Microorganisms

15 pages, 313 KB

Open AccessArticle

Viral Quasispecies Inference from Single Observations—Mutagens as Accelerators of Quasispecies Evolution

by Josep Gregori, Miquel Salicrú, Marta Ibáñez-Lligoña, Sergi Colomer-Castell, Carolina Campos, Alvaro González-Camuesco and Josep Quer

Microorganisms 2025, 13(9), 2029; https://doi.org/10.3390/microorganisms13092029 (registering DOI) - 30 Aug 2025

Abstract

RNA virus populations exist as quasispecies-complex, dynamic clouds of closely related but genetically diverse variants generated by high mutation rates during replication. Assessing quasispecies structure and diversity is crucial for understanding viral evolution, adaptation, and response to antiviral treatments. However, comparing single quasispecies [...] Read more.

RNA virus populations exist as quasispecies-complex, dynamic clouds of closely related but genetically diverse variants generated by high mutation rates during replication. Assessing quasispecies structure and diversity is crucial for understanding viral evolution, adaptation, and response to antiviral treatments. However, comparing single quasispecies observations from individual biosamples, especially at different infection or treatment time points, presents statistical challenges. Traditional inferential tests are inapplicable due to the lack of replicate observations, and resampling-based approaches such as the bootstrap and jackknife are limited by biases and non-independence, particularly for diversity indices sensitive to rare haplotypes. In this study, we address these limitations by applying the delta method to derive analytical variances for a set of quasispecies structure indicators specifically designed to assess the quasispecies maturation state. We demonstrate the utility of this approach using high-depth next-generation sequencing data from hepatitis C virus (HCV) quasispecies evolving in vitro under various conditions, including free evolution and exposure to antiviral or mutagenic treatments. Our results reveal that with highly fit HCV quasispecies, sofosbuvir inhibits quasispecies genetic diversity, while mutagenic treatments accelerate maturation, compared to untreated controls. We emphasize the interpretation of results through absolute differences, log-fold changes, and standardized effect sizes, moving beyond mere statistical significance. This framework enables robust, quantitative comparisons of quasispecies diversity from single observations, providing valuable insights into viral adaptation and treatment response. The R code and session info with required libraries and versions is provided in the supplementary material. Full article

(This article belongs to the Special Issue Bioinformatics Research on Viruses)

16 pages, 1646 KB

Open AccessArticle

Characterization of Prophages and Their Genetic Cargo in Clinical M. abscessus Isolates

by Sichun Luan, Yu Chen, Na Li, Qing Miao, Jue Pan and Bijie Hu

Microorganisms 2025, 13(9), 2028; https://doi.org/10.3390/microorganisms13092028 (registering DOI) - 30 Aug 2025

Abstract

Limited data exist regarding lysogenic phages carried by M. abscessus, as well as regarding their roles played in diseases. Strains identified as M. abscessus from patients were collected. Prophages, virulence factors, and antibiotic resistance genes present in genomes were predicted, and correlations [...] Read more.

Limited data exist regarding lysogenic phages carried by M. abscessus, as well as regarding their roles played in diseases. Strains identified as M. abscessus from patients were collected. Prophages, virulence factors, and antibiotic resistance genes present in genomes were predicted, and correlations between prophages, virulence factors, antibiotic resistance genes, and clinical patient prognoses were analyzed. A total of 145 prophage sequences were detected in 56 M. abscessus strains. Prophages contained more virulence factors and antibiotic resistance genes, compared to known mycobacteriophages. The average sequence similarity among prophage sequences from a single patient was significantly higher than that among prophages from different patients or between prophages and known phages. The study showed that M. abscessus commonly carries prophages, which are enriched in virulence factors and antibiotic resistance genes relative to known phages, but their relationship to clinical prognoses requires further study. Prophages present in strains from different patients were highly diverse and exhibited low similarity with known mycobacterial phages. Full article

(This article belongs to the Section Molecular Microbiology and Immunology)

19 pages, 4070 KB

Open AccessArticle

Optimization of Fermentation Conditions for Antarctic Bacteria and Investigation of Its Antimicrobial Mechanism Against Klebsiella pneumoniae

by Lukai Xu, Mengyu Li, Yangzhu Huang, Yuanchao Mao, Shouyuan Cai, Xinyuan Yang, Xiyan Hou, Lulu Wang, Chunshan Quan and Liming Jin

Microorganisms 2025, 13(9), 2027; https://doi.org/10.3390/microorganisms13092027 (registering DOI) - 30 Aug 2025

Abstract

Klebsiella pneumoniae is the second-most common opportunistic pathogen in clinical practice and has developed resistance to potent antibacterial drugs such as carbapenems. Therefore, developing safe and effective strategies for the prevention and treatment of K. pneumoniae infections remains a critical challenge. In this [...] Read more.

Klebsiella pneumoniae is the second-most common opportunistic pathogen in clinical practice and has developed resistance to potent antibacterial drugs such as carbapenems. Therefore, developing safe and effective strategies for the prevention and treatment of K. pneumoniae infections remains a critical challenge. In this study, a strain named Tie-10 isolated from Antarctic samples demonstrated potent antibacterial activity against K. pneumoniae, which was subsequently identified as Bacillus nakamurai. The fermentation medium and culture conditions were systematically optimized through single-factor experiments, orthogonal array testing, and response surface methodology. The optimal medium composition was determined to be beef extract, peptone, and KNO₃. The culture conditions included a time of 24 h, temperature of 37 °C, pH of 7.0, and bottling volume of 80 mL. Antagonistic experiments demonstrated that the crude extract of B. nakamurai Tie-10 exhibited significant inhibitory activity against K. pneumoniae. The alkaline protease (AKP) assay demonstrated that the crude extract effectively disrupted the cellular integrity of K. pneumoniae, a finding further corroborated by scanning electron microscopy (SEM) analysis. Furthermore, the crude extract significantly inhibited extracellular protease secretion in K. pneumoniae, downregulated the expression of virulence-associated genes, and effectively disrupted biofilm formation. The study presented innovative strategies for the management and containment of K. pneumoniae infections. Full article

(This article belongs to the Section Microbial Biotechnology)

► Show Figures

Figure 1

26 pages, 5439 KB

Open AccessArticle

Methods for Evaluating the Effects of 2D and 3D Culture Environment on Macrophage Response to Mycobacterium Infection

by Danielle L. Stolley, Komal S. Rasaputra and Elebeoba E. May

Microorganisms 2025, 13(9), 2026; https://doi.org/10.3390/microorganisms13092026 - 29 Aug 2025

Abstract

Macrophages are critical to the formation of infection- and non-infection-associated immune structures such as cancer spheroids, pathogen-, and non-pathogen-associated granulomas, contributing to the spatiotemporal and chemical immune response and eventual outcome of disease. While well established in cancer immunology, the prevalence of using [...] Read more.

Macrophages are critical to the formation of infection- and non-infection-associated immune structures such as cancer spheroids, pathogen-, and non-pathogen-associated granulomas, contributing to the spatiotemporal and chemical immune response and eventual outcome of disease. While well established in cancer immunology, the prevalence of using three-dimensional (3D) cultures to characterize later-stage structural immune response in pathogen-associated granulomas continues to increase, generating valuable insights for empirical and computational analysis. To enable integration of data from 3D in vitro studies with the vast bibliome of standard two-dimensional (2D) tissue culture data, methods that determine concordance between 2D and 3D immune response need to be established. Focusing on macrophage migration and oxidative species production, we develop experimental and computational methods to enable concurrent spatiotemporal and biochemical characterization of 2D versus 3D macrophage–mycobacterium interaction. We integrate standard biological sampling methods, time-lapse confocal imaging, and 4D quantitative image analysis to develop a 3D ex vivo model of Mycobacterium smegmatis infection using bone-marrow-derived macrophages (BMDMs) embedded in reconstituted basement membrane (RBM). Comparing features of 2D to 3D macrophage response that contribute to control and resolution of bacteria infection, we determined that macrophages in 3D environments increased production of reactive species, motility, and differed in cellular volume. Results demonstrate a viable and extensible approach for comparison of 2D and 3D datasets and concurrent biochemical plus spatiotemporal characterization of initial macrophage structural response during infection. Full article

(This article belongs to the Section Molecular Microbiology and Immunology)

► Show Figures

Figure 1

11 pages, 1171 KB

Open AccessArticle

The Trans-Kingdom Spectrum of Mpox-like Lesion Pustules of Suspect Patients in the Mpox Clade Ib Outbreak in Eastern Democratic Republic of the Congo

by Leandre Murhula Masirika, Benjamin Hewins, Ali Toloue Ostadgavahi, Mansi Dutt, Léandre Mutimbwa Mambo, Jean Claude Udahemuka, Pacifique Ndishimye, Justin Bengehya Mbiribindi, Freddy Belesi Siangoli, Patricia Kelvin, Morgan G. I. Langille, David J. Kelvin, Luis Flores, Gustavo Sganzerla Martinez and Anuj Kumar

Microorganisms 2025, 13(9), 2025; https://doi.org/10.3390/microorganisms13092025 - 29 Aug 2025

Abstract

During infectious disease outbreaks, acquiring genetic data across various kingdoms offers essential information to tailor precise treatment methodologies and bolster clinical, epidemiological, and public health awareness. Metagenomics sequencing has paved the way for personalized treatment approaches and streamlined the monitoring process for both [...] Read more.

During infectious disease outbreaks, acquiring genetic data across various kingdoms offers essential information to tailor precise treatment methodologies and bolster clinical, epidemiological, and public health awareness. Metagenomics sequencing has paved the way for personalized treatment approaches and streamlined the monitoring process for both co-infections and opportunistic infections. In this study, we conducted long-read metagenomic DNA sequencing on mpox-like lesion pustules from six suspected patients who were positive and confirmed to be infected with MPXV during the MPXV subclade Ib outbreak in the Eastern Democratic Republic of the Congo. The sequenced data were taxonomically classified as bacterial, fungal, and viral in composition. Our results show a wide spectrum of microorganisms present in the lesions. Bacteria such as Corynebacterium amycolatum, Gardnerella vaginalis, Enterococcus faecium, Enterobacter clocae, Staphylococcus epidermidis, and Stenotrophomonas maltophilia were found in the lesions. The viral classification of the reads pointed out the absolute predominance of the monkeypox virus. Taken together, the outcomes of this investigation underscore the potential involvement of microorganisms in mpox lesions and the possible role that co-infections played in exacerbating disease severity and transmission during the MPXV subclade Ib outbreak. Full article

(This article belongs to the Section Virology)

► Show Figures

Figure 1

24 pages, 3050 KB

Open AccessArticle

Comparison of Bacterial Community in the Jejunum, Ileum and Cecum of Suckling Lambs During Different Growth Stages

by Mengrong Su, Chunmei Du, Wenjie Zhang, Jie Liao, Tao Li, Shangquan Gan and Jian Ma

Microorganisms 2025, 13(9), 2024; https://doi.org/10.3390/microorganisms13092024 - 29 Aug 2025

Abstract

Given that suckling lambs with immature rumen development rely on intestinal microbiota for nutrient utilization, investigating the composition and functional characteristics of their intestinal microbiota is therefore of paramount importance. In this study, 16S rRNA gene amplicon sequencing technology was adopted to characterize [...] Read more.

Given that suckling lambs with immature rumen development rely on intestinal microbiota for nutrient utilization, investigating the composition and functional characteristics of their intestinal microbiota is therefore of paramount importance. In this study, 16S rRNA gene amplicon sequencing technology was adopted to characterize and analyze the diversity and composition of the jejunum, ileum and cecum bacterial communities of lambs at 0, 7 and 28 days of age, and to predict the functions of the bacterial communities. The α-diversity analysis results revealed that in the jejunum of lambs, the Chao1, PD, Simpson and Shannon indexes differed significantly among the three age groups (p < 0.05). In the ileum, Shannon and Simpson indexes of the 0-days-of-age group were slightly lower than those of the 7 (8.84% and 12.66% reductions, respectively) and 28-days-of-age groups (19.34% and 15.85% reductions, respectively) (0.05 < p < 0.10). In the cecum, Simpson and Shannon indexes differed significantly (p < 0.05) among the three age groups. At the phylum level, Firmicutes (64.68%) and Proteobacteria (21.76%) dominated the bacterial communities across all intestinal segments, with a total of 42 phyla detected. At the genus level, 19 dominant genera were identified in the jejunum. Except for Bifidobacterium, which showed no significant age-related variation (p > 0.05), the relative abundance of the remaining 18 genera changed significantly with age (p < 0.05). In the ileum, compared with the 0-days-of-age group, the Lactobacillus abundance was significantly higher in the 7- and 28-days-of-age groups (p < 0.05), while the Escherichia-Shigella, Mannheimia and Enterobacter abundances were significantly reduced (p < 0.05). In the cecum, the genera, including Blautia, Sellimonas and Ruminococcaceae UCG-014, exhibited significant age-related differences (p < 0.05), whereas other genera showed no significant variation (p > 0.05). Collectively, the bacterial community α-diversity, compositional structure and specific genus abundance in the jejunum, ileum and cecum of lambs demonstrated pronounced age-dependent variation and intestinal segment specificity patterns. This study provides a foundation for a deeper understanding of the succession patterns of the early digestive tract microbiota in lambs, and is conducive to the development of early nutrition strategies based on precise regulation of the microbiome. Full article

(This article belongs to the Section Gut Microbiota)

31 pages, 3096 KB

Open AccessArticle

Pathoadapative Genomic Determinants of Staphylococcus aureus Community Skin Infections and Nasal Colonization

by Cody A. Black, Wonhee So, Raymond Benavides, Julianne A. Mercer, Steven S. Dallas, James F. Shurko, Sarah M. Bandy, Benjamin A. Encino, Justina S. Lipscomb, Adriana Vargus, Christopher R. Frei and Grace C. Lee

Microorganisms 2025, 13(9), 2023; https://doi.org/10.3390/microorganisms13092023 - 29 Aug 2025

Abstract

Staphylococcus aureus is a leading cause of skin and soft tissue infections (SSTIs), yet the bacterial genomic adaptations underlying the transition from nasal colonization to invasive infection remain incompletely defined. We sequenced and analyzed 157 S. aureus isolates (126 from SSTIs and 31 [...] Read more.

Staphylococcus aureus is a leading cause of skin and soft tissue infections (SSTIs), yet the bacterial genomic adaptations underlying the transition from nasal colonization to invasive infection remain incompletely defined. We sequenced and analyzed 157 S. aureus isolates (126 from SSTIs and 31 from asymptomatic nasal colonization) from a primary care network in South Texas. Using genome-wide association studies, non-synonymous single-nucleotide variant (NSNV) profiling, and machine learning, we identified strain-specific adaptations in metabolic and regulatory pathways. SSTI isolates exhibited significant enrichment of nitrogen assimilation, purine biosynthesis, menaquinone production, and anaerobic respiration genes. Elevated copy number and colocalization of phage-linked metabolic genes—including nirB, narH, and nifR3—suggest a pathoadaptive genomic island supporting infection-specific energy generation. The enrichment of α/β-hydrolase domain-encoding genes was associated with clinical severity. To quantify severity, we developed the Purulent Ulcer Skin (PUS) score, which integrates wound size, drainage, and erythema. The α/β-hydrolase and lipoprotein genes were significantly associated with higher PUS scores (higher SSTI severity) and phage-encoded virulence gene products were linked to larger wound size. Machine learning prioritized purL and other metabolic loci as key infection classifiers. NSNVs and unitig-level changes co-localized within nutrient transport, stress resistance, and cytolytic genes, supporting a model of multi-layered genomic selection. Metagenomic assemblies of nasal microbiota were enriched for Staphylococcus, Enterococcus, and Micrococcus species, core metabolic pathways, and taxon-specific virulence determinants. This underscores the roles of metabolic and virulent co-networks within nasal commensals and their adaptive capacity for pathogenic transition. These findings provide a potential genomic blueprint of S. aureus pathoadaptation during SSTI and are a step towards the development of novel therapeutic targets. Full article

(This article belongs to the Special Issue New Trends in Medical Bacteriology: Diagnosis, Treatment and Prevention—Second Edition)

► Show Figures

Graphical abstract

15 pages, 2236 KB

Open AccessArticle

Adaptive Evolution of Aurantiochytrium limacinum for Efficient Production of Docosahexaenoic Acid Under Acidic and High-Temperature Conditions

by Tanapawarin Rampai, Rujirek Nopgasorn, Kobkul Laoteng and Siwaporn Wannawilai

Microorganisms 2025, 13(9), 2022; https://doi.org/10.3390/microorganisms13092022 - 29 Aug 2025

Abstract

Acid- and heat-tolerant industrial microbial strains are crucial for biotechnological production because they minimize the risk of microbial contamination and reduce energy consumption associated with cooling requirements. Here, adaptive laboratory evolution (ALE) of Aurantiochytrium limacinum was performed to improve the capability of the [...] Read more.

Acid- and heat-tolerant industrial microbial strains are crucial for biotechnological production because they minimize the risk of microbial contamination and reduce energy consumption associated with cooling requirements. Here, adaptive laboratory evolution (ALE) of Aurantiochytrium limacinum was performed to improve the capability of the strain to produce docosahexaenoic acid (DHA) under acidic and high-temperature conditions. A stepwise increase from 30 to 38 °C was applied during cultivation at pH 4.5. After 30 cycles of high-temperature exposure (34 °C), an adaptive strain (BBF002) was obtained. Cell growth and DHA production of BBF002 were higher than those of the parental strain (BBF001) by 32.95 and 7.12%, respectively, at pH 4.5 and 30 °C. Based on the experimental data obtained using glucose as a carbon source, a kinetic model was developed to describe cell growth, biomass maintenance, and DHA, and we used other metabolite methods to produce the native, parental, and adaptive strains. The growth traits of the three strains could be adequately described through logistic modeling. DHA was found to be a mixed-growth product produced during exponential and stationary phases, according to the Luedeking–Piret equation. Full article

(This article belongs to the Section Microbial Biotechnology)

► Show Figures

Figure 1

14 pages, 2365 KB

Open AccessArticle

Are “Free From” Foods Risk-Free? Lactose-Free Milk Fermentation Modulates Normal Colon in a Gut Microbiota in Vitro Model

by Flavia Casciano, Lorenzo Nissen, Alessandra Bordoni and Andrea Gianotti

Microorganisms 2025, 13(9), 2021; https://doi.org/10.3390/microorganisms13092021 - 29 Aug 2025

Abstract

Nowadays, the consumption of “free from” foods by non-specific consumers is increasing, partly due to a misperception of labels that make them seem healthier. These foods are formulated for consumers with allergies or diseases that limit their diet, and it is not known [...] Read more.

Nowadays, the consumption of “free from” foods by non-specific consumers is increasing, partly due to a misperception of labels that make them seem healthier. These foods are formulated for consumers with allergies or diseases that limit their diet, and it is not known if there are more benefits than risks for healthy consumers. For example, there is no work investigating the interaction between lactose-free milk and the colonic microbiome of healthy individuals. To focus on the potential modulation of gut microbiota of healthy subjects by lactose-free milk, we performed an in vitro simulation of digestion and fermentation, integrating microbiomics and metabolomics approaches to study changes in gut microbiota populations and metabolite production. Results indicated that lactose-free and lactose-containing milk differently modulated colonic microbiota based on several microbiological indicators, including the reduction in Bifidobacteriaceae (approximately more than two times) and Lactobacillales and the reduction in the beneficial production of microbial compounds (approximately six times less acetic acid and two times less butanoic acid). Such features suggest that lactose-free milk increases the risk of dysbiosis in healthy subjects. Our work identifies the drivers of this dysbiosis among hundreds of molecules and microbes of the gut microbiota, assigning specific names and ecological niches for the first time. It employs an in vitro model, which represents a new standard for sustainable research and improves translatability. Our findings support the European Society for Clinical Nutrition and Metabolism (ESPEN) guidelines, which do not recommend the routine consumption of lactose-free diets in the absence of diagnosed intolerance. Full article

(This article belongs to the Section Public Health Microbiology)

► Show Figures

Figure 1

7 pages, 389 KB

Open AccessCase Report

Vagococcus lutrae Isolation in a Cat with Feline Urological Syndrome in Italy: A Case Report

by Daniela Averaimo, Sabrina Vanessa Patrizia Defourny, Alessandra Alessiani, Marco Rulli, Alexandra Chiaverini, Marco Di Domenico, Iolanda Mangone, Cinzia Pompilii, Vanessa Piersanti, Roberta Giancristofaro, Lucilla Ricci and Antonio Petrini

Microorganisms 2025, 13(9), 2020; https://doi.org/10.3390/microorganisms13092020 - 29 Aug 2025

Abstract

Vagococcus lutrae is an emerging pathogen that can cause severe disease, especially in immunocompromised patients. Unlike Vagococcus fluvialis, which is recognized as a human and animal pathogen, there are few reports of V. lutrae from human and animal infections. In humans, it [...] Read more.

Vagococcus lutrae is an emerging pathogen that can cause severe disease, especially in immunocompromised patients. Unlike Vagococcus fluvialis, which is recognized as a human and animal pathogen, there are few reports of V. lutrae from human and animal infections. In humans, it has been reported in patients with severe skin lesions and bloodstream infections. In veterinary medicine, V. lutrae was accidentally isolated from a Eurasian otter and a largemouth bass, and only once from the genitourinary tract of a pig with a urinary tract infection. However, the prevalence may be underestimated due to difficulties in identification using traditional methods. In addition, V. lutrae could be a carrier of resistance genes and contribute to the spread of AMR. A neutered male cat with feline urological syndrome underwent urethrostomy surgery due to serious problems with dysuria and urolithiasis that could not be resolved through catheterizations. Urine culture revealed the presence of Vagococcus lutrae. The strain showed resistance genes against aminoglycoside, lincosamide, streptogramin a and b, pleuromutilin, macrolide, tetracycline, oxazolidinone, and amphenicol classes. We report the first isolation of V. lutrae from the urinary tract of a cat. Full article

(This article belongs to the Collection Feature Papers in Medical Microbiology)

► Show Figures

Figure 1

17 pages, 1912 KB

Open AccessArticle

Whole-Genome-Sequencing Analysis of the Pathogen Causing Spotting Disease and Molecular Response in the Strongylocentrotus intermedius

by Shufeng Li, Fenglin Tian, Yongjie Wang, Haoran Xiao, Zijie Zhou, Lina Cao, Lingshu Han, Junxiao Sun, Chong Zhao and Jun Ding

Microorganisms 2025, 13(9), 2019; https://doi.org/10.3390/microorganisms13092019 - 29 Aug 2025

Abstract

Sea urchin aquaculture has experienced remarkable growth in recent years. However, this growth has been accompanied by increased disease prevalence. Notably, spotting disease has particularly severe impacts. In this study, we isolated the pathogen HZ-3-2 from 10 sea urchins with spotting disease, and [...] Read more.

Sea urchin aquaculture has experienced remarkable growth in recent years. However, this growth has been accompanied by increased disease prevalence. Notably, spotting disease has particularly severe impacts. In this study, we isolated the pathogen HZ-3-2 from 10 sea urchins with spotting disease, and it was identified as Vibrio splendidus through morphological observations, 16S rDNA sequencing, and whole-genome sequencing. Subsequently, experimental infection confirmed that V. splendidus (HZ-3-2) is the causative agent of spotting disease in this outbreak. The drug sensitivity confirmed the presence of drug resistance genes, such as CPR, QNRS5, and rsmA, which were identified in the genome. The tests indicated that V. splendidus was sensitive to various antibiotics, including fluoroquinolones and florfenicol. Finally, we used the transcriptome to explore the molecular response of the diseased sea urchin. Compared to the control group, a group of sea urchins immersed in a pathogen suspension with a concentration of 10⁷ CFU/mL (group M) resulted in 439 annotated differentially expressed genes. KEGG pathway analysis indicated significant activation of cholesterol metabolism and starch and sucrose metabolism in the S. intermedius. This study highlights the genes NPC1, AMY2A, and MGAM as critical regulators of energy metabolism, and cholesterol synthesis in infected sea urchins. These findings confirm V. splendidus as the bacterium responsible for spotting disease and provide valuable insights into the intestinal molecular response of S. intermedius to infection. Full article

(This article belongs to the Special Issue Infectious Diseases in Aquaculture)

► Show Figures

Figure 1

16 pages, 864 KB

Open AccessReview

High-Value Bioactive Molecules Extracted from Microalgae

by Carla Arenas Colarte, Iván Balic, Óscar Díaz, Adrián A. Moreno, Maximiliano J. Amenabar, Tamara Bruna Larenas and Nelson Caro Fuentes

Microorganisms 2025, 13(9), 2018; https://doi.org/10.3390/microorganisms13092018 - 29 Aug 2025

Abstract

Microalgae are unicellular photosynthetic organisms with considerable genetic diversity and remarkable metabolic capacity, positioning them as sustainable cellular biorefineries. They can be cultivated in open or closed systems, influenced by physical and chemical variables such as light, temperature, and nutrient availability. These conditions [...] Read more.

Microalgae are unicellular photosynthetic organisms with considerable genetic diversity and remarkable metabolic capacity, positioning them as sustainable cellular biorefineries. They can be cultivated in open or closed systems, influenced by physical and chemical variables such as light, temperature, and nutrient availability. These conditions modulate the synthesis of valuable biomolecules, including proteins, lipids, polysaccharides, and secondary metabolites. Microalgae are especially notable for their high protein content (up to 70% w/w in Spirulina sp.), polyunsaturated fatty acids (e.g., DHA and EPA), and β-glucans with bioactive properties. Choosing the correct extraction method (mechanical, enzymatic or combined) is very important to obtain and preserve the functionality of these compounds. Despite their biotechnological potential in functional foods, pharmaceuticals, and biofuels, industrial development faces challenges such as extraction efficiency, scalability, and regulatory approval. This review compiles current knowledge on the nutritional and bioactive potential of microalgae, highlights advances in extraction technologies and discusses their potential applications in health-oriented industrial innovation. Full article

(This article belongs to the Special Issue Interaction Between Microorganisms and Environment)

► Show Figures

Figure 1

19 pages, 1498 KB

Open AccessArticle

Identification and Characterization of Antiyeast Organic Acids Produced by Lactiplantibacillus plantarum 3121M0s Derived from Mongolian Traditional Fermented Milk, Airag

by Md. Bakhtiar Lijon, Yuko Matsu-ura, Takumi Ukita, Kensuke Arakawa and Taku Miyamoto

Microorganisms 2025, 13(9), 2017; https://doi.org/10.3390/microorganisms13092017 - 29 Aug 2025

Abstract

Lactic acid bacteria are beneficial for food biopreservation by inhibiting not only bacteria but also fungi. However, reports on the control of fungi, especially yeasts, by lactic acid bacteria are limited. In this study, strain 3121M0s derived from Mongolian traditional fermented milk, airag, [...] Read more.

Lactic acid bacteria are beneficial for food biopreservation by inhibiting not only bacteria but also fungi. However, reports on the control of fungi, especially yeasts, by lactic acid bacteria are limited. In this study, strain 3121M0s derived from Mongolian traditional fermented milk, airag, was selected with relatively high antiyeast activity among 236 strains, and identified as Lactiplantibacillus plantarum. The activity was exhibited under acidic conditions and remained stable after heating. It was also highly resistant to catalase and proteases, indicating that the primary antiyeast substances of 3121M0s were neither H₂O₂ nor peptides. Then, organic acids (lactic acid, acetic acid, 4-hydroxyphenyllactic acid, 4-hydroxybenzoic acid, and 3-phenyllactic acid) were detected and quantified in the ethyl acetate extract of the 3121M0s culture supernatant. Among them, only acetic acid showed antiyeast activity on its own, and the activity was enhanced by lactic acid or 3-phenyllactic acid. Compared to the type strain of L. plantarum, the production of lactic acid from 3121M0s was almost equal, but acetic acid and 3-phenyllactic acid were about 1.5 times higher. These results suggest that strain 3121M0s would be useful as a biopreservative starter for fermented foods susceptible to yeast contamination due to being produced in open environments without final sterilization. Full article

(This article belongs to the Special Issue Microbial Fermentation in Food Processing)

► Show Figures

Figure 1

14 pages, 1131 KB

Open AccessArticle

Enzymatic Activity and Organic Acid Profile of Phosphate-Solubilizing Bacterial Inoculants and Their Agronomic Effectiveness in Soybean

by Luana Rainieri Massucato, Mayara Barbosa Silva, Mirela Mosela, Lycio Shinji Watanabe, Leandro Afonso, Antoni Wallace Marcos, Alison Fernando Nogueira, Nicholas Vieira de Sousa, Ricardo Cancio Fendrich, Marcos Ventura Faria and Leandro Simões Azeredo Gonçalves

Microorganisms 2025, 13(9), 2016; https://doi.org/10.3390/microorganisms13092016 - 29 Aug 2025

Abstract

Low phosphorus (P) availability in tropical soils is one of the main constraints to agricultural productivity and the sustainability of cropping systems. In this study, we evaluated the functional potential of four bacterial strains, including those present in two commercial inoculants: Nodubiophos (Ag87-CCT [...] Read more.

Low phosphorus (P) availability in tropical soils is one of the main constraints to agricultural productivity and the sustainability of cropping systems. In this study, we evaluated the functional potential of four bacterial strains, including those present in two commercial inoculants: Nodubiophos (Ag87-CCT 8090 and Ag94-CCT 8108), and Biomaphos (B119 and B2084), focusing on their production of phosphatase and phytase enzymes, organic acids, and their agronomic efficacy in soybean cultivation. In vitro assays showed that all strains exhibited phytase and both acid and alkaline phosphatase activities, with B2084 and Ag94 standing out in phytase-mediated mineralization. In contrast, B119 and B2084 showed the highest phosphatase activity. Organic acid production varied among strains and was influenced by the phosphate source, indicating a highly responsive metabolic regulation. Strains Ag87 and Ag94 were particularly effective in producing lactic, malic, and gluconic acids, displaying distinct profiles modulated by the available P source. In field trials, combined inoculation with Ag87 and Ag94 led to increased soybean yield, achieving performance comparable to conventional fertilization at 50% and 100% of the recommended P rate, despite applying only 30% of the total P. The results highlight complementary metabolic strategies among the evaluated strains, with the ability to solubilize and mineralize phosphorus through different mechanisms. They support their potential use as bioinoculants to enhance nutrient use efficiency and reduce fertilizer dependency in soybean cultivation. Full article

(This article belongs to the Special Issue Beneficial Microorganisms for Sustainable Agriculture)

► Show Figures

Figure 1

15 pages, 2139 KB

Open AccessArticle

Molecular Epidemiology of Carbapenem-Resistant P. aeruginosa and Enterobacterales Isolates from Clinical Infections and Their Susceptibility to Ceftazidime–Avibactam

by Jose-Rita Gerges, Sara Barada, Hadi Hussein, Ahmad Sleiman, Ziad Jabbour, Fatima El Rida, Abdallah Kurdi, Ghassan Matar, George Araj, Antoine Abou Fayad and Zeina Adnan Kanafani

Microorganisms 2025, 13(9), 2015; https://doi.org/10.3390/microorganisms13092015 - 29 Aug 2025

Abstract

The overuse of carbapenems has driven the rise of carbapenem-resistant Pseudomonas aeruginosa (CRPA) and Enterobacterales (CRE), against which ceftazidime–avibactam (CAZ-AVI) offers an alternative treatment. This study phenotypically determined resistance profiles of P. aeruginosa (PA), Escherichia coli (EC), and Klebsiella pneumoniae (KP) clinical isolates [...] Read more.

The overuse of carbapenems has driven the rise of carbapenem-resistant Pseudomonas aeruginosa (CRPA) and Enterobacterales (CRE), against which ceftazidime–avibactam (CAZ-AVI) offers an alternative treatment. This study phenotypically determined resistance profiles of P. aeruginosa (PA), Escherichia coli (EC), and Klebsiella pneumoniae (KP) clinical isolates to CAZ-AVI and investigated molecular resistance mechanisms genotypically. A total of 394 PA, 90 EC, and 84 KP isolates were collected from the American University of Beirut Medical Center. Antimicrobial susceptibility testing (AST) and whole-genome sequencing (WGS) were performed on 30 isolates per species. Results showed that 100% of KP, 63% of EC, and 100% of PA isolates were carbapenem-resistant. Among these, 73% of KP, 79% of EC, and 60% of PA were CAZ-AVI-resistant. WGS revealed diverse sequence types, plasmids, and antimicrobial resistance genes. Additionally, 100% of KP, 93% of EC, and 89% of PA isolates produced metallo-β-lactamases (MBLs). Mutations in ampD, ampR, and mexR were identified in CAZ-AVI-resistant, non-MBL-producing PA, whereas mutations in ompC, marR, and ampC were detected in CAZ-AVI-resistant, non-MBL-producing EC. While CAZ-AVI remains effective against most CRE and CRPA lacking MBLs, resistance to CAZ-AVI is multifactorial, commonly involving overexpression of efflux pumps and AmpC β-lactamases, loss of porin channels, and the presence of oxacillinases. Full article

(This article belongs to the Section Antimicrobial Agents and Resistance)

► Show Figures

Figure 1

20 pages, 5083 KB

Open AccessArticle

Shrub Expansion Impacts on Carbon, Nitrogen, and Sulfur Cycles and Microorganism Communities in Wetlands in Northeastern China

by Shenzheng Wang, Lin Li, Xiaoyu Fu, Haixiu Zhong, Rongtao Zhang and Xin Sui

Microorganisms 2025, 13(9), 2014; https://doi.org/10.3390/microorganisms13092014 - 28 Aug 2025

Abstract

Marsh wetland degradation and shrub expansion, driven by human activities and climate change, can impact carbon, nitrogen, and sulfur cycles by soil microorganisms. There is a paucity of systematic and in-depth research on the impact of shrub expansion in temperate wetlands on soil [...] Read more.

Marsh wetland degradation and shrub expansion, driven by human activities and climate change, can impact carbon, nitrogen, and sulfur cycles by soil microorganisms. There is a paucity of systematic and in-depth research on the impact of shrub expansion in temperate wetlands on soil element cycles, which is a pressing scientific issue that demands resolution. This study used metagenomic sequencing and soil analysis methods to investigate the impact of shrub expansion in the Sanjiang Plain wetlands on carbon, nitrogen, and sulfur cycles in temperate wetland soils, as well as on functional microbial communities. Shrub expansion significantly altered soil carbon, nitrogen, and sulfur cycle processes and the composition (β diversity) of associated functional microbial communities, despite minimal changes in overall α diversity. Significant shifts occurred in the abundance of cycle pathways and related functional genes. Ammonia nitrogen, moisture, and total phosphorus were identified as the primary factors influencing these cycles and the functional microbial communities. Changes in the abundance of specific cycling pathways following shrub expansion are key drivers of functional community structure transformation. These changes may significantly reduce the long-term carbon sequestration potential of wetlands and affect regional climate feedback by altering greenhouse gas fluxes. The findings provide a theoretical basis for managing shrub expansion and assessing wetland function. Full article

(This article belongs to the Section Environmental Microbiology)

► Show Figures

Figure 1

34 pages, 2021 KB

Open AccessReview

Untangling the Complexity of Two-Component Signal Transduction in Bacteria

by Patrycja Wadach, Dagmara Jakimowicz and Martyna Gongerowska-Jac

Microorganisms 2025, 13(9), 2013; https://doi.org/10.3390/microorganisms13092013 - 28 Aug 2025

Abstract

Two-component systems (TCSs) are ubiquitous in bacteria and are central to their ability to sense and respond to diverse environmental and intracellular cues. Classically composed of a sensor histidine kinase and a cognate response regulator, TCSs control processes ranging from metabolism and development [...] Read more.

Two-component systems (TCSs) are ubiquitous in bacteria and are central to their ability to sense and respond to diverse environmental and intracellular cues. Classically composed of a sensor histidine kinase and a cognate response regulator, TCSs control processes ranging from metabolism and development to virulence and antibiotic resistance. In addition to their biological roles, TCSs are garnering attention in synthetic biology and antimicrobial drug development. While canonical architectures have been extensively studied, increasing evidence highlights the remarkable diversity in their organization and regulation. Despite substantial progress, key questions remain regarding the prevalence and physiological relevance of non-canonical TCSs, the mechanisms ensuring signal fidelity, and the potential for engineering these systems. This review explores non-typical TCSs, focusing on their varied transcriptional regulation, alternative response regulator activities, varied control by phosphorylation, and negative control mechanisms. We discuss how bacteria manage signaling specificity among numerous TCSs through cross-talk, hierarchical interactions, and phosphorelay systems and how these features shape adaptive responses. By synthesizing current understanding and highlighting still existing knowledge gaps, this review offers a novel perspective on TCS diversity, indicating directions for future research and potential translational applications in biotechnology and medicine. Full article

(This article belongs to the Section Molecular Microbiology and Immunology)

20 pages, 5671 KB

Open AccessArticle

Precipitation Alleviates Adverse Effects of Nitrogen and Phosphorus Enrichment on Soil Microbial Co-Occurrence Network Complexity and Stability in Karst Shrubland

by Jiangnan Li, Jie Zhao, Xionghui Liao, Xianwen Long, Wenyu Wang, Peilei Hu, Wei Zhang and Kelin Wang

Microorganisms 2025, 13(9), 2012; https://doi.org/10.3390/microorganisms13092012 - 28 Aug 2025

Abstract

The karst region is highly ecologically fragile due to its unique geology and poor water and nutrient retention. Despite long-term restoration, vegetation often remains in the secondary shrubland stage. Soil microorganisms play a vital role in maintaining ecosystem functions, but how microbial communities [...] Read more.

The karst region is highly ecologically fragile due to its unique geology and poor water and nutrient retention. Despite long-term restoration, vegetation often remains in the secondary shrubland stage. Soil microorganisms play a vital role in maintaining ecosystem functions, but how microbial communities respond to combined water and nitrogen-phosphorus nutrient changes in karst shrubland remains poorly understood. This knowledge gap hinders effective restoration strategies in karst shrublands. Here, the effects of water, nitrogen, and phosphorous additions and their interactions on soil physico-chemical properties, soil microbial abundance, diversity, community composition, and the co-occurrence network were explored. A full factorial experiment (water × nitrogen × phosphorous, each at two levels) was conducted in a karst shrubland with over 20 years of vegetation restoration, with treatments including control, water (+120 mm yr⁻¹), nitrogen (+20 g N m⁻² yr⁻¹), phosphorus (+16 g P m⁻² yr⁻¹), and their four combinations. Our results suggested that water addition significantly increased soil water content and soil microbial abundance but reduced fungal diversity. Nitrogen addition significantly increased soil nitrate nitrogen content and fungal diversity, and fungal diversity showed an increasing trend under phosphorous addition. The addition of nitrogen and phosphorous did not significantly alter the soil microbial community composition, while water addition showed a tendency to change the soil fungal community composition. Network topological properties, robustness, and vulnerability analyses indicated that individual nitrogen or phosphorous additions, as well as their interactions, reduced network complexity and stability. In contrast, water addition alone or in combination with nitrogen and/or phosphorous alleviated these negative effects, and the water and phosphorous interaction exhibited the highest levels of network complexity and stability. Further analysis showed that the soil pH, available phosphorous, ratio of carbon to phosphorous, and ammonium nitrogen were explanatory variables contributing significantly to soil microbial abundance, diversity, community composition, and network complexity. Overall, these findings highlighted the pivotal role of water availability in enhancing soil microbial stability under nutrient enrichment, offering valuable insights into ecological restoration in karst ecosystems. Full article

(This article belongs to the Special Issue Soil Microbial Carbon/Nitrogen/Phosphorus Cycling: 2nd Edition)

► Show Figures

Figure 1

16 pages, 2200 KB

Open AccessArticle

GWAS Study Applied to Phenotypically Slow Growth Strains of Listeria monocytogenes Workflow and Outcome

by Maria Elisabetta De Angelis, Giovanna Alessia Robbe, Cesare Cammà, Massimo Ancora, Serena Bosica, Mattia Ferrara, Marina Torresi, Frank M. Aarestrup, Alexander Gmeiner, Narong Nuanmuang, Patrick Murigu Kamau Njage, Chiara Bravaccini, Viviana Belardo, Chiara Di Iorio, Silvia Di Zacomo, Paolo Fazii, Francesco Pomilio and Pimlapas Leekitcharoenphon

Microorganisms 2025, 13(9), 2011; https://doi.org/10.3390/microorganisms13092011 - 28 Aug 2025

Abstract

Listeria monocytogenes (Lm) is a serious public health foodborne pathogen cause of listeriosis, usually in elderly, pregnant and immunocompromised people, linked to consumption of contaminated food, especially ready-to-eat (RTE) products. Different protocols can be used to detect Lm, and ISO11290-1:2017 [...] Read more.

Listeria monocytogenes (Lm) is a serious public health foodborne pathogen cause of listeriosis, usually in elderly, pregnant and immunocompromised people, linked to consumption of contaminated food, especially ready-to-eat (RTE) products. Different protocols can be used to detect Lm, and ISO11290-1:2017 is the reference method in Europe. Through molecular techniques such as whole genome sequencing (WGS) it is possible to discriminate between Lm strains, which are unequally distributed between clinical cases, food or food related environments, probably also due to enrichment step bias towards some Lm serogroup (IIa) compared to IVb. In the present work a set of Lm strains, detected in clinical cases and food, was investigated to define Lm strains growth ability after incubation in Half Fraser broth, and Genome Wide Association Studies (GWAS) applied to correlate the growth phenotype traits to presence of relevant genes. GWAS enabled the identification of a more relevant cassette of genes associated to a holin region of bacteriophage A118 and the determination of the distribution of relevant genes, highlighted from GWAS analysis within a population of Lm IVb and IIa. Full article

(This article belongs to the Special Issue An Update on Listeria monocytogenes, Third Edition)

► Show Figures

Figure 1

Journal Description

Microorganisms

Latest Articles

Journal Menu

Journal Browser

Highly Accessed Articles

Latest Books

E-Mail Alert

News

Topics

Conferences

Special Issues

Topical Collections

Further Information

Guidelines

MDPI Initiatives

Follow MDPI