Postgenomic Microbial Physiology and Fermentation

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 submissions that pass pre-check are 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 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 2100 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.

• 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