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Applied Microbiology
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Exclusive Papers Collection of Editorial Board Members and Invited Scholars...
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Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2025)

A special issue of Applied Microbiology (ISSN 2673-8007).

Deadline for manuscript submissions: 31 December 2025 | Viewed by 4025

Special Issue Editor

Prof. Dr. Ian Connerton

E-Mail Website
Guest Editor
Division of Microbiology, Brewing and Biotechnology, University of Nottingham, Loughborough LE12 5RD, UK
Interests: foodborne disease; bacteriology; bacteriophages; probiotics; prebiotics; antimicrobial resistance; host-pathogen interactions; enzymology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous successful Special Issues, entitled “Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology” and “Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024)”.

As the Editor-in-Chief of Applied Microbiology, I am pleased to acknowledge the support of the research community and their request to extend this initiative. I therefore announce the continuation of the Special Issue entitled “Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2025)”. This Special Issue will be a collection of high-quality papers from Editorial Board Members and invited scholars. The aim is to provide a venue for networking and communication between Applied Microbiology and scholars in this field. All papers will be published as fully open access articles after peer review.

Prof. Dr. Ian Connerton
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 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. Applied Microbiology is an international peer-reviewed open access quarterly 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 1000 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 structure, growth, and metabolism
  • process and products
  • industrial microorganisms, fermentation, downstream processing, and product development
  • microbial enzymes, fuels, and industrial chemicals
  • enzymology and protein engineering
  • healthcare products
  • food and beverage fermentation, food additives and supplements
  • microbial biomass production
  • microbial biodeterioration of materials
  • applied genetics and molecular biotechnology
  • applied microbial and cell physiology
  • environmental biotechnology
  • antimicrobial agents
  • microbiomes
  • biofilms

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  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

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

Related Special Issues

Published Papers (6 papers)

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Research

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15 pages, 1965 KiB  
Article
Harnessing Environmental Yeasts—Pichia kudriavzevii Strain ZMUM_K002: The Quest for Isolates with Properties for Efficient Biotechnological Applications
by Tadeja Vajdič and Marjanca Starčič Erjavec
Appl. Microbiol. 2025, 5(1), 30; https://doi.org/10.3390/applmicrobiol5010030 - 13 Mar 2025
Viewed by 713
Abstract
The environment hosts a diversity of microorganisms whose potential for biotechnological applications has not yet been exhausted. The quest of our study was to find isolates of Pichia kudriavzevii from the environment that could be used as new biotechnological agents. Moreover, we aimed [...] Read more.
The environment hosts a diversity of microorganisms whose potential for biotechnological applications has not yet been exhausted. The quest of our study was to find isolates of Pichia kudriavzevii from the environment that could be used as new biotechnological agents. Moreover, we aimed to explore the resource efficiency for microbial cultivation, in particular the efficiency of spent coffee grounds (SCG), an easily accessible waste coffee product with a high unutilized organic content. In this study, Pichia kudriavzevii strain ZMUM_K002, a yeast strain isolated from a grape pomace compost, was investigated. Antifungal susceptibility, particularly fluconazole susceptibility, was assessed, and the strain’s biotechnological potential by comparing its ability to utilize low-cost carbon sources, including SCG, with a natural isolate of Saccharomyces cerevisiae (strain ZMUM_K003) was assessed. The P. kudriavzevii strain ZMUM_K002 exhibited higher fluconazole susceptibility and yielded more than 30% more biomass in optimized media formulations compared to S. cerevisiae ZMUM_K003. These findings demonstrate that P. kudriavzevii ZMUM_K002 has the potential for efficient biomass production in sustainable industrial biotechnology, particularly in processes requiring high biomass yields on alternative substrates. Full article
(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2025))
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15 pages, 2717 KiB  
Article
A Novel Bacteriophage Targeting mcr-9 Enterobacter kobei with Potential Application in Fresh Leafy Greens
by Alberto Pintor-Cora, Andrea Carpintero, Ángel Alegría, Apostolos Giannis, Teresa-María Lopez-Díaz, Jesús A. Santos and Jose M. Rodríguez-Calleja
Appl. Microbiol. 2025, 5(1), 25; https://doi.org/10.3390/applmicrobiol5010025 - 24 Feb 2025
Viewed by 422
Abstract
The presence of opportunistic pathogens, such as the Enterobacter cloacae complex (ECC), in fresh vegetables poses a significant health risk, particularly amid the ongoing antibiotic resistance crisis. Traditional chemical decontamination methods are often ineffective and these are associated with issues such as cross-resistance [...] Read more.
The presence of opportunistic pathogens, such as the Enterobacter cloacae complex (ECC), in fresh vegetables poses a significant health risk, particularly amid the ongoing antibiotic resistance crisis. Traditional chemical decontamination methods are often ineffective and these are associated with issues such as cross-resistance between antibiotics and biocides, highlighting the need for alternative approaches. This study describes the isolation of a novel phage, FENT2, with anti-ECC activity, obtained from cattle farm sewage. Belonging to the Seunavirus genus, FENT2 did not carry genes associated with lysogenic cycle, antimicrobial resistance, or virulence factors. The phage demonstrated lytic activity against the host strain E. kobei AG07E, which harbored the mcr-9 gene, exhibiting a narrow host range that also included E. ludwigii strains. In vitro assays using BioTrac (SY-LAB) impedance technology confirmed the sustained lytic activity of FENT2 under food-related stress conditions, including pH levels from 5 to 7 and NaCl concentrations up to 2%. Furthermore, FENT2 demonstrated bactericidal potential on lettuce leaves, achieving 1 log reduction in bacterial counts of the host strain after 30 min immersion treatment. These findings highlight FENT2 as a promising candidate for biocontrol applications, offering a sustainable alternative to conventional decontamination methods for reducing antimicrobial-resistant ECC contamination in fresh produce. Full article
(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2025))
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13 pages, 3826 KiB  
Article
Bacillus velezensis SM1: A Promising Biocontrol Solution for Phytophthora Durian Root Rot
by Ashara Pengnoo, Usman Lohlaeh, Fadila Maduerehand, Chuthamard Kaewmano, Sudanai Krualee, Pimchana Wongpisal, Wipa Homhaul, Pawika Boonyapipat, Sukhumaporn Saeng-ngam, Abbas Äkbärjan and Vipaporn Phuntumart
Appl. Microbiol. 2025, 5(1), 21; https://doi.org/10.3390/applmicrobiol5010021 - 17 Feb 2025
Viewed by 664
Abstract
Plant diseases, particularly root rot caused by Phytophthora species, pose a significant threat to plants. In this study, we investigated the antagonistic activity of a Bacillus velezensis strain (Bv-SM1) against Phytophthora palmivora isolates, NKST002 and CP002, which cause root rot in durian. In [...] Read more.
Plant diseases, particularly root rot caused by Phytophthora species, pose a significant threat to plants. In this study, we investigated the antagonistic activity of a Bacillus velezensis strain (Bv-SM1) against Phytophthora palmivora isolates, NKST002 and CP002, which cause root rot in durian. In vitro assays using dual-plate, pour-plate, and volatile organic compounds demonstrated a strong inhibition of Phytophthora mycelial growth by Bv-SM1. Phylogenomic analysis based on 1000 genes confirmed that Bv-SM1 is most closely related to B. velezensis. Genome analysis revealed the presence of key genes that contribute to biocontrol activity, including genes encoding cell wall-degrading enzymes (β-glucanase and cellulase) and siderophore production. Additionally, 13 biosynthetic gene clusters are responsible for the production of various antimicrobial compounds, such as fengycin, bacillaene, macrolactin, and bacilysin. These findings are the first to demonstrate the potential of Bv-SM1 as a promising biocontrol agent for managing Phytophthora-induced root rot in durian, with potential applications in other crops. Full article
(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2025))
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18 pages, 1405 KiB  
Article
Optimization of L-Asparaginase Production from Aspergillus caespitosus: Solid-State and Submerged Fermentation Using Low-Cost Substrates and Partial Purification
by Natana Gontijo Rabelo, Luara Aparecida Simões, Natália de Andrade Teixeira Fernandes, Angélica Cristina Souza, Maysa Lima Parente Fernandes, Lizzy Ayra Alcântara Veríssimo, Rosane Freitas Schwan and Disney Ribeiro Dias
Appl. Microbiol. 2025, 5(1), 19; https://doi.org/10.3390/applmicrobiol5010019 - 10 Feb 2025
Viewed by 675
Abstract
This work aimed to optimize the production of L-asparaginase (L-ASNase) from Aspergillus caespitosus CCDCA 11593 using Pereskia aculeata (Ora-pro-nóbis) leaf fiber as a substrate for solid-state fermentation (SSF), along with powdered whey protein as a substrate in submerged fermentation (SmF) processes. A centered [...] Read more.
This work aimed to optimize the production of L-asparaginase (L-ASNase) from Aspergillus caespitosus CCDCA 11593 using Pereskia aculeata (Ora-pro-nóbis) leaf fiber as a substrate for solid-state fermentation (SSF), along with powdered whey protein as a substrate in submerged fermentation (SmF) processes. A centered face design was applied to evaluate the effect of the different parameters. Additionally, L-ASNase was partially purified on an ion-exchange cryogel column. For SSF, the experimental condition, inoculum concentration 105 spores/mL, 120 h at 25 °C, 14% of substrate, and 1% of asparagine, corresponded to the highest enzymatic activity (2.75 U/mL) of L-ASNase. For SmF, the experimental condition of greater enzymatic activity (1.49 U/mL) was obtained in the medium containing 16% to 24% asparagine, 3.3% to 4.7% substrate, spore concentration of 7 × 106 to 107 spores/mL, temperature range of 29.8 to 34.8 °C, pH range of 5.7 to 6.3, and 87 to 105 h of fermentation. The L-ASNase obtained from SmF was subjected to adsorption tests, resulting in 4.4 U/mg of partially purified enzyme. This study suggested that whey protein and Ora-pro-nóbis leaf fiber could be a low-cost substrate for L-ASNase production. Additionally, using an ion-exchange cryogel column for enzyme purification holds promise for sustainable applications in the clinical and food industries. Full article
(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2025))
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17 pages, 2656 KiB  
Article
Quantifying Resilience in Single-Host/Single-Virus Infections
by Socheata Hour, Andrew Pierce, Sobroney Ying Heng, Ruth Plymale and Ruben Michael Ceballos
Appl. Microbiol. 2025, 5(1), 18; https://doi.org/10.3390/applmicrobiol5010018 - 10 Feb 2025
Viewed by 497
Abstract
Due to theoretical and practical applications in biomedical, environmental, and industrial microbiology, robust metrics for quantifying the virulence of pathogens is vital. For many virus–host systems, multiple virus strains propagate through host populations. Each strain may exhibit a different virulence level. Likewise, different [...] Read more.
Due to theoretical and practical applications in biomedical, environmental, and industrial microbiology, robust metrics for quantifying the virulence of pathogens is vital. For many virus–host systems, multiple virus strains propagate through host populations. Each strain may exhibit a different virulence level. Likewise, different hosts may manifest different levels of host resilience to infection by a given virus. Recent publications have assessed metrics for quantifying virulence (VR) from growth curve data. Regardless of the metric used, a feature that most methods have in common is focus on the exponential growth phase of virus–host interactions. Often ignored is mortality phase. Following a report introducing the Stacy–Ceballos Inhibition Index (ISC), a robust metric to quantify relative virulence (VR) between viruses, we have turned attention to quantifying relative resilience (RR) between hosts in single-virus/single-host (SVSH) experimental infections. Although resilience during viral infection impacts the entire host growth curve, RR has particular biological significance during the mortality phase. In this report, we argue that calculating RR using a modified ISC provides a robust metric for comparisons between SVSH infections. Wet lab data from fusellovirus infections in Sulfolobales, bacteriophage infections in Mycobacteriales, and simulated infected-host growth profiles form the basis for developing this metric, RR, for quantifying resilience. Full article
(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2025))
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Review

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18 pages, 638 KiB  
Review
Oxidative Stress Responses in Microalgae: Modern Insights into an Old Topic
by Aikaterini Koletti, Dimitrios Skliros, Irene Dervisi, Andreas Roussis and Emmanouil Flemetakis
Appl. Microbiol. 2025, 5(2), 37; https://doi.org/10.3390/applmicrobiol5020037 - 8 Apr 2025
Viewed by 435
Abstract
Microalgae are the primary producers in aquatic ecosystems, while simultaneously playing a vital role in various industrial sectors. Despite their significant ecological and bioeconomic importance, the impacts of oxidative stress on their populations remain poorly understood. In this mini-review, we summarize recent advancements [...] Read more.
Microalgae are the primary producers in aquatic ecosystems, while simultaneously playing a vital role in various industrial sectors. Despite their significant ecological and bioeconomic importance, the impacts of oxidative stress on their populations remain poorly understood. In this mini-review, we summarize recent advancements in understanding oxidative stress modulation in microalgae, with a focus on responses to climate change-related stressors. Additionally, we compare the valuable insights obtained from multi-omics studies on specific biochemical pathways and genes, correlating the responses and mechanisms by which microalgae respond to oxidative stress among different species. Full article
(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2025))
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