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Trends in Microbiology 2025
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Trends in Microbiology 2025

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Microbiology".

Deadline for manuscript submissions: 30 November 2025 | Viewed by 12772

Special Issue Editors

Dr. Pabulo Rampelotto

E-Mail Website
Guest Editor
Clinical Hospital of Porto Alegre (HCPA), affiliated with the Federal University of Rio Grande do Sul, Porto Alegre 91501-970, Brazil
Interests: microbiome; molecular microbiology; metagenomics; omics; biostatistics; next-generation sequencing; clinical research; bioinformatics; biotechnology; system biology; grand challenges
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Milan Kolar

E-Mail Website
Guest Editor
Faculty of Medicine and Dentistry and University Hospital, Palacky University, Olomouc, Czech Republic
Interests: bacterial infections; antibiotic therapy; antibiotic resistance
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We are excited to announce the call for papers for the 2025 edition of our Special Issue on "Trends in Microbiology". Building on the success of our previous edition, this Special Issue aims to compile a diverse collection of cutting-edge research articles, reviews, and perspectives that reflect the dynamic and rapidly evolving field of microbiology. We welcome original research articles, comprehensive reviews, and insightful perspectives that provide novel insights, introduce new methodologies, or present breakthrough discoveries. Our goal is to offer a platform for the latest advancements in both basic and applied microbiology, fostering the exchange of knowledge and ideas across the scientific community.

2024 edition: Life | Special Issue: Trends in Microbiology 2024

Dr. Pabulo H. Rampelotto
Prof. Dr. Milan Kolar
Guest Editors

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. Life 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 2600 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

  • agricultural microbiology
  • clinical microbiology
  • environmental microbiology
  • food microbiology
  • industrial microbiology
  • marine microbiology
  • microbial biochemistry
  • microbial biofuel and bioenergy
  • microbial ecology
  • microbial evolution
  • microbial genetics
  • microbial metabolism
  • microbial pathogenesis
  • microbial physiology

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (9 papers)

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Research

22 pages, 3216 KiB  
Article
Effect of Pseudomonas protegens EMM-1 Against Rhizopus oryzae in Interactions with Mexican Autochthonous Red Maize
by Bruce Manuel Morales-Barron, Violeta Larios-Serrato, Yolanda Elizabeth Morales-García, Verónica Quintero-Hernández, Paulina Estrada-de los Santos and Jesús Muñoz-Rojas
Life 2025, 15(4), 554; https://doi.org/10.3390/life15040554 - 28 Mar 2025
Viewed by 525
Abstract
In the present study, the strain Rhizopus oryzae EMM was isolated from germinated autochthonous red maize seeds, which were harvested in a region of San Diego-Buenavista, Papalotla, Tlaxcala, Mexico, where cobs with fungal infections have been observed. This fungal strain caused wilting in [...] Read more.
In the present study, the strain Rhizopus oryzae EMM was isolated from germinated autochthonous red maize seeds, which were harvested in a region of San Diego-Buenavista, Papalotla, Tlaxcala, Mexico, where cobs with fungal infections have been observed. This fungal strain caused wilting in the maize seedlings. Pseudomonas protegens EMM-1 was tested for its ability to inhibit R. oryzae EMM, both in culture media and in association with maize plantlets. P. protegens EMM-1 inhibited the growth of R. oryzae EMM under all culture media conditions explored. The ability of P. protegens EMM-1 to inhibit the growth of R. oryzae EMM associated with plants was evaluated in both a hydroponic system and in vermiculite. In both systems, P. protegens EMM-1 strongly inhibited the growth of R. oryzae EMM. The dry weight of root plants infected with R. oryzae EMM and inoculated with P. protegens EMM-1 increased to 0.43 g, while that of plants infected only with R. oryzae EMM reached just 0.19 g under hydroponic conditions. However, no differences were observed under vermiculite conditions. The dry weight of the aerial region of plants infected with R. oryzae EMM and inoculated with P. protegens EMM-1 was greater than that of plants infected only with R. oryzae EMM, both under hydroponic and vermiculite conditions. These results indicate that P. protegens EMM-1 inhibits the infection caused by R. oryzae EMM, thereby improving plant growth. Moreover, the genome analysis of P. protegens EMM-1 revealed the presence of several genes that potentially encode for antimicrobial compounds, which could strengthen the potential use of P. protegens EMM-1 as a biocontrol agent in maize plants. Full article
(This article belongs to the Special Issue Trends in Microbiology 2025)
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20 pages, 5088 KiB  
Article
Exploring Fungal Abundance and WHO Fungal Priority Pathogens in Agricultural Fields: A One Health Perspective in Northeast Thailand
by Chayaporn Lakmuang, Syahriar Nur Maulana Malik Ibrahim, Teeratat Kaewjon, Nattapol Kraisitudomsook, Naraporn Somboonna, Ratmanee Chanabun, Ariya Chindamporn and Nuttapon Pombubpa
Life 2025, 15(3), 488; https://doi.org/10.3390/life15030488 - 18 Mar 2025
Viewed by 426
Abstract
Fungal pathogens prevalent in agricultural areas pose a significant risk to human health, with some exhibiting high fatality rates, as reported by the WHO Fungal Pathogen Priority List (WHO FPPL). This study investigates fungal communities in northeast Thailand’s agricultural areas, focusing on potential [...] Read more.
Fungal pathogens prevalent in agricultural areas pose a significant risk to human health, with some exhibiting high fatality rates, as reported by the WHO Fungal Pathogen Priority List (WHO FPPL). This study investigates fungal communities in northeast Thailand’s agricultural areas, focusing on potential reservoirs of the WHO FPPL. Samples were collected from rice, cassava, rubber trees, and sugarcane fields across 18 provinces with distinct geological features. Metabarcoding of the ITS1 region and taxonomic analysis were conducted, and potential pathogens were selected according to WHO FPPL criteria. The results showed that overall fungal community richness and diversity were influenced by plant fields but not significantly different by geological features. Soil organic matter and water content affected fungal dynamics only in rubber tree fields. Fungal pathogens from the WHO FPPL were found in all four plant fields, with higher abundance in Chaiyaphum province, especially in sugarcane fields, and the lowest in Nong Bua Lam Phu. Candida tropicalis, a high-priority pathogen, was predominantly associated with rock salt features. This study underscores the need for vigilance among farmers and emphasizes the importance of confirming fungal pathogenicity. Full article
(This article belongs to the Special Issue Trends in Microbiology 2025)
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15 pages, 635 KiB  
Article
Antibacterial Effects of Er:YAG Laser Irradiation on Candida–Streptococcal Biofilms
by Zuzanna Grzech-Leśniak, Jakub Pyrkosz, Jagoda Szwach, Patrycja Kosidło, Jacek Matys, Rafał Wiench, Magdalena Pajączkowska, Joanna Nowicka, Marzena Dominiak and Kinga Grzech-Leśniak
Life 2025, 15(3), 474; https://doi.org/10.3390/life15030474 - 16 Mar 2025
Viewed by 590
Abstract
In contemporary dentistry, laser-based interventions have become one of the mainstays of care for patients with oral biofilm diseases, such as candidiasis, periodontal disease and peri-implantitis. The purpose of this study was to evaluate the effectiveness of Er:YAG laser (LightWalker, Ljubljana, Fotona, Slovenia) [...] Read more.
In contemporary dentistry, laser-based interventions have become one of the mainstays of care for patients with oral biofilm diseases, such as candidiasis, periodontal disease and peri-implantitis. The purpose of this study was to evaluate the effectiveness of Er:YAG laser (LightWalker, Ljubljana, Fotona, Slovenia) irradiation at varying irradiance levels (T1: 11.3 W/cm2 and T2: 120.54 W/cm2) on microbial viability in single- and dual-species biofilm models, focusing on Candida albicans, Candida glabrata and Streptococcus mutans, to address challenges in managing complex oral biofilms in clinically relevant settings. The results showed substantial microbial reduction, with C. albicans being the most susceptible microorganism (93–99.9%), while C. glabrata exhibited marked resistance at higher irradiance levels. Interestingly, S. mutans demonstrated varying reductions based on the biofilm composition, highlighting the influence of microbial interactions. This study concluded that the Er:YAG laser effectively reduced biofilm viability, with its efficacy depending on the microbial composition and irradiance settings. These findings highlight the need for tailored erbium laser parameters to optimize clinical outcomes, underscoring the need for individualized polymicrobial biofilm management, particularly in periodontal and peri-implant therapies. Full article
(This article belongs to the Special Issue Trends in Microbiology 2025)
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12 pages, 1316 KiB  
Article
Assessing Potential Reservoir of Multidrug-Resistant Bacteria in the Oral Microbiota of Captive Burmese and Royal Pythons
by Inês Marques, Ana R. Pinto, José J. Martins, Nuno Alvura, Paula Telinhos, Pedro Mendes, Mónica Correia, João F. Requicha and Maria J. Saavedra
Life 2025, 15(3), 442; https://doi.org/10.3390/life15030442 - 12 Mar 2025
Viewed by 437
Abstract
The oral microbiota has a diversity of microorganisms that together maintain the homeostasis of the oral cavity. Disruptions in the balance of these microbial populations can lead to the development of oral and dental diseases. To characterize the normal oral microbiota of captive [...] Read more.
The oral microbiota has a diversity of microorganisms that together maintain the homeostasis of the oral cavity. Disruptions in the balance of these microbial populations can lead to the development of oral and dental diseases. To characterize the normal oral microbiota of captive ophidians, samples were obtained from the oral cavity of eight Burmese pythons (Python bivittatus) and 11 royal pythons (Python regius), using oral swab, during routine evaluations. In the Laboratory-Antimicrobials, Biocides and Biofilms Unit at University of Trás-os-Montes e Alto Douro, the identification and antimicrobial susceptibility profile was determined using the Vitek® 2 Compact automated device (bioMérieux, Marcy-l’Étoile, France). Of the 106 bacterial isolates obtained, 69% were Gram-negative species and 31% were Gram-positive bacteria. The genus Pseudomonas was the most frequently isolated. Chryseobacterium indologenes, Escherichia coli and Pseudomonas aeruginosa were the most isolated species. Antimicrobial susceptibility testing revealed that the phenotypic resistance was highest for nitrofurans (47.2%), beta-lactams (45.8%) and sulfonamides (30.6%). Twenty-one multidrug-resistant isolates (58.3%) were identified with Acinetobacter baumannii, Serratia plymuthica, Chryseobacterium indologenes, Providencia rettgeri and Pseudomonas aeruginosa showing the highest resistance frequencies. Full article
(This article belongs to the Special Issue Trends in Microbiology 2025)
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11 pages, 1556 KiB  
Article
In Vitro and In Vivo Interventions Reveal the Health Benefits of Levan-Type Exopolysaccharide Produced by a Fish Gut Isolate Lactobacillus reuteri FW2
by Waqar Ahmad, Anam Nasir, Satya Prakash, Azam Hayat, Mujaddad ur Rehman, Shazia Khaliq, Kalsoom Akhtar, Munir Ahmad Anwar and Nayla Munawar
Life 2025, 15(1), 89; https://doi.org/10.3390/life15010089 - 13 Jan 2025
Cited by 1 | Viewed by 906
Abstract
Microorganisms synthesize diverse types of exopolysaccharides (EPSs). EPSs with varying structural and physical properties can demonstrate unique health benefits, which allow for their tailored applications as functional foods such as prebiotics. Levan, a fructose-based EPS, is gaining considerable attention as an effective prebiotic [...] Read more.
Microorganisms synthesize diverse types of exopolysaccharides (EPSs). EPSs with varying structural and physical properties can demonstrate unique health benefits, which allow for their tailored applications as functional foods such as prebiotics. Levan, a fructose-based EPS, is gaining considerable attention as an effective prebiotic to support the growth of beneficial gut bacteria. Consequently, this enhances digestive health, boosts the immune system, and reduces the risk of chronic diseases. Unfortunately, limited studies are available on levan-type EPSs to demonstrate their role as prebiotics. Therefore, in this study, we conducted in vitro and in vivo experiments, concerning intestinal cell integrity and metabolic syndrome, to assess the therapeutic potential of levan derived from Lactobacillus reuteri FW2. The in vitro experimental results revealed that levan improved the survival of impaired HT-29 epithelial cells of the intestine and also exerted antioxidant effects. In the in vivo experiments, mice fed with levan-supplemented feed exhibited low body weight gain, blood glucose, and serum cholesterol levels compared to the control group. These findings highlight the biotherapeutic potential of L. reuteri FW2-derived levan for improving metabolic syndrome and its associated aspects. It also signifies the need for a further detailed investigation based on clinical trials to include levan in dietary supplements for improved health and well-being. Full article
(This article belongs to the Special Issue Trends in Microbiology 2025)
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18 pages, 5346 KiB  
Article
Metagenome Analysis Identified Novel Microbial Diversity of Sandy Soils Surrounded by Natural Lakes and Artificial Water Points in King Salman Bin Abdulaziz Royal Natural Reserve, Saudi Arabia
by Yahya S. Al-Awthan, Rashid Mir, Fuad A. Alatawi, Abdulaziz S. Alatawi, Fahad M. Almutairi, Tamer Khafaga, Wael M. Shohdi, Amal M. Fakhry and Basmah M. Alharbi
Life 2024, 14(12), 1692; https://doi.org/10.3390/life14121692 - 20 Dec 2024
Viewed by 4694
Abstract
Background: Soil microbes play a vital role in the ecosystem as they are able to carry out a number of vital tasks. Additionally, metagenomic studies offer valuable insights into the composition and functional potential of soil microbial communities. Furthermore, analyzing the obtained data [...] Read more.
Background: Soil microbes play a vital role in the ecosystem as they are able to carry out a number of vital tasks. Additionally, metagenomic studies offer valuable insights into the composition and functional potential of soil microbial communities. Furthermore, analyzing the obtained data can improve agricultural restoration practices and aid in developing more effective environmental management strategies. Methodology: In November 2023, sandy soil samples were collected from ten sites of different geographical areas surrounding natural lakes and artificial water points in the Tubaiq conservation area of King Salman Bin Abdulaziz Royal Natural Reserve (KSRNR), Saudi Arabia. In addition, genomic DNA was extracted from the collected soil samples, and 16S rRNA sequencing was conducted using high-throughput Illumina technology. Several computational analysis tools were used for gene prediction and taxonomic classification of the microbial groups. Results: In this study, sandy soil samples from the surroundings of natural and artificial water resources of two distinct natures were used. Based on 16S rRNA sequencing, a total of 24,563 OTUs were detected. The metagenomic information was then categorized into 446 orders, 1036 families, 4102 genera, 213 classes, and 181 phyla. Moreover, the phylum Pseudomonadota was the most dominant microbial community across all samples, representing an average relative abundance of 34%. In addition, Actinomycetes was the most abundant class (26%). The analysis of clustered proteins assigned to COG categories provides a detailed understanding of the functional capabilities and adaptation of microbial communities in soil samples. Amino acid metabolism and transport were the most abundant categories in the soil environment. Conclusions: Metagenome analysis of sandy soils surrounding natural lakes and artificial water points in the Tubaiq conservation area of KSRNR (Saudi Arabia) has unveils rich microbial activity, highlighting the complex interactions and ecological roles of microbial communities in these environments. Full article
(This article belongs to the Special Issue Trends in Microbiology 2025)
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19 pages, 5564 KiB  
Article
Pathogenomic Insights into Xanthomonas oryzae pv. oryzae’s Resistome, Virulome, and Diversity for Improved Rice Blight Management
by Peter Adeolu Adedibu, Oksana Son, Liudmila Tekutyeva and Larissa Balabanova
Life 2024, 14(12), 1690; https://doi.org/10.3390/life14121690 - 20 Dec 2024
Viewed by 934
Abstract
Oryza sativa (rice) is a major staple food targeted for increased production to achieve food security. However, increased production is threatened by several biotic and abiotic factors, of which bacterial blight disease caused by Xanthomonas oryzae pathovar oryzae is severe. Developing effective control [...] Read more.
Oryza sativa (rice) is a major staple food targeted for increased production to achieve food security. However, increased production is threatened by several biotic and abiotic factors, of which bacterial blight disease caused by Xanthomonas oryzae pathovar oryzae is severe. Developing effective control strategies requires an up-to-date understanding of its pathogenomics. This study analyzes the genomes of 30 X. oryzae strains collected from rice-producing regions across five continents to identify genetic elements critical for its pathogenicity and adaptability and for an intraspecific diversity assessment using advanced genomics and bioinformatics tools. Resistome analysis revealed 28 distinct types of antibiotic resistance genes (ARGs), both innate and acquired, indicating a growing threat from multidrug-resistant X. oryzae strains. Sixteen virulent genes, including type III and VI secretion systems, motility genes, and effector proteins, were identified. A unique ‘MexCD-OprJ’ multidrug efflux system was detected in the Tanzanian strains, conferring resistance to multiple antibiotic classes. To curb further ARG emergence, there is a need to regulate the use of antibiotics for X. oryzae control and adopt resistant rice varieties. Transposable elements were also discovered to contribute to X. oryzae pathogenicity, facilitating the horizontal transfer of virulence genes. Pangenome analysis revealed intraspecific variation among the population, with 112 unique CDS having diverse functional roles. Strains registered in the Philippines had the most unique genes. Phylogenetic analysis confirmed the divergent evolution of X. oryzae. This study’s results will aid in identifying more effective management strategies and biocontrol alternatives for sustainable rice production. Full article
(This article belongs to the Special Issue Trends in Microbiology 2025)
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15 pages, 3246 KiB  
Article
Comparative Analysis of Gut Microbiota in Humans Living with and Without Companion Animals
by Kyung-Hyo Do, Jiwon Park, Nahee Kim, Dahye Ryu, Min-Gyu Kim, Hyunjung Ahn, Hakhyun Kim, Jun-Gi Hwang, Min-Kyu Park, Kwang-Won Seo and Wan-Kyu Lee
Life 2024, 14(12), 1621; https://doi.org/10.3390/life14121621 - 6 Dec 2024
Viewed by 1365
Abstract
Cohabitation with companion animals (CAs) has been suggested as a significant modifier of gut microbial diversity. This study investigated the influence of cohabitation with CAs on human gut microbiota composition. Using 16S rRNA gene sequencing, we analyzed the gut microbiota of 20 families [...] Read more.
Cohabitation with companion animals (CAs) has been suggested as a significant modifier of gut microbial diversity. This study investigated the influence of cohabitation with CAs on human gut microbiota composition. Using 16S rRNA gene sequencing, we analyzed the gut microbiota of 20 families with CAs (40 adults, 20 children) and 20 families without CAs (40 adults, 20 children). Alpha and beta diversity analyses were performed, and the differentially abundant genera were identified. There were significant differences in beta diversity across the groups (p-value = 0.001). The Bacillota/Bacteroidota ratio was considerably lower in the CAs group (0.67) than in the without-CAs group (1.02). Prevotellaceae_UCG-003 (log2 fold change: 7.3; adjusted p-value ≤ 0.001), Ruminococcaceae (log2 fold change: 6.3; adjusted p-value ≤ 0.001), and Oscillospira (log2 fold change: 5.1; adjusted p-value = 0.012) were elevated in the group cohabiting with CAs, whereas Megamonas (with CAs: 3.81%; without CAs: 13.52%) and Veillonella (with CAs: 3.77%; without CAs: 6.50%) were more prevalent in the group without CAs. Cohabitation with CAs may positively influence the gut microbiota by promoting the presence of beneficial bacteria and reducing the Bacillota/Bacteroidota ratio. This study highlights the potential for cohabitation with CAs to promote gut microbial health. Full article
(This article belongs to the Special Issue Trends in Microbiology 2025)
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17 pages, 6182 KiB  
Article
Oral Microbiome Dynamics in Treated Childhood Caries: A Comparative Study
by Zahirrah Begam Mohamed Rasheed, Chew Wei Sheng, Erika Norfitriah, Nurrul Shaqinah Nasruddin and Farinawati Yazid
Life 2024, 14(12), 1576; https://doi.org/10.3390/life14121576 - 1 Dec 2024
Cited by 1 | Viewed by 1626
Abstract
Background: Dental caries is a multifactorial disease that results from interactions of susceptible host, cariogenic microorganisms, and fermentable carbohydrate sources. Our study explored oral microbiome shifts in children before and after dental treatment. Methods: Initial saliva samples were collected from caries free, moderate [...] Read more.
Background: Dental caries is a multifactorial disease that results from interactions of susceptible host, cariogenic microorganisms, and fermentable carbohydrate sources. Our study explored oral microbiome shifts in children before and after dental treatment. Methods: Initial saliva samples were collected from caries free, moderate caries, and severe caries children based on the decayed, missing, and filled teeth index (DMFT/dmft) index. After three months of dental treatment, second saliva samples were gathered from the moderate and severe caries groups. The microbiota was analyzed by 16S rRNA gene-based high-throughput sequencing. Results: Most children with caries were between seven and eight years of age (40%), from middle-income group families (61%), highly educated parents (18% secondary level and 75% tertiary level) with good oral hygiene practices. There was a significant increase in alpha-diversity post-dental intervention. Firmicutes, Bacteroidota, and Proteobacteria were abundant across all samples. Post-treatment, Actinobacteria, and Firmicutes significantly decreased (p < 0.05) while Fusobacteria, Proteobacteria, Spirochaetota, and Synergistota significantly increased (p < 0.05). At genus level, a decreased trend was seen in Streptococcus, Prevotella_7, and Rothia and an increased trend was seen in Fusobacterium, Neisseria, Haemophilus, and Leptotrichia, but was not statistically significant. Conclusions: This study on Malaysian children highlights that dental caries are influenced by factors like age, socioeconomic status, and diet, with oral microbiome diversity increasing post-treatment, though some harmful bacteria persist, indicating a need for targeted oral health education and further research on probiotics’ role in caries prevention. Full article
(This article belongs to the Special Issue Trends in Microbiology 2025)
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