Ecological modelling approaches for predicting emergent properties in microbial communities
出版年份 2022 全文链接
标题
Ecological modelling approaches for predicting emergent properties in microbial communities
作者
关键词
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出版物
Nature Ecology & Evolution
Volume -, Issue -, Pages -
出版商
Springer Science and Business Media LLC
发表日期
2022-05-17
DOI
10.1038/s41559-022-01746-7
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- Constrained proteome allocation affects coexistence in models of competitive microbial communities
- (2021) Leonardo Pacciani-Mori et al. ISME Journal
- A trait‐based approach predicting community assembly and dominance of microbial invasive species
- (2021) C. Kruk et al. OIKOS
- Tracking, targeting, and conserving soil biodiversity
- (2021) Carlos A. Guerra et al. SCIENCE
- Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community
- (2021) Sonja Blasche et al. Nature Microbiology
- Polarization of microbial communities between competitive and cooperative metabolism
- (2021) Daniel Machado et al. Nature Ecology & Evolution
- Quantifying microbial control of soil organic matter dynamics at macrosystem scales
- (2021) Mark A. Bradford et al. Biogeochemistry
- Non-additive microbial community responses to environmental complexity
- (2021) Alan R. Pacheco et al. Nature Communications
- Community composition of microbial microcosms follows simple assembly rules at evolutionary timescales
- (2021) Nittay Meroz et al. Nature Communications
- Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments
- (2021) Sylvie Estrela et al. eLife
- Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model
- (2021) Shion Hosoda et al. BIOINFORMATICS
- Adaptive laboratory evolution of microbial co‐cultures for improved metabolite secretion
- (2021) Dimitrios Konstantinidis et al. Molecular Systems Biology
- Spatio-temporal modeling of the crowding conditions and metabolic variability in microbial communities
- (2021) Liliana Angeles-Martinez et al. PLoS Computational Biology
- Environmental fluctuations reshape an unexpected diversity-disturbance relationship in a microbial community
- (2021) Christopher P Mancuso et al. eLife
- Structural identifiability of the generalized Lotka–Volterra model for microbiome studies
- (2021) Christopher H. Remien et al. Royal Society Open Science
- A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)
- (2021) Ilija Dukovski et al. Nature Protocols
- metaGEM: reconstruction of genome scale metabolic models directly from metagenomes
- (2021) Francisco Zorrilla et al. NUCLEIC ACIDS RESEARCH
- Positive interactions are common among culturable bacteria
- (2021) Jared Kehe et al. Science Advances
- Distinct mechanisms shape soil bacterial and fungal co-occurrence networks in a mountain ecosystem
- (2020) Jiabao Li et al. FEMS MICROBIOLOGY ECOLOGY
- A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns
- (2020) Robert Marsland et al. Scientific Reports
- Strength of species interactions determines biodiversity and stability in microbial communities
- (2020) Christoph Ratzke et al. Nature Ecology & Evolution
- Gastrointestinal dysbiosis following diethylhexyl phthalate exposure in zebrafish (Danio rerio): Altered microbial diversity, functionality, and network connectivity
- (2020) Amanda N. Buerger et al. ENVIRONMENTAL POLLUTION
- Conservation of community functional structure across changes in composition in consumer-resource models
- (2020) Lee Worden JOURNAL OF THEORETICAL BIOLOGY
- Understanding the evolution of interspecies interactions in microbial communities
- (2020) Florien A. Gorter et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- Linking regional shifts in microbial genome adaptation with surface ocean biogeochemistry
- (2020) Catherine A. Garcia et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- The Community Simulator: A Python package for microbial ecology
- (2020) Robert Marsland et al. PLoS One
- Dynamic metabolic adaptation can promote species coexistence in competitive microbial communities
- (2020) Leonardo Pacciani-Mori et al. PLoS Computational Biology
- Microbial communities display alternative stable states in a fluctuating environment
- (2020) Clare I. Abreu et al. PLoS Computational Biology
- Compositional Lotka-Volterra describes microbial dynamics in the simplex
- (2020) Tyler A. Joseph et al. PLoS Computational Biology
- In sickness and health: Effects of gut microbial metabolites on human physiology
- (2020) Robert W. P. Glowacki et al. PLoS Pathogens
- Trait‐based approach to bacterial growth efficiency
- (2020) Mario E. Muscarella et al. ENVIRONMENTAL MICROBIOLOGY
- Emergent neutrality in consumer-resource dynamics
- (2020) Rafael D’Andrea et al. PLoS Computational Biology
- Trophic Interactions and the Drivers of Microbial Community Assembly
- (2020) Matti Gralka et al. CURRENT BIOLOGY
- Reconstructing organisms in silico: genome-scale models and their emerging applications
- (2020) Xin Fang et al. NATURE REVIEWS MICROBIOLOGY
- gauseR: Simple methods for fitting Lotka‐Volterra models describing Gause’s “Struggle for Existence”
- (2020) Lina K. Mühlbauer et al. Ecology and Evolution
- Resource plasticity-driven carbon-nitrogen budgeting enables specialization and division of labor in a clonal community
- (2020) Sriram Varahan et al. eLife
- Plant traits alone are poor predictors of ecosystem properties and long-term ecosystem functioning
- (2020) Fons van der Plas et al. Nature Ecology & Evolution
- A multi-scale eco-evolutionary model of cooperation reveals how microbial adaptation influences soil decomposition
- (2020) Elsa Abs et al. Communications Biology
- Artificial consortium demonstrates emergent properties of enhanced cellulosic-sugar degradation and biofuel synthesis
- (2020) Heejoon Park et al. npj Biofilms and Microbiomes
- Tradeoffs among microbial life history strategies influence the fate of microbial residues in subtropical forest soils
- (2020) Pengshuai Shao et al. SOIL BIOLOGY & BIOCHEMISTRY
- Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities
- (2019) Robert Marsland et al. PLoS Computational Biology
- Toxicity drives facilitation between 4 bacterial species
- (2019) Philippe Piccardi et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Making the Most of Trait-Based Approaches for Microbial Ecology
- (2019) Geneviève Lajoie et al. TRENDS IN MICROBIOLOGY
- Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH)
- (2019) Benedict Borer et al. PLoS Computational Biology
- Trait-based modelling in ecology: A review of two decades of research
- (2019) L. Zakharova et al. ECOLOGICAL MODELLING
- Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change
- (2019) Ashish A. Malik et al. ISME Journal
- Emergent properties of organic matter decomposition by soil enzymes
- (2019) Bin Wang et al. SOIL BIOLOGY & BIOCHEMISTRY
- Individual Based Model Links Thermodynamics, Chemical Speciation and Environmental Conditions to Microbial Growth
- (2019) Valentina Gogulancea et al. Frontiers in Microbiology
- An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data
- (2019) Chenhao Li et al. Microbiome
- Microbial Interactions in Oral Communities Mediate Emergent Biofilm Properties
- (2019) P.I. Diaz et al. JOURNAL OF DENTAL RESEARCH
- Metabolite-mediated modelling of microbial community dynamics captures emergent behaviour more effectively than species–species modelling
- (2019) J. D. Brunner et al. Journal of the Royal Society Interface
- Gut Microbiota: An Important Link between Western Diet and Chronic Diseases
- (2019) Zumin Shi Nutrients
- Multistability and regime shifts in microbial communities explained by competition for essential nutrients
- (2019) Veronika Dubinkina et al. eLife
- High-order interactions distort the functional landscape of microbial consortia
- (2019) Alicia Sanchez-Gorostiaga et al. PLOS BIOLOGY
- Higher-Order Interaction between Species Inhibits Bacterial Invasion of a Phototroph-Predator Microbial Community
- (2019) Harry Mickalide et al. Cell Systems
- The spatial and metabolic basis of colony size variation
- (2018) Jeremy M. Chacón et al. ISME Journal
- Fast automated reconstruction of genome-scale metabolic models for microbial species and communities
- (2018) Daniel Machado et al. NUCLEIC ACIDS RESEARCH
- Generic assembly patterns in complex ecological communities
- (2018) Matthieu Barbier et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Modifying and reacting to the environmental pH can drive bacterial interactions
- (2018) Christoph Ratzke et al. PLOS BIOLOGY
- Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features
- (2018) Niv Zmora et al. CELL
- Emergent simplicity in microbial community assembly
- (2018) Joshua E. Goldford et al. SCIENCE
- A shared limiting resource leads to competitive exclusion in a cross-feeding system
- (2018) Sarah P. Hammarlund et al. ENVIRONMENTAL MICROBIOLOGY
- The antibiotic action of methylarsenite is an emergent property of microbial communities
- (2018) Jian Chen et al. MOLECULAR MICROBIOLOGY
- Inference of Significant Microbial Interactions From Longitudinal Metagenomics Data
- (2018) Xuefeng Gao et al. Frontiers in Microbiology
- A mechanistic Individual-based Model of microbial communities
- (2017) Pahala Gedara Jayathilake et al. PLoS One
- Ocean biogeochemistry modeled with emergent trait-based genomics
- (2017) V. J. Coles et al. SCIENCE
- Consequences of drought tolerance traits for microbial decomposition in the DEMENT model
- (2017) Steven D. Allison et al. SOIL BIOLOGY & BIOCHEMISTRY
- A New Improved and Extended Version of the Multicell Bacterial Simulator gro
- (2017) Martín Gutiérrez et al. ACS Synthetic Biology
- BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities
- (2017) Eugen Bauer et al. PLoS Computational Biology
- Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions
- (2017) Babak Momeni et al. eLife
- Regulation-Structured Dynamic Metabolic Model Provides a Potential Mechanism for Delayed Enzyme Response in Denitrification Process
- (2017) Hyun-Seob Song et al. Frontiers in Microbiology
- Gaussian process emulation of an individual-based model simulation of microbial communities
- (2017) O.K. Oyebamiji et al. Journal of Computational Science
- Yeast Creates a Niche for Symbiotic Lactic Acid Bacteria through Nitrogen Overflow
- (2017) Olga Ponomarova et al. Cell Systems
- Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI
- (2017) Joshua J. Hamilton et al. mSystems
- Community structure follows simple assembly rules in microbial microcosms
- (2017) Jonathan Friedman et al. Nature Ecology & Evolution
- Synthetic Ecology of Microbes: Mathematical Models and Applications
- (2016) Ali R. Zomorrodi et al. JOURNAL OF MOLECULAR BIOLOGY
- Biofilms: an emergent form of bacterial life
- (2016) Hans-Curt Flemming et al. NATURE REVIEWS MICROBIOLOGY
- Advancing microbial sciences by individual-based modelling
- (2016) Ferdi L. Hellweger et al. NATURE REVIEWS MICROBIOLOGY
- The Human Intestinal Microbiome in Health and Disease
- (2016) Susan V. Lynch et al. NEW ENGLAND JOURNAL OF MEDICINE
- High-order species interactions shape ecosystem diversity
- (2016) Eyal Bairey et al. Nature Communications
- Resource Availability Modulates the Cooperative and Competitive Nature of a Microbial Cross-Feeding Mutualism
- (2016) Tim A. Hoek et al. PLOS BIOLOGY
- The Contribution of High-Order Metabolic Interactions to the Global Activity of a Four-Species Microbial Community
- (2016) Xiaokan Guo et al. PLoS Computational Biology
- Predicting the Responses of Soil Nitrite-Oxidizers to Multi-Factorial Global Change: A Trait-Based Approach
- (2016) Xavier Le Roux et al. Frontiers in Microbiology
- Next generation sequencing data of a defined microbial mock community
- (2016) Esther Singer et al. Scientific Data
- Local and global consequences of flow on bacterial quorum sensing
- (2016) Minyoung Kevin Kim et al. Nature Microbiology
- Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir
- (2016) Aaron M. Walsh et al. mSystems
- Using Genome-scale Models to Predict Biological Capabilities
- (2015) Edward J. O’Brien et al. CELL
- Phytoplankton traits predict ecosystem function in a global set of lakes
- (2015) Jacob A. Zwart et al. ECOLOGY
- Public Good Diffusion Limits Microbial Mutualism
- (2015) Rajita Menon et al. PHYSICAL REVIEW LETTERS
- Metabolic dependencies drive species co-occurrence in diverse microbial communities
- (2015) Aleksej Zelezniak et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples
- (2015) T. Korem et al. SCIENCE
- The ecology of the microbiome: Networks, competition, and stability
- (2015) K. Z. Coyte et al. SCIENCE
- Ecological communities by design
- (2015) J. K. Fredrickson SCIENCE
- Hydration and diffusion processes shape microbial community organization and function in model soil aggregates
- (2015) Ali Ebrahimi et al. WATER RESOURCES RESEARCH
- Microscale Heterogeneity Explains Experimental Variability and Non-Linearity in Soil Organic Matter Mineralisation
- (2015) Ruth E. Falconer et al. PLoS One
- Interaction effects of cell diffusion, cell density and public goods properties on the evolution of cooperation in digital microbes
- (2014) A. Dobay et al. JOURNAL OF EVOLUTIONARY BIOLOGY
- Towards Predictive Models of the Human Gut Microbiome
- (2014) Vanni Bucci et al. JOURNAL OF MOLECULAR BIOLOGY
- Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile
- (2014) Charlie G. Buffie et al. NATURE
- Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression
- (2014) Charles K. Fisher et al. PLoS One
- Evolutionary limits to cooperation in microbial communities
- (2014) Nuno M. Oliveira et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Untangling the fungal niche: the trait-based approach
- (2014) Thomas W. Crowther et al. Frontiers in Microbiology
- Emergence of microbial networks as response to hostile environments
- (2014) Dario Madeo et al. Frontiers in Microbiology
- When, where and how does microbial community composition matter?
- (2014) Diana R. Nemergut et al. Frontiers in Microbiology
- Deciphering microbial interactions and detecting keystone species with co-occurrence networks
- (2014) David Berry et al. Frontiers in Microbiology
- Mathematical Modeling of Microbial Community Dynamics: A Methodological Review
- (2014) Hyun-Seob Song et al. Processes
- Evidence of Microbial Regulation of Biogeochemical Cycles from a Study on Methane Flux and Land Use Change
- (2013) Loïc Nazaries et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Trait-based approaches to zooplankton communities
- (2013) Elena Litchman et al. JOURNAL OF PLANKTON RESEARCH
- Iron, phosphorus, and nitrogen supply ratios define the biogeography of nitrogen fixation
- (2013) Ben A. Ward et al. LIMNOLOGY AND OCEANOGRAPHY
- Variable Effects of Dispersal on Productivity of Bacterial Communities Due to Changes in Functional Trait Composition
- (2013) Ina Severin et al. PLoS One
- Heterogeneity in protein expression induces metabolic variability in a modeledEscherichia colipopulation
- (2013) Piyush Labhsetwar et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Mighty small: Observing and modeling individual microbes becomes big science
- (2013) J.-U. Kreft et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Mathematical modeling of primary succession of murine intestinal microbiota
- (2013) S. Marino et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota
- (2013) Richard R. Stein et al. PLoS Computational Biology
- Spatial self-organization favors heterotypic cooperation over cheating
- (2013) Babak Momeni et al. eLife
- Spatial dilemmas of diffusible public goods
- (2013) Benjamin Allen et al. eLife
- Competition, Not Cooperation, Dominates Interactions among Culturable Microbial Species
- (2012) Kevin R. Foster et al. CURRENT BIOLOGY
- A trait-based approach for modelling microbial litter decomposition
- (2012) S. D. Allison ECOLOGY LETTERS
- The human microbiome: at the interface of health and disease
- (2012) Ilseung Cho et al. NATURE REVIEWS GENETICS
- Microbial interactions: from networks to models
- (2012) Karoline Faust et al. NATURE REVIEWS MICROBIOLOGY
- Schools of fish and flocks of birds: their shape and internal structure by self-organization
- (2012) C. K. Hemelrijk et al. Interface Focus
- Trait-Based Representation of Biological Nitrification: Model Development, Testing, and Predicted Community Composition
- (2012) Nicholas J. Bouskill et al. Frontiers in Microbiology
- Individual-based modelling of adaptation in marine microbial populations using genetically defined physiological parameters
- (2011) James R. Clark et al. ECOLOGICAL MODELLING
- iDynoMiCS: next-generation individual-based modelling of biofilms
- (2011) Laurent A. Lardon et al. ENVIRONMENTAL MICROBIOLOGY
- The biomass objective function
- (2010) Adam M Feist et al. CURRENT OPINION IN MICROBIOLOGY
- A global network of coexisting microbes from environmental and whole-genome sequence data
- (2010) S. Chaffron et al. GENOME RESEARCH
- Emergent cooperation in microbial metabolism
- (2010) Edwin H Wintermute et al. Molecular Systems Biology
- What is flux balance analysis?
- (2010) Jeffrey D Orth et al. NATURE BIOTECHNOLOGY
- Emergence of Spatial Structure in Cell Groups and the Evolution of Cooperation
- (2010) Carey D. Nadell et al. PLoS Computational Biology
- What is microbial community ecology?
- (2009) Allan Konopka ISME Journal
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