Microbial Cell Factories for Natural Products

Topic Information

Dear Colleagues,

Microorganisms, in some way, are considered microbial cell factories and can aid in the production of natural products with applications in pharmaceuticals (human and animal health), agriculture, food, feed, cosmetics, and industry. Advances in microbial biotechnology, from classical strain selection to sophisticated metabolic engineering approaches boosted by synthetic biology methodologies, have significantly expanded the diversity, yield, and profit of bio-based compounds. These include primary and secondary metabolites that result in a diverse array of compounds such as antibiotics, biofertilizers, carotenoids, colorants, enzymes, immunosuppressants, proteins, or steroids, among others. At present, the development of high-throughput omics technologies (genomics, transcriptomics, proteomics, and metabolomics) is providing unprecedented insights into microbial metabolism, enhancing the selection, improvement, and optimization of industrial strains. Moreover, emerging metaomics approaches, such as metagenomics, metataxonomics, metatranscriptomics, and metaproteomics, in many cases assisted by AI, are also widening the scope of applications from novel biological data sources. As can be seen from the information presented above, microorganisms (bacteria, fungi, and yeasts), themselves or as microbial platforms, continue to evolve as powerful tools for sustainable bioproduction through rational engineering approaches or by means of non engineered adaptive strategies. As part of the Topics Project, this Special Issue invites submissions of research articles, reviews, and perspectives covering both fundamental and applied aspects of microbial cell factories for natural products. Topics of interest include, but are not limited to, the following:

• Strain selection and improvement strategies, including adaptive evolution and genome editing.
• Metabolic and synthetic biology approaches for pathway optimization.
• Omics-driven discovery and enhancement of microbial producers.
• Fermentation strategies and bioprocess optimization.
• Industrial applications of microbial cell factories for clinical, agricultural, food, feed, and cosmetics applications.
• Downstream processes to enhance the yield and quality of the products.

We also welcome contributions that explore new microbial platforms, innovative production strategies, and interdisciplinary approaches to enhance the biosynthesis of high-value natural products.

Dr. Carlos Barreiro
Dr. Ana Ibáñez
Dr. José L. Barredo
Topic Editors

Keywords

Participating Journals

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Applied Biosciences applbiosci	-	2.9	2022	22.8 Days	CHF 1200	Submit
Applied Microbiology applmicrobiol	-	2.8	2021	16.2 Days	CHF 1200	Submit
Fermentation fermentation	3.3	5.7	2015	19.5 Days	CHF 2100	Submit
Marine Drugs marinedrugs	5.4	10.1	2003	13.6 Days	CHF 2900	Submit
Microorganisms microorganisms	4.2	7.7	2013	20 Days	CHF 2700	Submit

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Published Papers (2 papers)

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All Applied Biosciences Applied Microbiology Fermentation Marine Drugs Microorganisms

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Open AccessArticle

The Metabolism of Streptomyces avermitilis Isolated from Agricultural Soils During the Four Seasons of the Year

by Janet Leandro Marmolejo, María Magdalena Crosby Galván, Elsa Margarita Crosby Galván, Laura Haydée Vallejo Hernández, María Teresa Sánchez-Torres Esqueda, César Cortez Romero and Ricardo Daniel Améndola Massiotti

Appl. Microbiol. 2025, 5(4), 138; https://doi.org/10.3390/applmicrobiol5040138 - 27 Nov 2025

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Abstract

Streptomyces avermitilis is a soil actinobacterium and has a complex metabolism in its natural habitat. Because of this, the environmental fluctuations present in the seasons can activate or silence the biosynthetic pathways involved in its metabolism. The objective of this research was to [...] Read more.

Streptomyces avermitilis is a soil actinobacterium and has a complex metabolism in its natural habitat. Because of this, the environmental fluctuations present in the seasons can activate or silence the biosynthetic pathways involved in its metabolism. The objective of this research was to analyze the morphological characteristics of the metabolism of Streptomyces avermitilis, isolated during the four seasons of the year and from four types of soil. Isolation was performed on oat agar ISP-3 and nystatin as an antifungal agent. The planting methods were rod drag and cross striations. The Petri dishes were incubated for 10 days at 30 °C in complete darkness. For 10 days, a colony count was performed to analyze the growth curves, as was an evaluation of the diffusible pigments in each Petri dish. The isolates presented the diffusible pigments white, yellow, orange, red and pink with a higher proportion in spring and summer compared to in autumn and winter. Under laboratory conditions, the isolates in summer presented the three phases of bacterial growth: lag (24 h), exponential (48–96 h) and stationary (120–168 h). A doubling time of 35.30–62.92 h was obtained. The morphological characteristics of the metabolism of Streptomyces avermitilis show differences according to the climatic conditions of each season of the year. Full article

(This article belongs to the Topic Microbial Cell Factories for Natural Products)

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23 pages, 2825 KB  

Open AccessReview

Metabolic Engineering of Yeasts for the Production of the Triterpene Squalene: Current Status and Future Prospective

by Shasha Zuo, Xinjia Tan, Jiwei Mao, Fanglin Hu, Jiaxu Chen, Liusha Fan, Qiyuan Lu, Yifei Zhao, Yongtong Wang, Zhiqiang Xiao, Siqi Zhang, Yang Shan, Juan Liu and Fuhua Fu

Microorganisms 2025, 13(11), 2422; https://doi.org/10.3390/microorganisms13112422 - 22 Oct 2025

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Abstract

Squalene, a linear triterpene compound characterized by its distinctive isoprenoid backbone with six transisoprene units, is widely used in the medicinal, nutraceutical, and cosmetic industries. The escalating global demand for squalene, coupled with growing ethical concerns over shark-derived sources and the inherent limitations [...] Read more.

Squalene, a linear triterpene compound characterized by its distinctive isoprenoid backbone with six transisoprene units, is widely used in the medicinal, nutraceutical, and cosmetic industries. The escalating global demand for squalene, coupled with growing ethical concerns over shark-derived sources and the inherent limitations of plant extraction (low yield) and chemical synthesis (environmental burden), has propelled microbial biosynthesis as a sustainable alternative. While substantial progress has been made in elucidating the mevalonate pathway and regulatory mechanisms of squalene biosynthesis, achieving industrially viable titers through microbial platforms remains an unresolved challenge. This review systematically summarizes recent advances in squalene biosynthesis using yeast chassis, with a focus on metabolic engineering strategies implemented in Saccharomyces cerevisiae and Yarrowia lipolytica. Furthermore, we elaborated on how squalene yields a diverse array of downstream derivatives through intricate enzymatic reactions. These derivatives—including triterpenoid saponins, triterpenoid acids, and steroids—exhibit significant applications in the pharmaceutical, nutraceutical, and cosmetic sectors. By integrating systems metabolic engineering with emerging synthetic biology tools, this work provides a roadmap for advancing strain engineering toward economically feasible squalene biomanufacturing. Full article

(This article belongs to the Topic Microbial Cell Factories for Natural Products)

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