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Fermentation
Special Issues
Fungal Secondary Metabolism: Discovery and Characterization of Biologically Active Compounds
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Fungal Secondary Metabolism: Discovery and Characterization of Biologically Active Compounds

A special issue of Fermentation (ISSN 2311-5637). This special issue belongs to the section "Microbial Metabolism, Physiology & Genetics".

Deadline for manuscript submissions: 30 November 2025 | Viewed by 1524

Special Issue Editors

Prof. Dr. Wen Huang

E-Mail Website
Guest Editor
College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
Interests: polysaccharides; triterpenes; immunoregulation; fungi; edible mushrooms
Special Issues, Collections and Topics in MDPI journals
Dr. Ying Liu

E-Mail Website
Guest Editor
College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
Interests: fungi; edible mushrooms; mycelial fermentation; biosynthesis; multiomics; functional food
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Fungi are biodiverse, with more than 97,000 fungal species described, accounting for only about 6% of the total. About 50% of biologically active microbial secondary metabolites are produced by filamentous fungi. These secondary metabolites have broad applications in the medical, agricultural, and food fields. At present, most of the antibiotics, immunomodulators, hypolipidemic, and cholesterol drugs with important clinical application value are derived from secondary metabolites of fungi. Due to the important application value of fungal secondary metabolites, the study of fungal secondary metabolism has always been a research hotspot. However, the yield of fungal secondary metabolites is low enough for large-scale extraction and purification. To address this limitation, the biosynthesis of these compounds is often enhanced through methods and strategies such as fermentation media optimization, gene-level modification, and exogenous stimulation. We mainly focus on the isolation and purification, structure identification, activity analysis, fermentation process optimization, metabolic pathway analysis, synthesis regulation, and other aspects of fungal secondary metabolites in the Special Issue.

Prof. Dr. Wen Huang
Dr. Ying Liu
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. 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.

Keywords

  • fungi
  • fermentation
  • secondary metabolism
  • functional component
  • separation and purification
  • bioactivity
  • structural characteristics
  • omics
  • metabolic pathways
  • biosynthesis

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Published Papers (3 papers)

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21 pages, 3369 KiB  
Article
Digestate-Based Liquid Growth Medium for Production of Microbial Chitosan
by Silvia Crognale, Cristina Russo, Eleonora Carota, Ilaria Armentano, Federico Di Gregorio, Alessandro D’Annibale, Alessio Cimini and Maurizio Petruccioli
Fermentation 2025, 11(8), 469; https://doi.org/10.3390/fermentation11080469 - 15 Aug 2025
Abstract
This study investigated the feasibility of using both the solid and the liquid fractions of waste from the anaerobic digestion process—the digestate—as a possible liquid growth medium for fungal production of chitosan. An enriched liquid phase (ELP), combining both fractions, and derived from [...] Read more.
This study investigated the feasibility of using both the solid and the liquid fractions of waste from the anaerobic digestion process—the digestate—as a possible liquid growth medium for fungal production of chitosan. An enriched liquid phase (ELP), combining both fractions, and derived from mild acid hydrolysis treatment at 120 °C with 6% H2SO4 (w/v) for 70 min, was screened for its ability to support biomass and chitosan production by 17 fungal strains. The best results were obtained with Absidia blakesleeana NRRL 2696 and Rhizopus oryzae NRRL 1510 cultures, which yielded chitosan volumetric productions of 444 and 324 mg L−1, respectively. The chitosan preparations of the former and the latter strain, characterized by infrared spectroscopy, elemental analysis, viscosimetry and thermogravimetric analysis, showed deacetylation degrees of 79% and 84.2%, respectively, and average viscosimetric molecular weights of around 20 and 5.4 kDa, respectively. Moreover, both fungal chitosan samples exerted significant antibacterial activity towards Gram-negative (i.e., Pseudomonas syringae and Escherichia coli) and Gram-positive (i.e., Bacillus subtilis) species. Full article
(This article belongs to the Special Issue Fungal Secondary Metabolism: Discovery and Characterization of Biologically Active Compounds)
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23 pages, 11314 KiB  
Article
Transcriptomic Analysis Reveals Opposing Roles of CEL1B in Sophorose- and Lactose-Induced Cellulase Expression in Trichoderma reesei Rut C30
by Lu Wang, Junping Fan, Xiao He, Jian Cheng, Xinyan Zhang, Tian Tian and Yonghao Li
Fermentation 2025, 11(8), 439; https://doi.org/10.3390/fermentation11080439 - 31 Jul 2025
Viewed by 394
Abstract
The β-glucosidase CEL1B has been linked to regulating cellulase expression in Trichoderma reesei, yet its inducer-specific functions and broader regulatory roles remain poorly characterized. In this study, CRISPR-Cas9-mediated gene knockout was applied in the industrial high-producing T. reesei Rut C30 to investigate [...] Read more.
The β-glucosidase CEL1B has been linked to regulating cellulase expression in Trichoderma reesei, yet its inducer-specific functions and broader regulatory roles remain poorly characterized. In this study, CRISPR-Cas9-mediated gene knockout was applied in the industrial high-producing T. reesei Rut C30 to investigate CEL1B function without the confounding effects of KU70 deletion. Unlike previous studies focused solely on cellulose or lactose induction, transcriptomic analysis of the CEL1B knockout strain revealed its regulatory roles under both lactose- and sophorose-rich conditions, with sophorose representing the most potent natural inducer of cellulase expression. Under lactose induction, CEL1B deletion resulted in a 52.4% increase in cellulase activity (p < 0.05), accompanied by transcriptome-wide upregulation of β-glucosidase genes (CEL3A: 729%, CEL3D: 666.8%, CEL3C: 110.9%), cellulose-sensing receptors (CRT1: 203.0%, CRT2: 105.8%), and key transcription factors (XYR1: 2.7-fold, ACE3: 2.8-fold, VIB1: 2.1-fold). Expression of ER proteostasis genes was significantly upregulated (BIP1: 3.3-fold, HSP70: 6.2-fold), contributing to enhanced enzyme secretion. Conversely, under sophorose induction, CEL1B deletion reduced cellulase activity by 25.7% (p < 0.05), which was associated with transcriptome profiling showing significant downregulation of β-glucosidase CEL3H (66.6%) and cellodextrin transporters (TrireC30_91594: 79.3%, TrireC30_127980: 76.3%), leading to reduced cellobiohydrolase expression (CEL7A: 57.8%, CEL6A: 67.8%). This first transcriptomic characterization of the CEL1B knockout strain reveals its dual opposing roles in modulating cellulase expression in response to lactose versus sophorose, providing new strategies for optimizing inducer-specific enzyme production in T. reesei. Full article
(This article belongs to the Special Issue Fungal Secondary Metabolism: Discovery and Characterization of Biologically Active Compounds)
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25 pages, 11690 KiB  
Article
Bioprospecting the Endophytic Fungus, Lasiodiplodia theobromae MMPI, for the Integrated Production of Mycoprotein and Exocellular (1→6)-β-Glucan
by Marcelo Luis Kuhn Marchioro, Gabrielli Aline Pietro Bom Candeia, Luana Malaquias Bertoleti, Aneli M. Barbosa-Dekker, Robert F. H. Dekker and Mário Antônio Alves da Cunha
Fermentation 2025, 11(4), 166; https://doi.org/10.3390/fermentation11040166 - 24 Mar 2025
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Abstract
In response to the growing demand for alternative protein sources and functional biomolecules for industrial applications, this study investigated the production of mycoprotein and extracellular (1→6)-β-D-glucan (lasiodiplodan) by the fungus Lasiodiplodia theobromae MMPI, establishing an integrated biotechnological platform. Soybean molasses were evaluated as [...] Read more.
In response to the growing demand for alternative protein sources and functional biomolecules for industrial applications, this study investigated the production of mycoprotein and extracellular (1→6)-β-D-glucan (lasiodiplodan) by the fungus Lasiodiplodia theobromae MMPI, establishing an integrated biotechnological platform. Soybean molasses were evaluated as a low-cost fermentation substrate and compared to a sucrose-based medium. The experimental design and response surface methodology defined conditions that maximized mycelial biomass and lasiodiplodan production. Mycelial biomass from soybean molasses was rich in essential amino acids, lipids, and polyunsaturated fatty acids like gamma-linolenic and alpha-linolenic acids, while sucrose favored higher lasiodiplodan production. Antioxidant compounds like gallic acid and catechin were also found in the biomass, showing potential for scavenging free radicals. Soybean molasses promoted lipid-rich biomass, suggesting L. theobromae MMPI’s potential for biofuel production. This study highlights the fungus’ utility in producing mycoproteins, lipids, and lasiodiplodan for food, animal feed, and industrial uses. Full article
(This article belongs to the Special Issue Fungal Secondary Metabolism: Discovery and Characterization of Biologically Active Compounds)
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