Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
7.4
4.1
Journals
Microorganisms
Special Issues
New Methods in Microbial Research, 4th Edition
share announcement

New Methods in Microbial Research, 4th Edition

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbial Biotechnology".

Deadline for manuscript submissions: closed (15 April 2025) | Viewed by 7196

Special Issue Editors

Dr. Juan M. Gonzalez

E-Mail Website
Guest Editor
Departament of Biogeochemistry, Plant and Microbial Ecology, Instituto de Recursos Naturales y Agrobiología de Sevilla, CSIC, Avenida Reina Mercedes 10, c.p. 41012 Sevilla, Spain
Interests: microbiology; microbial diversity; environmental microbiology; biotechnology; genomics; extremophiles
Special Issues, Collections and Topics in MDPI journals
Dr. Alba Cuecas

E-Mail
Guest Editor Assistant
Department of Geoecology, Biogeochemistry and Microbial Ecology, CSIC, Avenida Reina Mercedes 10, c.p. 41012 Sevilla, Spain
Interests: microbiology; molecular biology; microbial ecology; methodologies

Special Issue Information

Dear Colleagues,

This Special Issue is the continuation of our previous special issue “New Methods in Microbial Research 3.0”.

Earth is a microbial dependent planet. However, our understanding of the microbial world is limited, and at present, there are important gaps on comprehending the actual microbial diversity, functionality, and role of microorganisms in the environment and in the wellbeing of animals and plants. Microorganisms, in addition to their reduced size, present incredible abundance, diversity, and complexity which complicates microbial research. The major advances in microbiology are generally linked to new methodologies or the application of techniques imported from other sciences. Due to the dependence on novel methods to foster our understanding of microorganisms and the microbial communities, it is critical to promote an active platform for the dissemination of novel improvements, methods, strategies, and hypothesis-driven perspectives on microorganisms and microbial communities.

This Special Issue seeks relevant contributions of novel methods, techniques, and initiatives to better understand the microbial world. Articles are expected to provide a clear description of the proposed novel methodology and complement it with results showing its relevance to the advancement of microbiology for any discipline, such as the environment, ecology, the microbiomes, biotechnology, and the clinical field, among others.

Dr. Juan M. Gonzalez
Guest Editor

Dr. Alba Cuecas
Guest Editor Assistant

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. Microorganisms 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

  • method
  • microbiology
  • microbial world
  • microbial community
  • novel techniques
  • microorganisms
  • omics
  • microscopy
  • growth rate
  • microbial metabolism
  • microbial monitoring
  • microbiome
  • gene expression
  • comparative genomics
  • lateral gene transfer
  • biofilms
  • microbial interactions
  • microbial biogeography
  • single-cell analysis

Benefits of Publishing in a Special Issue

  • 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.

Published Papers (5 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

23 pages, 2886 KiB  
Article
Limitations of 18S rDNA Sequence in Species-Level Classification of Dictyostelids
by Thanyaporn Chittavichai, Sukhita Sathitnaitham, Supanut Utthiya, Wanasilp Prompichai, Kamonchat Prommarit, Supachai Vuttipongchaikij and Passorn Wonnapinij
Microorganisms 2025, 13(2), 275; https://doi.org/10.3390/microorganisms13020275 - 26 Jan 2025
Viewed by 698
Abstract
Dictyostelid species classification has traditionally relied on morphology, a time-intensive method requiring expert knowledge. This study evaluated the potential and limitations of using the 18S rDNA sequence for species-level classification. 18S rDNA sequences of 16 samples from the Dicty stock center, including 14 [...] Read more.
Dictyostelid species classification has traditionally relied on morphology, a time-intensive method requiring expert knowledge. This study evaluated the potential and limitations of using the 18S rDNA sequence for species-level classification. 18S rDNA sequences of 16 samples from the Dicty stock center, including 14 samples found in Thailand, were analyzed. Signature sequence analyses confirmed genus-level identification with high accuracy. These sequences were analyzed alongside 309 database entries retrieved from the GenBank database. The analyses confirmed genus-level identification accuracy but highlighted challenges in distinguishing species due to overlapping intraspecific and interspecific variations, negative barcoding gaps, and incorrectly grouped samples to putative taxa by species delimitation analyses. Species delimitation methods, including maximum likelihood (ML) phylogenetic analysis, achieved limited success, with ML showing the highest accuracy but not exceeding 50%. However, species with high barcoding gaps, such as Raperostelium and Rostrostelium, demonstrated potential for accurate classification. These findings support using 18S rDNA for genus-level identification and suggest its possible application for certain species. Expanded sampling is needed to improve species-level classification and to identify more robust DNA markers for dictyostelid diversity studies. Full article
(This article belongs to the Special Issue New Methods in Microbial Research, 4th Edition)
►▼ Show Figures

Figure 1

18 pages, 4442 KiB  
Article
Engineering Inorganic Pyrophosphate Metabolism as a Strategy to Generate a Fluoride-Resistant Saccharomyces cerevisiae Strain
by José R. Perez-Castiñeira, Francisco J. Ávila-Oliva and Aurelio Serrano
Microorganisms 2025, 13(2), 226; https://doi.org/10.3390/microorganisms13020226 - 21 Jan 2025
Viewed by 2534
Abstract
Fluorine accounts for 0.3 g/kg of the Earth’s crust, being widely distributed in the environment as fluoride. The toxic effects of this anion in humans and other organisms have been known for a long time. Fluoride has been reported to alter several cellular [...] Read more.
Fluorine accounts for 0.3 g/kg of the Earth’s crust, being widely distributed in the environment as fluoride. The toxic effects of this anion in humans and other organisms have been known for a long time. Fluoride has been reported to alter several cellular processes although the mechanisms involved are largely unknown. Inorganic pyrophosphatases (PPases) are ubiquitous enzymes that hydrolyze inorganic pyrophosphate (PPi), a metabolite generated from ATP. In Saccharomyces cerevisiae, the enzyme responsible for PPi hydrolysis in the cytosol (IPP1) is strongly inhibited by fluoride in vitro. The essentiality of IPP1 for growth has been previously demonstrated using YPC3, a yeast mutant with conditional expression of the corresponding gene. Here, YPC3 was used to generate cells that tolerate high concentrations of fluoride by (a) the overexpression of IPP1 or its human ortholog, or (b) the substitution of IPP1 by the fluoride-insensitive PPase from Streptococcus mutans. The results obtained suggest that maintaining appropriate levels of PPase activity in the cytosol is essential for the adaptation of S. cerevisiae to high fluoride concentrations. The increase in fluoride tolerance allows YPC3 cells transformed with suitable plasmids to be selected on rich non-selective medium supplemented with this anion. Full article
(This article belongs to the Special Issue New Methods in Microbial Research, 4th Edition)
►▼ Show Figures

Figure 1

14 pages, 1663 KiB  
Article
Investigating the Role of Gut Microbiota in Pediatric Patients with Severe COVID-19 or MIS-C
by Elena Franchitti, Paolo Bottino, Francesca Sidoti, Andrea Carpino, Giulia Pruccoli, Ugo Ramenghi, Cristina Costa, Ugo Ala, Emilia Parodi and Deborah Traversi
Microorganisms 2025, 13(1), 83; https://doi.org/10.3390/microorganisms13010083 - 4 Jan 2025
Viewed by 712
Abstract
Severe COVID-19 and MIS-C are rare but serious outcomes associated with SARS-CoV-2 infection. The onset of MIS-C often involves the gastrointestinal system, suggesting a potential connection with gut microbiota. This study aims to compare the gut microbiota of children with severe COVID-19 and [...] Read more.
Severe COVID-19 and MIS-C are rare but serious outcomes associated with SARS-CoV-2 infection. The onset of MIS-C often involves the gastrointestinal system, suggesting a potential connection with gut microbiota. This study aims to compare the gut microbiota of children with severe COVID-19 and those with MIS-C using various biomolecular approaches. Gut microbiota composition and specific microbial modulations were analyzed using fecal samples collected at hospital admission. The study included hospitalized patients (mean age 6 ± 5 years) diagnosed with severe COVID-19 (37 patients) or MIS-C (37 patients). Microbial differences were assessed using both NGS and qRT-PCR methodologies. In 75% of cases, pharmacological treatments included antibiotics and corticosteroids, which influenced the microbiota composition. Early age was found to have the most significant impact on microbiota diversity. Significant differences in alpha and beta diversity were observed between COVID-19 and MIS-C patients, particularly concerning low-abundance species. Levels of Bacteroides spp., Bifidobacterium spp., and Akkermansia muciniphila were comparable between groups, while an increased activity of Bifidobacterium spp. was noted in children with positive fecal samples (p = 0.019). An in-depth evaluation of lesser-known gut species may be key to reducing the risk of severe outcomes and developing microbiota-based biomarkers for the early diagnosis of MIS-C. Full article
(This article belongs to the Special Issue New Methods in Microbial Research, 4th Edition)
►▼ Show Figures

Figure 1

11 pages, 470 KiB  
Article
Effects of Prospective Audit and Feedback in Patients with Extended-Spectrum β-Lactamase-Producing Escherichia coli Bacteremia
by Yota Yamada, Motoyasu Miyazaki, Hisako Kushima, Hitomi Hirata, Arata Ogawa, Yukie Komiya, Chika Hagiwara, Akio Nakashima, Hiroshi Ishii and Osamu Imakyure
Microorganisms 2024, 12(11), 2275; https://doi.org/10.3390/microorganisms12112275 - 9 Nov 2024
Viewed by 850
Abstract
Antimicrobial stewardship (AS) Guidelines by the Infectious Diseases Society of America recommend employing prospective audit and feedback (PAF) as an effective intervention in AS programs. Since July 2022, our hospital has implemented PAF for all patients with positive blood cultures, including those with [...] Read more.
Antimicrobial stewardship (AS) Guidelines by the Infectious Diseases Society of America recommend employing prospective audit and feedback (PAF) as an effective intervention in AS programs. Since July 2022, our hospital has implemented PAF for all patients with positive blood cultures, including those with extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (EC) bacteremia. Our study examined the effect of PAF on clinical outcomes in patients with ESBL-EC bacteremia. We enrolled 62 patients diagnosed with ESBL-EC via blood culture who were undergoing antibiotic treatment. The patients were divided into the pre-PAF and post-PAF implementation groups. The rate of antibiotic de-escalation from broad-spectrum antibiotics to narrow-spectrum cefmetazole was significantly higher in the post-PAF group than in the pre-PAF group (80.7% vs. 32.4%, p = 0.0003). The treatment failure rate in the pre-PAF group was higher than that in the post-PAF group (38.7% vs. 12.9%, p = 0.04). The results of this study indicate that the implementation of PAF is advantageous not only in terms of process indicators but also in improved clinical outcomes, including reduced treatment failure rates. We hope that this study will encourage the implementation of PAF in more facilities to instigate a collective effort to reduce the incidence of antimicrobial resistance. Full article
(This article belongs to the Special Issue New Methods in Microbial Research, 4th Edition)
►▼ Show Figures

Figure 1

22 pages, 3640 KiB  
Article
Differential Reshaping of Skin and Intestinal Microbiota by Stocking Density and Oxygen Availability in Farmed Gilthead Sea Bream (Sparus aurata): A Behavioral and Network-Based Integrative Approach
by Socorro Toxqui-Rodríguez, Paul George Holhorea, Fernando Naya-Català, Josep Àlvar Calduch-Giner, Ariadna Sitjà-Bobadilla, Carla Piazzon and Jaume Pérez-Sánchez
Microorganisms 2024, 12(7), 1360; https://doi.org/10.3390/microorganisms12071360 - 2 Jul 2024
Cited by 5 | Viewed by 1859
Abstract
Fish were kept for six weeks at three different initial stocking densities and water O2 concentrations (low-LD, 8.5 kg/m3 and 95–70% O2 saturation; medium-MD, 17 kg/m3 and 55–75% O2 saturation; high-HD, 25 kg/m3 and 60–45% O2 [...] Read more.
Fish were kept for six weeks at three different initial stocking densities and water O2 concentrations (low-LD, 8.5 kg/m3 and 95–70% O2 saturation; medium-MD, 17 kg/m3 and 55–75% O2 saturation; high-HD, 25 kg/m3 and 60–45% O2 saturation), with water temperature increasing from 19 °C to 26–27 °C. The improvement in growth performance with the decrease in stocking density was related to changes in skin and intestinal mucosal microbiomes. Changes in microbiome composition were higher in skin, with an increased abundance of Alteromonas and Massilia in HD fish. However, these bacteria genera were mutually exclusive, and Alteromonas abundance was related to a reactive behavior and systemic growth regulation via the liver Gh/Igf system, while Massilia was correlated to a proactive behavior and a growth regulatory transition towards muscle rather than liver. At the intestinal level, microbial abundance showed an opposite trend for two bacteria taxa, rendering in a low abundance of Reyranella and a high abundance of Prauserella in HD fish. This trend was correlated with up-regulated host gene expression, affecting the immune response, epithelial cell turnover, and abiotic stress response. Most of the observed responses are adaptive in nature, and they would serve to infer new welfare indicators for increased stress resilience. Full article
(This article belongs to the Special Issue New Methods in Microbial Research, 4th Edition)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-5
Back to TopTop