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Biosynthesis of Metabolites from Microorganisms, or Microorganism-Host Interaction? (Volume II)
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Biosynthesis of Metabolites from Microorganisms, or Microorganism-Host Interaction? (Volume II)

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Microbiology".

Deadline for manuscript submissions: 1 September 2025 | Viewed by 11838

Special Issue Editors

Dr. Fengli Zhang

E-Mail Website
Guest Editor
State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
Interests: biosynthesis; biological activity; microbial metabolites; microbe–host reaction
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Zhiqiang Liu

E-Mail Website
Guest Editor
School of Life and Health, Hainan University, Haikou 570228, China
Interests: pathogenic fungi; microorganism-host interaction; secondary metabolites; pathogenesis
Prof. Dr. Michel Denis
*
E-Mail
Guest Editor
Mediterranean Institute of Oceanography UM 110, Aix-Marseille University, Toulon University, CNRS, IRD, Marseille, France
Interests: marine phytoplankton; marine microbial ecology; marine microzooplankton
* Retired
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Microbial metabolites are compounds that microorganisms use to complete their own life activities. They include primary metabolites such as amino acids, lipids, and organic acids, and secondary metabolites such as antibiotics. Different microorganisms produce different metabolites, resulting in diverse structures of metabolites that are widely used in medicine and industry. The biosynthesis of metabolites also provides new ideas and breakthroughs for research in the life sciences.

For this Special Issue, research on the regulation mechanism of metabolite biosynthesis and analyses of the metabolite biosynthesis process are welcome for submission. Moreover, submissions of research on the biological activity of metabolites are also welcome.

Dr. Fengli Zhang
Prof. Dr. Zhiqiang Liu
Prof. Dr. Michel Denis
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. Biology 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

  • biosynthesis
  • biological activity
  • biosynthesis regulation
  • microbial metabolites
  • microbe–host reaction

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Related Special Issue

Published Papers (5 papers)

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Research

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19 pages, 3955 KiB  
Article
Study on the Degradation of Aflatoxin B1 by Myroides odoratimimus 3J2MO
by Xue Wang, Yao-Yao Gao, Dun Wang, Qi Zhang, Hao-Ran Wang, Ting-Ting Zhang, Meng-Jie Zhu, Jing Dong, Dong Ling, Peng Feng, Xue-Hui Tang and Pei-Wu Li
Biology 2025, 14(6), 724; https://doi.org/10.3390/biology14060724 - 19 Jun 2025
Viewed by 290
Abstract
To address the issue of aflatoxin contamination, which poses a significant threat to food safety and human health, we have conducted extensive research. We have isolated a strain of Myroides odoratimimus (3J2MO) from the soil that exhibited remarkable efficiency in degrading various aflatoxin [...] Read more.
To address the issue of aflatoxin contamination, which poses a significant threat to food safety and human health, we have conducted extensive research. We have isolated a strain of Myroides odoratimimus (3J2MO) from the soil that exhibited remarkable efficiency in degrading various aflatoxin types, including AFB1, AFB2, AFG1, AFG2, and AFM1. SDS-PAGE analysis confirmed the purity of the enzymes to be over 95%. Through fluorescence assays, we quantified the enzymatic activity, with an AFB1 degradation rate of 95% achieved at 37 °C and a pH of 8.0. Further analysis using HPLC-MS/MS identified the degradation intermediates, revealing the mechanisms of lactone ring cleavage and epoxy group hydrolysis. GO/COG/KEGG annotations provided insights into the functions of these enzymes, with peroxidase linked to reactive oxygen species (ROS) generation and helicase associated with ATP-dependent conformational changes. Helicase, on the other hand, hydrolyzes ATP, driving conformational changes in AFB1 and facilitating its breakdown into non-toxic metabolites. The potential industrial-scale application of this discovery could significantly mitigate aflatoxin-related economic losses while minimizing chemical residues in the food chain. Full article
(This article belongs to the Special Issue Biosynthesis of Metabolites from Microorganisms, or Microorganism-Host Interaction? (Volume II))
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20 pages, 1383 KiB  
Article
Determination of the Roles of H. pylori Outer Membrane Virulence Factors and Pyroptosis-Associated NLRP3, ASC, Caspase-1, Gasdermin D, IL-1β, and IL-18 in Ulcer and Gastritis Pathogenesis
by Yaren Buyukcolak-Cebeci, Emel Timucin, Sumeyye Akcelik-Deveci, Nesteren Mansur-Ozen, Tuana Aydinlar, Arzu Tiftikci and Sinem Oktem-Okullu
Biology 2025, 14(6), 634; https://doi.org/10.3390/biology14060634 - 30 May 2025
Viewed by 486
Abstract
Background: This study aims to investigate the association between pyroptosis and the outer membrane virulence factor of H. pylori in patients with gastritis and ulcers. Methods: DNA, RNA, and protein were extracted from a single tissue sample taken from the antrum region of [...] Read more.
Background: This study aims to investigate the association between pyroptosis and the outer membrane virulence factor of H. pylori in patients with gastritis and ulcers. Methods: DNA, RNA, and protein were extracted from a single tissue sample taken from the antrum region of the stomach of volunteer patients. The expression of bacterial outer membrane virulence genes was analyzed at the gene level, and the expression levels of key pyroptosis markers were compared between H. pylori-infected and uninfected gastritis and ulcer patient groups. Results: H. pylori infection induced significant alterations in the expression levels of pyroptosis markers, including ASC, NLRP3, caspase-1, GSDMD, IL-18, and IL-1β, indicating a strong association with gastritis and ulcer pathology. Statistically significant correlations were observed between elevated levels of these markers and the activation of caspase-1 across different patient cohorts, supporting effective detection of pyroptosis. Both pro and active forms of caspase-1, GSDMD, IL-18, and IL-1β were assessed, revealing pyroptotic activity in specific patient samples. The vacA m2 allele showed a distinct ASC response in gastritis versus ulcer patients and was associated with increased GSDMD expression in ulcerative cases. Along with the babB gene, this allele appears to play a critical role in the interaction between H. pylori virulence and host pyroptotic responses. A statistically significant negative association was identified between the presence of the H. pylori alpA gene and Gasdermin D expression (odds ratio = 0, p < 0.01), suggesting that Gasdermin D was absent in all alpA-positive samples. Conclusion: This study provides novel insights into the interrelation between the virulence factors of H. pylori and pyroptosis in gastritis and ulcer diseases. Our findings demonstrate that H. pylori infection significantly alters the expression levels of pyroptosis markers, including ASC, NLRP3, caspase-1, GSDMD, IL-18, and IL-1β, in gastric tissues. Notably, the vacA m2 allele was associated with a differential response in ASC expression among patients with gastritis and ulcers, correlating with increased GSDMD levels in ulcerative conditions. The presence of the H. pylori alpA gene is markedly associated with the lack of Gasdermin D activation, indicating a possible suppressive function or immune evasion tactic. These results underscore the critical role of H. pylori virulence determinants in modulating pyroptosis and suggest that understanding this relationship may pave the way for developing targeted therapeutic strategies to mitigate H. pylori-associated pathologies. Full article
(This article belongs to the Special Issue Biosynthesis of Metabolites from Microorganisms, or Microorganism-Host Interaction? (Volume II))
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16 pages, 4088 KiB  
Article
Whole Genome Sequencing of Kodamaea ohmeri SSK and Its Characterization for Degradation of Inhibitors from Lignocellulosic Biomass
by Yong-Qiang Yang, Xu Li, Zhi-Fei Wang, Yu-Long Deng, Zhen-Zhi Wang, Xing-Yu Fang, Mao-Dong Zhang, Wei Sun, Xin-Qing Zhao, Zhi-Qiang Liu and Feng-Li Zhang
Biology 2025, 14(5), 458; https://doi.org/10.3390/biology14050458 - 24 Apr 2025
Viewed by 403
Abstract
Lignocellulosic biomass is widely recognized as a renewable resource for bioconversion. However, the presence of inhibitors such as furfural, 5-HMF, and acetic acid can inhibit cell growth, thereby affecting the overall efficiency of the bioconversion process. The studies on the degradation of lignocellulosic [...] Read more.
Lignocellulosic biomass is widely recognized as a renewable resource for bioconversion. However, the presence of inhibitors such as furfural, 5-HMF, and acetic acid can inhibit cell growth, thereby affecting the overall efficiency of the bioconversion process. The studies on the degradation of lignocellulosic hydrolysate inhibitors by Saccharomyces cerevisiae have been limited. In this research, a yeast strain Kodamaea ohmeri can degrade inhibitors furfural, 5-HMF, and acetic acid, and the genome sequence of the strain was analyzed. Furthermore, the molecular detoxification mechanism of K. ohmeri SSK against lignocellulosic hydrolysate inhibitors was predicted using whole genome sequencing. Annotation based on the COG/KEGG databases identified 57 key detoxification genes, including the alcohol dehydrogenase (ADH) gene, aldo-keto/aldehyde reductase (AKR/ARI) gene, and aldehyde dehydrogenase (ALDH) gene. Stress tolerance experiments revealed that the maximum tolerance concentration for the strain was 5.2 g/L of furfural, 2.5 g/L of 5-HMF, and 5.9 g/L of acetic acid, respectively. A NAD(P)+-dependent bifunctional enzyme with possible ADH and ARI activities was found by conserved domain analysis. Phylogenetic analysis indicated that this enzyme shared 99% homology with the detoxification enzyme from S. cerevisiae S288C (GenBank: Q04894.1). This study represents the first comprehensive analysis of the inhibitor detoxification network in K. ohmeri SSK from a genome perspective, providing theoretical targets and design strategies for developing highly efficient biorefinery strains. Full article
(This article belongs to the Special Issue Biosynthesis of Metabolites from Microorganisms, or Microorganism-Host Interaction? (Volume II))
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19 pages, 3453 KiB  
Article
CopG1, a Novel Transcriptional Regulator Affecting Symbiosis in Bradyrhizobium sp. SUTN9-2
by Praneet Wangthaisong, Pongdet Piromyou, Pongpan Songwattana, Tarnee Phimphong, Apisit Songsaeng, Natcha Pruksametanan, Pakpoom Boonchuen, Jenjira Wongdee, Kamonluck Teamtaisong, Nantakorn Boonkerd, Shusei Sato, Panlada Tittabutr and Neung Teaumroong
Biology 2024, 13(6), 415; https://doi.org/10.3390/biology13060415 - 5 Jun 2024
Viewed by 4889
Abstract
The symbiotic interaction between leguminous and Bradyrhizobium sp. SUTN9-2 mainly relies on the nodulation process through Nod factors (NFs), while the type IV secretion system (T4SS) acts as an alternative pathway in this symbiosis. Two copies of T4SS (T4SS1 and T4SS2 [...] Read more.
The symbiotic interaction between leguminous and Bradyrhizobium sp. SUTN9-2 mainly relies on the nodulation process through Nod factors (NFs), while the type IV secretion system (T4SS) acts as an alternative pathway in this symbiosis. Two copies of T4SS (T4SS1 and T4SS2) are located on the chromosome of SUTN9-2. ΔT4SS1 reduces both nodule number and nitrogenase activity in all SUTN9-2 nodulating legumes. The functions of three selected genes (copG1, traG1, and virD21) within the region of T4SS1 were examined. We generated deleted mutants and tested them in Vigna radiata cv. SUT4. ΔtraG1 and ΔvirD21 exhibited lower invasion efficiency at the early stages of root infection but could be recently restored. In contrast, ΔcopG1 completely hindered nodule organogenesis and nitrogenase activity in all tested legumes. ΔcopG1 showed low expression of the nodulation gene and ttsI but exhibited high expression levels of the T4SS genes, traG1 and trbE1. The secreted proteins from ΔT4SS1 were down-regulated compared to the wild-type. Although ΔcopG1 secreted several proteins after flavonoid induction, T3SS (nopP and nopX) and the C4-dicarboxylate transporter (dct) were not detected. These results confirm the crucial role of the copG1 gene as a novel key regulator in the symbiotic relationship between SUTN9-2 and legumes. Full article
(This article belongs to the Special Issue Biosynthesis of Metabolites from Microorganisms, or Microorganism-Host Interaction? (Volume II))
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Review

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46 pages, 3736 KiB  
Review
Exploring Extremotolerant and Extremophilic Microalgae: New Frontiers in Sustainable Biotechnological Applications
by Dorian Rojas-Villalta, David Rojas-Rodríguez, Melany Villanueva-Ilama, Rossy Guillén-Watson, Francinie Murillo-Vega, Olman Gómez-Espinoza and Kattia Núñez-Montero
Biology 2024, 13(9), 712; https://doi.org/10.3390/biology13090712 - 11 Sep 2024
Cited by 5 | Viewed by 4844
Abstract
Exploring extremotolerant and extremophilic microalgae opens new frontiers in sustainable biotechnological applications. These microorganisms thrive in extreme environments and exhibit specialized metabolic pathways, making them valuable for various industries. The study focuses on the ecological adaptation and biotechnological potential of these microalgae, highlighting [...] Read more.
Exploring extremotolerant and extremophilic microalgae opens new frontiers in sustainable biotechnological applications. These microorganisms thrive in extreme environments and exhibit specialized metabolic pathways, making them valuable for various industries. The study focuses on the ecological adaptation and biotechnological potential of these microalgae, highlighting their ability to produce bioactive compounds under stress conditions. The literature reveals that extremophilic microalgae can significantly enhance biomass production, reduce contamination risks in large-scale systems, and produce valuable biomolecules such as carotenoids, lipids, and proteins. These insights suggest that extremophilic microalgae have promising applications in food, pharmaceutical, cosmetic, and biofuel industries, offering sustainable and efficient alternatives to traditional resources. The review concludes that further exploration and utilization of these unique microorganisms can lead to innovative and environmentally friendly solutions in biotechnology. Full article
(This article belongs to the Special Issue Biosynthesis of Metabolites from Microorganisms, or Microorganism-Host Interaction? (Volume II))
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