New Methods in Microbial Research 3.0

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

Deadline for manuscript submissions: closed (15 December 2023) | Viewed by 18079

Special Issue Editor


E-Mail
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

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 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

Published Papers (10 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

Jump to: Review

11 pages, 3428 KiB  
Article
Impact of Zero-Valent Iron Nanoparticles and Ampicillin on Adenosine Triphosphate and Lactate Metabolism in the Cyanobacterium Fremyella diplosiphon
by Yavuz S. Yalcin, Busra N. Aydin and Viji Sitther
Microorganisms 2024, 12(3), 612; https://doi.org/10.3390/microorganisms12030612 - 19 Mar 2024
Viewed by 812
Abstract
In cyanobacteria, the interplay of ATP and lactate dynamics underpins cellular energetics; their pronounced shifts in response to zero-valent iron (nZVI) nanoparticles and ampicillin highlight the nuanced metabolic adaptations to environmental challenges. In this study, we investigated the impact of nZVIs and ampicillin [...] Read more.
In cyanobacteria, the interplay of ATP and lactate dynamics underpins cellular energetics; their pronounced shifts in response to zero-valent iron (nZVI) nanoparticles and ampicillin highlight the nuanced metabolic adaptations to environmental challenges. In this study, we investigated the impact of nZVIs and ampicillin on Fremyella diplosiphon cellular energetics as determined by adenosine triphosphate (ATP) content, intracellular and extracellular lactate levels, and their impact on cell morphology as visualized by transmission electron microscopy. While a significant increase in ATP concentration was observed in 0.8 mg/L ampicillin-treated cells compared to the untreated control, a significant decline was noted in cells treated with 3.2 mg/L nZVIs. ATP levels in the combination regimen of 0.8 mg/L ampicillin and 3.2 mg/L nZVIs were significantly elevated (p < 0.05) compared to the 3.2 mg/L nZVI treatment. Intracellular and extracellular lactate levels were significantly higher in 0.8 mg/L ampicillin, 3.2 mg/L nZVIs, and the combination regimen compared to the untreated control; however, extracellular lactate levels were the highest in cells treated with 3.2 mg/L nZVIs. Visualization of morphological changes indicated increased thylakoid membrane stacks and inter-thylakoidal distances in 3.2 mg/L nZVI-treated cells. Our findings demonstrate a complex interplay of nanoparticle and antibiotic-induced responses, highlighting the differential impact of these stressors on F. diplosiphon metabolism and cellular integrity. Full article
(This article belongs to the Special Issue New Methods in Microbial Research 3.0)
Show Figures

Figure 1

8 pages, 1695 KiB  
Communication
Application of Fourier Transform Infrared Spectroscopy to Discriminate Two Closely Related Bacterial Species: Bacillus anthracis and Bacillus cereus Sensu Stricto
by Viviana Manzulli, Miriam Cordovana, Luigina Serrecchia, Valeria Rondinone, Lorenzo Pace, Donatella Farina, Dora Cipolletta, Marta Caruso, Rosa Fraccalvieri, Laura Maria Difato, Francesco Tolve, Valerio Vetritto and Domenico Galante
Microorganisms 2024, 12(1), 183; https://doi.org/10.3390/microorganisms12010183 - 17 Jan 2024
Cited by 2 | Viewed by 1221
Abstract
Fourier transform infrared spectroscopy (FTIRS) is a diagnostic technique historically used in the microbiological field for the characterization of bacterial strains in relation to the specific composition of their lipid, protein, and polysaccharide components. For each bacterial strain, it is possible to obtain [...] Read more.
Fourier transform infrared spectroscopy (FTIRS) is a diagnostic technique historically used in the microbiological field for the characterization of bacterial strains in relation to the specific composition of their lipid, protein, and polysaccharide components. For each bacterial strain, it is possible to obtain a unique absorption spectrum that represents the fingerprint obtained based on the components of the outer cell membrane. In this study, FTIRS was applied for the first time as an experimental diagnostic tool for the discrimination of two pathogenic species belonging to the Bacillus cereus group, Bacillus anthracis and Bacillus cereus sensu stricto; these are two closely related species that are not so easy to differentiate using classical microbiological methods, representing an innovative technology in the field of animal health. Full article
(This article belongs to the Special Issue New Methods in Microbial Research 3.0)
Show Figures

Figure 1

11 pages, 886 KiB  
Article
Direct Impact of the Air on Mutant Cells for Mutagenicity Assessments in Urban Environments
by Chiara Caredda, Elena Franchitti, Giorgio Gilli, Cristina Pignata and Deborah Traversi
Microorganisms 2024, 12(1), 3; https://doi.org/10.3390/microorganisms12010003 - 19 Dec 2023
Viewed by 812
Abstract
Background: Urban air pollution is recognized as a critical problem for public health and is classified as a carcinogen for humans. A great number of studies have focused on the monitoring of urban air mutagenicity. One of the best-known and applied methods for [...] Read more.
Background: Urban air pollution is recognized as a critical problem for public health and is classified as a carcinogen for humans. A great number of studies have focused on the monitoring of urban air mutagenicity. One of the best-known and applied methods for assessing mutagenicity is the Ames test, a bacterial reverse mutation test. The classic protocol for assessing air mutagenicity involves the concentration of particulate matter (PM) on filters and subsequent extraction using organic solvents. This work aimed to develop a method for the evaluation of air mutagenicity directly impacted by air on microbial plates already containing an Ames’ microbial sensor. Methods: A specific six-month sampling campaign was carried out in Turin in a period with high air pollution. Samples were tested for mutagenicity on Salmonella typhimurium strains TA98, TA100, and YG1024 with the traditional method and with the new direct method. Results: The new protocol is able to evaluate the mutagenicity of the sampled air and obtain repeatable results. The final sensitivity is similar to the traditional method (≈10 net revertants/m3); however, the mutagenic response is due to the complete air pollution mixture, including volatile and semivolatile pollutants avoiding the concentration of filters and the following laborious extraction procedures. Conclusions. Despite some critical issues in contamination control, the method is easier, faster, and less expensive than traditional methods. Full article
(This article belongs to the Special Issue New Methods in Microbial Research 3.0)
Show Figures

Figure 1

12 pages, 1995 KiB  
Article
Phylogenetic Analysis and Emerging Drug Resistance against Different Nucleoside Analogues in Hepatitis B Virus Positive Patients
by Maryam Gohar, Irshad Ur Rehman, Amin Ullah, Muhammad Ajmal Khan, Humaira Yasmin, Jamshaid Ahmad, Sadia Butt and Ajaz Ahmad
Microorganisms 2023, 11(11), 2622; https://doi.org/10.3390/microorganisms11112622 - 24 Oct 2023
Cited by 1 | Viewed by 1483
Abstract
Several nucleotide analogues have been approved for use in treating hepatitis B virus (HBV) infection. Long-term exposure to therapy leads to the emergence of mutations within the HBV DNA polymerase gene, resulting in drug resistance, a major factor contributing to therapy failure. Chronic [...] Read more.
Several nucleotide analogues have been approved for use in treating hepatitis B virus (HBV) infection. Long-term exposure to therapy leads to the emergence of mutations within the HBV DNA polymerase gene, resulting in drug resistance, a major factor contributing to therapy failure. Chronic HBV patients from the Khyber Pakhtunkhwa province, Pakistan, who had completed 6 months of therapy participated in this study. Samples were collected from 60 patients. In this study, the entire reverse transcriptase domain of the HBV polymerase gene was amplified using nested polymerase chain reaction and sequenced. Drug-resistant mutations were detected in nine (22.5%) patients. All of these patients had lamivudine-resistant mutations (rtM204V + L180M), while seven individuals (17.5%) had both lamivudine- plus entecavir-resistant mutations (L180M + M204V + S202G). N236T, a mutation that gives rise to tenofovir and adefovir resistance, was observed in two (5%) patients. T184A, a partial drug-resistant mutation to entecavir, was found in five (12.5%) patients. Furthermore, other genotypic variants (100%) and vaccine escape mutations (5%) were additionally observed. Moreover, pN459Y (35%), pN131D (20%), pL231S (20%), pP130Q (17.5%), pS189Q (12.5%), pP161S (5%), pH160P (2.5%), pT322S (2.5%), and pA223S (2.5%) mutations in the polymerase gene, as well as sA166V (17.5%), sQ181K (12.5%), sV184R (7.5%), sA17E (5%), sP153S/K (5%), sW156C (5%), sC76Y (2.5%), and S132F (2.5%) mutations in the small surface gene, were identified for the first time in this study. Phylogenetic analysis showed that genotype D was predominant amongst the HBV carriers. Subtype D1 was found in most patients, while two patients were subtype D9. These novel findings may contribute to the body of knowledge and have clinical significance for treating and curing HBV infections in Pakistan. Full article
(This article belongs to the Special Issue New Methods in Microbial Research 3.0)
Show Figures

Figure 1

16 pages, 7771 KiB  
Article
The World’s First Acne Dysbiosis-like Model of Human 3D Ex Vivo Sebaceous Gland Colonized with Cutibacterium acnes and Staphylococcus epidermidis
by Nico Forraz, Cécile Bize, Anne-Laure Desroches, Clément Milet, Pauline Payen, Pauline Chanut, Catherine Kern, Christine Garcia and Colin McGuckin
Microorganisms 2023, 11(9), 2183; https://doi.org/10.3390/microorganisms11092183 - 29 Aug 2023
Cited by 1 | Viewed by 2394
Abstract
Acne-prone skin is associated with dysbiosis involving Cutibacterium acnes (C. acnes) and Staphylococcus epidermidis (S. epidermidis) causing increased seborrhea in sebaceous glands (SG) and inflammation. Human primary sebocytes were cultivated using 1.106 UFC/mL C. acnes Type IA (facial [...] Read more.
Acne-prone skin is associated with dysbiosis involving Cutibacterium acnes (C. acnes) and Staphylococcus epidermidis (S. epidermidis) causing increased seborrhea in sebaceous glands (SG) and inflammation. Human primary sebocytes were cultivated using 1.106 UFC/mL C. acnes Type IA (facial acne, ATCC6919) and/or 1.105 UFC/mL S. epidermidis (unknown origin, ATCC12228) for 48 h in our SEB4GLN-optimized media without antibiotics. Bacteria and sebocytes were enumerated and assessed to determine their viability. Lipid production was imaged and quantified via Nile Red staining. SG with hair follicles were microdissected from healthy skin and cultured using 1.105 UFC/mL C. acnes Type 1A and/or 1.104 UFC/mL S. epidermidis (wild-type facial skin strain) through prior fixation and immunostaining for MC5R, C. acnes and nuclei (DAPI) via Z-stack confocal microscopy bioimaging (Leica SP5X & FIJI software, Version 2.9.0). C. acnes growth was not impacted when co-cultivated with sebocytes (2D) or SG (3D) models. Phylotype IA stimulated sebocyte lipid production, which had no impact on viability. The S. epidermidis reference strain overproliferated, inducing sebocyte mortality. For 3D SG model, culture conditions were optimized using a wild-type facial skin strain at a lower concentration, 1:10 ratio to C. acnes, reduced contact time, sequential inoculation and rinsing step. Bioimaging revealed strong C. acnes labeling in the active areas of the pilosebaceous unit. S. epidermidis formed biofilm, which was distributed across the SG via non-specific fluorescence imaging. We developed an innovative model of a sebaceous gland that mimics acne-prone skin with lipid overproduction and virulent phylotype IA C. acnes inoculation. Full article
(This article belongs to the Special Issue New Methods in Microbial Research 3.0)
Show Figures

Figure 1

12 pages, 4091 KiB  
Article
Global Risk Maps of Climate Change Impacts on the Distribution of Acinetobacter baumannii Using GIS
by Amal Sabour
Microorganisms 2023, 11(9), 2174; https://doi.org/10.3390/microorganisms11092174 - 28 Aug 2023
Cited by 5 | Viewed by 1342
Abstract
Impacts of climate change rank among the century’s most significant ecological and medical concerns. As a result of climatic changes, the distribution of some bacterial species will alter across time and space. Numerous bacterial infections will reorganize as a result worldwide. Acinetobacter baumannii [...] Read more.
Impacts of climate change rank among the century’s most significant ecological and medical concerns. As a result of climatic changes, the distribution of some bacterial species will alter across time and space. Numerous bacterial infections will reorganize as a result worldwide. Acinetobacter baumannii Bouvet and Grimont is one of the most significant and frequently occurring bacteria identified in soil and air. The COVID-19 pandemic has changed how bacteriologists perceive this species as a new threat to human health. In order to estimate the existing and future worldwide distribution of A. baumannii under various climate change scenarios, about 1000 A. baumannii occurrence records were employed. Given its superior accuracy and dependability versus alternative modeling techniques, maximum entropy implemented in MaxEnt was selected as the modeling tool. The bioclimatic variable that contributes the most to the distribution of A. baumannii is the mean temperature of the coldest quarter (bio_11). The created current distribution model agreed with the species’ actual globally dispersed distribution. It is projected that A. baumannii will experience a severe range expansion due to the increase in temperature brought on by global warming in different regions of its range. According to the risk maps created for 2050 and 2070 using two alternative RCPs, there are various regions that will be under risk of this bacterium as a result of rising temperature. Future data science and GIS evaluation of the current results are necessary, especially on a local level. Full article
(This article belongs to the Special Issue New Methods in Microbial Research 3.0)
Show Figures

Figure 1

13 pages, 2435 KiB  
Article
Information Scale Correction for Varying Length Amplicons Improves Eukaryotic Microbiome Data Integration
by Tong Zhou, Feng Zhao and Kuidong Xu
Microorganisms 2023, 11(4), 949; https://doi.org/10.3390/microorganisms11040949 - 6 Apr 2023
Cited by 1 | Viewed by 1513
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 [...] Read more.
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)
Show Figures

Figure 1

13 pages, 39190 KiB  
Article
Urany-Less Low Voltage Transmission Electron Microscopy: A Powerful Tool for Ultrastructural Studying of Cyanobacterial Cells
by Katerina Mrazova, Jaromir Bacovsky, Zuzana Sedrlova, Eva Slaninova, Stanislav Obruca, Ines Fritz and Vladislav Krzyzanek
Microorganisms 2023, 11(4), 888; https://doi.org/10.3390/microorganisms11040888 - 29 Mar 2023
Cited by 3 | Viewed by 2534
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 [...] Read more.
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)
Show Figures

Graphical abstract

11 pages, 3417 KiB  
Article
A Simple In-Vivo Method for Evaluation of Antibiofilm and Wound Healing Activity Using Excision Wound Model in Diabetic Swiss Albino Mice
by Mohammed Alrouji, Fahd A. Kuriri, Mohammed Hussein Alqasmi, Hamood AlSudais, Mohammed Alissa, Meshari A. Alsuwat, Mohammed Asad, Babu Joseph and Yasir Almuhanna
Microorganisms 2023, 11(3), 692; https://doi.org/10.3390/microorganisms11030692 - 8 Mar 2023
Cited by 4 | Viewed by 2558
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 [...] Read more.
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)
Show Figures

Figure 1

Review

Jump to: Research

13 pages, 1225 KiB  
Review
Using Genomics to Decipher the Enigmatic Properties and Survival Adaptation of Candidate Phyla Radiation
by Mohamad Maatouk, Jean-Marc Rolain and Fadi Bittar
Microorganisms 2023, 11(5), 1231; https://doi.org/10.3390/microorganisms11051231 - 7 May 2023
Cited by 1 | Viewed by 2140
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, [...] Read more.
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)
Show Figures

Figure 1

Back to TopTop