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Special Issue "New Methods in Microbial Research 3.0"

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

Deadline for manuscript submissions: 30 June 2023 | Viewed by 3366

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Special Issue Editor

Prof. Dr. Juan M. Gonzalez

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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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Special Issue Information

Dear Colleagues,

This Special Issue is the continuation of our previous special issues "New Methods in Microbial Research 2.0" and "New Methods in Microbial Research 1.0".

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.

Prof. Dr. Juan M. Gonzalez
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. 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 2200 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

Published Papers (4 papers)

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Research

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Open AccessArticle

Information Scale Correction for Varying Length Amplicons Improves Eukaryotic Microbiome Data Integration

Tong Zhou

Feng Zhao

and

Kuidong Xu

Microorganisms 2023, 11(4), 949; https://doi.org/10.3390/microorganisms11040949 - 06 Apr 2023

Viewed by 617

Abstract

The integration and reanalysis of big data provide valuable insights into microbiome studies. However, the significant difference in information scale between amplicon data poses a key challenge in data analysis. Therefore, reducing batch effects is crucial to enhance data integration for large-scale molecular ecology data. To achieve this, the information scale correction (ISC) step, involving cutting different length amplicons into the same sub-region, is essential. In this study, we used the Hidden Markov model (HMM) method to extract 11 different 18S rRNA gene v4 region amplicon datasets with 578 samples in total. The length of the amplicons ranged from 344 bp to 720 bp, depending on the primer position. By comparing the information scale correction of amplicons with varying lengths, we explored the extent to which the comparability between samples decreases with increasing amplicon length. Our method was shown to be more sensitive than V-Xtractor, the most popular tool for performing ISC. We found that near-scale amplicons exhibited no significant change after ISC, while larger-scale amplicons exhibited significant changes. After the ISC treatment, the similarity among the data sets improved, especially for long amplicons. Therefore, we recommend adding ISC processing when integrating big data, which is crucial for unlocking the full potential of microbial community studies and advancing our knowledge of microbial ecology. Full article

(This article belongs to the Special Issue New Methods in Microbial Research 3.0)

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Open AccessArticle

Urany-Less Low Voltage Transmission Electron Microscopy: A Powerful Tool for Ultrastructural Studying of Cyanobacterial Cells

and

Microorganisms 2023, 11(4), 888; https://doi.org/10.3390/microorganisms11040888 - 29 Mar 2023

Viewed by 794

Abstract

Sample preparation protocols for conventional high voltage transmission electron microscopy (TEM) heavily rely on the usage of staining agents containing various heavy metals, most commonly uranyl acetate and lead citrate. However high toxicity, rising legal regulations, and problematic waste disposal of uranyl acetate have increased calls for the reduction or even complete replacement of this staining agent. One of the strategies for uranyless imaging is the employment of low-voltage transmission electron microscopy. To investigate the influence of different imaging and staining strategies on the final image of cyanobacterial cells, samples stained by uranyl acetate with lead citrate, as well as unstained samples, were observed using TEM and accelerating voltages of 200 kV or 25 kV. Moreover, to examine the possibilities of reducing chromatic aberration, which often causes issues when imaging using electrons of lower energies, samples were also imaged using a scanning transmission electron microscopy at 15 kV accelerating voltages. The results of this study demonstrate that low-voltage electron microscopy offers great potential for uranyless electron microscopy. Full article

(This article belongs to the Special Issue New Methods in Microbial Research 3.0)

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Open AccessArticle

A Simple In-Vivo Method for Evaluation of Antibiofilm and Wound Healing Activity Using Excision Wound Model in Diabetic Swiss Albino Mice

Mohammed Alrouji

Fahd A. Kuriri

Mohammed Hussein Alqasmi

and

Microorganisms 2023, 11(3), 692; https://doi.org/10.3390/microorganisms11030692 - 08 Mar 2023

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Abstract

The study developed a simple and inexpensive method to induce biofilm formation in-vivo for the evaluation of the antibiofilm activity of pharmacological agents using Swiss albino mice. Animals were made diabetic using streptozocin and nicotinamide. A cover slip containing preformed biofilm along with MRSA culture was introduced into the excision wound in these animals. The method was effective in developing biofilm on the coverslip after 24 h incubation in MRSA broth which was confirmed by microscopic examination and a crystal violet assay. Application of preformed biofilm along with microbial culture induced a profound infection with biofilm formation on excision wounds in 72 h. This was confirmed by macroscopic, histological, and bacterial load determination. Mupirocin, a known antibacterial agent effective against MRSA was used to demonstrate antibiofilm activity. Mupirocin was able to completely heal the excised wounds in 19 to 21 days while in the base-treated group, healing took place between 30 and 35 days. The method described is robust and can be reproduced easily without the use of transgenic animals and sophisticated methods such as confocal microscopy. Full article

(This article belongs to the Special Issue New Methods in Microbial Research 3.0)

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Review

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Open AccessReview

Using Genomics to Decipher the Enigmatic Properties and Survival Adaptation of Candidate Phyla Radiation

Mohamad Maatouk

Jean-Marc Rolain

and

Fadi Bittar

Microorganisms 2023, 11(5), 1231; https://doi.org/10.3390/microorganisms11051231 - 07 May 2023

Viewed by 727

Abstract

Microbial ecology is a critical field for understanding the composition, diversity, and functions of microorganisms in various environmental and health-related processes. The discovery of Candidate Phyla Radiation (CPR) through culture-independent methods has introduced a new division of microbes characterized by a symbiotic/parasitic lifestyle, small cell size, and small genome. Despite being poorly understood, CPRs have garnered significant attention in recent years due to their widespread detection in a variety of environmental and clinical samples. These microorganisms have been found to exhibit a high degree of genetic diversity compared to other microbes. Several studies have shed light on their potential importance in global biogeochemical cycles and their impact on various human activities. In this review, we provide a systematic overview of the discovery of CPRs. We then focus on describing how the genomic characteristics of CPRs have helped them interact with and adapt to other microbes in different ecological niches. Future works should focus on discovering the metabolic capacities of CPRs and, if possible, isolating them to obtain a better understanding of these microorganisms. Full article

(This article belongs to the Special Issue New Methods in Microbial Research 3.0)

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