DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Towards a deeper understanding of microbial communities: integrating experimental data with dynamic models

Journal Article · · Current Opinion in Microbiology

Not Available

Sponsoring Organization:
USDOE
OSTI ID:
1786395
Journal Information:
Current Opinion in Microbiology, Journal Name: Current Opinion in Microbiology Journal Issue: C Vol. 62; ISSN 1369-5274
Publisher:
ElsevierCopyright Statement
Country of Publication:
United Kingdom
Language:
English

References (71)

Inferring human microbial dynamics from temporal metagenomics data: Pitfalls and lessons journal December 2016
Species packing and competitive equilibrium for many species journal May 1970
Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli journal September 2002
Bacteriotherapy for Chronic Relapsing Clostridium Difficile Diarrhoea in six Patients journal May 1989
A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action journal May 2019
Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics journal May 2014
Microbial Interaction Network Inference in Microfluidic Droplets journal September 2019
The dynamic microbiome journal February 2014
Altered bile acid profile associates with cognitive impairment in Alzheimer's disease-An emerging role for gut microbiome journal October 2018
Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space journal June 2004
Longitudinal dynamics of a tracked vehicle: Simulation and experiment journal April 2012
Recent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law formalisms journal January 2021
d-OptCom: Dynamic Multi-level and Multi-objective Metabolic Modeling of Microbial Communities journal November 2013
Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments journal July 2010
Modeling time-series data from microbial communities journal August 2017
Gut microbiome remodeling induces depressive-like behaviors through a pathway mediated by the host’s metabolism journal April 2016
Metabolic modeling of a mutualistic microbial community journal January 2007
Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli journal January 2007
A core gut microbiome in obese and lean twins journal November 2008
Structure, function and diversity of the healthy human microbiome journal June 2012
Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile journal October 2014
Quantitative microbiome profiling links gut community variation to microbial load journal November 2017
What is flux balance analysis? journal March 2010
Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection journal January 2014
Prediction and quantification of bioactive microbiota metabolites in the mouse gut journal November 2014
Trophic network architecture of root-associated bacterial communities determines pathogen invasion and plant health journal September 2015
Reaction–diffusion theory explains hypoxia and heterogeneous growth within microbial biofilms associated with chronic infections journal June 2016
Use and abuse of correlation analyses in microbial ecology journal June 2019
Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities journal November 2017
Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems journal January 2019
Design of synthetic human gut microbiome assembly and butyrate production journal May 2021
Short-range interactions govern the dynamics and functions of microbial communities journal February 2020
Strength of species interactions determines biodiversity and stability in microbial communities journal February 2020
Highly multiplexed spatial mapping of microbial communities journal December 2020
Trends in U.S. Burden of Clostridioides difficile Infection and Outcomes journal April 2020
Range expansion promotes cooperation in an experimental microbial metapopulation journal April 2013
Metabolic dependencies drive species co-occurrence in diverse microbial communities journal May 2015
Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework journal February 2015
SER-109, an Investigational Microbiome Drug to Reduce Recurrence After Clostridioides difficile Infection: Lessons Learned From a Phase 2 Trial journal April 2020
Determinants of Reduced Genetic Capacity for Butyrate Synthesis by the Gut Microbiome in Crohn’s Disease and Ulcerative Colitis journal October 2017
On Interpretability of Artificial Neural Networks: A Survey journal January 2021
Modelling the emergent dynamics and major metabolites of the human colonic microbiota: Emergent microbial dynamics in the colon journal October 2014
The mechanistic basis for higher-order interactions and non-additivity in competitive communities journal January 2019
Metabolic multistability and hysteresis in a model aerobe-anaerobe microbiome community journal August 2020
Detecting Causality in Complex Ecosystems journal September 2012
Fecal microbiota transplant overcomes resistance to anti–PD-1 therapy in melanoma patients journal February 2021
Modeling of the Coral Microbiome: the Influence of Temperature and Microbial Network journal April 2020
Machine Learning Reveals Missing Edges and Putative Interaction Mechanisms in Microbial Ecosystem Networks journal October 2018
Designing Metabolic Division of Labor in Microbial Communities journal April 2019
The Gut Microbiome and Its Role in Cardiovascular Diseases journal March 2017
Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut journal January 2013
MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses journal June 2016
Uncovering and resolving challenges of quantitative modeling in a simplified community of interacting cells journal February 2019
Social Interaction, Noise and Antibiotic-Mediated Switches in the Intestinal Microbiota journal April 2012
Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota journal December 2013
Two dynamic regimes in the human gut microbiome journal February 2017
Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal journal April 2017
BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities journal May 2017
Spatial dynamics of synthetic microbial mutualists and their parasites journal August 2017
BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data journal April 2019
Machine and deep learning meet genome-scale metabolic modeling journal July 2019
Microbial communities display alternative stable states in a fluctuating environment journal May 2020
Modeling microbial cross-feeding at intermediate scale portrays community dynamics and species coexistence journal August 2020
A mechanistic Individual-based Model of microbial communities journal August 2017
Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling journal January 2020
Deciphering microbial interactions in synthetic human gut microbiome communities journal June 2018
Estimating Community Stability and Ecological Interactions from Time-Series data journal May 2003
Modeling Metabolic Interactions in a Consortium of the Infant Gut Microbiome journal December 2017
Calibration and analysis of genome-based models for microbial ecology journal October 2015
Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions journal March 2017
Computer-guided design of optimal microbial consortia for immune system modulation journal April 2018

Similar Records

Towards a deeper understanding of microbial communities: integrating experimental data with dynamic models
Journal Article · 2021 · Current Opinion in Microbiology · OSTI ID:1849050

Toward a Deeper Understanding of Plutonium
Journal Article · 2007 · Journal of Computer-Aided Materials Design, vol. 14, no. 3, September 30, 2007, pp. 329-330 · OSTI ID:942027

Toward a deeper understanding of how experiments constrain the underlying physics of heavy-ion collisions
Journal Article · 2016 · Physical Review C · OSTI ID:1237781

Related Subjects