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

Special Issue Editor

Guest Editor
Dr. Nicolai S. Panikov

Northeastern University, College of Sciences, Boston, United States
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Special Issue Information

Dear Colleagues,

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
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1000 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers

This special issue is now open for submission.
Microorganisms EISSN 2076-2607 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
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