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: 15 April 2025 | Viewed by 2004

Special Issue Editors


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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
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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

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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.

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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

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Published Papers (2 papers)

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Research

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 462
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)
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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 3 | Viewed by 1241
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)
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