1
|
Muñoz-Cazalla A, de Quinto I, Álvaro-Llorente L, Rodríguez-Beltrán J, Herencias C. The role of bacterial metabolism in human gut colonization. Int Microbiol 2025; 28:401-410. [PMID: 38937311 PMCID: PMC11906536 DOI: 10.1007/s10123-024-00550-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/29/2024]
Abstract
Can we anticipate the emergence of the next pandemic antibiotic-resistant bacterial clone? Addressing such an ambitious question relies on our ability to comprehensively understand the ecological and epidemiological factors fostering the evolution of high-risk clones. Among these factors, the ability to persistently colonize and thrive in the human gut is crucial for most high-risk clones. Nonetheless, the causes and mechanisms facilitating successful gut colonization remain obscure. Here, we review recent evidence that suggests that bacterial metabolism plays a pivotal role in determining the ability of high-risk clones to colonize the human gut. Subsequently, we outline novel approaches that enable the exploration of microbial metabolism at an unprecedented scale and level of detail. A thorough understanding of the constraints and opportunities of bacterial metabolism in gut colonization will foster our ability to predict the emergence of high-risk clones and take appropriate containment strategies.
Collapse
Affiliation(s)
- Ada Muñoz-Cazalla
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Ignacio de Quinto
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Laura Álvaro-Llorente
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Jerónimo Rodríguez-Beltrán
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas-CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain.
| | - Cristina Herencias
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas-CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain.
| |
Collapse
|
2
|
Villablanca EJ. Organismal mucosal immunology: A perspective through the eyes of game theory. Mucosal Immunol 2025; 18:16-25. [PMID: 39672543 DOI: 10.1016/j.mucimm.2024.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 12/03/2024] [Accepted: 12/06/2024] [Indexed: 12/15/2024]
Abstract
In complex organisms, functional units must interact cohesively to maintain homeostasis, especially within mucosal barriers that house diverse, specialized cell exposed to constant environmental challenges. Understanding how homeostasis at mucosal barriers is maintained and how its disruption can lead to autoimmune diseases or cancer, requires a holistic view. Although omics approaches and systems immunology have become powerful tools, they are not without limitations; interpretations may reflect researchers' assumptions, even if other explanations exist. In this perspective, I propose that applying game theory concepts to mucosal immunology could help interpret complex data, offering fresh perspectives and supporting the exploration of alternative scenarios. By framing the mucosal immune system as a network of strategic interactions with multiple possible outcomes, game theory, which analyzes strategic interactions and decision-making processes, could illuminate novel cell types and functions, cell interactions, and responses to pathogens and commensals, leading to a more comprehensive understanding of immune homeostasis and diseases. In addition, game theory might encourage researchers to consider a broader range of possibilities, reduce the risk of myopic thinking, and ultimately enable a more refined and comprehensive understanding of the complexity of the immune system at mucosal barriers. This perspective aims to introduce game theory as a complementary framework for mucosal immunologists, encouraging them to incorporate these concepts into data interpretation and system modeling.
Collapse
Affiliation(s)
- Eduardo J Villablanca
- Division of Immunology and Respiratory Medicine, Department of Medicine Solna, Karolinska Institute and University Hospital, Stockholm, Sweden; Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden; Center of Molecular Medicine, Stockholm, Sweden.
| |
Collapse
|
3
|
Venkataraman P, Mahilkar A, Raj N, Saini S. Empirical evidence of resource dependent evolution of payoff matrices in Saccharomyces cerevisiae populations. J Evol Biol 2025; 38:122-128. [PMID: 39387146 PMCID: PMC11696675 DOI: 10.1093/jeb/voae128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 08/24/2024] [Accepted: 10/08/2024] [Indexed: 10/12/2024]
Abstract
In evolutionary game theory, a relative comparison of the cost and benefit associated with obtaining a resource, called payoff, is used as an indicator of fitness of an organism. Payoffs of different strategies, quantitatively represented as payoff matrices, are used to understand complex inter-species and intra-species interactions like cooperation, mutualism, and altruism. Payoff matrices, however, are usually treated as invariant with time-largely due to the absence of any empirical data quantifying their evolution. In this paper, we present empirical evidence of three types of resource-dependent changes in the payoff matrices of evolving Saccharomyces cerevisiae populations. We show that depending on the carbon source and participating genotypes, N-player games could collapse, be born, or be maintained. Our results highlight the need to consider the dynamic nature of payoff matrices while making even short-term predictions about population interactions and dynamics.
Collapse
Affiliation(s)
- Pavithra Venkataraman
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Anjali Mahilkar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Namratha Raj
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Supreet Saini
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| |
Collapse
|
4
|
Scott H, Segrè D. Metabolic Flux Modeling in Marine Ecosystems. ANNUAL REVIEW OF MARINE SCIENCE 2025; 17:593-620. [PMID: 39259978 DOI: 10.1146/annurev-marine-032123-033718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Ocean metabolism constitutes a complex, multiscale ensemble of biochemical reaction networks harbored within and between the boundaries of a myriad of organisms. Gaining a quantitative understanding of how these networks operate requires mathematical tools capable of solving in silico the resource allocation problem each cell faces in real life. Toward this goal, stoichiometric modeling of metabolism, such as flux balance analysis, has emerged as a powerful computational tool for unraveling the intricacies of metabolic processes in microbes, microbial communities, and multicellular organisms. Here, we provide an overview of this approach and its applications, future prospects, and practical considerations in the context of marine sciences. We explore how flux balance analysis has been employed to study marine organisms, help elucidate nutrient cycling, and predict metabolic capabilities within diverse marine environments, and highlight future prospects for this field in advancing our knowledge of marine ecosystems and their sustainability.
Collapse
Affiliation(s)
- Helen Scott
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Bioinformatics Program, Faculty of Computing and Data Science, Boston University, Boston, Massachusetts, USA; ,
| | - Daniel Segrè
- Department of Biology, Department of Physics, and Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Bioinformatics Program, Faculty of Computing and Data Science, Boston University, Boston, Massachusetts, USA; ,
| |
Collapse
|
5
|
Dieckow S, Szafrański SP, Grischke J, Qu T, Doll-Nikutta K, Steglich M, Yang I, Häussler S, Stiesch M. Structure and composition of early biofilms formed on dental implants are complex, diverse, subject-specific and dynamic. NPJ Biofilms Microbiomes 2024; 10:155. [PMID: 39719447 DOI: 10.1038/s41522-024-00624-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 11/26/2024] [Indexed: 12/26/2024] Open
Abstract
Biofilm-associated peri-implant infections pose a major problem in modern medicine. The understanding of biofilm development is hampered by biofilm complexity and the lack of robust clinical models. This study comprehensively characterized the dynamics of early biofilm formation in the transmucosal passage of implant abutments in 12 patients. Biofilm structures and compositions were complex, diverse, subject-specific and dynamic. A total of 371 different bacterial species were detected. 100 phylogenetically diverse unnamed species and 35 taxonomically diverse disease-associated species comprised an average 4.3% and 3.1% of the community, respectively, but reached up to 12.7% and 21.7% in some samples. Oral taxa formed numerous positive associations and clusters and were characterized by a high potential for metabolic interactions. The subspecies diversity was highly patient-specific and species-dependent, with 1427 ASVs identified in total. The unprecedented depth of early biofilm characterization in this study will support the development of individualized preventive and early diagnostic strategies.
Collapse
Affiliation(s)
- Sophie Dieckow
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Hannover, Germany
| | - Szymon P Szafrański
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Hannover, Germany
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE), Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Jasmin Grischke
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Hannover, Germany
| | - Taoran Qu
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Hannover, Germany
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE), Hannover, Germany
| | - Katharina Doll-Nikutta
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Hannover, Germany
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE), Hannover, Germany
| | - Matthias Steglich
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Hannover, Germany
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE), Hannover, Germany
| | - Ines Yang
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Hannover, Germany
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE), Hannover, Germany
| | - Susanne Häussler
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Molecular Bacteriology, Twincore, Centre for Clinical and Experimental Infection Research, Hannover, Germany
- Department of Clinical Microbiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Meike Stiesch
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Hannover, Germany.
- Lower Saxony Centre for Biomedical Engineering, Implant Research and Development (NIFE), Hannover, Germany.
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany.
| |
Collapse
|
6
|
Huelsmann M, Schubert OT, Ackermann M. A framework for understanding collective microbiome metabolism. Nat Microbiol 2024; 9:3097-3109. [PMID: 39604625 DOI: 10.1038/s41564-024-01850-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 10/10/2024] [Indexed: 11/29/2024]
Abstract
Microbiome metabolism underlies numerous vital ecosystem functions. Individual microbiome members often perform partial catabolism of substrates or do not express all of the metabolic functions required for growth. Microbiome members can complement each other by exchanging metabolic intermediates and cellular building blocks to achieve a collective metabolism. We currently lack a mechanistic framework to explain why microbiome members adopt partial metabolism and how metabolic functions are distributed among them. Here we argue that natural selection for proteome efficiency-that is, performing essential metabolic fluxes at a minimal protein investment-explains partial metabolism of microbiome members, which underpins the collective metabolism of microbiomes. Using the carbon cycle as an example, we discuss motifs of collective metabolism, the conditions under which these motifs increase the proteome efficiency of individuals and the metabolic interactions they result in. In summary, we propose a mechanistic framework for how collective metabolic functions emerge from selection on individuals.
Collapse
Affiliation(s)
- Matthias Huelsmann
- Department of Environmental Systems Science, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich, Switzerland.
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland.
- PharmaBiome AG, Schlieren, Switzerland.
| | - Olga T Schubert
- Department of Environmental Systems Science, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich, Switzerland
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
| | - Martin Ackermann
- Department of Environmental Systems Science, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich, Switzerland
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
- School of Architecture, Civil and Environmental Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| |
Collapse
|
7
|
Eshoa E, Zomorrodi AR. Precision game engineering through reshaping strategic payoffs. Sci Rep 2024; 14:25226. [PMID: 39448647 PMCID: PMC11502784 DOI: 10.1038/s41598-024-72543-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 09/09/2024] [Indexed: 10/26/2024] Open
Abstract
Nash equilibrium is a key concept in game theory fundamental for elucidating the equilibrium state of strategic interactions, with applications in diverse fields such as economics, political science, and biology. However, the Nash equilibrium may not always align with desired outcomes within the broader system. This article introduces a novel game engineering framework that tweaks strategic payoffs within a game to achieve a pre-defined desired Nash equilibrium while averting undesired ones. Leveraging mixed-integer linear programming, this framework identifies intricate combinations of players and strategies and optimal perturbations to their payoffs that enable the shift from undesirable Nash equilibria to more favorable ones. We demonstrate the effectiveness and scalability of our approach on games of varying complexity, ranging from simple prototype games such as the Prisoner's Dilemma and Snowdrift games with two or more players to complex game configurations with up to10 6 entries in the payoff matrix. These studies showcase the capability of this framework in efficiently identifying the alternative ways of reshaping strategic payoffs to secure desired Nash equilibria and preclude undesired equilibrium states. Our game engineering framework offers a versatile toolkit for precision strategic decision-making with far-reaching implications across diverse domains.
Collapse
Affiliation(s)
- Elie Eshoa
- Computer Science Department, Harvard John A. Paulson School of Engineering and Applied Sciences, Boston, MA, USA
- Harvard Kenneth C. Griffin Graduate School of Arts and Sciences, Cambridge, MA, USA
- Mucosal Immunology and Biology Research Center, Pediatrics Department, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Ali R Zomorrodi
- Mucosal Immunology and Biology Research Center, Pediatrics Department, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
8
|
Puente-Sánchez F, Pascual-García A, Bastolla U, Pedrós-Alió C, Tamames J. Cross-biome microbial networks reveal functional redundancy and suggest genome reduction through functional complementarity. Commun Biol 2024; 7:1046. [PMID: 39181977 PMCID: PMC11344793 DOI: 10.1038/s42003-024-06616-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 07/23/2024] [Indexed: 08/27/2024] Open
Abstract
The structure of microbial communities arises from a multitude of factors, including the interactions of microorganisms with each other and with the environment. In this work, we sought to disentangle those drivers by performing a cross-study, cross-biome meta-analysis of microbial occurrence data in more than 5000 samples, applying a novel network clustering algorithm aimed to capture conditional taxa co-occurrences. We then examined the phylogenetic and functional composition of the resulting clusters, and searched for global patterns of assembly both at the community level and in the presence/absence of individual metabolic pathways.Our analysis highlighted the prevalence of functional redundancy in microbial communities, particularly between taxa that co-occur in more than one environment, pointing to a relationship between functional redundancy and environmental adaptation. In spite of this, certain pathways were observed in fewer taxa than expected by chance, suggesting the presence of auxotrophy, and presumably cooperation among community members. This hypothetical cooperation may play a role in genome reduction, since we observed a negative relationship between the size of bacterial genomes and the size of the community they belong to.Overall, our results suggest the microbial community assembly is driven by universal principles that operate consistently across different biomes and taxonomic groups.
Collapse
Affiliation(s)
- Fernando Puente-Sánchez
- Systems Biology Department, Centro Nacional de Biotecnología (CSIC), C/ Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain.
- Department of Aquatic Sciences and Assessment, Swedish University for Agricultural Sciences (SLU), Lennart Hjelms väg 9, 756 51, Uppsala, Sweden.
| | - Alberto Pascual-García
- Systems Biology Department, Centro Nacional de Biotecnología (CSIC), C/ Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Ugo Bastolla
- Computational Biology and Bioinformatics, Centro de Biología Molecular Severo Ochoa (Universidad Autónoma de Madrid - CSIC), C/ Nicolás Cabrera 1, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Carlos Pedrós-Alió
- Systems Biology Department, Centro Nacional de Biotecnología (CSIC), C/ Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Javier Tamames
- Systems Biology Department, Centro Nacional de Biotecnología (CSIC), C/ Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| |
Collapse
|
9
|
Loo EPI, Durán P, Pang TY, Westhoff P, Deng C, Durán C, Lercher M, Garrido-Oter R, Frommer WB. Sugar transporters spatially organize microbiota colonization along the longitudinal root axis of Arabidopsis. Cell Host Microbe 2024; 32:543-556.e6. [PMID: 38479394 DOI: 10.1016/j.chom.2024.02.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 02/01/2024] [Accepted: 02/21/2024] [Indexed: 04/13/2024]
Abstract
Plant roots are functionally heterogeneous in cellular architecture, transcriptome profile, metabolic state, and microbial immunity. We hypothesized that axial differentiation may also impact spatial colonization by root microbiota along the root axis. We developed two growth systems, ArtSoil and CD-Rhizotron, to grow and then dissect Arabidopsis thaliana roots into three segments. We demonstrate that distinct endospheric and rhizosphere bacterial communities colonize the segments, supporting the hypothesis of microbiota differentiation along the axis. Root metabolite profiling of each segment reveals differential metabolite enrichment and specificity. Bioinformatic analyses and GUS histochemistry indicate microbe-induced accumulation of SWEET2, 4, and 12 sugar uniporters. Profiling of root segments from sweet mutants shows altered spatial metabolic profiles and reorganization of endospheric root microbiota. This work reveals the interdependency between root metabolites and microbial colonization and the contribution of SWEETs to spatial diversity and stability of microbial ecosystem.
Collapse
Affiliation(s)
- Eliza P-I Loo
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute for Molecular Physiology, 40225 Düsseldorf, Germany; Cluster of Excellence on Plant Sciences, 40225 Düsseldorf, Germany.
| | - Paloma Durán
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Cluster of Excellence on Plant Sciences, 40225 Düsseldorf, Germany
| | - Tin Yau Pang
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute for Computer Science and Department of Biology, 40225 Düsseldorf, Germany; Heinrich Heine University Düsseldorf, Medical Faculty and University Hospital Düsseldorf, Division of Cardiology, Pulmonology and Vascular Medicine, 40225 Düsseldorf, Germany
| | - Philipp Westhoff
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Plant Metabolism and Metabolomics Laboratory, 40225 Düsseldorf, Germany; Cluster of Excellence on Plant Sciences, 40225 Düsseldorf, Germany
| | - Chen Deng
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute for Molecular Physiology, 40225 Düsseldorf, Germany
| | - Carlos Durán
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Martin Lercher
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute for Computer Science and Department of Biology, 40225 Düsseldorf, Germany; Heinrich Heine University Düsseldorf, Medical Faculty and University Hospital Düsseldorf, Division of Cardiology, Pulmonology and Vascular Medicine, 40225 Düsseldorf, Germany
| | - Ruben Garrido-Oter
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Cluster of Excellence on Plant Sciences, 40225 Düsseldorf, Germany; Earlham Institute, Norwich NR4 7UZ, UK
| | - Wolf B Frommer
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute for Molecular Physiology, 40225 Düsseldorf, Germany; Cluster of Excellence on Plant Sciences, 40225 Düsseldorf, Germany; Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, 464-8601 Nagoya, Japan.
| |
Collapse
|
10
|
Srinivasan S, Jnana A, Murali TS. Modeling Microbial Community Networks: Methods and Tools for Studying Microbial Interactions. MICROBIAL ECOLOGY 2024; 87:56. [PMID: 38587642 PMCID: PMC11001700 DOI: 10.1007/s00248-024-02370-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 03/28/2024] [Indexed: 04/09/2024]
Abstract
Microbial interactions function as a fundamental unit in complex ecosystems. By characterizing the type of interaction (positive, negative, neutral) occurring in these dynamic systems, one can begin to unravel the role played by the microbial species. Towards this, various methods have been developed to decipher the function of the microbial communities. The current review focuses on the various qualitative and quantitative methods that currently exist to study microbial interactions. Qualitative methods such as co-culturing experiments are visualized using microscopy-based techniques and are combined with data obtained from multi-omics technologies (metagenomics, metabolomics, metatranscriptomics). Quantitative methods include the construction of networks and network inference, computational models, and development of synthetic microbial consortia. These methods provide a valuable clue on various roles played by interacting partners, as well as possible solutions to overcome pathogenic microbes that can cause life-threatening infections in susceptible hosts. Studying the microbial interactions will further our understanding of complex less-studied ecosystems and enable design of effective frameworks for treatment of infectious diseases.
Collapse
Affiliation(s)
- Shanchana Srinivasan
- Department of Public Health Genomics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Apoorva Jnana
- Department of Public Health Genomics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Thokur Sreepathy Murali
- Department of Public Health Genomics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India.
| |
Collapse
|
11
|
Jing J, Garbeva P, Raaijmakers JM, Medema MH. Strategies for tailoring functional microbial synthetic communities. THE ISME JOURNAL 2024; 18:wrae049. [PMID: 38537571 PMCID: PMC11008692 DOI: 10.1093/ismejo/wrae049] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/26/2024] [Indexed: 04/12/2024]
Abstract
Natural ecosystems harbor a huge reservoir of taxonomically diverse microbes that are important for plant growth and health. The vast diversity of soil microorganisms and their complex interactions make it challenging to pinpoint the main players important for the life support functions microbes can provide to plants, including enhanced tolerance to (a)biotic stress factors. Designing simplified microbial synthetic communities (SynComs) helps reduce this complexity to unravel the molecular and chemical basis and interplay of specific microbiome functions. While SynComs have been successfully employed to dissect microbial interactions or reproduce microbiome-associated phenotypes, the assembly and reconstitution of these communities have often been based on generic abundance patterns or taxonomic identities and co-occurrences but have only rarely been informed by functional traits. Here, we review recent studies on designing functional SynComs to reveal common principles and discuss multidimensional approaches for community design. We propose a strategy for tailoring the design of functional SynComs based on integration of high-throughput experimental assays with microbial strains and computational genomic analyses of their functional capabilities.
Collapse
Affiliation(s)
- Jiayi Jing
- Bioinformatics Group, Department of Plant Science, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Department of Plant Science, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| |
Collapse
|
12
|
Ghadermazi P, Chan SHJ. Microbial interactions from a new perspective: reinforcement learning reveals new insights into microbiome evolution. Bioinformatics 2024; 40:btae003. [PMID: 38212999 PMCID: PMC10799744 DOI: 10.1093/bioinformatics/btae003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 12/24/2023] [Accepted: 01/10/2024] [Indexed: 01/13/2024] Open
Abstract
MOTIVATION Microbes are essential part of all ecosystems, influencing material flow and shaping their surroundings. Metabolic modeling has been a useful tool and provided tremendous insights into microbial community metabolism. However, current methods based on flux balance analysis (FBA) usually fail to predict metabolic and regulatory strategies that lead to long-term survival and stability especially in heterogenous communities. RESULTS Here, we introduce a novel reinforcement learning algorithm, Self-Playing Microbes in Dynamic FBA, which treats microbial metabolism as a decision-making process, allowing individual microbial agents to evolve by learning and adapting metabolic strategies for enhanced long-term fitness. This algorithm predicts what microbial flux regulation policies will stabilize in the dynamic ecosystem of interest in the presence of other microbes with minimal reliance on predefined strategies. Throughout this article, we present several scenarios wherein our algorithm outperforms existing methods in reproducing outcomes, and we explore the biological significance of these predictions. AVAILABILITY AND IMPLEMENTATION The source code for this article is available at: https://github.com/chan-csu/SPAM-DFBA.
Collapse
Affiliation(s)
- Parsa Ghadermazi
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80521, United States
| | - Siu Hung Joshua Chan
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80521, United States
| |
Collapse
|
13
|
Srinivasan A, Sajeevan A, Rajaramon S, David H, Solomon AP. Solving polymicrobial puzzles: evolutionary dynamics and future directions. Front Cell Infect Microbiol 2023; 13:1295063. [PMID: 38145044 PMCID: PMC10748482 DOI: 10.3389/fcimb.2023.1295063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/03/2023] [Indexed: 12/26/2023] Open
Abstract
Polymicrobial infections include various microorganisms, often necessitating different treatment methods than a monomicrobial infection. Scientists have been puzzled by the complex interactions within these communities for generations. The presence of specific microorganisms warrants a chronic infection and impacts crucial factors such as virulence and antibiotic susceptibility. Game theory is valuable for scenarios involving multiple decision-makers, but its relevance to polymicrobial infections is limited. Eco-evolutionary dynamics introduce causation for multiple proteomic interactions like metabolic syntropy and niche segregation. The review culminates both these giants to form evolutionary dynamics (ED). There is a significant amount of literature on inter-bacterial interactions that remain unsynchronised. Such raw data can only be moulded by analysing the ED involved. The review culminates the inter-bacterial interactions in multiple clinically relevant polymicrobial infections like chronic wounds, CAUTI, otitis media and dental carries. The data is further moulded with ED to analyse the niche colonisation of two notoriously competitive bacteria: S.aureus and P.aeruginosa. The review attempts to develop a future trajectory for polymicrobial research by following recent innovative strategies incorporating ED to curb polymicrobial infections.
Collapse
Affiliation(s)
| | | | | | | | - Adline Princy Solomon
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| |
Collapse
|
14
|
Roitershtein A, Rastegar R, Chapkin RS, Ivanov I. Extinction scenarios in evolutionary processes: a multinomial Wright-Fisher approach. J Math Biol 2023; 87:63. [PMID: 37751048 PMCID: PMC10586398 DOI: 10.1007/s00285-023-01993-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 08/16/2023] [Accepted: 08/31/2023] [Indexed: 09/27/2023]
Abstract
We study a discrete-time multi-type Wright-Fisher population process. The mean-field dynamics of the stochastic process is induced by a general replicator difference equation. We prove several results regarding the asymptotic behavior of the model, focusing on the impact of the mean-field dynamics on it. One of the results is a limit theorem that describes sufficient conditions for an almost certain path to extinction, first eliminating the type which is the least fit at the mean-field equilibrium. The effect is explained by the metastability of the stochastic system, which under the conditions of the theorem spends almost all time before the extinction event in a neighborhood of the equilibrium. In addition to the limit theorems, we propose a maximization principle for a general deterministic replicator dynamics and study its implications for the stochastic model.
Collapse
Affiliation(s)
| | - Reza Rastegar
- Occidental Petroleum Corporation, Houston, TX, 77046, USA
| | - Robert S Chapkin
- Department of Nutrition - Program in Integrative Nutrition & Complex Diseases, Texas A &M University, College Station, TX, 77843, USA
| | - Ivan Ivanov
- Department of Veterinary Physiology and Pharmacology, Texas A &M University, College Station, TX, 77843, USA.
| |
Collapse
|
15
|
Theorell A, Stelling J. Assumptions on decision making and environment can yield multiple steady states in microbial community models. BMC Bioinformatics 2023; 24:262. [PMID: 37349675 DOI: 10.1186/s12859-023-05325-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/05/2023] [Indexed: 06/24/2023] Open
Abstract
BACKGROUND Microbial community simulations using genome scale metabolic networks (GSMs) are relevant for many application areas, such as the analysis of the human microbiome. Such simulations rely on assumptions about the culturing environment, affecting if the culture may reach a metabolically stationary state with constant microbial concentrations. They also require assumptions on decision making by the microbes: metabolic strategies can be in the interest of individual community members or of the whole community. However, the impact of such common assumptions on community simulation results has not been investigated systematically. RESULTS Here, we investigate four combinations of assumptions, elucidate how they are applied in literature, provide novel mathematical formulations for their simulation, and show how the resulting predictions differ qualitatively. Our results stress that different assumption combinations give qualitatively different predictions on microbial coexistence by differential substrate utilization. This fundamental mechanism is critically under explored in the steady state GSM literature with its strong focus on coexistence states due to crossfeeding (division of labor). Furthermore, investigating a realistic synthetic community, where the two involved strains exhibit no growth in isolation, but grow as a community, we predict multiple modes of cooperation, even without an explicit cooperation mechanism. CONCLUSIONS Steady state GSM modelling of microbial communities relies both on assumed decision making principles and environmental assumptions. In principle, dynamic flux balance analysis addresses both. In practice, our methods that address the steady state directly may be preferable, especially if the community is expected to display multiple steady states.
Collapse
Affiliation(s)
- Axel Theorell
- Department of Biosystems Science and Engineering (D-BSSE) and SIB Swiss Institute of Bioinformatics, ETH Zurich, 4058, Basel, Switzerland.
| | - Jörg Stelling
- Department of Biosystems Science and Engineering (D-BSSE) and SIB Swiss Institute of Bioinformatics, ETH Zurich, 4058, Basel, Switzerland.
| |
Collapse
|
16
|
Aulakh SK, Sellés Vidal L, South EJ, Peng H, Varma SJ, Herrera-Dominguez L, Ralser M, Ledesma-Amaro R. Spontaneously established syntrophic yeast communities improve bioproduction. Nat Chem Biol 2023:10.1038/s41589-023-01341-2. [PMID: 37248413 PMCID: PMC10374442 DOI: 10.1038/s41589-023-01341-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 04/14/2023] [Indexed: 05/31/2023]
Abstract
Nutritional codependence (syntrophy) has underexplored potential to improve biotechnological processes by using cooperating cell types. So far, design of yeast syntrophic communities has required extensive genetic manipulation, as the co-inoculation of most eukaryotic microbial auxotrophs does not result in cooperative growth. Here we employ high-throughput phenotypic screening to systematically test pairwise combinations of auxotrophic Saccharomyces cerevisiae deletion mutants. Although most coculture pairs do not enter syntrophic growth, we identify 49 pairs that spontaneously form syntrophic, synergistic communities. We characterized the stability and growth dynamics of nine cocultures and demonstrated that a pair of tryptophan auxotrophs grow by exchanging a pathway intermediate rather than end products. We then introduced a malonic semialdehyde biosynthesis pathway split between different pairs of auxotrophs, which resulted in increased production. Our results report the spontaneous formation of stable syntrophy in S. cerevisiae auxotrophs and illustrate the biotechnological potential of dividing labor in a cooperating intraspecies community.
Collapse
Affiliation(s)
- Simran Kaur Aulakh
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
- The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lara Sellés Vidal
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Eric J South
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Huadong Peng
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Sreejith Jayasree Varma
- Department of Biochemistry, Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Lucia Herrera-Dominguez
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
- Department of Biochemistry, Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Markus Ralser
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
- The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Department of Biochemistry, Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.
| |
Collapse
|
17
|
Mataigne V, Vannier N, Vandenkoornhuyse P, Hacquard S. Multi-genome metabolic modeling predicts functional inter-dependencies in the Arabidopsis root microbiome. MICROBIOME 2022; 10:217. [PMID: 36482420 PMCID: PMC9733318 DOI: 10.1186/s40168-022-01383-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 09/23/2022] [Indexed: 05/28/2023]
Abstract
BACKGROUND From a theoretical ecology point of view, microbiomes are far more complex than expected. Besides competition and competitive exclusion, cooperative microbe-microbe interactions have to be carefully considered. Metabolic dependencies among microbes likely explain co-existence in microbiota. METHODOLOGY In this in silico study, we explored genome-scale metabolic models (GEMs) of 193 bacteria isolated from Arabidopsis thaliana roots. We analyzed their predicted producible metabolites under simulated nutritional constraints including "root exudate-mimicking growth media" and assessed the potential of putative metabolic exchanges of by- and end-products to avoid those constraints. RESULTS We found that the genome-encoded metabolic potential is quantitatively and qualitatively clustered by phylogeny, highlighting metabolic differentiation between taxonomic groups. Random, synthetic combinations of increasing numbers of strains (SynComs) indicated that the number of producible compounds by GEMs increased with average phylogenetic distance, but that most SynComs were centered around an optimal phylogenetic distance. Moreover, relatively small SynComs could reflect the capacity of the whole community due to metabolic redundancy. Inspection of 30 specific end-product metabolites (i.e., target metabolites: amino acids, vitamins, phytohormones) indicated that the majority of the strains had the genetic potential to produce almost all the targeted compounds. Their production was predicted (1) to depend on external nutritional constraints and (2) to be facilitated by nutritional constraints mimicking root exudates, suggesting nutrient availability and root exudates play a key role in determining the number of producible metabolites. An answer set programming solver enabled the identification of numerous combinations of strains predicted to depend on each other to produce these targeted compounds under severe nutritional constraints thus indicating a putative sub-community level of functional redundancy. CONCLUSIONS This study predicts metabolic restrictions caused by available nutrients in the environment. By extension, it highlights the importance of the environment for niche potential, realization, partitioning, and overlap. Our results also suggest that metabolic dependencies and cooperation among root microbiota members compensate for environmental constraints and help maintain co-existence in complex microbial communities. Video Abstract.
Collapse
Affiliation(s)
- Victor Mataigne
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, 35000, Rennes, France
- Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, 50829, Cologne, Germany
| | - Nathan Vannier
- Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, 50829, Cologne, Germany
| | | | - Stéphane Hacquard
- Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, 50829, Cologne, Germany.
| |
Collapse
|
18
|
Kleshnina M, McKerral JC, González-Tokman C, Filar JA, Mitchell JG. Shifts in evolutionary balance of phenotypes under environmental changes. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220744. [PMID: 36340514 PMCID: PMC9627443 DOI: 10.1098/rsos.220744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Environments shape communities by driving individual interactions and the evolutionary outcome of competition. In static, homogeneous environments a robust, evolutionary stable, outcome is sometimes reachable. However, inherently stochastic, this evolutionary process need not stabilize, resulting in a dynamic ecological state, often observed in microbial communities. We use evolutionary games to study the evolution of phenotypic competition in dynamic environments. Under the assumption that phenotypic expression depends on the environmental shifts, existing periodic relationships may break or result in formation of new periodicity in phenotypic interactions. The exact outcome depends on the environmental shift itself, indicating the importance of understanding how environments influence affected systems. Under periodic environmental fluctuations, a stable state preserving dominant phenotypes may exist. However, rapid environmental shifts can lead to critical shifts in the phenotypic evolutionary balance. This might lead to environmentally favoured phenotypes dominating making the system vulnerable. We suggest that understanding of the robustness of the system's current state is necessary to anticipate when it will shift to a new equilibrium via understanding what level of perturbations the system can take before its equilibrium changes. Our results provide insights in how microbial communities can be steered to states where they are dominated by desired phenotypes.
Collapse
Affiliation(s)
| | - Jody C. McKerral
- College of Science and Engineering, Flinders University, Adelaide, Australia
| | | | - Jerzy A. Filar
- School of Mathematics and Physics, University of Queensland, Brisbane, Australia
| | - James G. Mitchell
- College of Science and Engineering, Flinders University, Adelaide, Australia
| |
Collapse
|
19
|
Tang Q, Huang J, Zhang S, Qin H, Dong Y, Wang C, Li D, Zhou R. Characterizing the correlation between species/strain-specific starter with community assembly and metabolic regulation in Xiaoqu Pei. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100170. [DOI: 10.1016/j.crmicr.2022.100170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
20
|
Beura S, Kundu P, Das AK, Ghosh A. Metagenome-scale community metabolic modelling for understanding the role of gut microbiota in human health. Comput Biol Med 2022; 149:105997. [DOI: 10.1016/j.compbiomed.2022.105997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/03/2022] [Accepted: 08/14/2022] [Indexed: 11/03/2022]
|
21
|
Giri S, Yousif G, Shitut S, Oña L, Kost C. Prevalent emergence of reciprocity among cross-feeding bacteria. ISME COMMUNICATIONS 2022; 2:71. [PMID: 37938764 PMCID: PMC9723789 DOI: 10.1038/s43705-022-00155-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/15/2022] [Accepted: 07/05/2022] [Indexed: 05/25/2023]
Abstract
Explaining the de novo evolution of obligate cooperative cross-feeding interactions among bacteria is a fundamental problem. A critical step during this process is the emergence of reciprocity among two interaction partners, because a mutually beneficial exchange of metabolic byproducts can subsequently favour the evolution of cooperative cross-feeding. However, so far, the propensity with which unidirectional cross-feeding interactions transition into bidirectional interactions remains unknown. To address this issue, we systematically cocultured four amino acid auxotrophic genotypes of two bacterial species with potential amino acid donors belonging to 25 different bacterial species. Surprisingly, the results of this experiment revealed that in around 40% of all cases analysed, both the auxotrophic recipient and the metabolically autonomous donor gained a significant growth advantage in coculture. Subsequent experiments clarified that the auxotrophy-causing mutation did not induce the growth-enhancing effect of recipients, but that it was rather due to a generally high propensity of different species to engage in synergistic metabolic interactions. Together, these findings show that reciprocity commonly emerges spontaneously in unidirectional cross-feeding interactions, thus paving the way for the evolution of even tighter metabolic interactions.
Collapse
Affiliation(s)
- Samir Giri
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany.
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, 49076, Osnabrück, Germany.
- Genome Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
| | - Ghada Yousif
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, 49076, Osnabrück, Germany
- Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Shraddha Shitut
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, 49076, Osnabrück, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Leonardo Oña
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, 49076, Osnabrück, Germany
| | - Christian Kost
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany.
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, 49076, Osnabrück, Germany.
| |
Collapse
|
22
|
McAvoy A, Kates-Harbeck J, Chatterjee K, Hilbe C. Evolutionary instability of selfish learning in repeated games. PNAS NEXUS 2022; 1:pgac141. [PMID: 36714856 PMCID: PMC9802390 DOI: 10.1093/pnasnexus/pgac141] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 07/22/2022] [Indexed: 02/01/2023]
Abstract
Across many domains of interaction, both natural and artificial, individuals use past experience to shape future behaviors. The results of such learning processes depend on what individuals wish to maximize. A natural objective is one's own success. However, when two such "selfish" learners interact with each other, the outcome can be detrimental to both, especially when there are conflicts of interest. Here, we explore how a learner can align incentives with a selfish opponent. Moreover, we consider the dynamics that arise when learning rules themselves are subject to evolutionary pressure. By combining extensive simulations and analytical techniques, we demonstrate that selfish learning is unstable in most classical two-player repeated games. If evolution operates on the level of long-run payoffs, selection instead favors learning rules that incorporate social (other-regarding) preferences. To further corroborate these results, we analyze data from a repeated prisoner's dilemma experiment. We find that selfish learning is insufficient to explain human behavior when there is a trade-off between payoff maximization and fairness.
Collapse
Affiliation(s)
| | | | | | - Christian Hilbe
- Max Planck Research Group: Dynamics of Social Behavior, Max Planck Institute for Evolutionary Biology, Plön, Germany
| |
Collapse
|
23
|
Liu Y, Xu P. Quantitative and analytical tools to analyze the spatiotemporal population dynamics of microbial consortia. Curr Opin Biotechnol 2022; 76:102754. [PMID: 35809433 DOI: 10.1016/j.copbio.2022.102754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/30/2022] [Accepted: 06/06/2022] [Indexed: 12/27/2022]
Abstract
Microorganisms occupy almost every niche on earth. They play critical roles in maintaining ecological balance, atmospheric C/N cycle, and human health. Microbes live in consortia with metabolite exchange or signal communication. Quantitative and analytical tools are becoming increasingly important to study microbial consortia dynamics. We argue that a combined reductionist and holistic approach will be important to understanding the assembly rules and spatiotemporal population dynamics of the microbial community (MICOM). Reductionism allows us to reconstruct complex MICOM from isolated or simple synthetic consortia. Holism allows us to understand microbes as a community with cooperation and competition. Here we review the recent development of quantitative and analytical tools to uncover the underlying principles in microbial communities that govern their spatiotemporal change and interaction dynamics. Mathematical models and analytical tools will continue to provide essential knowledge and expand our capability to manipulate and control microbial consortia.
Collapse
Affiliation(s)
- Yugeng Liu
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology, Shantou, Guangdong 515063, China
| | - Peng Xu
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology, Shantou, Guangdong 515063, China; Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion-Israel Institute of Technology, Shantou, Guangdong 515063, China.
| |
Collapse
|
24
|
Bannon C, Rapp I, Bertrand EM. Community Interaction Co-limitation: Nutrient Limitation in a Marine Microbial Community Context. Front Microbiol 2022; 13:846890. [PMID: 35711751 PMCID: PMC9196195 DOI: 10.3389/fmicb.2022.846890] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/29/2022] [Indexed: 11/20/2022] Open
Abstract
The simultaneous limitation of productivity by two or more nutrients, commonly referred to as nutrient co-limitation, affects microbial communities throughout the marine environment and is of profound importance because of its impacts on various biogeochemical cycles. Multiple types of co-limitation have been described, enabling distinctions based on the hypothesized mechanisms of co-limitation at a biochemical level. These definitions usually pertain to individuals and do not explicitly, or even implicitly, consider complex ecological dynamics found within a microbial community. However, limiting and co-limiting nutrients can be produced in situ by a subset of microbial community members, suggesting that interactions within communities can underpin co-limitation. To address this, we propose a new category of nutrient co-limitation, community interaction co-limitation (CIC). During CIC, one part of the community is limited by one nutrient, which results in the insufficient production or transformation of a biologically produced nutrient that is required by another part of the community, often primary producers. Using cobalamin (vitamin B12) and nitrogen fixation as our models, we outline three different ways CIC can arise based on current literature and discuss CIC's role in biogeochemical cycles. Accounting for the inherent and complex roles microbial community interactions play in generating this type of co-limitation requires an expanded toolset - beyond the traditional approaches used to identify and study other types of co-limitation. We propose incorporating processes and theories well-known in microbial ecology and evolution to provide meaningful insight into the controls of community-based feedback loops and mechanisms that give rise to CIC in the environment. Finally, we highlight the data gaps that limit our understanding of CIC mechanisms and suggest methods to overcome these and further identify causes and consequences of CIC. By providing this framework for understanding and identifying CIC, we enable systematic examination of the impacts this co-limitation can have on current and future marine biogeochemical processes.
Collapse
Affiliation(s)
- Catherine Bannon
- Department of Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
| | - Insa Rapp
- Department of Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Marine Biogeochemistry Division, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Erin M. Bertrand
- Department of Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
| |
Collapse
|
25
|
Sepich-Poore GD, Guccione C, Laplane L, Pradeu T, Curtius K, Knight R. Cancer's second genome: Microbial cancer diagnostics and redefining clonal evolution as a multispecies process: Humans and their tumors are not aseptic, and the multispecies nature of cancer modulates clinical care and clonal evolution: Humans and their tumors are not aseptic, and the multispecies nature of cancer modulates clinical care and clonal evolution. Bioessays 2022; 44:e2100252. [PMID: 35253252 PMCID: PMC10506734 DOI: 10.1002/bies.202100252] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 01/31/2022] [Accepted: 02/16/2022] [Indexed: 12/13/2022]
Abstract
The presence and role of microbes in human cancers has come full circle in the last century. Tumors are no longer considered aseptic, but implications for cancer biology and oncology remain underappreciated. Opportunities to identify and build translational diagnostics, prognostics, and therapeutics that exploit cancer's second genome-the metagenome-are manifold, but require careful consideration of microbial experimental idiosyncrasies that are distinct from host-centric methods. Furthermore, the discoveries of intracellular and intra-metastatic cancer bacteria necessitate fundamental changes in describing clonal evolution and selection, reflecting bidirectional interactions with non-human residents. Reconsidering cancer clonality as a multispecies process similarly holds key implications for understanding metastasis and prognosing therapeutic resistance while providing rational guidance for the next generation of bacterial cancer therapies. Guided by these new findings and challenges, this Review describes opportunities to exploit cancer's metagenome in oncology and proposes an evolutionary framework as a first step towards modeling multispecies cancer clonality. Also see the video abstract here: https://youtu.be/-WDtIRJYZSs.
Collapse
Affiliation(s)
| | - Caitlin Guccione
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Lucie Laplane
- Institut d’histoire et de philosophie des sciences et des techniques (UMR8590), CNRS & Panthéon-Sorbonne University, 75006 Paris, France
- Hematopoietic stem cells and the development of myeloid malignancies (UMR1287), Gustave Roussy Cancer Campus, 94800 Villejuif, France
| | - Thomas Pradeu
- ImmunoConcept (UMR5164), CNRS & University of Bordeaux, 33076 Bordeaux Cedex, France
| | - Kit Curtius
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| |
Collapse
|
26
|
Oña L, Kost C. Cooperation increases robustness to ecological disturbance in microbial cross-feeding networks. Ecol Lett 2022; 25:1410-1420. [PMID: 35384221 DOI: 10.1111/ele.14006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 01/26/2022] [Accepted: 02/22/2022] [Indexed: 12/19/2022]
Abstract
Microorganisms mainly exist within complex networks of ecological interactions. Given that the growth and survival of community members frequently depend on an obligate exchange of essential metabolites, it is generally unclear how such communities can persist despite the destabilising force of ecological disturbance. Here we address this issue using a population dynamics model. In contrast to previous work that suggests the potential for obligate interaction networks to emerge is limited, we find the opposite pattern: ecological disturbance favours both specific network topologies and cooperative cross-feeding among community members. These results establish environmental perturbations as a key driver shaping the architecture of microbial interaction networks.
Collapse
Affiliation(s)
- Leonardo Oña
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
| | - Christian Kost
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
| |
Collapse
|
27
|
Moran MA, Kujawinski EB, Schroer WF, Amin SA, Bates NR, Bertrand EM, Braakman R, Brown CT, Covert MW, Doney SC, Dyhrman ST, Edison AS, Eren AM, Levine NM, Li L, Ross AC, Saito MA, Santoro AE, Segrè D, Shade A, Sullivan MB, Vardi A. Microbial metabolites in the marine carbon cycle. Nat Microbiol 2022; 7:508-523. [PMID: 35365785 DOI: 10.1038/s41564-022-01090-3] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/23/2022] [Indexed: 01/08/2023]
Abstract
One-quarter of photosynthesis-derived carbon on Earth rapidly cycles through a set of short-lived seawater metabolites that are generated from the activities of marine phytoplankton, bacteria, grazers and viruses. Here we discuss the sources of microbial metabolites in the surface ocean, their roles in ecology and biogeochemistry, and approaches that can be used to analyse them from chemistry, biology, modelling and data science. Although microbial-derived metabolites account for only a minor fraction of the total reservoir of marine dissolved organic carbon, their flux and fate underpins the central role of the ocean in sustaining life on Earth.
Collapse
Affiliation(s)
- Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, USA.
| | - Elizabeth B Kujawinski
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| | - William F Schroer
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Shady A Amin
- Division of Science, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Nicholas R Bates
- Bermuda Institute of Ocean Sciences, St George's, Bermuda.,School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - Erin M Bertrand
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Rogier Braakman
- Departments of Earth, Atmospheric and Planetary Sciences, and Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - C Titus Brown
- Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Scott C Doney
- Department of Environmental Sciences, University of Virginia, Charlottesville, VA, USA
| | - Sonya T Dyhrman
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, USA.,Department of Earth and Environmental Science, Columbia University, Palisades, NY, USA
| | - Arthur S Edison
- Departments of Biochemistry and Genetics, Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - A Murat Eren
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA.,Helmholtz-Institute for Functional Marine Biodiversity (HIFMB), University of Oldenburg, Oldenburg, Germany
| | - Naomi M Levine
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, Ontario, Canada
| | - Mak A Saito
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Alyson E Santoro
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
| | - Daniel Segrè
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA, USA
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental, and Geodetic Engineering, and Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
28
|
Bombin A, Yan S, Bombin S, Mosley JD, Ferguson JF. Obesity influences composition of salivary and fecal microbiota and impacts the interactions between bacterial taxa. Physiol Rep 2022; 10:e15254. [PMID: 35384379 PMCID: PMC8980904 DOI: 10.14814/phy2.15254] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 03/04/2022] [Accepted: 03/17/2022] [Indexed: 04/23/2023] Open
Abstract
Obesity is an increasing global health concern and is associated with a broad range of morbidities. The gut microbiota are increasingly recognized as important contributors to obesity and cardiometabolic health. This study aimed to characterize oral and gut microbial communities, and evaluate host: microbiota interactions between clinical obesity classifications. We performed 16S rRNA sequencing on fecal and salivary samples, global metabolomics profiling on plasma and stool samples, and dietary profiling in 135 healthy individuals. We grouped individuals by obesity status, based on body mass index (BMI), including lean (BMI 18-124.9), overweight (BMI 25-29.9), or obese (BMI ≥30). We analyzed differences in microbiome composition, community inter-relationships, and predicted microbial function by obesity status. We found that salivary bacterial communities of lean and obese individuals were compositionally and phylogenetically distinct. An increase in obesity status was positively associated with strong correlations between bacterial taxa, particularly with bacterial groups implicated in metabolic disorders including Fretibacterium, and Tannerella. Consumption of sweeteners, especially xylitol, significantly influenced compositional and phylogenetic diversities of salivary and fecal bacterial communities. In addition, obesity groups exhibited differences in predicted bacterial metabolic activity, which was correlated with host's metabolite concentrations. Overall, obesity was associated with distinct changes in bacterial community dynamics, particularly in saliva. Consideration of microbiome community structure and inclusion of salivary samples may improve our ability to understand pathways linking microbiota to obesity and cardiometabolic disease.
Collapse
Affiliation(s)
- Andrei Bombin
- Division of Clinical PharmacologyDepartment of MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Shun Yan
- Department of GeneticsThe University of AlabamaBirminghamAlabamaUSA
| | - Sergei Bombin
- Department of Biological SciencesThe University of AlabamaTuscaloosaAlabamaUSA
| | - Jonathan D. Mosley
- Division of Clinical PharmacologyDepartment of MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of Biomedical InformaticsVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Jane F. Ferguson
- Division of Cardiovascular MedicineDepartment of MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
- Vanderbilt Microbiome Innovation Center (VMIC)NashvilleTennesseeUSA
| |
Collapse
|
29
|
Wendering P, Nikoloski Z. COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions. PLoS Comput Biol 2022; 18:e1009906. [PMID: 35320266 PMCID: PMC8942231 DOI: 10.1371/journal.pcbi.1009906] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 02/09/2022] [Indexed: 11/18/2022] Open
Abstract
Composition and functions of microbial communities affect important traits in diverse hosts, from crops to humans. Yet, mechanistic understanding of how metabolism of individual microbes is affected by the community composition and metabolite leakage is lacking. Here, we first show that the consensus of automatically generated metabolic reconstructions improves the quality of the draft reconstructions, measured by comparison to reference models. We then devise an approach for gap filling, termed COMMIT, that considers metabolites for secretion based on their permeability and the composition of the community. By applying COMMIT with two soil communities from the Arabidopsis thaliana culture collection, we could significantly reduce the gap-filling solution in comparison to filling gaps in individual reconstructions without affecting the genomic support. Inspection of the metabolic interactions in the soil communities allows us to identify microbes with community roles of helpers and beneficiaries. Therefore, COMMIT offers a versatile fully automated solution for large-scale modelling of microbial communities for diverse biotechnological applications.
Collapse
Affiliation(s)
- Philipp Wendering
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Zoran Nikoloski
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- * E-mail:
| |
Collapse
|
30
|
Network Reconstruction and Modelling Made Reproducible with moped. Metabolites 2022; 12:metabo12040275. [PMID: 35448462 PMCID: PMC9032245 DOI: 10.3390/metabo12040275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/24/2022] [Accepted: 03/15/2022] [Indexed: 11/23/2022] Open
Abstract
Mathematical modeling of metabolic networks is a powerful approach to investigate the underlying principles of metabolism and growth. Such approaches include, among others, differential-equation-based modeling of metabolic systems, constraint-based modeling and metabolic network expansion of metabolic networks. Most of these methods are well established and are implemented in numerous software packages, but these are scattered between different programming languages, packages and syntaxes. This complicates establishing straight forward pipelines integrating model construction and simulation. We present a Python package moped that serves as an integrative hub for reproducible construction, modification, curation and analysis of metabolic models. moped supports draft reconstruction of models directly from genome/proteome sequences and pathway/genome databases utilizing GPR annotations, providing a completely reproducible model construction and curation process within executable Python scripts. Alternatively, existing models published in SBML format can be easily imported. Models are represented as Python objects, for which a wide spectrum of easy-to-use modification and analysis methods exist. The model structure can be manually altered by adding, removing or modifying reactions, and gap-filling reactions can be found and inspected. This greatly supports the development of draft models, as well as the curation and testing of models. Moreover, moped provides several analysis methods, in particular including the calculation of biosynthetic capacities using metabolic network expansion. The integration with other Python-based tools is facilitated through various model export options. For example, a model can be directly converted into a CobraPy object for constraint-based analyses. moped is a fully documented and expandable Python package. We demonstrate the capability to serve as a hub for integrating reproducible model construction and curation, database import, metabolic network expansion and export for constraint-based analyses.
Collapse
|
31
|
Mall A, Kasarlawar S, Saini S. Limited Pairwise Synergistic and Antagonistic Interactions Impart Stability to Microbial Communities. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.648997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
One of the central goals of ecology is to explain and predict coexistence of species. In this context, microbial communities provide a model system where community structure can be studied in environmental niches and in laboratory conditions. A community of microbial population is stabilized by interactions between participating species. However, the nature of these stabilizing interactions has remained largely unknown. Theory and experiments have suggested that communities are stabilized by antagonistic interactions between member species, and destabilized by synergistic interactions. However, experiments have also revealed that a large fraction of all the interactions between species in a community are synergistic in nature. To understand the relative significance of the two types of interactions (synergistic vs. antagonistic) between species, we perform simulations of microbial communities with a small number of participating species using two frameworks—a replicator equation and a Lotka-Volterra framework. Our results demonstrate that synergistic interactions between species play a critical role in maintaining diversity in cultures. These interactions are critical for the ability of the communities to survive perturbations and maintain diversity. We follow up the simulations with quantification of the extent to which synergistic and antagonistic interactions are present in a bacterial community present in a soil sample. Overall, our results show that community stability is largely achieved with the help of synergistic interactions between participating species. However, we perform experiments to demonstrate that antagonistic interactions, in specific circumstances, can also contribute toward community stability.
Collapse
|
32
|
A Single-Cell Omics Network Model of Cell Crosstalk during the Formation of Primordial Follicles. Cells 2022; 11:cells11030332. [PMID: 35159142 PMCID: PMC8834074 DOI: 10.3390/cells11030332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/04/2022] [Accepted: 01/11/2022] [Indexed: 12/27/2022] Open
Abstract
The fate of fetal germ cells (FGCs) in primordial follicles is largely determined by how they interact with the surrounding granulosa cells. However, the molecular mechanisms underlying this interactive process remain poorly understood. Here, we develop a computational model to characterize how individual genes program and rewire cellular crosstalk across FGCs and somas, how gene regulatory networks mediate signaling pathways that functionally link these two cell types, and how different FGCs diversify and evolve through cooperation and competition during embryo development. We analyze single-cell RNA-seq data of human female embryos using the new model, identifying previously uncharacterized mechanisms behind follicle development. The majority of genes (70%) promote FGC–soma synergism, only with a small portion (4%) that incur antagonism; hub genes function reciprocally between the FGC network and soma network; and germ cells tend to cooperate between different stages of development but compete in the same stage within a developmental embryo. Our network model could serve as a powerful tool to unravel the genomic signatures that mediate folliculogenesis from single-cell omics data.
Collapse
|
33
|
Mataigne V, Vannier N, Vandenkoornhuyse P, Hacquard S. Microbial Systems Ecology to Understand Cross-Feeding in Microbiomes. Front Microbiol 2021; 12:780469. [PMID: 34987488 PMCID: PMC8721230 DOI: 10.3389/fmicb.2021.780469] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/25/2021] [Indexed: 12/26/2022] Open
Abstract
Understanding how microorganism-microorganism interactions shape microbial assemblages is a key to deciphering the evolution of dependencies and co-existence in complex microbiomes. Metabolic dependencies in cross-feeding exist in microbial communities and can at least partially determine microbial community composition. To parry the complexity and experimental limitations caused by the large number of possible interactions, new concepts from systems biology aim to decipher how the components of a system interact with each other. The idea that cross-feeding does impact microbiome assemblages has developed both theoretically and empirically, following a systems biology framework applied to microbial communities, formalized as microbial systems ecology (MSE) and relying on integrated-omics data. This framework merges cellular and community scales and offers new avenues to untangle microbial coexistence primarily by metabolic modeling, one of the main approaches used for mechanistic studies. In this mini-review, we first give a concise explanation of microbial cross-feeding. We then discuss how MSE can enable progress in microbial research. Finally, we provide an overview of a MSE framework mostly based on genome-scale metabolic-network reconstruction that combines top-down and bottom-up approaches to assess the molecular mechanisms of deterministic processes of microbial community assembly that is particularly suitable for use in synthetic biology and microbiome engineering.
Collapse
Affiliation(s)
- Victor Mataigne
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Rennes, France
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Nathan Vannier
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Rennes, France
| | | | | |
Collapse
|
34
|
Tan P, Liu H, Zhao J, Gu X, Wei X, Zhang X, Ma N, Johnston LJ, Bai Y, Zhang W, Nie C, Ma X. Amino acids metabolism by rumen microorganisms: Nutrition and ecology strategies to reduce nitrogen emissions from the inside to the outside. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 800:149596. [PMID: 34426337 DOI: 10.1016/j.scitotenv.2021.149596] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 06/13/2023]
Abstract
For the ruminant animal industry, the emission of nitrogenous substances, such as nitrous oxide (N2O) and ammonia (NH3), not only challenges environmental sustainability but also restricts its development. The metabolism of proteins and amino acids by rumen microorganisms is a key factor affecting nitrogen (N) excretion in ruminant animals. Rumen microorganisms that affect N excretion mainly include three types: proteolytic and peptidolytic bacteria (PPB), ureolytic bacteria (UB), and hyper-ammonia-producing bacteria (HAB). Microbes residing in the rumen, however, are influenced by several complex factors, such as diet, which results in fluctuations in the rumen metabolism of proteins and amino acids and ultimately affects N emission. Combining feed nutrition strategies (including ingredient adjustment and feed additives) and ecological mitigation strategies of N2O and NH3 in industrial practice can reduce the emission of nitrogenous pollutants from the ruminant breeding industry. In this review, the characteristics of the rumen microbial community related to N metabolism in ruminants were used as the metabolic basis. Furthermore, an effective strategy to increase N utilisation efficiency in combination with nutrition and ecology was reviewed to provide an inside-out approach to reduce N emissions from ruminants.
Collapse
Affiliation(s)
- Peng Tan
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Han Liu
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832000, China; College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Jing Zhao
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832000, China; College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Xueling Gu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xiaobing Wei
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Xiaojian Zhang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Ning Ma
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Lee J Johnston
- West Central Research & Outreach Center, University of Minnesota, Morris, MN 56267, USA
| | - Yueyu Bai
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Wenju Zhang
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832000, China
| | - Cunxi Nie
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832000, China
| | - Xi Ma
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832000, China.
| |
Collapse
|
35
|
Predicting Microbiome Metabolism and Interactions through Integrating Multidisciplinary Principles. mSystems 2021; 6:e0076821. [PMID: 34609169 PMCID: PMC8547421 DOI: 10.1128/msystems.00768-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
In this Commentary, we will discuss some of the current trends and challenges in modeling microbiome metabolism. A focus will be the state of the art in the integration of metabolic networks, ecological and evolutionary principles, and spatiotemporal considerations, followed by envisioning integrated frameworks incorporating different principles and data to generate predictive models in the future.
Collapse
|
36
|
Yao J, Zeng Y, Wang M, Tang YQ. Energy Availability Determines Strategy of Microbial Amino Acid Synthesis in Volatile Fatty Acid-Fed Anaerobic Methanogenic Chemostats. Front Microbiol 2021; 12:744834. [PMID: 34671332 PMCID: PMC8521154 DOI: 10.3389/fmicb.2021.744834] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/30/2021] [Indexed: 12/03/2022] Open
Abstract
In natural communities, microbes exchange a variety of metabolites (public goods) with each other, which drives the evolution of auxotroph and shapes interdependent patterns at community-level. However, factors that determine the strategy of public goods synthesis for a given community member still remains to be elucidated. In anaerobic methanogenic communities, energy availability of different community members is largely varied. We hypothesized that this uneven energy availability contributed to the heterogeneity of public goods synthesis ability among the members in these communities. We tested this hypothesis by analyzing the synthetic strategy of amino acids of the bacterial and archaeal members involved in four previously enriched anaerobic methanogenic communities residing in thermophilic chemostats. Our analyses indicate that most of the members in the communities did not possess ability to synthesize all the essential amino acids, suggesting they exchanged these essential public goods to establish interdependent patterns for survival. Importantly, we found that the amino acid synthesis ability of a functional group was largely determined by how much energy it could obtain from its metabolism in the given environmental condition. Moreover, members within a functional group also possessed different amino acid synthesis abilities, which are related to their features of energy metabolism. Our study reveals that energy availability is a key driver of microbial evolution in presence of metabolic specialization at community level and suggests the feasibility of managing anaerobic methanogenic communities for better performance through controlling the metabolic interactions involved.
Collapse
Affiliation(s)
| | | | - Miaoxiao Wang
- College of Architecture and Environment, Sichuan University, Chengdu, China
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, Chengdu, China
| |
Collapse
|
37
|
Cell Growth Model with Stochastic Gene Expression Helps Understand the Growth Advantage of Metabolic Exchange and Auxotrophy. mSystems 2021; 6:e0044821. [PMID: 34342540 PMCID: PMC8407474 DOI: 10.1128/msystems.00448-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During cooperative growth, microbes often experience higher fitness by sharing resources via metabolite exchange. How competitive species evolve to cooperate is, however, not known. Moreover, existing models (based on optimization of steady-state resources or fluxes) are often unable to explain the growth advantage for the cooperating species, even for simple reciprocally cross-feeding auxotrophic pairs. We present here an abstract model of cell growth that considers the stochastic burst-like gene expression of biosynthetic pathways of limiting biomass precursor metabolites and directly connect the amount of metabolite produced to cell growth and division, using a "metabolic sizer/adder" rule. Our model recapitulates Monod's law and yields the experimentally observed right-skewed long-tailed distribution of cell doubling times. The model further predicts the growth effect of secretion and uptake of metabolites by linking it to changes in the internal metabolite levels. The model also explains why auxotrophs may grow faster when supplied with the metabolite they cannot produce and why two reciprocally cross-feeding auxotrophs can grow faster than prototrophs. Overall, our framework allows us to predict the growth effect of metabolic interactions in independent microbes and microbial communities, setting up the stage to study the evolution of these interactions. IMPORTANCE Cooperative behaviors are highly prevalent in the wild, but their evolution is not understood. Metabolic flux models can demonstrate the viability of metabolic exchange as cooperative interactions, but steady-state growth models cannot explain why cooperators grow faster. We present a stochastic model that connects growth to the cell's internal metabolite levels and quantifies the growth effect of metabolite exchange and auxotrophy. We show that a reduction in gene expression noise can explain why cells that import metabolites or become auxotrophs can grow faster and why reciprocal cross-feeding of metabolites between complementary auxotrophs allows them to grow faster. Furthermore, our framework can simulate the growth of interacting cells, which will enable us to understand the possible trajectories of the evolution of cooperation in silico.
Collapse
|
38
|
Qian Y, Lan F, Venturelli OS. Towards a deeper understanding of microbial communities: integrating experimental data with dynamic models. Curr Opin Microbiol 2021; 62:84-92. [PMID: 34098512 PMCID: PMC8286325 DOI: 10.1016/j.mib.2021.05.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/03/2021] [Accepted: 05/06/2021] [Indexed: 12/15/2022]
Abstract
Microbial communities and their functions are shaped by complex networks of interactions among microbes and with their environment. While the critical roles microbial communities play in numerous environments have become increasingly appreciated, we have a very limited understanding of their interactions and how these interactions combine to generate community-level behaviors. This knowledge gap hinders our ability to predict community responses to perturbations and to design interventions that manipulate these communities to our benefit. Dynamic models are promising tools to address these questions. We review existing modeling techniques to construct dynamic models of microbial communities at different scales and suggest ways to leverage multiple types of models and data to facilitate our understanding and engineering of microbial communities.
Collapse
Affiliation(s)
- Yili Qian
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Freeman Lan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Ophelia S Venturelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States; Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, United States.
| |
Collapse
|
39
|
Tuganbaev T, Honda K. Non-zero-sum microbiome immune system interactions. Eur J Immunol 2021; 51:2120-2136. [PMID: 34242413 PMCID: PMC8457126 DOI: 10.1002/eji.202049065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 06/01/2021] [Accepted: 07/08/2021] [Indexed: 12/14/2022]
Abstract
Fundamental asymmetries between the host and its microbiome in enzymatic activities and nutrient storage capabilities have promoted mutualistic adaptations on both sides. As a result, the enteric immune system has evolved so as not to cause a zero‐sum sterilization of non‐self, but rather achieve a non‐zero‐sum self‐reinforcing cooperation with its evolutionary partner the microbiome. In this review, we attempt to integrate the accumulated knowledge of immune—microbiome interactions into an evolutionary framework and trace the pattern of positive immune—microbiome feedback loops across epithelial, enteric nervous system, innate, and adaptive immune circuits. Indeed, the immune system requires commensal signals for its development and function, and reciprocally protects the microbiome from nutrient shortage and pathogen outgrowth. In turn, a healthy microbiome is the result of immune system curatorship as well as microbial ecology. The paradigms of host–microbiome asymmetry and the cooperative nature of their interactions identified in the gut are applicable across all tissues influenced by microbial activities. Incorporation of immune system influences into models of microbiome ecology will be a step forward toward defining what constitutes a healthy human microbiome and guide discoveries of novel host–microbiome mutualistic adaptations that may be harnessed for the promotion of human health.
Collapse
Affiliation(s)
- Timur Tuganbaev
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Kenya Honda
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan.,RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| |
Collapse
|
40
|
Leggieri PA, Liu Y, Hayes M, Connors B, Seppälä S, O'Malley MA, Venturelli OS. Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes. Annu Rev Biomed Eng 2021; 23:169-201. [PMID: 33781078 PMCID: PMC8277735 DOI: 10.1146/annurev-bioeng-082120-022836] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Microbiomes are complex and ubiquitous networks of microorganisms whose seemingly limitless chemical transformations could be harnessed to benefit agriculture, medicine, and biotechnology. The spatial and temporal changes in microbiome composition and function are influenced by a multitude of molecular and ecological factors. This complexity yields both versatility and challenges in designing synthetic microbiomes and perturbing natural microbiomes in controlled, predictable ways. In this review, we describe factors that give rise to emergent spatial and temporal microbiome properties and the meta-omics and computational modeling tools that can be used to understand microbiomes at the cellular and system levels. We also describe strategies for designing and engineering microbiomes to enhance or build novel functions. Throughout the review, we discuss key knowledge and technology gaps for elucidating the networks and deciphering key control points for microbiome engineering, and highlight examples where multiple omics and modeling approaches can be integrated to address these gaps.
Collapse
Affiliation(s)
- Patrick A Leggieri
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Yiyi Liu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Madeline Hayes
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
| | - Bryce Connors
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Susanna Seppälä
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Ophelia S Venturelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| |
Collapse
|
41
|
Dillard LR, Payne DD, Papin JA. Mechanistic models of microbial community metabolism. Mol Omics 2021; 17:365-375. [PMID: 34125127 PMCID: PMC8202304 DOI: 10.1039/d0mo00154f] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 02/25/2021] [Indexed: 11/21/2022]
Abstract
Microbial communities affect many facets of human health and well-being. Naturally occurring bacteria, whether in nature or the human body, rarely exist in isolation. A deeper understanding of the metabolic functions of these communities is now possible with emerging computational models. In this review, we summarize frameworks for constructing mechanistic models of microbial community metabolism and discuss available algorithms for model analysis. We highlight essential decision points that greatly influence algorithm selection, as well as model analysis. Polymicrobial metabolic models can be utilized to gain insights into host-pathogen interactions, bacterial engineering, and many more translational applications.
Collapse
Affiliation(s)
- Lillian R. Dillard
- Department of Biochemistry and Molecular Genetics, University of VirginiaCharlottesvilleVA 22908USA
| | - Dawson D. Payne
- Department of Biomedical Engineering, University of VirginiaBox 800759, Health SystemCharlottesvilleVA 22908USA
| | - Jason A. Papin
- Department of Biochemistry and Molecular Genetics, University of VirginiaCharlottesvilleVA 22908USA
- Department of Biomedical Engineering, University of VirginiaBox 800759, Health SystemCharlottesvilleVA 22908USA
| |
Collapse
|
42
|
Yamagishi JF, Saito N, Kaneko K. Adaptation of metabolite leakiness leads to symbiotic chemical exchange and to a resilient microbial ecosystem. PLoS Comput Biol 2021; 17:e1009143. [PMID: 34161322 PMCID: PMC8260005 DOI: 10.1371/journal.pcbi.1009143] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/06/2021] [Accepted: 06/03/2021] [Indexed: 02/03/2023] Open
Abstract
Microbial communities display remarkable diversity, facilitated by the secretion of chemicals that can create new niches. However, it is unclear why cells often secrete even essential metabolites after evolution. Based on theoretical results indicating that cells can enhance their own growth rate by leaking even essential metabolites, we show that such "leaker" cells can establish an asymmetric form of mutualism with "consumer" cells that consume the leaked chemicals: the consumer cells benefit from the uptake of the secreted metabolites, while the leaker cells also benefit from such consumption, as it reduces the metabolite accumulation in the environment and thereby enables further secretion, resulting in frequency-dependent coexistence of multiple microbial species. As supported by extensive simulations, such symbiotic relationships generally evolve when each species has a complex reaction network and adapts its leakiness to optimize its own growth rate under crowded conditions and nutrient limitations. Accordingly, symbiotic ecosystems with diverse cell species that leak and exchange many metabolites with each other are shaped by cell-level adaptation of leakiness of metabolites. Moreover, the resultant ecosystems with entangled metabolite exchange are resilient against structural and environmental perturbations. Thus, we present a theory for the origin of resilient ecosystems with diverse microbes mediated by secretion and exchange of essential chemicals.
Collapse
Affiliation(s)
- Jumpei F. Yamagishi
- Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Nen Saito
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- Research Center for Complex Systems Biology, Universal Biology Institute, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Kunihiko Kaneko
- Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
- Research Center for Complex Systems Biology, Universal Biology Institute, The University of Tokyo, Meguro-ku, Tokyo, Japan
| |
Collapse
|
43
|
Johnson B, Altrock PM, Kimmel GJ. Two-dimensional adaptive dynamics of evolutionary public goods games: finite-size effects on fixation probability and branching time. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210182. [PMID: 34084549 PMCID: PMC8150049 DOI: 10.1098/rsos.210182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
Public goods games (PGGs) describe situations in which individuals contribute to a good at a private cost, but others can free-ride by receiving a share of the public benefit at no cost. The game occurs within local neighbourhoods, which are subsets of the whole population. Free-riding and maximal production are two extremes of a continuous spectrum of traits. We study the adaptive dynamics of production and neighbourhood size. We allow the public good production and the neighbourhood size to coevolve and observe evolutionary branching. We explain how an initially monomorphic population undergoes evolutionary branching in two dimensions to become a dimorphic population characterized by extremes of the spectrum of trait values. We find that population size plays a crucial role in determining the final state of the population. Small populations may not branch or may be subject to extinction of a subpopulation after branching. In small populations, stochastic effects become important and we calculate the probability of subpopulation extinction. Our work elucidates the evolutionary origins of heterogeneity in local PGGs among individuals of two traits (production and neighbourhood size), and the effects of stochasticity in two-dimensional trait space, where novel effects emerge.
Collapse
Affiliation(s)
- Brian Johnson
- Department of Integrated Mathematical Oncology, H. Lee Moffit Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Philipp M. Altrock
- Department of Integrated Mathematical Oncology, H. Lee Moffit Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Gregory J. Kimmel
- Department of Integrated Mathematical Oncology, H. Lee Moffit Cancer Center and Research Institute, Tampa, FL 33612, USA
| |
Collapse
|
44
|
Wang M, Liu X, Nie Y, Wu XL. Selfishness driving reductive evolution shapes interdependent patterns in spatially structured microbial communities. THE ISME JOURNAL 2021; 15:1387-1401. [PMID: 33343001 PMCID: PMC8115099 DOI: 10.1038/s41396-020-00858-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 11/14/2020] [Accepted: 11/24/2020] [Indexed: 12/28/2022]
Abstract
Microbes release a wide variety of metabolites to the environment that benefit the whole population, called public goods. Public goods sharing drives adaptive function loss, and allows the rise of metabolic cross-feeding. However, how public goods sharing governs the succession of communities over evolutionary time scales remains unclear. To resolve this issue, we constructed an individual-based model, where an autonomous population that possessed functions to produce three essential public goods, was allowed to randomly lose functions. Simulations revealed that function loss genotypes could evolve from the autonomous ancestor, driven by the selfish public production trade-off at the individual level. These genotypes could then automatically develop to three possible types of interdependent patterns: complete functional division, one-way dependency, and asymmetric functional complementation, which were influenced by function cost and function redundancy. In addition, we found random evolutionary events, i.e., the priority and the relative spatial positioning of genotype emergence, are also important in governing community assembly. Moreover, communities occupied by interdependent patterns exhibited better resistance to environmental perturbation, suggesting such patterns are selectively favored. Our work integrates ecological interactions with evolution dynamics, providing a new perspective to explain how reductive evolution shapes microbial interdependencies and governs the succession of communities.
Collapse
Affiliation(s)
- Miaoxiao Wang
- College of Engineering, Peking University, 100871, Beijing, China
| | - Xiaonan Liu
- College of Engineering, Peking University, 100871, Beijing, China
| | - Yong Nie
- College of Engineering, Peking University, 100871, Beijing, China.
| | - Xiao-Lei Wu
- College of Engineering, Peking University, 100871, Beijing, China.
- Institute of Ocean Research, Peking University, 100871, Beijing, China.
- Institute of Ecology, Peking University, 100871, Beijing, China.
| |
Collapse
|
45
|
Saraiva JP, Worrich A, Karakoç C, Kallies R, Chatzinotas A, Centler F, Nunes da Rocha U. Mining Synergistic Microbial Interactions: A Roadmap on How to Integrate Multi-Omics Data. Microorganisms 2021; 9:microorganisms9040840. [PMID: 33920040 PMCID: PMC8070991 DOI: 10.3390/microorganisms9040840] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/13/2021] [Accepted: 04/08/2021] [Indexed: 11/24/2022] Open
Abstract
Mining interspecies interactions remain a challenge due to the complex nature of microbial communities and the need for computational power to handle big data. Our meta-analysis indicates that genetic potential alone does not resolve all issues involving mining of microbial interactions. Nevertheless, it can be used as the starting point to infer synergistic interspecies interactions and to limit the search space (i.e., number of species and metabolic reactions) to a manageable size. A reduced search space decreases the number of additional experiments necessary to validate the inferred putative interactions. As validation experiments, we examine how multi-omics and state of the art imaging techniques may further improve our understanding of species interactions’ role in ecosystem processes. Finally, we analyze pros and cons from the current methods to infer microbial interactions from genetic potential and propose a new theoretical framework based on: (i) genomic information of key members of a community; (ii) information of ecosystem processes involved with a specific hypothesis or research question; (iii) the ability to identify putative species’ contributions to ecosystem processes of interest; and, (iv) validation of putative microbial interactions through integration of other data sources.
Collapse
Affiliation(s)
- Joao Pedro Saraiva
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Anja Worrich
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Canan Karakoç
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Rene Kallies
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, 04103 Leipzig, Germany
| | - Florian Centler
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- Correspondence:
| |
Collapse
|
46
|
Liu F, Giometto A, Wu M. Microfluidic and mathematical modeling of aquatic microbial communities. Anal Bioanal Chem 2021; 413:2331-2344. [PMID: 33244684 PMCID: PMC7990691 DOI: 10.1007/s00216-020-03085-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/05/2020] [Accepted: 11/19/2020] [Indexed: 01/27/2023]
Abstract
Aquatic microbial communities contribute fundamentally to biogeochemical transformations in natural ecosystems, and disruption of these communities can lead to ecological disasters such as harmful algal blooms. Microbial communities are highly dynamic, and their composition and function are tightly controlled by the biophysical (e.g., light, fluid flow, and temperature) and biochemical (e.g., chemical gradients and cell concentration) parameters of the surrounding environment. Due to the large number of environmental factors involved, a systematic understanding of the microbial community-environment interactions is lacking. In this article, we show that microfluidic platforms present a unique opportunity to recreate well-defined environmental factors in a laboratory setting in a high throughput way, enabling quantitative studies of microbial communities that are amenable to theoretical modeling. The focus of this article is on aquatic microbial communities, but the microfluidic and mathematical models discussed here can be readily applied to investigate other microbiomes.
Collapse
Affiliation(s)
- Fangchen Liu
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Andrea Giometto
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Mingming Wu
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, 14853, USA.
| |
Collapse
|
47
|
García-Jiménez B, Torres-Bacete J, Nogales J. Metabolic modelling approaches for describing and engineering microbial communities. Comput Struct Biotechnol J 2020; 19:226-246. [PMID: 33425254 PMCID: PMC7773532 DOI: 10.1016/j.csbj.2020.12.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 12/02/2020] [Accepted: 12/05/2020] [Indexed: 12/17/2022] Open
Abstract
Microbes do not live in isolation but in microbial communities. The relevance of microbial communities is increasing due to growing awareness of their influence on a huge number of environmental, health and industrial processes. Hence, being able to control and engineer the output of both natural and synthetic communities would be of great interest. However, most of the available methods and biotechnological applications involving microorganisms, both in vivo and in silico, have been developed in the context of isolated microbes. In vivo microbial consortia development is extremely difficult and costly because it implies replicating suitable environments in the wet-lab. Computational approaches are thus a good, cost-effective alternative to study microbial communities, mainly via descriptive modelling, but also via engineering modelling. In this review we provide a detailed compilation of examples of engineered microbial communities and a comprehensive, historical revision of available computational metabolic modelling methods to better understand, and rationally engineer wild and synthetic microbial communities.
Collapse
Affiliation(s)
- Beatriz García-Jiménez
- Department of Systems Biology, Centro Nacional de Biotecnología (CSIC), 28049 Madrid, Spain
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo-UPM, 28223-Pozuelo de Alarcón, Madrid, Spain
| | - Jesús Torres-Bacete
- Department of Systems Biology, Centro Nacional de Biotecnología (CSIC), 28049 Madrid, Spain
| | - Juan Nogales
- Department of Systems Biology, Centro Nacional de Biotecnología (CSIC), 28049 Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC), Madrid, Spain
| |
Collapse
|
48
|
Cai J, Tan T, Joshua Chan SH. Predicting Nash equilibria for microbial metabolic interactions. Bioinformatics 2020; 36:5649-5655. [PMID: 33315094 DOI: 10.1093/bioinformatics/btaa1014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 11/15/2020] [Accepted: 11/24/2020] [Indexed: 12/16/2022] Open
Abstract
MOTIVATION Microbial metabolic interactions impact ecosystems, human health and biotechnology profoundly. However, their determination remains elusive, invoking an urgent need for predictive models seamlessly integrating metabolism with evolutionary principles that shape community interactions. RESULTS Inspired by the evolutionary game theory, we formulated a bi-level optimization framework termed NECom for which any feasible solutions are Nash equilibria of microbial community metabolic models with/without an outer-level (community) objective function. Distinct from discrete matrix games, NECom models the continuous interdependent strategy space of metabolic fluxes. We showed that NECom successfully predicted several classical games in the context of metabolic interactions that were falsely or incompletely predicted by existing methods, including prisoner's dilemma, snowdrift and cooperation. The improved capability originates from the novel formulation to prevent 'forced altruism' hidden in previous static algorithms while allowing for sensing all potential metabolite exchanges to determine evolutionarily favorable interactions between members, a feature missing in dynamic methods. The results provided insights into why mutualism is favorable despite seemingly costly cross-feeding metabolites and demonstrated similarities and differences between games in the continuous metabolic flux space and matrix games. NECom was then applied to a reported algae-yeast co-culture system that shares typical cross-feeding features of lichen, a model system of mutualism. 488 growth conditions corresponding to 3,221 experimental data points were simulated. Without training any parameters using the data, NECom is more predictive of species' growth rates given uptake rates compared with flux balance analysis with an overall 63.5% and 81.7% reduction in root-mean-square error for the two species. AVAILABILITY Simulation code and data are available at https://github.com/Jingyi-Cai/NECom.git. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Jingyi Cai
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing, China
| | - Tianwei Tan
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing, China
| | - S H Joshua Chan
- Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, USA
| |
Collapse
|
49
|
Fang X, Lloyd CJ, Palsson BO. Reconstructing organisms in silico: genome-scale models and their emerging applications. Nat Rev Microbiol 2020; 18:731-743. [PMID: 32958892 PMCID: PMC7981288 DOI: 10.1038/s41579-020-00440-4] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2020] [Indexed: 02/06/2023]
Abstract
Escherichia coli is considered to be the best-known microorganism given the large number of published studies detailing its genes, its genome and the biochemical functions of its molecular components. This vast literature has been systematically assembled into a reconstruction of the biochemical reaction networks that underlie E. coli's functions, a process which is now being applied to an increasing number of microorganisms. Genome-scale reconstructed networks are organized and systematized knowledge bases that have multiple uses, including conversion into computational models that interpret and predict phenotypic states and the consequences of environmental and genetic perturbations. These genome-scale models (GEMs) now enable us to develop pan-genome analyses that provide mechanistic insights, detail the selection pressures on proteome allocation and address stress phenotypes. In this Review, we first discuss the overall development of GEMs and their applications. Next, we review the evolution of the most complete GEM that has been developed to date: the E. coli GEM. Finally, we explore three emerging areas in genome-scale modelling of microbial phenotypes: collections of strain-specific models, metabolic and macromolecular expression models, and simulation of stress responses.
Collapse
Affiliation(s)
- Xin Fang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Colton J Lloyd
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
| |
Collapse
|
50
|
Pacheco AR, Segrè D. A multidimensional perspective on microbial interactions. FEMS Microbiol Lett 2020; 366:5513995. [PMID: 31187139 PMCID: PMC6610204 DOI: 10.1093/femsle/fnz125] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/10/2019] [Indexed: 12/16/2022] Open
Abstract
Beyond being simply positive or negative, beneficial or inhibitory, microbial interactions can involve a diverse set of mechanisms, dependencies and dynamical properties. These more nuanced features have been described in great detail for some specific types of interactions, (e.g. pairwise metabolic cross-feeding, quorum sensing or antibiotic killing), often with the use of quantitative measurements and insight derived from modeling. With a growing understanding of the composition and dynamics of complex microbial communities for human health and other applications, we face the challenge of integrating information about these different interactions into comprehensive quantitative frameworks. Here, we review the literature on a wide set of microbial interactions, and explore the potential value of a formal categorization based on multidimensional vectors of attributes. We propose that such an encoding can facilitate systematic, direct comparisons of interaction mechanisms and dependencies, and we discuss the relevance of an atlas of interactions for future modeling and rational design efforts.
Collapse
Affiliation(s)
- Alan R Pacheco
- Graduate Program in Bioinformatics and Biological Design Center, Boston University, 24 Cummington Mall, Boston, MA, 02215, USA
| | - Daniel Segrè
- Graduate Program in Bioinformatics and Biological Design Center, Boston University, 24 Cummington Mall, Boston, MA, 02215, USA.,Department of Biomedical Engineering, Department of Biology and Department of Physics, Boston University, 24 Cummington Mall, Boston, MA, 02215, USA
| |
Collapse
|