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Fermentation
Special Issues
Microbial Metabolism Focusing on Bioactive Molecules
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Microbial Metabolism Focusing on Bioactive Molecules

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

Deadline for manuscript submissions: 28 February 2026 | Viewed by 2256

Special Issue Editor

Prof. Dr. Ismael Maciel de Mancilha

E-Mail Website1 Website2
Guest Editor
Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Estrada Municipal do Campinho n° 100, Ponte Nova, Lorena, São Paulo 12.602.810, Brazil
Interests: industrial and fermentation microbiology; food science and technology; industrial biotechnology; fermentation technology; probiotics

Special Issue Information

Dear Colleagues,

Over time, microbial metabolism has brought a range of benefits to humanity in relevant areas such as agriculture, food science and technology, human and animal health, the environment, and the sustainable energy sector. In this context, it is worth highlighting microbial metabolism, through which microorganisms meet their own needs and, as a consequence, generate a variety of bioactive metabolites, and some of them have been explored by humans for their own benefit. Due to this evolution, biotechnology emerges, which can be defined as the application of biological materials, including cells or cell derivatives from microorganisms, plants, and animals, for the generation of useful products and inputs.

This Special Issue proposes to discuss recent findings related to microbial metabolism and its potential to produce functional compounds. We aim to receive contributions that explore microbial pathways and their biotechnological applications in health, food production, and sustainability, highlighting how these metabolic products can contribute to innovation and scientific advancement.

Prof. Dr. Ismael Maciel de Mancilha
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

  • microbial metabolism
  • bioactive metabolites
  • biotechnology
  • microbial pathways
  • metabolic products

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (3 papers)

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Research

23 pages, 1790 KB  
Article
Genomic and Metabolomic Characterization of Kitasatospora griseola JNUCC 62 from Mulyeongari Oreum and Its Cosmeceutical Potential
by Mi-Sun Ko, Mi-Yeon Moon and Chang-Gu Hyun
Fermentation 2025, 11(12), 671; https://doi.org/10.3390/fermentation11120671 - 29 Nov 2025
Viewed by 329
Abstract
The actinobacterial strain Kitasatospora griseola JNUCC 62 was isolated from volcanic wetland soil at Mulyeongari Oreum, Jeju Island, and taxonomically identified through 16S rRNA gene and whole-genome analyses. The complete genome, assembled from PacBio Sequel I reads, spans 8.31 Mb with a GC [...] Read more.
The actinobacterial strain Kitasatospora griseola JNUCC 62 was isolated from volcanic wetland soil at Mulyeongari Oreum, Jeju Island, and taxonomically identified through 16S rRNA gene and whole-genome analyses. The complete genome, assembled from PacBio Sequel I reads, spans 8.31 Mb with a GC content of 72.8% and contains 7265 coding sequences. Comparative genomic indices (Average nucleotide identity, ANI 97.46%; digital DNA–DNA hybridization, dDDH 84.4%) confirmed its conspecific relationship with K. griseola JCM 3339T. Genome mining using antiSMASH 8.0 revealed 30 biosynthetic gene clusters (BGCs), including polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS), ribosomally synthesized and post-translationally modified peptide (RiPP), lanthipeptide, and terpene types, accounting for 18.6% of the genome. Several BGCs displayed homology to known formicamycin-, lankacidin-, and lanthipeptide-type clusters, while others were novel or cryptic, reflecting adaptation to the nutrient-poor volcanic environment. Ethyl acetate extraction of the culture broth, especially under tryptophan-supplemented conditions, yielded four metabolites—1-acetyl-β-carboline, perlolyrine, tryptopol, and 1H-pyrrole-2-carboxylic acid—identified by UV and NMR spectroscopy. These compounds correspond to NRPS–PKS hybrid and arylpolyene-type gene clusters predicted in the genome, suggesting precursor-directed biosynthesis of indole and pyrrole alkaloids. The ethyl acetate extract (JNUCC62 EA) exhibited strong antioxidant capacity in the ABTS assay, anti-inflammatory activity via inhibition of nitric oxide (31.09 ± 3.69% of control) and cytokines (IL-6, IL-1β, TNF-α) in lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophages, and anti-melanogenic effects in α-melanocyte-stimulating hormone (MSH)-stimulated B16F10 melanoma cells, where melanin content and tyrosinase activity decreased to 61.49 ± 1.24% and 24.32 ± 0.31% of the control, respectively, without cytotoxicity. A human primary skin irritation test confirmed no irritation up to 50 µg/mL, establishing excellent dermal safety. Collectively, these findings highlight K. griseola JNUCC 62 from Mulyeongari Oreum as a volcanic wetland-derived actinomycete harboring rich biosynthetic potential for novel indole alkaloids with antioxidant, anti-inflammatory, and whitening properties, supporting its development as a safe and multifunctional cosmeceutical ingredient. Full article
(This article belongs to the Special Issue Microbial Metabolism Focusing on Bioactive Molecules)
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17 pages, 771 KB  
Article
In Vitro Characterization of Veillonella atypica ATCC 17744 Regarding Its Functional Properties
by Julia Cristina Fernandes, Fernanda Weber Bordini, Anuj Kumar Chandel and Ismael Maciel de Mancilha
Fermentation 2025, 11(11), 612; https://doi.org/10.3390/fermentation11110612 - 28 Oct 2025
Viewed by 906
Abstract
The growing demand for functional foods has stimulated the search for novel microbial strains with probiotic potential, such as Veillonella atypica ATCC 17744, which has been emerging as a promising strain. Therefore, the present study aimed to perform an in vitro characterization of [...] Read more.
The growing demand for functional foods has stimulated the search for novel microbial strains with probiotic potential, such as Veillonella atypica ATCC 17744, which has been emerging as a promising strain. Therefore, the present study aimed to perform an in vitro characterization of this strain, focusing on safety aspects and functional properties such as stress tolerance (pH, bile salts, and simulated gastrointestinal conditions), adhesion capacity (hydrophobicity, auto-aggregation, and biofilm formation), anti-pathogenic activity, antioxidant activity, antibiotic susceptibility, and enzymatic synthesis ability (gelatinase, lipase, catalase, and hemolytic activity). Stress tolerance assays revealed that this strain is sensitive to pH values below 4.00; however, no reduction in cell viability was observed at pH 3.00 in the presence of pepsin or 0.3% and 0.6% bile salts. Hydrophobicity testing showed moderate tolerance to toluene and low tolerance to xylene. Regarding biofilm synthesis, this strain formed a weak biofilm after 48 h of incubation. No anti-pathogenic activity was observed against Streptococcus aureus or Escherichia coli, and it exhibited low antioxidant activity in the DPPH assay. Regarding its safety properties, this strain was sensitive to all tested antibiotics and did not synthesize gelatinase, lipase, catalase, or exhibit β-hemolytic activity. Therefore, Veillonella atypica ATCC 17744 presents promising characteristics supporting its potential application in the development of functional food formulations, although further studies are required to ensure its safety for human consumption. Full article
(This article belongs to the Special Issue Microbial Metabolism Focusing on Bioactive Molecules)
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14 pages, 884 KB  
Article
The Effect of Carbon Sources on Carotenoid Synthesis by the Novel Rhodococcus corynebacterioides TAO1
by Elif Yürümez Canpolat and Tuba Artan Onat
Fermentation 2025, 11(10), 599; https://doi.org/10.3390/fermentation11100599 - 21 Oct 2025
Viewed by 855
Abstract
The financial feasibility of microbial carotenoid synthesis can be markedly improved by using widely available and renewable carbon sources. In this study, different carbon sources including molasses, were tested as carbon sources for Rhodococcus corynebacteioides TAO1. The effect of different molasses concentrations (50–250 [...] Read more.
The financial feasibility of microbial carotenoid synthesis can be markedly improved by using widely available and renewable carbon sources. In this study, different carbon sources including molasses, were tested as carbon sources for Rhodococcus corynebacteioides TAO1. The effect of different molasses concentrations (50–250 mL/L) on bacterial growth, carotenoid synthesis, and exopolysaccharide production was determined during a 30-day period. The results demonstrated an upward trend between molasses concentration and bacterial dry weight up to 200 mL/L, with the highest dry weight measured as 0.656 ± 0.049 g. Bacterial growth was decreased at 250 mL/L molasses concentration due to possible carbon-source inhibition. However, carotenoid production exhibited a negative interaction with a maximum yield of 1.572 ± 0.108 mg/g in basal medium, while the lowest carotenoid production was determined as 0.84 ± 0.007 mg/g at 250 mL/L molasses concentration, showing that increased carbon availability might inhibit pigment biosynthesis. FTIR analysis indicated significant functional groups, such as C=O, O-H, C=C, and =CH, with significant peaks at 1713, 1655, and 1459 cm−1, indicating the presence of carotenoid intermediates. The data highlight the interaction between carbon source concentration and microbial metabolism, emphasizing the importance of optimal nutrient factors for improving both carotenoid and EPS production. This research presents significant insights into economical biotechnological methods for the production of microbial pigments and biopolymers from industrial by-products. Full article
(This article belongs to the Special Issue Microbial Metabolism Focusing on Bioactive Molecules)
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