Calibration and analysis of genome-based models for microbial ecology

نویسندگان

  • Stilianos Louca
  • Michael Doebeli
  • Wenying Shou
چکیده

Microbial ecosystem modeling is complicated by the large number of unknown parameters and the lack of appropriate calibration tools. Here we present a novel computational framework for modeling microbial ecosystems, which combines genome-based model construction with statistical analysis and calibration to experimental data. Using this framework, we examined the dynamics of a community of Escherichia coli strains that emerged in laboratory evolution experiments, during which an ancestral strain diversified into two coexisting ecotypes. We constructed a microbial community model comprising the ancestral and the evolved strains, which we calibrated using separate monoculture experiments. Simulations reproduced the successional dynamics in the evolution experiments, and pathway activation patterns observed in microarray transcript profiles. Our approach yielded detailed insights into the metabolic processes that drove bacterial diversification, involving acetate cross-feeding and competition for organic carbon and oxygen. Our framework provides a missing link towards a data-driven mechanistic microbial ecology.

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

On Calibration and Application of Logit-Based Stochastic Traffic Assignment Models

There is a growing recognition that discrete choice models are capable of providing a more realistic picture of route choice behavior. In particular, influential factors other than travel time that are found to affect the choice of route trigger the application of random utility models in the route choice literature. This paper focuses on path-based, logit-type stochastic route choice models, i...

متن کامل

Genome-Scale Metabolic Network Models of Bacillus Species Suggest that Model Improvement is Necessary for Biotechnological Applications

Background: A genome-scale metabolic network model (GEM) is a mathematical representation of an organism’s metabolism. Today, GEMs are popular tools for computationally simulating the biotechnological processes and for predicting biochemical properties of (engineered) strains.Objectives: In the present study, we have evaluated the predictive power of two ...

متن کامل

BacArena - An Agent-Based Modeling Framework for Cellular Communities

Microbial communities are essential for global ecosystems and human health. Computational modeling of microbial consortia is thus a major goal in systems biology and microbial ecology. BacArena is a project to simulate bacterial behavior in communities. A lot of progress is done in the last years to create genome wide metabolic reconstructions of certain organisms, which open a wide field of ma...

متن کامل

Comparison of Conduction Based and Mediator Based Models for Microbial Fuel Cells

Microbial fuel cells (MFCs) are processes used for simultanuous bioenergy capturing and waste treatment. In this study, a model for MFCs based upon a conduction mechanism for electron transfer is proposed, which integrates substrate utilization, current production and conduction and  microbial distribution and growth in batch flow mode. The outputs of the model and that of a mediator based mode...

متن کامل

Automatic Calibration of HEC-HMS Model Using Multi-Objective Fuzzy Optimal Models

Estimation of parameters of a hydrologic model is undertaken using a procedure called “calibration” in order to obtain predictions as close as possible to observed values. This study aimed to use the particle swarm optimization (PSO) algorithm for automatic calibration of the HEC-HMS hydrologic model, which includes a library of different event-based models for simulating the rainfall-runoff pr...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:

دوره 4  شماره 

صفحات  -

تاریخ انتشار 2015