Special Issue "Postgenomic Microbial Physiology and Fermentation"

A special issue of Fermentation (ISSN 2311-5637).

Deadline for manuscript submissions: closed (31 August 2018)

Special Issue Editor

Guest Editor
Dr. Nicolai S. Panikov

Northeastern University, Biotechnology Programs, Boston, USA
Website | E-Mail
Interests: predictive quantitative microbiology; development of theoretical principles; instruments and methods for controlled cultivation of microbial and mammalian cells; directed evolution of microorganisms, mechanisms of acquiring of multiple drug-resistance

Special Issue Information

Dear Colleagues,

Fermentations are virtually as old as civilization itself; about hundred years ago, we began to understand the nature of fermentation as metabolic reactions of living (mostly microbial) cells, and the last two to three decades, we face an enormous expansion of the range of fermentation products inspired by genomic revolution. Microbial physiology and biochemistry have been historically a primary scientific background in development of industrial fermentations. Microbial physiology is the study of microbial structure and function, in particular, how cells proliferate and lyse, adapt and respond to changeable environment (nutrient sources, aeration, toxicity, pH, temperature, etc.) and to presence of other organisms in mixed fermentations. Specific areas of microbial physiology focus on production of secondary metabolites (e.g., antibiotics, pigments), cellular differentiation (e.g., formation of dormant cells, persisters, extracellular vesicles), and spontaneous mutations followed by autoselection in long-term continuous cultures and other events. Quantitative microbial physiology combining experimental studies with mostly macroscopic mathematical modeling are synonymous to microbiological kinetics, bioenergetics and stoichiometry that are crucial for bioprocesses development. Now, in the postgenomic era, biotechnologists have access to recombinant techniques to carry out metabolic engineering of microbial strains with a given set of functionalities. Full genome sequences of industrially-important microorganisms, efficient molecular and computational tools gave new impetus to study and optimize industrial fermentations. Unsurprisingly, deeper insight into molecular mechanisms in majority of published reports represent a move towards reductionism compared with the classical macroscopic physiological studies, as the focus is on the role of specific proteins, genes or pathways without a global picture of the whole cellular (as a rule heterogeneous) population. The goal of systems biology is to generate a holistic picture of physiological response of the cell, based on available sequencing and other ‘omics’ data but this goal cannot yet be reached in a real biotech world.

This Special Issue of Fermentation focuses on modern physiological research approaching at least partially the ultimate goal of systems biology and make practical steps to overcome mentioned above reductionism. We encourage potential authors to submit manuscripts (either review or original experimental studies, mathematical models and methodological developments) aimed to ‘see the forest among trees’ in fermentation studies. Ask yourself whether my contribution uses modern approaches including molecular omics data to improve the mechanistic understanding of microbial physiology. If your answer is positive, then do not hesitate to submit paper to us.

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. Fermentation is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) is waived for well-prepared manuscripts submitted to this issue. 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.


  • growth rate
  • death rate
  • lysis
  • affinity to substrate
  • yield variation
  • differentiation
  • dormancy
  • persisters
  • secondary metabolism
  • flux balance analysis
  • genome-based predictive mathematical modeling of microbial growth
  • maintenance requirements
  • overflow catabolism
  • substrate-accelerated death
  • minimal growth rate
  • near-zero growth rate
  • spontaneous mutations
  • fitness of mutants
  • chemostat culture
  • retentiostat, auxostat
  • GASP mutations
  • epigenetic changes
  • gene expression profile as dependent on environmental conditions

Published Papers (1 paper)

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Open AccessReview Transcription Factors Controlling Primary and Secondary Metabolism in Filamentous Fungi: The β-Lactam Paradigm
Fermentation 2018, 4(2), 47; https://doi.org/10.3390/fermentation4020047
Received: 3 April 2018 / Revised: 4 June 2018 / Accepted: 15 June 2018 / Published: 19 June 2018
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Transcription factors are key regulatory proteins in all living beings. In fungi, transcription factors include either broad-domain regulatory proteins that affect the expression of many genes involved in biosynthetic processes, or proteins encoded by cluster-associated (also called pathway-specific) regulatory genes. Belonging to the
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Transcription factors are key regulatory proteins in all living beings. In fungi, transcription factors include either broad-domain regulatory proteins that affect the expression of many genes involved in biosynthetic processes, or proteins encoded by cluster-associated (also called pathway-specific) regulatory genes. Belonging to the most interesting transcription factors in fungi are binuclear zinc finger proteins. In addition to the transcription factors in the strict sense, other proteins play a very important role in the expression of genes for primary and secondary metabolism in fungi, such as winged helix regulators, the LaeA protein and the velvet complex. LaeA appears to be involved in heterochromatin reorganization, and the velvet complex proteins, which are nuclear factors that associate with LaeA, also have a determining role in both differentiation (sporulation) and secondary metabolite biosynthesis. The genes involved in the biosynthesis of β-lactam antibiotics are well known and serve as an excellent model to understand the transcriptional control of genes involved in the biosynthesis of secondary metabolites. Interaction between different regulatory proteins in the promoter regions may represent a cross-talk regulation between different gene clusters. Full article
(This article belongs to the Special Issue Postgenomic Microbial Physiology and Fermentation)

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