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Novel and Old Insights for Biotechnological Exploitation of Actinomycetota Strain...
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Novel and Old Insights for Biotechnological Exploitation of Actinomycetota Strain Fermentations

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

Deadline for manuscript submissions: 30 April 2026 | Viewed by 1702

Special Issue Editor

Dr. Giuseppe Gallo

E-Mail Website
Guest Editor
1. Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, Palermo University, 90128 Palermo, Italy
2. National Biodiversity Future Center, Piazza Marina n. 61, 90133 Palermo, Italy
Interests: morpho-physiological and molecular characterization of strains belonging to actinobacteria; analysis of membrane extracellular vesicles produced by streptomycetes; antibiotic production by actinobacterial strain fermentation; biosynthesis of microbial bioactive metabolites; analysis of biosynthetic gene clusters; isolation and characterization of plant growth promoting bacteria; analysis of microbiome of biotic or abiotic matrices; sewage sludge/soil/plant microbiome modulation

Special Issue Information

Dear Colleagues,

I would like to invite you to contribute to the Special Issue ‘Novel and Old Insights for Biotechnological Exploitation of Actinomycetota Strain Fermentations,’ which aims to bring together researchers worldwide to explore the diverse metabolic and biochemical potential of these bacteria.

Members of the phylum Actinomycetota (formerly known as Actinobacteria) are renowned for their biotechnological and industrial relevance, particularly for bioactive compound and enzyme production. Genera such as Streptomyces have historically played a pivotal role in the biosynthesis of valuable products. Today, omics-based approaches are revolutionizing our understanding of Actinomycetota biology, driving both traditional and innovative biotechnological applications. However, several challenges remain, including improving product yield and quality, as well as uncovering cryptic compounds.

This Special Issue welcomes contributions that highlight both classical and emerging approaches for fermenting well-studied or rare Actinomycetota strains, particularly focusing on the following topics: strain improvement, fermentation optimization, metabolic engineering, omics investigation, microbial interactions in co-cultures, extracellular vesicle isolation, biogenic nanomaterial production, and the discovery of novel bioactive compounds.

I encourage you to share your latest research to promote new perspectives and advance the knowledge in the field of Actinomycetota strain fermentation.

Best regards,

Dr. Giuseppe Gallo
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 250 words) can be sent to the Editorial Office for assessment.

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

  • actinomycetota
  • actinobacteria
  • fermentation
  • biotechnological exploitation
  • metabolic engineering
  • bioactive compounds
  • strain improvement
  • omics studies
  • mixed cultures
  • enzyme production
  • microbial interactions

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Published Papers (2 papers)

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Research

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15 pages, 2628 KB  
Article
Enhanced Cultivation of Actinomycetota Strains from Millipedes (Diplopoda) Using a Helper Strain-Assisted Method
by Yingying Shi, Eun-Young Seo, Jeffrey S. Owen, Zhaoyun He, Liufei Shi, Chang Yan, Wenhan Lin, Dawoon Jung and Shan He
Fermentation 2026, 12(1), 16; https://doi.org/10.3390/fermentation12010016 - 27 Dec 2025
Viewed by 468
Abstract
The limited cultivability of Actinomycetota strains restricts the exploration of their novel antibiotics, highlighting the need for improved isolation techniques. This study employed a helper strain-assisted cultivation method which utilizes culture supernatants from helper strains to isolate diverse members of the Actinomycetota from [...] Read more.
The limited cultivability of Actinomycetota strains restricts the exploration of their novel antibiotics, highlighting the need for improved isolation techniques. This study employed a helper strain-assisted cultivation method which utilizes culture supernatants from helper strains to isolate diverse members of the Actinomycetota from millipedes and compared its efficacy with a standard method. Using a preliminary dual-layer solid media assay and subsequent confirmation experiments, eight helper strains (M3, M9, M13, N3, N4, N6, N8, and N9) were identified, whose supernatants promoted the growth of Actinomycetota and other microbes. Application of this method to millipede samples established a novel cultivation strategy based on co-cultivation with helper strains. The new method enabled the isolation of 233 bacterial species in total, of which 143 were species of the phylum Actinomycetota, including 49 novel species. In contrast, the standard method yielded only 42 total bacterial species and 29 species of Actinomycetota, with merely 8 novel species. Comparative diversity analysis revealed that the helper strain-assisted method yielded Actinomycetota strains from 85 genera, which was 3.5 times higher than the standard method. This demonstrates that the helper strain-assisted approach is a highly effective strategy for accessing diverse and novel microbial majority. Among the isolated Actinomycetota strains, 75 strains predicted to have high biosynthetic gene clusters (BGCs) numbers or expected to be novel species were screened for antibacterial activity. Fourteen strains (17%) exhibited inhibitory effects against at least one indicator bacterium. One novel strain, Streptomyces sp. N8-31, was selected for whole-genome sequencing. AntiSMASH analysis predicted 40 biosynthetic gene clusters in N8-31, with 60% showing less than 70% similarity to known clusters; among these, 20 clusters showed less than 50% similarity. These findings indicate that strain N8-31 is a rich reservoir of novel genetic resources, and its broad-spectrum antibacterial activity is likely linked to these unique secondary metabolite gene clusters. Critically, this study confirms that helper strain-assisted cultivation is a powerful tool for unlocking the hidden biosynthetic potential of previously inaccessible Actinomycetota. Full article
(This article belongs to the Special Issue Novel and Old Insights for Biotechnological Exploitation of Actinomycetota Strain Fermentations)
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Review

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21 pages, 1980 KB  
Review
Secondary Metabolites from Actinokineospora spp.: Insights into a Sparsely Studied Genus of Actinomycetes
by Oleksandr Yushchuk
Fermentation 2025, 11(12), 663; https://doi.org/10.3390/fermentation11120663 - 27 Nov 2025
Viewed by 742
Abstract
The genus Actinokineospora (family Pseudonocardiaceae) has recently emerged as a prolific source of structurally diverse, biologically active specialized metabolites. Actinokineospora spp. are filamentous actinomycetes isolated from various terrestrial biotopes. The genus is still sparsely represented taxonomically, with only 19 species holding validly [...] Read more.
The genus Actinokineospora (family Pseudonocardiaceae) has recently emerged as a prolific source of structurally diverse, biologically active specialized metabolites. Actinokineospora spp. are filamentous actinomycetes isolated from various terrestrial biotopes. The genus is still sparsely represented taxonomically, with only 19 species holding validly published names and genome sequences available for an additional six strains. Nevertheless, Actinokineospora appears to have one of the highest biosynthetic novelty index values among actinomycetes, making it a prime candidate for the discovery of new specialized metabolites. To date, several Actinokineospora strains have shown antimicrobial activity, including Actinokineospora acnipugnans R434T, Actinokineospora alba 03-9939T, Actinokineospora fastidiosa NRRL B-16697T, Actinokineospora riparia C-39162T, Actinokineospora sp. G85, and Actinokineospora sp. PR83; the active compounds from these strains remain to be identified and characterized. By contrast, detailed chemical characterization has been achieved for several producers: Actinokineospora spheciospongiae EG49T (polyketides actinospene and actinosporins; the lasso peptide actinokineosin), Actinokineospora bangkokensis 44EHWT (polyene thailandins), Actinokineospora fastidiosa ATCC 202099 (nocathiacin thiopeptides), Actinokineospora sp. UTMC 2448 (persiathiacin thiopeptides), and Actinokineospora auranticolor DSM 44650T (kineomіcin glycopeptides). Collectively, these findings establish Actinokineospora as a promising yet underexplored genus for antibiotic discovery and biosynthetic engineering. In this review, we summarize current knowledge on Actinokineospora spp. and provide an in-depth account of specialized metabolite production for those compounds whose structures have been elucidated. Full article
(This article belongs to the Special Issue Novel and Old Insights for Biotechnological Exploitation of Actinomycetota Strain Fermentations)
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