Feature Papers in Microbial Biology

A topical collection in Biology (ISSN 2079-7737). This collection belongs to the section "Microbiology".

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Editors


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Collection Editor
Clinical Hospital of Porto Alegre (HCPA), Federal University of Rio Grande do Sul, Porto Alegre 91501-970, Brazil
Interests: microbiome; molecular microbiology; metagenomics; omics; next-generation sequencing; microbial ecology; bioinformatics; biotechnology; system biology; grand challenges
Special Issues, Collections and Topics in MDPI journals

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Collection Editor
Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain
Interests: microbial ecotoxicology; heavy metals; metallic nanoparticles; metallothioneins; gene expression regulation; biosensors; protozoa; ciliates
Special Issues, Collections and Topics in MDPI journals

Topical Collection Information

Dear Colleagues,

Microbiology is the fundamental biological science that studies microscopic organisms, including bacteria, archaea, protists, fungi and viruses. Understanding microbes' structure, life cycle, metabolism and growth is essential for further studies within various biological sciences, including genetics, ecology, evolution, health and biotechnology. Recent advances in microbiology, driven by cutting-edge technologies such as multi-omics and bioinformatics offer unprecedented potential to address major societal challenges. Scientists can now delve into previously unexplored questions, leading to breakthrough discoveries that highlight the crucial role of microbes in biology.

Our Topical Collection aims to showcase cutting-edge advances in microbial biology through a collection of feature papers that explore innovative work and rigorous scientific methodologies. Review articles are expected to synthesize ideas, challenge existing paradigms and establish new frameworks that advance our comprehension of the microbial world. We encourage researchers from related fields to submit their articles highlighting the latest developments in microbial biology, or to invite other relevant experts and colleagues to do so.

Prof. Dr. Pabulo H. Rampelotto
Prof. Dr. Juan Carlos Gutiérrez
Collection Editors

Manuscript Submission Information

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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

  • antimicrobials
  • agricultural microbiology
  • biomining and bioremediation
  • clinical microbiology
  • environmental microbiology
  • food microbiology
  • geomicrobiology
  • host–microbe interaction
  • industrial microbiology
  • marine microbiology
  • microbial biochemistry
  • microbial biofilms
  • microbial biofuel and bioenergy
  • microbial biotechnology
  • microbial ecology
  • microbial evolution
  • microbial genetics
  • microbial metabolism
  • microbial omics
  • microbial pathogenesis
  • microbial physiology
  • pharmaceutical microbiology
  • probiotics
  • veterinary microbiology

Published Papers (7 papers)

2024

17 pages, 9466 KiB  
Article
Characterization of New Tropicoporus Species (Basidiomycota, Hymenochaetales, Hymenochaetaceae) Discovered in Tamil Nadu, India
by Elangovan Arumugam, Ramesh Murugadoss, Sugantha Gunaseelan, Samantha C. Karunarathna, Abdallah M. Elgorban, Pabulo Henrique Rampelotto and Malarvizhi Kaliyaperumal
Biology 2024, 13(10), 770; https://doi.org/10.3390/biology13100770 - 27 Sep 2024
Viewed by 570
Abstract
This study aimed to investigate the morphological characteristics and phylogenetic relationships of three new species of Tropicoporus from the southern parts of India. The analyses of the ITS and nLSU regions revealed the novelty of these species, which have been named T. pannaensis [...] Read more.
This study aimed to investigate the morphological characteristics and phylogenetic relationships of three new species of Tropicoporus from the southern parts of India. The analyses of the ITS and nLSU regions revealed the novelty of these species, which have been named T. pannaensis, T. subindicus, and T. xerophyticus. All three species possess pileate basidiomes, a monomitic hyphal system in the context, and the presence of cystidioles and setae. However, they differ significantly in their phylogenetic placements and other morpho-taxonomic features. Tropicoporus pannaensis is characterized by a meagrely ungulate basidiome, indistinct zones, and an obtuse margin. Tropicoporus subindicus has a triquetrous basidiome and a radially cracked, crusted pileal surface with an acute margin, while T. xerophyticus is distinguished by an imbricate, perennial basidiome with an abundantly warted pileal surface. A phylogenetic tree is provided to show the placement of the three new species, along with detailed descriptions and illustrations. Additionally, a key for the identification of the Asian species of Tropicoporus is presented. Full article
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17 pages, 8040 KiB  
Article
The Putative Virulence Plasmid pYR4 of the Fish Pathogen Yersinia ruckeri Is Conjugative and Stabilized by a HigBA Toxin–Antitoxin System
by Fisentzos Floras, Chantell Mawere, Manvir Singh, Victoria Wootton, Luke Hamstead, Gareth McVicker and Jack C. Leo
Biology 2024, 13(9), 652; https://doi.org/10.3390/biology13090652 - 23 Aug 2024
Viewed by 663
Abstract
The bacterium Yersinia ruckeri causes enteric redmouth disease in salmonids and hence has substantial economic implications for the farmed fish industry. The Norwegian Y. ruckeri outbreak isolate NVH_3758 carries a relatively uncharacterized plasmid, pYR4, which encodes both type 4 pili and a type [...] Read more.
The bacterium Yersinia ruckeri causes enteric redmouth disease in salmonids and hence has substantial economic implications for the farmed fish industry. The Norwegian Y. ruckeri outbreak isolate NVH_3758 carries a relatively uncharacterized plasmid, pYR4, which encodes both type 4 pili and a type 4 secretion system. In this study, we demonstrate that pYR4 does not impose a growth burden on the Y. ruckeri host bacterium, nor does the plasmid contribute to twitching motility (an indicator of type 4 pilus function) or virulence in a Galleria mellonella larval model of infection. However, we show that pYR4 is conjugative. We also reveal, through mutagenesis, that pYR4 encodes a functional post-segregational killing system, HigBA, that is responsible for plasmid maintenance within Y. ruckeri. This is the first toxin–antitoxin system to be characterized for this organism. Whilst further work is needed to elucidate the virulence role of pYR4 and whether it contributes to bacterial disease under non-laboratory conditions, our results suggest that the plasmid possesses substantial stability and transfer mechanisms that imply importance within the organism. These results add to our understanding of the mobile genetic elements and evolutionary trajectory of Y. ruckeri as an important commercial pathogen, with consequences for human food production. Full article
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11 pages, 5368 KiB  
Article
The A226D Mutation of OmpC Leads to Increased Susceptibility to β-Lactam Antibiotics in Escherichia coli
by Jiaming Zhu, Peng Guo, Yuting Zheng, Shiqing Xiang, Yang Zhao, Xinyu Liu, Chengzhang Fu, Youming Zhang, Hai Xu, Ling Li, Wenjia Wang and Mingyu Wang
Biology 2024, 13(8), 600; https://doi.org/10.3390/biology13080600 - 9 Aug 2024
Viewed by 1049
Abstract
Bacterial resistance to antibiotics can lead to long-lasting, hard-to-cure infections that pose significant threats to human health. One key mechanism of antimicrobial resistance (AMR) is to reduce the antibiotic permeation of cellular membranes. For instance, the lack of outer membrane porins (OMPs) can [...] Read more.
Bacterial resistance to antibiotics can lead to long-lasting, hard-to-cure infections that pose significant threats to human health. One key mechanism of antimicrobial resistance (AMR) is to reduce the antibiotic permeation of cellular membranes. For instance, the lack of outer membrane porins (OMPs) can lead to elevated AMR levels. However, knowledge on whether mutations of OMPs can also influence antibiotic susceptibility is limited. This work aims to address this question and identified an A226D mutation in OmpC, a trimeric OMP, in Escherichia coli. Surveillance studies found that this mutation is present in 50 E. coli strains for which whole genomic sequences are available. Measurement of minimum inhibition concentrations (MICs) found that this mutation leads to a 2-fold decrease in MICs for β-lactams ampicillin and piperacillin. Further survival assays confirmed the role this mutation plays in β-lactam susceptibility. With molecular dynamics, we found that the A226D mutation led to increased overall flexibility of the protein, thus facilitating antibiotic uptake, and that binding with piperacillin was weakened, leading to easier antibiotic penetration. This work reports a novel mutation that plays a role in antibiotic susceptibility, along with mechanistic studies, and further confirms the role of OMPs in bacterial tolerance to antibiotics. Full article
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15 pages, 9139 KiB  
Article
Comparative Analysis of the Gut Microbiota of Bat Species with Different Feeding Habits
by Diego Antonio Mena Canata, Mara Silveira Benfato, Francielly Dias Pereira, María João Ramos Pereira, Fernanda Schäfer Hackenhaar, Michele Bertoni Mann, Ana Paula Guedes Frazzon and Pabulo Henrique Rampelotto
Biology 2024, 13(6), 363; https://doi.org/10.3390/biology13060363 - 22 May 2024
Viewed by 1327
Abstract
Bats are a diverse and ecologically important group of mammals that exhibit remarkable diversity in their feeding habits. These diverse feeding habits are thought to be reflected in the composition and function of their gut microbiota, which plays important roles in nutrient acquisition, [...] Read more.
Bats are a diverse and ecologically important group of mammals that exhibit remarkable diversity in their feeding habits. These diverse feeding habits are thought to be reflected in the composition and function of their gut microbiota, which plays important roles in nutrient acquisition, immune function, and overall health. Despite the rich biodiversity of bat species in South America, there is a lack of microbiome studies focusing on bats from this region. Such studies could offer major insights into conservation efforts and the preservation of biodiversity in South America. In this work, we aimed to compare the gut microbiota of four bat species with different feeding habits from Southern Brazil, including nectarivorous, frugivorous, insectivorous, and hematophagous bats. Our findings demonstrate that feeding habits can have a significant impact on the diversity and composition of bat gut microbiotas, with each species exhibiting unique metabolic potentials related to their dietary niches. In addition, the identification of potentially pathogenic bacteria suggests that the carriage of microbial pathogens by bats may vary, depending on feeding habits and host-specific factors. These findings provide novel insights into the relationship between bat feeding habits and gut microbiota composition, highlighting the need to promote diverse habitats and food sources to support these ecologically important species. Full article
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17 pages, 2716 KiB  
Article
Antibacterial and Antibiofilm Potential of Bacterial Cellulose Hydrogel Containing Vancomycin against Multidrug-Resistant Staphylococcus aureus and Staphylococcus epidermidis
by Ana Alice Venancio Correia, Luís André de Almeida Campos, Hanne Lazla Rafael de Queiroz Macêdo, Davi de Lacerda Coriolano, Maria Anndressa Alves Agreles, Danilo Elias Xavier, Rafaela de Siqueira Ferraz-Carvalho, José Lamartine de Andrade Aguiar and Isabella Macário Ferro Cavalcanti
Biology 2024, 13(5), 354; https://doi.org/10.3390/biology13050354 - 17 May 2024
Cited by 1 | Viewed by 1654
Abstract
The present study aimed to evaluate the in vitro antibacterial and antibiofilm activity of bacterial cellulose hydrogel produced by Zoogloea sp. (HYDROGEL) containing vancomycin (VAN) against bacterial strains that cause wound infections, such as multidrug-resistant (MDR) Staphylococcus aureus and Staphylococcus epidermidis. Initially, [...] Read more.
The present study aimed to evaluate the in vitro antibacterial and antibiofilm activity of bacterial cellulose hydrogel produced by Zoogloea sp. (HYDROGEL) containing vancomycin (VAN) against bacterial strains that cause wound infections, such as multidrug-resistant (MDR) Staphylococcus aureus and Staphylococcus epidermidis. Initially, HYDROGEL was obtained from sugar cane molasses, and scanning electron microscopy (SEM) was performed to determine morphological characteristics. Then, VAN was incorporated into HYDROGEL (VAN-HYDROGEL). The antibacterial activity of VAN, HYDROGEL, and VAN-HYDROGEL was assessed using the broth microdilution method to determine the minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) against methicillin-sensitive S. aureus (MSSA) ATCC 25923, methicillin-resistant S. aureus (MRSA) ATCC 33591, S. epidermidis INCQS 00016 (ATCC 12228), five clinical isolates of MRSA, and nine clinical isolates of methicillin-resistant S. epidermidis, following the Clinical and Laboratory Standards Institute (CLSI) guidelines. Additionally, the antibacterial activity of VAN, HYDROGEL, and VAN-HYDROGEL was studied using the time-kill assay. Subsequently, the antibiofilm activity of VAN, HYDROGEL, and VAN-HYDROGEL was evaluated using crystal violet and Congo red methods, as well as SEM analysis. VAN and VAN-HYDROGEL showed bacteriostatic and bactericidal activity against MRSA and methicillin-resistant S. epidermidis strains. HYDROGEL did not show any antibacterial activity. Analysis of the time-kill assay indicated that HYDROGEL maintained the antibacterial efficacy of VAN, highlighting its efficiency as a promising carrier. Regarding antibiofilm activity, VAN and HYDROGEL inhibited biofilm formation but did not demonstrate biofilm eradication activity against methicillin-resistant S. aureus and S. epidermidis strains. However, it was observed that the biofilm eradication potential of VAN was enhanced after incorporation into HYDROGEL, a result also proven through images obtained by SEM. From the methods carried out in this study, it was possible to observe that HYDROGEL preserved the antibacterial activity of vancomycin, aside from exhibiting antibiofilm activity and enhancing the antibiofilm effect of VAN. In conclusion, this study demonstrated the potential of HYDROGEL as a candidate and/or vehicle for antibiotics against MDR bacteria that cause wound infections. Full article
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14 pages, 2627 KiB  
Article
Response Mechanism of cbbM Carbon Sequestration Microbial Community Characteristics in Different Wetland Types in Qinghai Lake
by Ni Zhang, Kelong Chen, Xinye Wang, Wei Ji, Ziwei Yang, Xia Wang and Junmin Li
Biology 2024, 13(5), 333; https://doi.org/10.3390/biology13050333 - 10 May 2024
Cited by 1 | Viewed by 1022
Abstract
Carbon-sequestering microorganisms play an important role in the carbon cycle of wetland ecosystems. However, the response mechanism of carbon-sequestering microbial communities to wetland type changes and their relationship with soil carbon remain unclear. To explore these differences and identify the main influencing factors, [...] Read more.
Carbon-sequestering microorganisms play an important role in the carbon cycle of wetland ecosystems. However, the response mechanism of carbon-sequestering microbial communities to wetland type changes and their relationship with soil carbon remain unclear. To explore these differences and identify the main influencing factors, this study selected marsh wetlands, river wetlands and lakeside wetlands around Qinghai Lake as research subjects. High-throughput sequencing was employed to analyze the functional gene cbbM of carbon-sequestering microorganisms. The results revealed that the alpha diversity of cbbM carbon-sequestering microorganisms mirrored the trend in total carbon content, with the highest diversity observed in marsh wetlands and the lowest in lakeside wetlands. The dominant bacterial phylum was Proteobacteria, with prevalent genera including Thiothrix, Acidithiobacillus, and Thiodictyon. Acidithiobacillus served as a biomarker in lakeside wetlands, while two other genera were indicative of marsh wetlands. The hierarchical partitioning analysis indicated that the diversity of cbbM carbon-fixing microorganisms was primarily influenced by the total nitrogen content, while the community structure was significantly affected by the soil total carbon content. Moreover, an increased soil temperature and humidity were found to favor the carbon fixation processes of Thiomicrospira, Thiomonas, Polaromonas, and Acidithiobacillus. In summary, changes in wetland types seriously affected the characteristics of cbbM carbon sequestration in microbial communities, and a warm and humid climate may be conducive to wetland carbon sequestration. Full article
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21 pages, 10505 KiB  
Article
Cellular Response of Adapted and Non-Adapted Tetrahymena thermophila Strains to Europium Eu(III) Compounds
by Patricia Alonso, Javier Blas, Francisco Amaro, Patricia de Francisco, Ana Martín-González and Juan Carlos Gutiérrez
Biology 2024, 13(5), 285; https://doi.org/10.3390/biology13050285 - 23 Apr 2024
Viewed by 1265
Abstract
Europium is one of the most reactive lanthanides and humans use it in many different applications, but we still know little about its potential toxicity and cellular response to its exposure. Two strains of the eukaryotic microorganism model Tetrahymena thermophila were adapted to [...] Read more.
Europium is one of the most reactive lanthanides and humans use it in many different applications, but we still know little about its potential toxicity and cellular response to its exposure. Two strains of the eukaryotic microorganism model Tetrahymena thermophila were adapted to high concentrations of two Eu(III) compounds (EuCl3 or Eu2O3) and compared to a control strain and cultures treated with both compounds. In this ciliate, EuCl3 is more toxic than Eu2O3. LC50 values show that this microorganism is more resistant to these Eu(III) compounds than other microorganisms. Oxidative stress originated mainly by Eu2O3 is minimized by overexpression of genes encoding important antioxidant enzymes. The overexpression of metallothionein genes under treatment with Eu(III) compounds supports the possibility that this lanthanide may interact with the -SH groups of the cysteine residues from metallothioneins and/or displace essential cations of these proteins during their homeostatic function. Both lipid metabolism (lipid droplets fusing with europium-containing vacuoles) and autophagy are involved in the cellular response to europium stress. Bioaccumulation, together with a possible biomineralization to europium phosphate, seems to be the main mechanism of Eu(III) detoxification in these cells. Full article
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