Microorganisms

11 pages, 1612 KiB

Open AccessArticle

A Lectin AtTL-2 Obtained from Acropora aff. tenuis Induced Stimualation of Phagocytosis of Symbiodiniaceae

by Mitsuru Jimbo, Nami Kuniya, Yuna Fujimaki, Daiki Yoshikawa, Naoki Kamiya, Haruna Amano, Ko Yasumoto, Ikuko Yuyama, Go Suzuki and Saki Harii

Microorganisms 2025, 13(5), 1095; https://doi.org/10.3390/microorganisms13051095 - 8 May 2025

Abstract

The coral Acropora aff. tenuis selectively acquired various zooxanthella (Symbiodiniaceae) strains, and one of the selective factors was lectins. The A. aff. tenuis lectin AtTL-2 was identified as a factor for Symbiodiniaceae acquisition by the coral, but the mechanism is not fully [...] Read more.

The coral Acropora aff. tenuis selectively acquired various zooxanthella (Symbiodiniaceae) strains, and one of the selective factors was lectins. The A. aff. tenuis lectin AtTL-2 was identified as a factor for Symbiodiniaceae acquisition by the coral, but the mechanism is not fully known. The acquisition process involves three steps: chemotaxis, entry into the coral, and phagocytosis. In this study, we examined the function of AtTL-2 in more detail. Immunohistochemistry analysis was performed to examine the distribution of AtTL-2. The effect of AtTL-2 on the number of Symbiodiniaceae acquired was measured in A. aff. tenuis juvenile polyps with and without AtTL-2 siRNA treatment. The effect of AtTL-2 fixation was examined by monitoring the acquisition of AtTL-2–fixed beads by A. aff. tenuis. AtTL-2 was distributed in nematocysts, spirocysts, and around Symbiodiniaceae. AtTL-2 siRNA inhibited the acquisition of Symbiodiniaceae by juvenile polyps. Fixation of AtTL-2 promoted bead acquisition by juvenile polyps more than fixation of bovine serum albumin (BSA). Moreover, more AtTL-2–fixed beads were bound to the Symbiodiniaceae-enclosed cells than BSA-fixed beads. AtTL-2 is released from spirocysts and binds to Symbiodiniaceae. AtTL-2 then promotes the phagocytosis of Symbiodiniaceae by gastrodermal cells of A. aff. tenuis. Full article

(This article belongs to the Special Issue The Molecular Mechanisms for Infection and Phenotypic Changes of the Host in Procaryote–Eukaryote and Eukaryote-Eukaryote Endosymbioses)

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17 pages, 2615 KiB

Open AccessArticle

In Silico Characterization of Resistance and Virulence Genes in Aeromonas jandaei Strains Isolated from Oreochromis niloticus in Brazil

by Marcela Laryssa Oliveira Duarte, Diego Lucas Neres Rodrigues, Gabryel Bernardo Vieira de Lima, Juan Carlos Ariute, Gisele Veneroni Gouveia, João José de Simoni Gouveia, Vasco Azevedo, Bertram Brenig, Eric Guédon, Guilherme Campos Tavares, Mateus Matiuzzi da Costa, Ulisses de Pádua Pereira and Flávia Figueira Aburjaile

Microorganisms 2025, 13(5), 1094; https://doi.org/10.3390/microorganisms13051094 - 8 May 2025

Abstract

Understanding the genetic characteristics of Aeromonas jandaei in Brazilian aquaculture is crucial for developing effective control strategies against this fish pathogen. The present study conducted a genomic analysis of Brazilian A. jandaei strains with the objective of investigating their virulence potential and resistance [...] Read more.

Understanding the genetic characteristics of Aeromonas jandaei in Brazilian aquaculture is crucial for developing effective control strategies against this fish pathogen. The present study conducted a genomic analysis of Brazilian A. jandaei strains with the objective of investigating their virulence potential and resistance profiles. Four Brazilian isolates were subjected to sequencing, and comparative genomic analyses were conducted in conjunction with 48 publicly available A. jandaei genomes. The methods employed included quality assessment, de novo assembly, annotation, and analyses of antimicrobial resistance and virulence factors. The results demonstrated the presence of fluoroquinolone resistance genes within the core genome. Notably, these antibiotics are not authorized for use in aquaculture in Brazil, suggesting that their resistance determinants may originate from other selective pressures or horizontal gene transfer unrelated to aquaculture practices. The analysis identified significant virulence mechanisms, including T2SS, T3SS, and notably T6SS (vgrG3 gene), which was more prevalent in Brazilian isolates. Additionally, genes associated with motility, adhesion, and heavy metal resistance were identified. These findings highlight the enhanced adaptability of Brazilian A. jandaei strains and raise concerns about antimicrobial resistance in aquaculture, emphasizing the need for improved regulatory oversight and control strategies. Full article

(This article belongs to the Special Issue Microbial Genomics in the Age of Omics and Artificial Intelligence)

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15 pages, 3167 KiB

Open AccessArticle

Assessment of Antimicrobial Activity and Safety of Pediococcus pentosaceus Isolated from Ginseng as a Functional Cosmetic Ingredient

by Xiangji Jin, Qiwen Zheng, Trang Thi Minh Nguyen, Gyeong-Seon Yi, Su-Jin Yang and Tae-Hoo Yi

Microorganisms 2025, 13(5), 1093; https://doi.org/10.3390/microorganisms13051093 - 8 May 2025

Abstract

Lactic acid bacteria (LAB) are gaining increasing attention as functional ingredients in the cosmetic industry, particularly those derived from natural plant sources. Although various LAB strains have been widely applied in cosmetic formulations, studies investigating the effects of naturally derived LAB on the [...] Read more.

Lactic acid bacteria (LAB) are gaining increasing attention as functional ingredients in the cosmetic industry, particularly those derived from natural plant sources. Although various LAB strains have been widely applied in cosmetic formulations, studies investigating the effects of naturally derived LAB on the skin remain limited. In this study, we isolated an LAB strain from ginseng and evaluated its potential as a functional cosmetic ingredient. The antimicrobial activity of the strain was assessed against skin-associated pathogens Staphylococcus aureus and Staphylococcus epidermidis, while cytotoxicity was evaluated using HaCaT and Caco-2 cells. Considering the limitations of vertebrate animal testing, infection and survival assays were conducted using Galleria mellonella larvae as an alternative in vivo model. The ginseng-derived strain exhibited 99.93% similarity to Pediococcus pentosaceus and was designated P. pentosaceus THG-219. It exhibited an MIC of 0.625 mg/mL and 1.25 mg/mL against S. aureus KCTC 3881 and S. epidermidis KCTC 1917, respectively. Its antimicrobial activity was further enhanced following ethyl acetate fractionation. P. pentosaceus THG-219 showed no toxicity in G. mellonella larvae and exerted antibacterial effects in this model. No cytotoxicity was observed in HaCaT and Caco-2 cells. Furthermore, P. pentosaceus THG-219 promoted host cell adhesion while inhibiting pathogen adhesion. It also exhibited excellent acid, bile, and heat tolerance, suggesting strong survivability under harsh conditions. Collectively, these results indicate that P. pentosaceus THG-219, isolated from ginseng, is a promising, safe, and stable candidate for development as a functional cosmetic ingredient. Full article

(This article belongs to the Special Issue Microorganisms in Functional Foods)

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16 pages, 636 KiB

Open AccessReview

The Vineyard Microbiome: How Climate and the Main Edaphic Factors Shape Microbial Communities

by Vanessa Silva, Isabel Brito and Ana Alexandre

Microorganisms 2025, 13(5), 1092; https://doi.org/10.3390/microorganisms13051092 - 8 May 2025

Abstract

The soil microbiome is a complex system that encompasses millions of microbes including archaea, bacteria, fungi, protozoa and viruses. The role of abiotic factors is crucial in shaping the distribution patterns of microorganisms, its abundance and also the interactions between species, from local [...] Read more.

The soil microbiome is a complex system that encompasses millions of microbes including archaea, bacteria, fungi, protozoa and viruses. The role of abiotic factors is crucial in shaping the distribution patterns of microorganisms, its abundance and also the interactions between species, from local to the global level. In the particular case of the vineyard, the microbial communities have a potential impact in both the grapevine development and health and, later on, in the grape production and quality. The present review focuses on how the composition of soil microbial communities is influenced by climate and several edaphic factors, such as soil moisture, soil nutrients and soil pH. It also discusses the role of microorganisms and their metabolic activity on the fermentation process, influencing the sensorial characterisation of the wine and suggesting the definition of a microbial terroir. Full article

(This article belongs to the Special Issue Interactions of Mycorrhizal Fungi and Other Soil Microorganisms with Plants)

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19 pages, 4124 KiB

Open AccessArticle

Reducing Functional Domain of Histatin 5 Improves Antifungal Activity and Prevents Proteolytic Degradation

by Carolina R. Zambom, Gabriel Dalio Bernardes da Silva, Fauller Henrique da Fonseca, Gabriela Vieira Silva Zolin, Mariana de Melo Faceto Portella, Lina Maria Marin, Edson Crusca, Ed S. Krol, Walter L. Siqueira and Saulo Santesso Garrido

Microorganisms 2025, 13(5), 1091; https://doi.org/10.3390/microorganisms13051091 - 8 May 2025

Abstract

Histatin 5 (Hst5) is an antifungal peptide (AFP) naturally produced by parotid glands with strong activity against Candida albicans. One of its mechanisms of action is the generation of reactive oxygen species (ROS) inside the C. albicans cells. Despite being an important [...] Read more.

Histatin 5 (Hst5) is an antifungal peptide (AFP) naturally produced by parotid glands with strong activity against Candida albicans. One of its mechanisms of action is the generation of reactive oxygen species (ROS) inside the C. albicans cells. Despite being an important peptide for the human innate immune response, its activity is reduced or inactivated by proteolytic degradation caused by salivary enzymes. To overcome this barrier, we used solid phase peptide synthesis (SPPS) to modify the Hst5 amino acid sequence improving its antifungal action and minimizing its degradation. We synthesized five peptides, three of which were based on the Hst5 functional domain. We determined that the smallest peptides (8WH5, 7WH5 and 6WH5) demonstrated the greatest antifungal action against C. albicans, including one fluconazole-resistant strain. Besides that, cationic-PAGE and HPLC assays showed that the degradation in saliva was slower for the smaller peptides than for 0WHst5 and WP113. Furthermore, 8WH5, 7WH5 and 6WH5 were found in the samples even after 8 h in whole saliva, while 0WHst5 and WP113 completely disappear after 1.5 h. Finally, we found that the smaller peptides were less fragmented than the 0WHst5 and WP113, so they were the smallest fragments of Hst5 to preserve its antifungal action with reduced degradation in whole saliva. Thus, they can be considered promising molecules for the treatment of C. albicans in the oral cavity. Full article

(This article belongs to the Special Issue Advances in Antimicrobial Peptides)

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18 pages, 2152 KiB

Open AccessArticle

Development and Laboratory Validation of Rapid, Bird-Side Molecular Diagnostic Assays for Avian Influenza Virus Including Panzootic H5Nx

by Matthew Coopersmith, Remco Dijkman, Maggie L. Bartlett, Richard Currie, Sander Schuurman and Sjaak de Wit

Microorganisms 2025, 13(5), 1090; https://doi.org/10.3390/microorganisms13051090 - 8 May 2025

Abstract

Avian influenza A viruses (AIV) significantly impact both animal and human health. Reliable diagnostics are crucial for controlling AIV, including the highly pathogenic strains like H5Nx. In this study, we developed and validated the on-site Alveo Sense Poultry Avian Influenza Tests to rapidly [...] Read more.

Avian influenza A viruses (AIV) significantly impact both animal and human health. Reliable diagnostics are crucial for controlling AIV, including the highly pathogenic strains like H5Nx. In this study, we developed and validated the on-site Alveo Sense Poultry Avian Influenza Tests to rapidly detect the AIV M-gene and subtypes H5, H7, and H9 in unprocessed samples using reverse-transcription loop-mediated isothermal amplification (RT-LAMP) and impedance-based measurements. The Alveo Sense tests, using single-use microfluidic cartridges, deliver results within 45 min. Each cartridge includes assays for the AIV M gene and specific H5 and H7 or H9 subtypes, with internal process controls. The laboratory validation involved specificity, limit of detection (LoD), diagnostic sensitivity, reproducibility, and robustness tests using various AIV strains, other avian pathogens, and field samples. The assays showed 100% specificity for AIV subtypes without cross-reactivity with non-AIV pathogens. The LoD95 for H5, H7, and H9 ranged between RT-PCR Ct values of 29–33 in both cloacal and oropharyngeal samples and were able to detect avian influenza virus in both spiked samples and field samples. Reproducibility and repeatability studies showed perfect agreement across operators and laboratories and remained stable and accurate under different pre-analytical conditions. The Alveo Sense tests offer rapid, accurate, and reliable on-site diagnostics for AIV subtypes H5, H7, and H9 on samples from fresh dead and sick birds, valuable for early flock-level detection and outbreak control. Further field validation will improve the understanding of their diagnostic performance across various avian species. Full article

(This article belongs to the Section Virology)

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13 pages, 5013 KiB

Open AccessArticle

Porcine Epidemic Diarrhea Virus Is Inhibited by GS-441524 During an In Vitro Infection

by Shijuan Dong, Rujing Sun, Bingqing Chen, Fusheng Si, Chunhua Li, Daojing Zhang, Ruisong Yu and Huili Liu

Microorganisms 2025, 13(5), 1089; https://doi.org/10.3390/microorganisms13051089 - 8 May 2025

Abstract

Porcine epidemic diarrhea virus (PEDV), the etiology of porcine epidemic diarrhea (PED), continues to impose severe economic burdens on pig farms in China. The continuous emergence of new variant strains makes it difficult for vaccinated sows to provide protective immunity to piglets. Hence, [...] Read more.

Porcine epidemic diarrhea virus (PEDV), the etiology of porcine epidemic diarrhea (PED), continues to impose severe economic burdens on pig farms in China. The continuous emergence of new variant strains makes it difficult for vaccinated sows to provide protective immunity to piglets. Hence, there is an urgent need for efficacious therapeutic drugs in clinical practice. In the present study, the antiviral activity of GS-441524, a nucleoside analogue, against PEDV was evaluated. It can efficiently inhibit the proliferation of trypsin-dependent and trypsin-independent PEDVs in a dose-dependent manner, exhibiting greater efficacy against the trypsin-independent strain. GS-441524 can inhibit trypsin-independent PEDV proliferation in Vero cells with EC₅₀ and CC₅₀ values of 2.6 μM and 104.4 μM, respectively. As expected, GS-441524 exerts its inhibitory effect during the replication phase of the four stages of the PEDV proliferation cycle. Even at a high viral infection dose of MOI 0.5 or added 6 h post-viral infection, 20 μM GS-441524 can still effectively inhibit PEDV proliferation. These findings emphasize the potent antiviral activity of GS-441524 against PEDV, and its therapeutic efficacy on PEDV-infected piglets warrants further investigation. Full article

(This article belongs to the Special Issue Advances in Porcine Virus: From Pathogenesis to Control Strategies)

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17 pages, 6481 KiB

Open AccessArticle

Impact of SARS-CoV-2 P.1 Variant Infection on the Nasopharyngeal Commensal Bacterial Microbiome of Individuals from the Brazilian Amazon

by Amanda Mendes Silva Cruz, Jedson Ferreira Cardoso, Kenny Costa Pinheiro, Jessylene Almeida Ferreira, Luana Soares Barbagelata, Sandro Patroca Silva, Wanderley Dias Chagas Junior, Patrícia Santos Lobo, Dielle Monteiro Teixeira, Walter André Junior, Inaiah Ordenes Silva, Mirleide Cordeiro Santos, Luana Silva Soares Farias, Maisa Silva Sousa and Fernando Neto Tavares

Microorganisms 2025, 13(5), 1088; https://doi.org/10.3390/microorganisms13051088 - 8 May 2025

Abstract

It is important to understand which bacterial taxa are most abundant during SARS-CoV-2 infection and to promote mitigation strategies for conditions subsequent to infection. Nasopharyngeal swab samples were collected from patients infected with SARS-CoV-2 and their family contacts (uninfected and asymptomatic) during the [...] Read more.

It is important to understand which bacterial taxa are most abundant during SARS-CoV-2 infection and to promote mitigation strategies for conditions subsequent to infection. Nasopharyngeal swab samples were collected from patients infected with SARS-CoV-2 and their family contacts (uninfected and asymptomatic) during the outbreak of the P.1 variant of SARS-CoV-2 in Parintins, Amazonas–Brazil, in March 2021. The samples were investigated by a shotgun sequencing metagenomic approach using the NextSeq 500 Illumina® system. The samples were stratified according to the presence or absence of SARS-CoV-2, household group, sex, and age. Of the total of 63 individuals, 37 (58.73%) were positive for SARS-CoV-2 and 26 (41.27%) were negative for SARS-CoV-2 and other respiratory viruses (FLU, AdV, HBoV, HCoV, HMPV, RSV, PIV, HRV). The alpha diversity indexes Chao1, species observed, Simpson, and Inv Simpson demonstrated a significant difference (p < 0.05) in both the diversity of observed species and the abundance of some taxa between positive and negative individuals. We also observed an abundance of opportunists such as Klebsiella pneumoniae, Staphylococcus spp, and Shigella sonnei, previously associated with the severity of COVID-19. Our results suggest that SARS-CoV-2 infection causes changes in the microenvironment of the nasopharyngeal region, allowing greater proliferation of opportunistic bacteria and decreased abundance of commensal bacteria. Full article

(This article belongs to the Section Virology)

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16 pages, 4993 KiB

Open AccessArticle

Genetic Basis of Gap Formation Between Migrating Helicobacter pylori Colonies in Soft Agar Assays

by Yasmine Elshenawi, Skander Hathroubi, Shuai Hu, Xiaolin Liu and Karen M. Ottemann

Microorganisms 2025, 13(5), 1087; https://doi.org/10.3390/microorganisms13051087 - 7 May 2025

Abstract

Helicobacter pylori is a motile bacterial pathogen that causes severe gastric diseases. H. pylori motility and chemotaxis are key colonization factors. Motility and chemotaxis are studied in many microbes, including H. pylori, using soft agar assays. In these assays, bacteria are inoculated [...] Read more.

Helicobacter pylori is a motile bacterial pathogen that causes severe gastric diseases. H. pylori motility and chemotaxis are key colonization factors. Motility and chemotaxis are studied in many microbes, including H. pylori, using soft agar assays. In these assays, bacteria are inoculated into low-percentage agar and expand in a motility- and chemotaxis-dependent manner. H. pylori similarly expands in soft agar, but, if a plate was inoculated at multiple points, the expanded H. pylori colonies did not merge and left gaps. The basis of these gaps was unknown. We report here that gap formation was not affected by media components such as nutrient and agar concentrations, nor did it require chemotaxis, but it did rely on quorum sensing. To broaden our understanding of this H. pylori property, an H. pylori Tn7 transposon library was screened for mutants that lost gap formation. Fourteen mutants were identified, with transposon sites mapped to genes encoding outer membrane proteins, cysteine-rich proteins, phosphatidyl glycerophosphate synthase, an endorestriction nuclease, and several hypothetical proteins. Our results suggest that H. pylori may use specific proteins to avoid contact with other H. pylori, a behavior that may relate to previous observations that different H. pylori strains do not mix populations in stomach glands. Full article

(This article belongs to the Section Biofilm)

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16 pages, 528 KiB

Open AccessArticle

Characterization of a Novel 2018 Influenza Virus Outbreak on the Yucatan Peninsula, Mexico, in the Summer

by Lumumba Arriaga-Nieto, David Alejandro Cabrera-Gaytán, Alfonso Vallejos-Parás, Porfirio Felipe Hernández-Bautista, Clara Esperanza Santacruz-Tinoco, Julio Elías Alvarado-Yaah, Yu-Mei Anguiano-Hernández, Bernardo Martínez-Miguel, María Erandhí Prieto-Torres, Concepción Grajales-Muñiz, Nancy Sandoval-Gutiérrez and Horacia Celina Velarde-Scull

Microorganisms 2025, 13(5), 1086; https://doi.org/10.3390/microorganisms13051086 - 7 May 2025

Abstract

Background: During the 2017–2018 influenza season, there was high influenza activity, with a predominance of influenza A(H1N1)pdm09 circulation in the country. The influenza circulation pattern in the area of the Yucatan Peninsula was different from that of the rest of the country. However, [...] Read more.

Background: During the 2017–2018 influenza season, there was high influenza activity, with a predominance of influenza A(H1N1)pdm09 circulation in the country. The influenza circulation pattern in the area of the Yucatan Peninsula was different from that of the rest of the country. However, in the summer of 2018, there was a sudden increase in the number of identified cases. Methods: A retrospective analysis was performed using data generated by four molecular diagnostic laboratories of the Mexican Social Security Institute. Demographics, influenza positivity, seasonality and case fatality rates were recorded. We used odds ratios to compare outpatients who were confirmed by laboratory tests to be positive with those who were confirmed to be negative. The Kaplan–Meier method and Cox multivariate analysis were used to calculate cumulative risk. Results: There were 4460 cases of ILI/SARI between Yucatan and Quintana Roo, which represented 53.1% of the total number of cases reported. Compared with that in 2009, the epidemic wave in 2018 was shorter and more expansive, with a greater number of reported cases, as well as a greater number of people who required hospitalization. Conclusions: The dominant pattern of A(H1N1)pdm09 influenza activity on the Yucatan Peninsula in the summer of 2018 has not been observed since the influenza pandemic of 2009. Full article

(This article belongs to the Special Issue Pandemics and Infectious Diseases)

12 pages, 235 KiB

Open AccessArticle

Effectiveness of Vascular Catheter Removal Versus Retention in Non-ICU Patients with CRBSI or CABSI in Retrospective, Single-Center Study

by Giovanni De Capitani, Marta Colaneri, Claudia Conflitti, Fabio Borgonovo, Lucia Galli, Giovanni Scaglione, Camilla Genovese, Rebecca Fattore, Monica Schiavini, Beatrice Caloni, Daniele Zizzo, Nicola Busatto, Antonio Gidaro, Alba Taino, Maria Calloni, Francesco Casella, Arianna Bartoli, Chiara Cogliati, Emanuele Palomba, Spinello Antinori, Andrea Gori and Antonella Foschi Show full author list Hide full author list

Microorganisms 2025, 13(5), 1085; https://doi.org/10.3390/microorganisms13051085 - 7 May 2025

Abstract

Catheter-associated bloodstream infections (CABSIs) and catheter-related bloodstream infections (CRBSIs) are significant causes of morbidity and mortality worldwide. The current practice favors the removal of vascular access devices (VADs); however, the evidence on this topic remains inconclusive. This study evaluates the clinical outcomes in [...] Read more.

Catheter-associated bloodstream infections (CABSIs) and catheter-related bloodstream infections (CRBSIs) are significant causes of morbidity and mortality worldwide. The current practice favors the removal of vascular access devices (VADs); however, the evidence on this topic remains inconclusive. This study evaluates the clinical outcomes in terms of in-hospital mortality and catheter retention vs. removal in CABSI and CRBSI cases. A retrospective, observational, single-center study was conducted at Luigi Sacco Hospital, Milan, Italy (May 2021–December 2023), and it analyzed non-ICU adult patients with VADs diagnosed with CRBSIs or CABSIs. Clinical and microbiological data were collected to assess the outcomes based on catheter management. Among 1874 patients with VADs, 147 were included, with 164 VAD infection events (92 CABSIs and 72 CRBSIs). Overall, 35 (23.8%) patients with CABSIs and CRBSIs died. Out of those who retained the catheter 19 (35.8%) patients died, while among removal patients 16 (17%) died (p = 0.018). A Candida spp. isolation was found to be significantly associated with a higher likelihood of catheter removal (p = 0.04). Our findings suggest that, in non-ICU CRBSI and CABSI cases, VAD removal may be associated with improved outcomes when feasible. Full article

(This article belongs to the Special Issue Healthcare-Associated Infections and Antimicrobial Therapy—2nd Edition)

22 pages, 1280 KiB

Open AccessReview

Gut Microbiota: An Immersion in Dysbiosis, Associated Pathologies, and Probiotics

by Valentina Origüela and Alvaro Lopez-Zaplana

Microorganisms 2025, 13(5), 1084; https://doi.org/10.3390/microorganisms13051084 - 7 May 2025

Abstract

The importance of the microbiome, particularly the gut microbiota and its implications for health, is well established. However, an increasing number of studies further strengthen the link between an imbalanced gut microbiota and a greater predisposition to different diseases. The gut microbiota constitutes [...] Read more.

The importance of the microbiome, particularly the gut microbiota and its implications for health, is well established. However, an increasing number of studies further strengthen the link between an imbalanced gut microbiota and a greater predisposition to different diseases. The gut microbiota constitutes a fundamental ecosystem for maintaining human health. Its alteration, known as dysbiosis, is associated with a wide range of conditions, including intestinal, metabolic, immunological, or neurological pathologies, among others. In recent years, there has been a substantial increase in knowledge about probiotics—bacterial species that enhance health or address various diseases—with numerous studies reporting their benefits in preventing or improving these conditions. This review aims to analyze the most common pathologies resulting from an imbalance in the gut microbiota, as well as detail the most important and known gut probiotics, their functions, and mechanisms of action in relation to these conditions. Full article

(This article belongs to the Section Gut Microbiota)

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23 pages, 13093 KiB

Open AccessArticle

Survival of Filamentous Cyanobacteria Through Martian ISRU: Combined Effects of Desiccation and UV-B Radiation

by Miguel Arribas Tiemblo, Inês P. E. Macário, Antonio Tornero, Ana Yáñez, Slavka Andrejkovičová and Felipe Gómez

Microorganisms 2025, 13(5), 1083; https://doi.org/10.3390/microorganisms13051083 - 7 May 2025

Abstract

Cyanobacteria are a widespread group of photosynthesizing prokaryotes potentially relevant for space exploration, as they can produce both oxygen and organic matter. These organisms have been repeatedly proposed as tools for colonizing planetary bodies in the solar system. We used several Martian regolith [...] Read more.

Cyanobacteria are a widespread group of photosynthesizing prokaryotes potentially relevant for space exploration, as they can produce both oxygen and organic matter. These organisms have been repeatedly proposed as tools for colonizing planetary bodies in the solar system. We used several Martian regolith simulants to support the growth of three widespread filamentous cyanobacteria (Desmonostoc muscorum UTAD N213, Anabaena cylindrica UTAD A212 and an uncharacterized Desmonostoc sp.). All cyanobacteria grew well on the surface of the commercial simulants MGS-1 and MMS-2 and in soluble extracts obtained from them, suggesting that these Martian regolith analogs contain everything necessary to sustain cyanobacterial growth, at least in the short term. We also evaluated the survival of the two Desmonostoc species under desiccation and UV-B radiation, using the same regolith simulants and two clays: Montmorillonite and nontronite. Desiccation hindered growth, but both cyanobacteria were able to recover in less than 30 days in all cases after desiccation. Short irradiation times (up to 1000 kJ/m²) did not consistently affect survival, but longer ones (24,000 kJ/m²) could fully sterilize some samples, although cyanobacteria within MGS-1, montmorillonite and nontronite showed signs of recovery in the long term (>70 days). Clays led to very fast recoveries, particularly montmorillonite. Full article

(This article belongs to the Special Issue Potential for Microbial Habitability on Mars: In Situ Resource Utilization Technologies for Human Missions to Mars)

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21 pages, 6426 KiB

Open AccessArticle

Probiotic Administration Contributes to the Improvement in Intestinal Dysregulation Induced by Allergic Contact Dermatitis

by Eduardo Mendes, Evelyn Roxana Perez Umana, Daniel Di Pace Soares Penna, Fernando Augusto de Oliveira, Leandro Nascimento Lemos, Willian Rodrigues Ribeiro, Mateus Barbosa Casaro, Mariana Lazarini, Valéria Maia Oliveira and Caroline Marcantonio Ferreira

Microorganisms 2025, 13(5), 1082; https://doi.org/10.3390/microorganisms13051082 - 7 May 2025

Abstract

Recent studies have emphasized the impact of gut microbiota on skin health, but the reverse, how skin diseases affect gut homeostasis, has received less attention. Allergic contact dermatitis (ACD), a common skin disorder affecting one in four people worldwide, can be accompanied by [...] Read more.

Recent studies have emphasized the impact of gut microbiota on skin health, but the reverse, how skin diseases affect gut homeostasis, has received less attention. Allergic contact dermatitis (ACD), a common skin disorder affecting one in four people worldwide, can be accompanied by intestinal disturbances. To explore this, we used an experimental model of ACD to investigate the intestinal changes induced by the disease. Parameters assessed included intestinal microbiota, short-chain fatty acids (SCFAs), gene expression related to intestinal permeability, inflammatory cytokines, and mucus production. To evaluate potential therapeutic interventions, the probiotic Bifidobacterium longum strain BB536 was administered via gavage, starting 10 days before dermatitis induction and continuing until the last day of disease induction. ACD caused alterations in the composition of intestinal microbiota compared to naïve mice but did not affect SCFA production. The probiotic altered microbiota composition and increased acetate production in dermatitis-induced mice. ACD decreased the gene expression of TjP1, ATHO1, and MUC2, while probiotic treatment restored TjP1 and ATHO1 to normal levels. The cytokine IL-6 increased in the ACD group compared to naïve mice, whereas IL-10 decreased; probiotic treatment also restored these levels. Intestinal mucus production, affected by ACD, was partially restored by probiotic treatment. The findings suggest that probiotics could be a therapeutic strategy to prevent intestinal issues caused by skin diseases. Full article

(This article belongs to the Special Issue Leaky Skin Syndrome)

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21 pages, 3602 KiB

Open AccessArticle

Ferric Uptake Regulator Contributes to Pseudomonas donghuensis HYS-Induced Iron Metabolic Disruption in Caenorhabditis elegans

by Donghao Gao, Liwen Shen, Yelong Lin, Shuo Huang and Zhixiong Xie

Microorganisms 2025, 13(5), 1081; https://doi.org/10.3390/microorganisms13051081 - 6 May 2025

Abstract

Iron is essential for vital biological processes, with its metabolism closely linked to host–pathogen interactions. Pseudomonas donghuensis HYS, with its superior iron uptake capacity, demonstrates pronounced virulence toward Caenorhabditis elegans. However, the virulence mechanisms remain unexplored. Ferric uptake regulator (Fur) regulates iron [...] Read more.

Iron is essential for vital biological processes, with its metabolism closely linked to host–pathogen interactions. Pseudomonas donghuensis HYS, with its superior iron uptake capacity, demonstrates pronounced virulence toward Caenorhabditis elegans. However, the virulence mechanisms remain unexplored. Ferric uptake regulator (Fur) regulates iron homeostasis and pathogenicity in bacteria, yet its role in HYS-mediated C. elegans pathogenesis requires systematic investigation. In this study, comparing the pathogenic processes of HYS and P. aeruginosa PA14 revealed that HYS causes stronger, irreversible toxicity via distinct mechanisms. Transcriptomics revealed that HYS infection disrupts C. elegans iron metabolism pathways, specifically iron transport, and iron–sulfur cluster utilization. Fur was identified as a pivotal regulator in HYS virulence and was indispensable for its colonization. Specifically, Fur was critical for disrupting nematode iron metabolism, as fur deletion eliminated this effect. While Fur regulated two HYS siderophores, neither of them mediated in the iron metabolism disruption of C. elegans. Screening identified Fur-regulated virulence factors to further investigate the function of Fur in HYS virulence, particularly alkaline proteases, and type II secretion system components. This study highlight that HYS can disrupt the iron metabolism pathway in C. elegans; Fur serves as a pivotal positive regulator in HYS-induced damage, particularly in disrupting iron metabolism through a siderophore-independent pathway. These findings expand the understanding of Pseudomonas pathogenicity and Fur-mediated virulence regulation. Full article

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

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16 pages, 3906 KiB

Open AccessArticle

Diversity, Composition, and Ecological Function of Endophytic Fungal Communities Associated with Erigeron breviscapus in China

by Yi Zhao, Hui Wu, Fang Wang, Liangzhou Zhao, Weijun Gong and Haiyan Li

Microorganisms 2025, 13(5), 1080; https://doi.org/10.3390/microorganisms13051080 - 6 May 2025

Abstract

Endophytic fungi (EF) play crucial roles in accelerating the accumulation of medicinal components and regulating the survival and reproduction of medicinal plants. Erigeron breviscapus is a well-known traditional Chinese medicinal plant with effective therapeutic effects and a wide application, but little is known [...] Read more.

Endophytic fungi (EF) play crucial roles in accelerating the accumulation of medicinal components and regulating the survival and reproduction of medicinal plants. Erigeron breviscapus is a well-known traditional Chinese medicinal plant with effective therapeutic effects and a wide application, but little is known about the diversity, community structure, and ecological roles of EF in this plant. Here, the EF communities associated with different tissues of E. breviscapus at two seasons were studied by high-throughput sequencing methods. Furthermore, FUNGuild was performed to predict the ecological functions of the fungi. Didymella was found to be the most dominant genus across all four tissues, followed by Plectosphaerella, Filobasidium, Cystofilobasidium, and Cladosporium. Notably, the dominant and unique genera and biomarkers of four tissues were different. Interestingly, it was found that the roots had the highest fungal richness and diversity in summer. Moreover, both PCoA plots and PERMANOVA analyses indicated that the tissue and season were main factors contributing to the differences in the fungal communities of E. breviscapus. FUNGuild prediction revealed that pathotroph–saprotroph fungi and undefined taxa accounted for a high proportion in the EF of E. breviscapus. We also found some valuable endophytes that encouraged deeper investigation. These findings provide a theoretical reference for the further development and utilization of EF resources in E. breviscapus. Full article

(This article belongs to the Special Issue Earth Systems: Shaped by Microbial Life)

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7 pages, 374 KiB

Open AccessCommunication

Occurrence of Multiple stx1 Genes and Rare Genomic Variation in stx1 Shiga Toxin-Producing Escherichia coli

by Michaela Projahn, Maria Borowiak, Matthias Contzen, Ekkehard Hiller, Christiane Werckenthin, Elisabeth Schuh and Carlus Deneke

Microorganisms 2025, 13(5), 1079; https://doi.org/10.3390/microorganisms13051079 - 6 May 2025

Abstract

Shiga toxin-producing Escherichia coli are important foodborne pathogens. There are several subtypes of the Shiga toxin Stx known, with Stx2 (a–o) being more diverse than Stx1 (a, c, d). Multiple occurrences of stx2 genes as well as combinations of stx1 and stx2 have [...] Read more.

Shiga toxin-producing Escherichia coli are important foodborne pathogens. There are several subtypes of the Shiga toxin Stx known, with Stx2 (a–o) being more diverse than Stx1 (a, c, d). Multiple occurrences of stx2 genes as well as combinations of stx1 and stx2 have been reported. However, there is a lack of knowledge on the occurrence of multiple stx1 genes in STEC strains. Here, we report two strains from food and animal feces which show genomic variations in the stx1 operon. The first strain harbors stx1a and stx1c genes, and the second strain shows an inactive stx1 operon due to an insertion in the stxA1a subunit gene. The screening of publicly available complete genome sequences of STEC revealed further strains harboring multiple stx1 genes, indicating that those strains also occur in human infections. This should be kept in mind when applying routine diagnostic methods like PCR, that do not detect multiple occurrences of stx1 genes of the same subtype. Moreover, the impact on the severity of human infections due to multiple stx1 genes has not been investigated well. Full article

(This article belongs to the Special Issue Shiga Toxin-Producing Escherichia coli: Diagnostics, Characterization, and Pathogenesis)

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17 pages, 554 KiB

Open AccessArticle

MRSA Profiles Reveal Age- and Gender-Specificity in a Tertiary Care Hospital: High Burden in ICU Elderly and Emerging Community Patterns in Youth

by Kamaleldin B. Said, Khalid Alshammari, Ruba M. Elsaid Ahmed, Fawwaz Alshammari, Ahmed H. Jadani, Ihab Rakha, Salem A. Almijrad, Anwar E. Almallahi, Bader Alkharisi, Naif M. Altamimi, Tarig Mahmoud, Nada A. Abozaid and Amal D. Alshammari

Microorganisms 2025, 13(5), 1078; https://doi.org/10.3390/microorganisms13051078 - 6 May 2025

Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) is a devastating global health concern. Hypervirulent strains are on the rise, causing morbidities and mortalities worldwide. In tertiary care hospitals, critically ill patients, those undergoing invasive procedures, and pediatric and geriatric patients are at risk. It is not [...] Read more.

Methicillin-resistant Staphylococcus aureus (MRSA) is a devastating global health concern. Hypervirulent strains are on the rise, causing morbidities and mortalities worldwide. In tertiary care hospitals, critically ill patients, those undergoing invasive procedures, and pediatric and geriatric patients are at risk. It is not fully clear how strains adapt and specialize in humans and emerge despite the well-established commonality of the S. aureus genome from humans and animals. This study investigates the influence of age-, gender-, and source-specific profiles (clinical, intensive care unit (ICU vs. non-ICU)) on the evolution of hospital-associated (HA)-MRSA versus community-associated (CA)-MRSA lineages. A total of 253 non-duplicate S. aureus isolates were obtained from May 2023 to March 2025. The patients were stratified by age and gender in ICUs and non-ICUs. Standard microbiology methods and Clinical and Laboratory Standards Institute (CLSI) guidelines were used for identification and susceptibility testing, with cefoxitin and oxacillin disk diffusions and molecular diagnosis confirming MRSA. Mann–Whitney U and Chi-square tests assessed the demographic distributions, clinical specimen sources, and MRSA/methicillin-sensitive S. aureus (MSSA) prevalence. Of 253, 41.9% originated from ICUs (71% male; 29% female) and 58.1% from non-ICU wards (64% male; 36% female). In both settings, MRSA colonized the two extremes of age (10–29 and 70+) for males and females, with different mid-life peaks or declines by gender. However, the overall demographic distribution did not differ significantly between the ICU and non-ICU groups (p = 0.287). Respiratory specimens constituted 37% and had the highest MRSA rate (42%), followed by blood (24.5%) and wounds (10.3%). In contrast, MSSA dominated wounds (20.3%). Overall, 73.9% were resistant to cefoxitin and cefotaxime, whereas vancomycin, linezolid, daptomycin, and tigecycline remained highly effective. Younger non-ICU patients (10–29) had higher MSSA, whereas older ICU ones showed pronounced HA-MRSA profiles. By the virtue of methicillin resistance, all MRSA were classified as multidrug resistance. Thus, MRSA colonization of the two extremes of life mostly in ICU seniors and the dominance of invasive MSSA and CA-MRSA patterns in non-ICU youth imply early age- and gender-specific adaptations of the three lineages. MRSA colonizes both ICU and non-ICU populations at extremes of age and gender specifically. High β-lactam resistance underscores the importance of robust stewardship and age- and gender-specific targeting in screening. These findings also indicate host- and organ-specificity in the sequalae of MSSA, CA-MRSA, and HA-MRSA evolutionary dynamics, emphasizing the need for continued surveillance to mitigate MRSA transmission and optimize patient outcomes in tertiary care settings. Full article

(This article belongs to the Section Medical Microbiology)

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22 pages, 3973 KiB

Open AccessArticle

Dysregulated Adaptive Immune Responses to SARS-CoV-2 in Immunocompromised Individuals

by Núria Mayola Danés, Demi Brownlie, Rebecca Folkman, Anna Nordlander, Kim Blom, Renata Varnaite, Julia Niessl, Oskar Karlsson Lindsjö, Sandra Söderholm, Mira Akber, Puran Chen, Marcus Buggert, Andreas Bråve, Jonas Klingström, Piotr Nowak, Nicole Marquardt, Klara Sondén, Ola Blennow and Sara Gredmark-Russ

Microorganisms 2025, 13(5), 1077; https://doi.org/10.3390/microorganisms13051077 - 6 May 2025

Abstract

The SARS-CoV-2 virus poses a significant risk to immunocompromised patients, who display weakened immunity and reduced seroconversion following infection and vaccination. In this study, we recruited 19 hospitalized patients with immune disorders (ImCo) and 4 immunocompetent controls (ICC) with COVID-19. We evaluated their [...] Read more.

The SARS-CoV-2 virus poses a significant risk to immunocompromised patients, who display weakened immunity and reduced seroconversion following infection and vaccination. In this study, we recruited 19 hospitalized patients with immune disorders (ImCo) and 4 immunocompetent controls (ICC) with COVID-19. We evaluated their serological, humoral, and cellular immune responses at <30 days and >90 days post-symptom onset. ICC patients showed robust B and T cell responses against SARS-CoV-2, indicated by detectable antibody levels, memory antibody-secreting cells (mASCs) towards the spike protein and spike-specific CD4⁺ and CD8⁺ T cells. ImCo patients showed impaired immune responses, with lower levels of B cell responses. Further subdivision of the ImCo patients demonstrates that solid organ transplant (SOT) patients generated B cell responses similar to ICC patients, whereas the other ImCo patients, including patients with hematological malignancies and anti-CD20 therapy, did not. Absolute T cell numbers and spike-specific CD4⁺ and CD8⁺ T cell responses were low in the ImCo patients at <30 days but increased at later time points. Our findings suggest that even when B cell responses were reduced, patients could present a T cell response, suggesting a more successful line of passive immunization for immunocompromised individuals focusing on boosting T cell responses. Full article

(This article belongs to the Special Issue Immune Modulation to SARS-CoV-2 Vaccination and Infection)

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