Rongling Wu, rwu@bjfu.edu.cn. A rule of thumb is proposed to reveal how microbes interact with each other in microbial community assembly. Received 9 September 2019 Accepted 23 September 2019 Published METHODS AND PROTOCOLS Ecological and Evolutionary Science September/October 2019 Volume 4 Issue 5 e00550-19 msystems.asm.org 1 29 October 2019 on May 31, 2020 by guest http://msystems.asm.org/ Downloaded from