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Microorganisms
Special Issues
Advances in Microbial Cell Factories, 3rd Edition
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Advances in Microbial Cell Factories, 3rd Edition

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

Deadline for manuscript submissions: 30 November 2025 | Viewed by 1404

Special Issue Editors

Prof. Dr. Thomas Brück

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Guest Editor
Werner Siemens Chair of Synthetic Biotechnology, School of Natural Sciences, Department of Chemistry, Technical University of Munich (TUM), D-85748 Garching bei München, Germany
Interests: biocatalysis; system biology; enzyme and metabolic engineering; synthetic biology; sustainable bioprocess engineering
Special Issues, Collections and Topics in MDPI journals
Dr. Dania Awad

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Guest Editor
Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), D-85748 Garching bei München, Germany
Interests: synthetic biotechnology; bioprocess development; proteomics; bioinformatics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue continues our previous Special Issues "Advances in Microbial Cell Factories, 2nd Edition” and “Advances in Microbial Cell Factories”.

In the “cell factory” concept, microorganisms convert substrates into desirable products. Well-established fermentation products include beer, antibiotics and insulin. Recent developments enabled by native and engineered microbial cell factories include oleochemicals, biopolymers, biofuels, animal feed, biopesticides, nutraceuticals and flavors. Currently, the availability of standardized and newly developed cloning and expression vectors, the accessibility and affordability of de novo DNA synthesis, the advancement in bioinformatics tools and the expansion of biological databases have allowed cells to become more programmable. In this revolutionized era, the design and modeling of bioprocesses, AI-guided automation and high-throughput process monitoring significantly reduce bioprocess development time and costs. Despite all this progress, only a few biotechnological processes have been adopted at an industrial level outside the confines of laboratory settings. Challenges and bottlenecks still need to be addressed at several levels, including feedstock flexibility, bioreactor design, metabolic burdens and downstream processing and iterative scale-up.

This Special Issue of Microorganisms provides a platform for authors to present novel tools and scientific concepts on microbial cell factories through research articles, reviews and Editorials. We invite you to send contributions relating to the development of microbial production platforms of eukaryotic and prokaryotic origin.

Prof. Dr. Thomas Brück
Dr. Dania Awad
Guest Editors

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

  • sustainability
  • biotechnology
  • bioengineering
  • biocatalysis
  • fermentation

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Published Papers (3 papers)

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Research

18 pages, 8726 KiB  
Article
Dynamic Response Mechanisms of Anammox Reactors Under Nitrogen-Loading Fluctuations: Nitrogen Removal Performance, Microbial Community Succession, and Metabolic Functions
by Xuemei Liu, Kai Wan, Chunqiao Xiao, Jingang Hu, Xiangyi Deng and Ruan Chi
Microorganisms 2025, 13(4), 899; https://doi.org/10.3390/microorganisms13040899 - 14 Apr 2025
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Abstract
The leachate from ion-adsorbed rare earth tailings poses challenges to the application of the anaerobic ammonium oxidation (anammox) process in this field due to its large fluctuations in ammonia nitrogen concentration (50–300 mg/L) and high flow rate (4000–10,000 m3/d). This study [...] Read more.
The leachate from ion-adsorbed rare earth tailings poses challenges to the application of the anaerobic ammonium oxidation (anammox) process in this field due to its large fluctuations in ammonia nitrogen concentration (50–300 mg/L) and high flow rate (4000–10,000 m3/d). This study investigated the effects of nitrogen-loading rate (NLR) regulation on denitrification performance through reactor operation and elucidated the mechanisms of NLR impacts on anammox processes via microbial community analysis and metabolic profiling. The results revealed a nonlinear relationship between nitrogen loading and system performance. As NLR increased, both denitrification efficiency and anammox bacterial abundance (rising from 5.85% in phase P1 to 11.43% in P3) showed synchronous enhancement. However, excessive nitrogen loading (>3.68 kg/m3·d) or nitrogen starvation led to performance deterioration and reduced anammox bacterial abundance. Microbial communities adopted modular collaboration to counteract loading stress, with modularity indices of 0.563 and 0.545 observed in the inhibition phase (P2) and starvation phase (P4), respectively. Zi-Pi plot analysis demonstrated a significant increase in inter-module connectivity, indicating reinforced interspecies interactions among microorganisms to resist nitrogen-loading fluctuations. Full article
(This article belongs to the Special Issue Advances in Microbial Cell Factories, 3rd Edition)
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20 pages, 10288 KiB  
Article
Automation of RNA-Seq Sample Preparation and Miniaturized Parallel Bioreactors Enable High-Throughput Differential Gene Expression Studies
by Karlis Blums, Josha Herzog, Jonathan Costa, Lara Quirico, Jonas Turber and Dirk Weuster-Botz
Microorganisms 2025, 13(4), 849; https://doi.org/10.3390/microorganisms13040849 - 8 Apr 2025
Viewed by 432
Abstract
A powerful strategy to accelerate bioprocess development is to complement parallel bioreactor systems with an automated approach, often achieved using liquid handling stations. The benefit of such high-throughput experiments is determined by the employed monitoring procedures. To gain a molecular understanding of the [...] Read more.
A powerful strategy to accelerate bioprocess development is to complement parallel bioreactor systems with an automated approach, often achieved using liquid handling stations. The benefit of such high-throughput experiments is determined by the employed monitoring procedures. To gain a molecular understanding of the microbial production strains in miniaturized parallel single-use bioreactors, we extended the at-line monitoring procedures to transcriptome analysis in a parallel approach using RNA-Seq. To perform automated RNA-Seq experiments, we developed a sample preparation workflow consisting of at-line cell disruption by enzymatic cell lysis, total RNA extraction, nucleic acid concentration normalization, and Nanopore cDNA Library preparation. The pH-controlled aerobic batch growth of Saccharomyces cerevisiae was studied with six different carbon sources (glucose, pyruvate, fructose, galactose, sucrose, and mannose) on a 11 mL scale using 24 parallel stirred tank bioreactors integrated into a liquid handling station while performing at-line sample preparation for RNA-Seq on the same deck. With four biological replicates per condition, 24 cDNA libraries were prepared over 11.5 h. Off-line Nanopore sequencing yielded 20.97 M classified reads with a Q-score > 9. Differential gene expression analysis revealed significant differences in transcriptomic profiles when comparing growth with glucose (exponential growth) to growth with pyruvate (stress conditions), allowing identification of 674 downregulated and 709 upregulated genes. Insignificant changes in gene expression patterns were measured when comparing growth with glucose and fructose, yielding only 64 differentially expressed genes. The expected differences in cellular responses identified in this study show a promising approach for transcriptomic profiling of bioreactor cultures, providing valuable insights on a molecular level at-line in a high-throughput fashion. Full article
(This article belongs to the Special Issue Advances in Microbial Cell Factories, 3rd Edition)
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15 pages, 2271 KiB  
Article
Alien Chromosome Serves as a Novel Platform for Multiple Gene Expression in Kluyveromyces marxianus
by Yilin Lyu, Jungang Zhou, Yao Yu and Hong Lu
Microorganisms 2025, 13(3), 509; https://doi.org/10.3390/microorganisms13030509 - 25 Feb 2025
Viewed by 454
Abstract
Kluyveromyces marxianus is an emerging yeast cell host for diverse products, but multiple-gene expression in K. marxianus faces challenges due to limited current knowledge of cis-regulatory elements and insertion loci. Our previous study transferred an alien Saccharomyces cerevisiae chromosome I (R1) into [...] Read more.
Kluyveromyces marxianus is an emerging yeast cell host for diverse products, but multiple-gene expression in K. marxianus faces challenges due to limited current knowledge of cis-regulatory elements and insertion loci. Our previous study transferred an alien Saccharomyces cerevisiae chromosome I (R1) into K. marxianus, resulting in the creation of the monochromosomal hybrid yeast KS-R1. All R1 genes were actively transcribed, providing a series of loci with varying transcriptional activities. Here, we explore the use of R1 as a novel platform for stable, multi-gene integration and expression. By deleting three essential K. marxianus genes while complementing their functions with orthologs on R1, we achieved stable propagation of R1 in the absence of selective pressure. We characterized several loci on R1 that exhibit stable transcriptional activities under various conditions. GFP inserted in place of genes at six such loci demonstrated varying expression levels. Strains with GFP at two loci exhibited significantly higher expression than those with GFP at a single locus. Furthermore, we replaced five R1 genes with disulfide bond formation genes from Pichia pastoris at distinct loci, resulting in the active expression of all five genes and significantly enhanced production of heterologous glucoamylases BadGLA and TeGlaA. Our findings demonstrate that alien chromosomes offer a stable and versatile platform for the coordinated expression of multiple heterologous genes, serving as valuable tools for metabolic engineering and synthetic biology. Full article
(This article belongs to the Special Issue Advances in Microbial Cell Factories, 3rd Edition)
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