Special Issue "Genome-Scale Modeling to Predict and Optimize Microbial Capabilities"
A special issue of Microorganisms (ISSN 2076-2607).
Deadline for manuscript submissions: 31 August 2019
Dr. Nicolai S. Panikov
Northeastern University, College of Sciences, Boston, United States
Presently, NCBI lists nearly 150,000 completed whole-genome projects! With 1,278 sequenced fungal species, 1,422 archaeal, and 21,380 bacterial species, we can state that most of the medically, industrially, and environmentally significant microorganisms have been already sequenced. Genomic data are used in a wide range of fundamental studies as well as diverse medical and industrial applications. However, the practical implementations of genomic data are well below the expected potential. To this gap, we rely on systems biology bottom-up approaches, such as genome-scale models (GEM). Typically GEMs are cellular metabolic network reconstructions converted into a mathematical format and lend themselves to computational treatment. The first GEM was created for viruses (Edwards and Palsson, 1999), but now GEMs have been applied to diverse forms of microbial life and even natural and artificial bacterial communities including human microbiome. GEMs vary from relatively simple and robust FBA (flux balance analysis) to highly sophisticated models simulating gene expression patterns coupled with metabolic networks or even whole-cell dynamic simulation of bacteria with small genomes.
Most efforts are focused on the development of computational tools, which are applied to simplified microbiological data, such as the homogeneous microbial growth of a few model organisms under the simplest possible cultivation conditions (nutrients excess, constant maximum growth rate without any inhibitory or perturbation effects). In real life, environmental factors vary, affecting gene expression, posttranslational modification, and other processes; biosynthesis of the most valuable target products (e.g. antibiotics) occurs during idiophase when growth rate declines, and natural microbial populations in soils, water or human gut only rarely display intensive growth. This Special Issue of the journal Microorganisms aims to bring GEMs closer to real life and the practical challenges of fundamental and applied microbiology. We encourage the submission of papers that address relevant topics, such as the following:
- Development of robust GEM simulating microbial metabolism and growth under non-optimal conditions (nutrient limited, intoxicated, under various stress conditions) to dissect molecular mechanisms of stress-response
- Experimental validation of GEMs under conditions beyond short-term exponential growth phase (lag-, stationary phase)
- Simulation of microbial biosynthesis of secondary metabolites including antibiotics that are not proportional to cell growth
- Accounts of changeable cell composition as dependent on environmental factors
- GEMs for difficult to culture microorganisms and enigmatic physiological phenomena (substrate-accelerated death, VBNC, phage-induced lysis, drug-resistance)
- GEMs of microbial communities taking into account interactions between individual populations
Experimental studies, critical reviews, and ‘current opinion’ comments are all welcome. We especially encourage constructive and productive reports on failures associated with the application of GEMs, such as false negative or false positive predictions contradicting experimental observations that could provide a great opportunity for ‘unplanned’ biological discoveries.Dr. Nicolai S. Panikov
Manuscript Submission Information
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