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Microorganisms
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Editorial Board Members’ Collection Series: How Microbial Cell Factories Can...
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Editorial Board Members’ Collection Series: How Microbial Cell Factories Can Help Change the World

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbial Biotechnology".

Deadline for manuscript submissions: 31 July 2025 | Viewed by 4546

Special Issue Editor

Dr. Mireille Fouillaud

E-Mail Website
Guest Editor
CHEMBIOPRO Chimie et Biotechnologie des Produits Naturels, Faculté des Sciences et Technologies, Université de la Réunion, F-97490 Sainte-Clotilde, Ile de La Réunion, France
Interests: microbiology; biotechnology; specialized metabolites; fermentations; pigments
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Recent developments in microbiology enabled us to understand that micro-organisms whether terrestrial, marine or aerial, are integral players in our planet evolution. We are co-evolving, and bacteria, fungi, microalgae, viruses etc. are essential partners in what we will be able to undertake, now and in the future, in order to meet the major barriers facing human beings on planet earth and perhaps beyond. The full range of technologies now available in all fields of research (physics, chemistry, biology, geography and sociology, etc.) and above all multidisciplinary approaches, are more essential than ever to advance our understanding of the “Microbial Cell Factory” and take advantage of a controlled collaboration with the microbial world. The microbial cell must be considered as a true scientific partner and, as such, studied from every angle. Thus, all articles providing new knowledge on the use of the microbial cells to overcome the major challenges of our time: microbial strains with novel physiological capacities, original bioprocesses or biotechnologies adapted for the management of a sustainable environment, renewable energies or bioproducts of interest in the food, pharmacological, cosmetic, environmental fields, etc., are some of the aspects that can be developed in this special issue, highlighting the microbial world and the microbial cell factories as allies in our future world.

Dr. Mireille Fouillaud
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. 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 2700 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.

Keywords

  • bacteria
  • fungi
  • microalgae
  • virus
  • biotechnology
  • bioprocess, specialized metabolite
  • genetic
  • omic sciences
  • industrial application
  • sustainable environment

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Published Papers (4 papers)

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Research

18 pages, 1851 KiB  
Article
Immobilization and Monitoring of Clostridium carboxidivorans and Clostridium kluyveri in Synthetic Biofilms
by Josha Herzog, Anna C. Jäkel, Friedrich C. Simmel and Dirk Weuster-Botz
Microorganisms 2025, 13(2), 387; https://doi.org/10.3390/microorganisms13020387 - 10 Feb 2025
Cited by 1 | Viewed by 690
Abstract
The growing need for sustainable biotechnological solutions to address environmental challenges, such as climate change and resource depletion, has intensified interest in microbial-based production systems. Synthetic biofilms, which mimic natural microbial consortia, offer a promising platform for optimizing complex metabolic processes that can [...] Read more.
The growing need for sustainable biotechnological solutions to address environmental challenges, such as climate change and resource depletion, has intensified interest in microbial-based production systems. Synthetic biofilms, which mimic natural microbial consortia, offer a promising platform for optimizing complex metabolic processes that can convert renewable feedstocks into valuable chemicals. In this context, understanding and harnessing the interactions between co-immobilized microorganisms are critical for advancing bioprocesses that contribute to circular bioeconomy goals. In this study, we investigated the viability and metabolic activity of Clostridium carboxidivorans and Clostridium kluyveri within a synthetic, dual-layered biofilm composed of agar hydrogel. This setup compartmentalized each bacterial species. Embedding the bacteria in a structured biofilm offers numerous opportunities for bioproduction, but the inability to monitor cell growth or movement within the immobilization matrix limits process insights. To address this, we adapted a fluorescence in situ hybridization (FISH) protocol, enabling precise, species-specific visualization of bacterial distribution and growth within the gel matrix. Batch processes with the dual-layered biofilm in anaerobic flasks, designed with a metabolic advantage for C. kluyveri, revealed distinct growth dynamics. C. kluyveri exhibited significant metabolic activity, forming clusters at low initial cell concentrations and converting ethanol and acetate into 1-butyrate and 1-hexanoate, indicating viability and cell growth. C. carboxidivorans remained evenly distributed without significant growth or product formation, suggesting that while the cells were viable, they were not metabolically active under the experimental conditions. Both bacterial species were confined to their respective compartments throughout the process, with C. kluyveri showing enhanced substrate conversion at higher initial cell densities in the hydrogel. The pH drop throughout the batch experiment likely contributed to incomplete substrate consumption, particularly for C. kluyveri, which thrives within a narrow pH range. These findings highlight synthetic biofilms as a promising platform for optimizing microbial interactions and improving bioprocess efficiency, especially in applications involving complex metabolic exchanges between co-immobilized microorganisms. Further research will focus on applying conditions to support the growth and metabolic activity of C. carboxidivorans to explore spatial dynamics of bacterial migration and cooperative relationships in the synthetic biofilm. Full article
(This article belongs to the Special Issue Editorial Board Members’ Collection Series: How Microbial Cell Factories Can Help Change the World)
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11 pages, 3366 KiB  
Article
Isolation and Characterization of Carbonosomes from Pseudomonas sp. phDV1 Grown Using Phenol as Carbon Source
by Ermis Dionysios Geladas, Alexandros Lyratzakis, Athina Drakonaki, Georgios Gkikas and Georgios Tsiotis
Microorganisms 2025, 13(2), 369; https://doi.org/10.3390/microorganisms13020369 - 8 Feb 2025
Viewed by 571
Abstract
The Pseudomonas sp. strain phDV1 was found to utilize monocyclic aromatic compounds as a sole carbon source and has a variety of potential applications in the bioremediation and biosynthesis of biodegradable plastics. It was possible to produce polyhydroxybutyrate when cultivated in the presence [...] Read more.
The Pseudomonas sp. strain phDV1 was found to utilize monocyclic aromatic compounds as a sole carbon source and has a variety of potential applications in the bioremediation and biosynthesis of biodegradable plastics. It was possible to produce polyhydroxybutyrate when cultivated in the presence of monocyclic aromatic compounds as the sole carbon source. This study provides the small-scale optimization for phenol bioremediation and polyhydroxybutyrate production. The bacterium was cultivated in minimal medium supplemented with different concentrations of phenol. The formation and localization of the polyhydroxybutyrate granules (carbonosomes) in the cell were determined after 72 h of cultivation using Nile Red stain in combination with fluorescence microscopy. Analytical HPLC was also used to quantify the PHB content in the cells and to optimize the production. Finally, comparative proteomic analysis of isolated carbonosomes was used to characterize of their protein composition. Full article
(This article belongs to the Special Issue Editorial Board Members’ Collection Series: How Microbial Cell Factories Can Help Change the World)
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19 pages, 2821 KiB  
Article
Genetic Code Expansion for Controlled Surfactin Production in a High Cell-Density Bacillus subtilis Strain
by Alexander Hermann, Eric Hiller, Philipp Hubel, Lennart Biermann, Elvio Henrique Benatto Perino, Oscar Paul Kuipers, Rudolf Hausmann and Lars Lilge
Microorganisms 2025, 13(2), 353; https://doi.org/10.3390/microorganisms13020353 - 6 Feb 2025
Viewed by 1105
Abstract
Background: In biotechnology, B. subtilis is established for heterologous protein production. In addition, the species provides a variety of bioactive metabolites, including the non-ribosomally produced surfactin lipopeptide. However, to control the formation of the target product-forming enzyme, different expression systems could be introduced, [...] Read more.
Background: In biotechnology, B. subtilis is established for heterologous protein production. In addition, the species provides a variety of bioactive metabolites, including the non-ribosomally produced surfactin lipopeptide. However, to control the formation of the target product-forming enzyme, different expression systems could be introduced, including the principle of genetic code expansion by the incorporation of externally supplied non-canonical amino acids. Methods: Integration of an amber stop codon into the srfA operon and additional chromosomal integration of an aminoacyl-tRNA synthetase/tRNA mutant pair from Methanococcus jannaschii enabled site-directed incorporation of the non-canonical amino acid O-methyl-L-tyrosine (OMeY). In different fed-batch bioreactor approaches, OMeY-associated surfactin production was quantified by high-performance thin-layer chromatography (HPTLC). Physiological adaptations of the B. subtilis production strain were analyzed by mass spectrometric proteomics. Results: Using a surfactin-forming B. subtilis production strain, which enables high cell density fermentation processes, the principle of genetic code expansion was introduced. Accordingly, the biosynthesis of the surfactin-forming non-ribosomal peptide synthetase (NRPS) was linked to the addition of the non-canonical amino acid OMeY. In OMeY-associated fed-batch bioreactor fermentation processes, a maximum surfactin titre of 10.8 g/L was achieved. In addition, the effect of surfactin induction was investigated by mass spectrometric proteome analyses. Among other things, adaptations in the B. subtilis motility towards a more sessile state and increased abundances of surfactin precursor-producing enzymes were detected. Conclusions: The principle of genetic code expansion enabled a precise control of the surfactin bioproduction as a representative of bioactive secondary metabolites in B. subtilis. This allowed the establishment of inducer-associated regulation at the post-transcriptional level with simultaneous use of the native promoter system. In this way, inductor-dependent control of the production of the target metabolite-forming enzyme could be achieved. Full article
(This article belongs to the Special Issue Editorial Board Members’ Collection Series: How Microbial Cell Factories Can Help Change the World)
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18 pages, 1852 KiB  
Article
Recombinant Production of Bovine αS1-Casein in Genome-Reduced Bacillus subtilis Strain IIG-Bs-20-5-1
by Lennart Biermann, Lea Rahel Tadele, Elvio Henrique Benatto Perino, Reed Nicholson, Lars Lilge and Rudolf Hausmann
Microorganisms 2025, 13(1), 60; https://doi.org/10.3390/microorganisms13010060 - 2 Jan 2025
Cited by 1 | Viewed by 1781
Abstract
Background: Cow’s milk represents an important protein source. Here, especially casein proteins are important components, which might be a promising source of alternative protein production by microbial expression systems. Nevertheless, caseins are difficult-to-produce proteins, making heterologous production challenging. However, the potential of genome-reduced [...] Read more.
Background: Cow’s milk represents an important protein source. Here, especially casein proteins are important components, which might be a promising source of alternative protein production by microbial expression systems. Nevertheless, caseins are difficult-to-produce proteins, making heterologous production challenging. However, the potential of genome-reduced Bacillus subtilis was applied for the recombinant production of bovine αS1-casein protein. Methods: A plasmid-based gene expression system was established in B. subtilis allowing the production of his-tagged codon-optimized bovine αS1-casein. Upscaling in a fed-batch bioreactor system for high cell-density fermentation processes allowed for efficient recombinant αS1-casein production. After increasing the molecular abundance of the recombinant αS1-casein protein using immobilized metal affinity chromatography, zeta potential and particle size distribution were determined in comparison to native bovine αS1-casein. Results: Non-sporulating B. subtilis strain BMV9 and genome-reduced B. subtilis strain IIG-Bs-20-5-1 were applied for recombinant αS1-casein production. Casein was detectable only in the insoluble protein fraction of the genome-reduced B. subtilis strain. Subsequent high cell-density fed-batch bioreactor cultivations using strain IIG-Bs-20-5-1 resulted in a volumetric casein titer of 56.9 mg/L and a yield of 1.6 mgcasein/gCDW after reducing the B. subtilis protein content. Comparative analyses of zeta potential and particle size between pre-cleaned recombinant and native αS1-casein showed pH-mediated differences in aggregation behavior. Conclusions: The study demonstrates the potential of B. subtilis for the recombinant production of bovine αS1-casein and underlines the potential of genome reduction for the bioproduction of difficult-to-produce proteins. Full article
(This article belongs to the Special Issue Editorial Board Members’ Collection Series: How Microbial Cell Factories Can Help Change the World)
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