Microorganisms

14 pages, 7705 KiB

Open AccessArticle

The Distribution of Neospora caninum Secretory Proteins in Mouse and Calf Brains

by Nanako Ushio-Watanabe, Rio Fujiwara, Kenichi Watanabe, Manabu Yamada, Yoshiyasu Kobayashi and Yoshifumi Nishikawa

Microorganisms 2025, 13(9), 1970; https://doi.org/10.3390/microorganisms13091970 - 22 Aug 2025

Abstract

Neospora caninum, as well as Toxoplasma gondii, secrete proteins that facilitate the invasion of host cells and the regulation of host immune response and metabolism. However, the localization of the secretory proteins in infected animal brains has not been studied in [...] Read more.

Neospora caninum, as well as Toxoplasma gondii, secrete proteins that facilitate the invasion of host cells and the regulation of host immune response and metabolism. However, the localization of the secretory proteins in infected animal brains has not been studied in detail. Here, we investigate the brain and intracellular distribution of the secretory proteins in experimentally infected mice and naturally infected calves through histopathology and immunohistochemistry (IHC) to detect surface antigen 1 (NcSAG1), cyclophilin (NcCYP), profilin (NcPF), dense granule protein 6 (NcGRA6), and NcGRA7. These methods revealed that numerous tachyzoites positive for NcSAG1, NcCYP, NcPF, NcGRA6, and NcGRA7 were localized in and around the animals’ necrotic lesions, and NcGRA7 was diffusely observed in the necrotic lesions of the infected mice. Moreover, IHC revealed that NcGRA6 and NcGRA7 were distributed in the cytoplasm of infected neurons around the parasites in the infected mice and calves. This suggests that NcGRA6 and NcGRA7 might be directly related to the alteration of neuronal metabolism and activity, and that NcGRA7 might be related to the formation of necrotic lesions. Full article

(This article belongs to the Special Issue Advances in Veterinary Microbiology)

14 pages, 2917 KiB

Open AccessArticle

Drebrin Is Involved in the Life Cycle of Pseudorabies Virus by Regulating the Actin Cytoskeleton

by Kun Xu, Xiao-Han Wang, Yan-Pei Ku, Jie-Yuan Guo, Shu-Han Fan, Miao-Miao Xue, Jiang Wang, Shuang Guo, Jia-Jia Pan and Bei-Bei Chu

Microorganisms 2025, 13(9), 1969; https://doi.org/10.3390/microorganisms13091969 - 22 Aug 2025

Abstract

Pseudorabies virus (PRV), a highly pathogenic alphaherpesvirus, poses a potential threat to public health and safety due to its broad host range and risk of cross-species transmission. Viruses have evolved multiple strategies to exploit host factors for entry into and survival in host [...] Read more.

Pseudorabies virus (PRV), a highly pathogenic alphaherpesvirus, poses a potential threat to public health and safety due to its broad host range and risk of cross-species transmission. Viruses have evolved multiple strategies to exploit host factors for entry into and survival in host cells. Drebrin is an actin-binding protein that restricts rotavirus entry by inhibiting dynamin-mediated endocytosis. However, its role and mechanism in DNA virus infection, particularly in herpesviruses, remain unexplored. In this study, we investigated the role of Drebrin in PRV infection using pharmacological inhibition (BTP−2) and CRISPR-Cas9-mediated gene knockout. Both the Drebrin inhibitor BTP−2 and gene knockout significantly suppressed PRV replication. Intriguingly, Drebrin exhibited stage-specific effects on the viral life cycle: its inhibition enhanced viral internalization during early infection but impaired viral replication at later stages, suggesting that Drebrin plays a complex role in the regulation of PRV infection. PRV infection partially disrupted actin stress fibers and caused an increase in cell size. Drebrin knockout also altered the host-cell morphology, reduced the cell surface area, and induced actin cytoskeleton rearrangement, which was further modulated in PRV-infected cells. In summary, our data demonstrate that Drebrin functions as a critical host factor governing the entire PRV life cycle by regulating actin cytoskeleton reorganization. Full article

(This article belongs to the Section Virology)

15 pages, 7985 KiB

Open AccessArticle

Short-Term Maize Rotation Suppresses Verticillium Wilt and Restructures Soil Microbiomes in Xinjiang Cotton Fields

by Faisal Hayat Khan, Zhanjiang Tie, Xueqin Zhang, Yanjun Ma, Yu Yu, Sifeng Zhao, Xuekun Zhang and Hui Xi

Microorganisms 2025, 13(9), 1968; https://doi.org/10.3390/microorganisms13091968 - 22 Aug 2025

Abstract

Verticillium wilt, a prevalent soil-borne disease, poses a significant challenge to cotton production in Xinjiang, China. Continuous cotton monoculture has increased disease incidence and affected soil microbial diversity in Xinjiang, while crop rotation is recognized as an effective strategy for soil pathogen control. [...] Read more.

Verticillium wilt, a prevalent soil-borne disease, poses a significant challenge to cotton production in Xinjiang, China. Continuous cotton monoculture has increased disease incidence and affected soil microbial diversity in Xinjiang, while crop rotation is recognized as an effective strategy for soil pathogen control. This study investigates how a one-year maize rotation affects Verticillium wilt incidence and soil microbiome composition in cotton fields across northern and southern Xinjiang. The results demonstrated that short-term rotation significantly reduced Verticillium wilt occurrence in both northern and southern Xinjiang. Using high-throughput sequencing of fungal ITS and bacterial 16S rRNA regions, microbial community analysis revealed minimal changes in alpha-diversity but significant structural reorganization between continuous cropping (CC) and rotation (CR) systems, particularly in fungal and bacterial genera composition, with distinct spatial patterns between northern and southern fields. Crop rotation promoted beneficial taxa such as Sphingomonas and Pseudogymnoascus, while reducing the abundance of pathogens such as Verticillium dahliae. LEfSe study suggested Tepidisphaerales and Lasiosphaeriaceae as biomarkers for CR systems, whereas Hypocreales and Blastocatellia dominated in CC soils. Co-occurrence network analysis revealed more bacterial connectivity and modularity under CR, suggesting better microbial interactions and ecological resilience. The increased structural complexity of bacterial networks under CR indicates their greater contribution to soil health maintenance and ecosystem resilience. Our findings demonstrate that short-term crop rotation not only effectively reduces Verticillium wilt incidence but also restructures soil microbial communities, providing an actionable strategy for sustainable cotton cultivation in Xinjiang. Full article

(This article belongs to the Special Issue Advances in the Plant Microbiome: Rhizosphere, Endosphere and Phyllosphere)

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16 pages, 1920 KiB

Open AccessArticle

Novel Thiazolidinedione Derivatives as Potential ZIKV Antiviral Inhibitors

by Isabella Luiza Ralph de Oliveira, José Arion da Silva Moura, Patricia Recordon-Pinson, Floriane Lagadec, Michelle Melgarejo da Rosa, Sayonara Maria Calado Gonçalves, Douglas Carvalho Francisco Viana, Paulo André Teixeira de Moraes Gomes, Marina Galdino da Rocha Pitta, Moacyr Jesus Barreto de Melo Rêgo, Michelly Cristiny Pereira, Mathieu Métifiot, Marie-Line Andreola and Maira Galdino da Rocha Pitta

Microorganisms 2025, 13(9), 1967; https://doi.org/10.3390/microorganisms13091967 - 22 Aug 2025

Abstract

Zika virus (ZIKV) remains a pressing global health concern due to its association with congenital Zika syndrome and the current lack of approved antiviral therapies. In this study, we evaluated the antiviral activity of three novel thiazolidinedione derivatives, GQ-402, GQ-396, and ZKC-10, against [...] Read more.

Zika virus (ZIKV) remains a pressing global health concern due to its association with congenital Zika syndrome and the current lack of approved antiviral therapies. In this study, we evaluated the antiviral activity of three novel thiazolidinedione derivatives, GQ-402, GQ-396, and ZKC-10, against ZIKV in vitro and investigated their potential molecular targets through in silico analysis. GQ-402 exhibited the highest antiviral potency, with an IC₅₀ of 15.7 µM, while ZKC-10 achieved the most substantial reduction in viral RNA levels, as determined by RT-qPCR. Molecular docking studies identified GQ-396 as the top-ranked inhibitor of the NS2B-NS3 protease and NS5 RNA-dependent RNA polymerase, suggesting distinct mechanisms of action among the compounds. These findings highlight the therapeutic potential of thiazolidinedione derivatives and underscore the need for further investigation to develop effective treatments for ZIKV infection. Full article

(This article belongs to the Special Issue Emerging Infectious Diseases and Multidrug Resistance)

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14 pages, 1972 KiB

Open AccessArticle

Oral Microbiome and Edentulism During Pregnancy: 16S rRNA Gene Analysis of an Indigenous Community—A Pilot Study

by Pablo Vásquez-Toasa, Juan C. Fernández-Cadena and Derly Andrade-Molina

Microorganisms 2025, 13(9), 1966; https://doi.org/10.3390/microorganisms13091966 - 22 Aug 2025

Abstract

Background: Edentulism, or toothlessness, is a significant public health issue with profound implications for physical and systemic health, especially during pregnancy, when hormonal and behavioral changes increase the risk of oral diseases. Indigenous populations are particularly vulnerable due to socioeconomic and cultural factors [...] Read more.

Background: Edentulism, or toothlessness, is a significant public health issue with profound implications for physical and systemic health, especially during pregnancy, when hormonal and behavioral changes increase the risk of oral diseases. Indigenous populations are particularly vulnerable due to socioeconomic and cultural factors that limit access to dental care. Methods: This pilot study assessed the oral microbiota of nine women, both pregnant and non-pregnant, aged 18–35 from the Salasaca indigenous community in Ecuador, using 16S rRNA gene sequencing. Samples were collected from dentin, saliva, and oral mucosa, and analyzed for alpha and beta diversity levels, taxonomic composition, and ecological metrics using the DADA2 pipeline and a canonical correspondence analysis. Results: Pregnant participants exhibited significantly lower microbial diversity compared to non-pregnant individuals, with notable differences in species richness and community structure. Dominant phyla included Bacillota, Bacteroidota, and Pseudomonadota. Prevotella sp., Neisseria sp., and Haemophilus sp. were among the prevalent genera, with the canonical correspondence analysis highlighting associations between microbial profiles and variables such as gestational status, marital status, and BMI. Conclusion: The findings suggest that pregnancy influences the oral microbiota composition, potentially predisposing women to dysbiosis and dental pathology. This study highlights the need for targeted oral health strategies during pregnancy and serves as a foundation for larger studies in underserved indigenous populations. Full article

(This article belongs to the Section Medical Microbiology)

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19 pages, 1337 KiB

Open AccessArticle

Yeast Ecology in White Brined Cheeses: Correlations with Physicochemical Parameters in Artisanal and Industrial Products

by Neli Ermenlieva, Sylvia Stamova, Nadezhda Ivanova, Petya Atanasova, Velichka Marinova, Sevginar Ibryamova, Ivan Ivanov and Emilia Georgieva

Microorganisms 2025, 13(9), 1965; https://doi.org/10.3390/microorganisms13091965 - 22 Aug 2025

Abstract

Yeasts are essential contributors to the ripening and flavor development of white brined cheeses. This study aimed to investigate and compare the microbial load and yeast species composition in artisanal and industrial white brined cheeses. The influence of key physicochemical parameters (salt content, [...] Read more.

Yeasts are essential contributors to the ripening and flavor development of white brined cheeses. This study aimed to investigate and compare the microbial load and yeast species composition in artisanal and industrial white brined cheeses. The influence of key physicochemical parameters (salt content, acidity, fat content, moisture, and ripening stage) on yeast count and species composition was analyzed. A total of 100 white brined cheese samples produced in Bulgaria were analyzed. Yeast species were identified using MALDI–TOF MS, and physicochemical properties were assessed according to ISO standards. The predominant yeast species identified were Torulaspora delbrueckii, Debaryomyces hansenii, Saccharomyces cerevisiae, and Candida sphaerica. D. hansenii was the dominant species in industrial samples, while S. cerevisiae was more frequently isolated from artisanal cheeses. Statistical analyses showed that the physicochemical parameters most influencing yeast species composition were salt content and acidity. A statistically significant correlation between yeast count and salt content was observed only in industrial cheeses, with D. hansenii showing greater salt tolerance. Yeast counts were higher in cheeses with higher salt content, particularly in industrial samples. This study highlights the distinct influence of production methods and physicochemical parameters on the yeast ecology of white brined cheeses. Full article

(This article belongs to the Section Food Microbiology)

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26 pages, 7929 KiB

Open AccessArticle

Genomic and Metabolomic Insights into the Antimicrobial Activities and Plant-Promoting Potential of Streptomyces olivoreticuli YNK-FS0020

by Xin Liu, Yongqin Liao, Zhufeng Shi, Te Pu, Zhuli Shi, Jianpeng Jia, Yu Wang, Feifei He and Peiwen Yang

Microorganisms 2025, 13(9), 1964; https://doi.org/10.3390/microorganisms13091964 - 22 Aug 2025

Abstract

Streptomycetes are vital microbial resources used in agriculture and biotechnology and are diverse secondary metabolites. The Streptomyces olivoreticuli YNK-FS0020 strain was isolated from the rhizosphere soil in Yunnan’s Wuliangshan Forest; its functions were explored via a series of experiments and genomic analysis. Indoor [...] Read more.

Streptomycetes are vital microbial resources used in agriculture and biotechnology and are diverse secondary metabolites. The Streptomyces olivoreticuli YNK-FS0020 strain was isolated from the rhizosphere soil in Yunnan’s Wuliangshan Forest; its functions were explored via a series of experiments and genomic analysis. Indoor assays showed that this strain inhibits seven plant pathogens (including Fusarium oxysporum f. sp. cubense Tropical Race 4) and exhibits phosphorus solubilization, siderophore production, and plant-growth promotion. Genomic analysis revealed 47 secondary metabolite biosynthetic gene clusters: 12 shared over 60% similarity with known clusters (4 exhibited 100% similarity, involving antimycin and ectoine), while 19 showed low similarity or unknown functions, indicating the strain’s potential in the development of novel compounds. Genes related to tryptophan-IAA synthesis, phosphate metabolism, and siderophore systems were annotated, while metabolomics detected indole-3-acetic acid and kitasamycin, revealing mechanisms like hormonal regulation and antimicrobial secretion. In summary, YNK-FS0020 has potential for use in plant-growth promotion and disease control, aiding agricultural microbial resource utilization. Full article

(This article belongs to the Section Plant Microbe Interactions)

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17 pages, 4342 KiB

Open AccessArticle

Metagenomic Signatures of Colorectal Cancer in the Jordanian Population: A Regional Case-Control Analysis Using 16S rRNA Profiling

by Lo’ai Alanagreh, Minas A. Mustafa, Mohammad Borhan Al-Zghoul, Muhannad I. Massadeh, Osamah Batiha, Maher Sughayer, Rashed Taiseer Almashakbeh, Haya Bader Abu Suilike, Faten S. Tout and Foad Alzoughool

Microorganisms 2025, 13(8), 1963; https://doi.org/10.3390/microorganisms13081963 - 21 Aug 2025

Abstract

The gut microbiota plays a pivotal role in developing colorectal cancer (CRC) through interactions with host immunity, metabolism, and inflammation. However, microbiome-based studies remain scarce in Middle Eastern populations, limiting regional insights into microbial signatures associated with CRC. This study aimed to characterize [...] Read more.

The gut microbiota plays a pivotal role in developing colorectal cancer (CRC) through interactions with host immunity, metabolism, and inflammation. However, microbiome-based studies remain scarce in Middle Eastern populations, limiting regional insights into microbial signatures associated with CRC. This study aimed to characterize the gut microbiota profiles of Jordanian CRC patients using 16S rRNA gene sequencing and compare them to those of healthy controls from the GutFeeling KnowledgeBase (GutFeelingKB). Stool samples from 50 CRC patients were analyzed using Illumina iSeq targeting the V3–V4 region. Taxonomic profiling was conducted with a standardized 16S metagenomics pipeline and compared with GutFeelingKB reference data. CRC samples were enriched in Streptococcus, Enterococcus, Klebsiella, Escherichia, Citrobacter, Veillonella, Megamonas, and Eggerthella, while beneficial butyrate-producing genera such as Roseburia, Ruminococcus, Akkermansia, Faecalibacterium, and Bacteroides were significantly depleted. The absence of Fusobacterium nucleatum and Bacteroides fragilis—commonly seen in global studies—suggests region-specific microbial patterns. This study is the first metagenomic study profiling CRC-associated microbiota in Jordan. The findings reveal a dysbiotic microbial signature that reflects both global changes associated with CRC and local ecological influences. This research emphasizes the importance of population-specific microbiome studies and highlights the need to include appropriately matched controls in future investigations. Full article

(This article belongs to the Section Gut Microbiota)

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13 pages, 1677 KiB

Open AccessArticle

A Single Tertiary-Care Center Case Series Using Vertical Rectus Abdominis Myocutaneous Flap in the Management of Complex Periprosthetic Joint Infection of the Hip

by Omar Salem, Jing Zhang, George Grammatopoulos, Simon Garceau and Hesham Abdelbary

Microorganisms 2025, 13(8), 1962; https://doi.org/10.3390/microorganisms13081962 - 21 Aug 2025

Abstract

Prosthetic joint infections (PJIs) pose significant challenges, often requiring multiple surgeries that lead to soft tissue loss, dead space, and fibrosis. Wound breakdown increases the risk of polymicrobial infection and treatment failure. The vertical rectus abdominis myocutaneous (VRAM) flap is a proven method [...] Read more.

Prosthetic joint infections (PJIs) pose significant challenges, often requiring multiple surgeries that lead to soft tissue loss, dead space, and fibrosis. Wound breakdown increases the risk of polymicrobial infection and treatment failure. The vertical rectus abdominis myocutaneous (VRAM) flap is a proven method for complex wound coverage, but its role in managing hip PJI is underexplored. This study evaluates outcomes of VRAM flap reconstruction in polymicrobial hip PJI. We retrospectively reviewed five patients who underwent VRAM flap reconstruction for polymicrobial hip PJI between December 2020 and December 2023. Primary outcomes included flap survival, infection control, and wound healing. Secondary outcomes were implant retention, postoperative complications, and functional status. At a mean follow-up of 28 months, four patients achieved wound healing and remained infection-free, while one had persistent sinus drainage but retained the implant. Flap survival was 100%, with no necrosis or failure. No major complications requiring reoperation occurred. Two patients developed deep collections, managed with ultrasound-guided drainage (Clavien-Dindo IIIa). Minor complications included donor-site dehiscence (three), flap dehiscence (one), edge necrosis (two), and hernias (two), all managed non-surgically (Clavien-Dindo I/II). All patients retained implants and remained ambulatory. VRAM flap reconstruction is a reliable option for managing complex polymicrobial hip PJI. Flap survival was excellent, and most patients achieved infection control. However, persistent infection and the need for suppressive antibiotics highlight the ongoing challenges in these cases. Full article

(This article belongs to the Special Issue Challenges of Biofilm-Associated Bone and Joint Infections)

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16 pages, 1800 KiB

Open AccessArticle

Extracellular Cr(VI) Reduction by the Salt-Tolerant Strain Bacillus safensis BSF-4

by Yilan Liu, Weiping Yu, Tianying Nie, Lu Wang and Yusheng Niu

Microorganisms 2025, 13(8), 1961; https://doi.org/10.3390/microorganisms13081961 - 21 Aug 2025

Abstract

Microbial reduction in hexavalent chromium (Cr(VI)) is a well characterized bioremediation strategy, yet the mechanistic diversity among bacterial taxa necessitates detailed investigations into strain-specific pathways. Here, we report the isolation and characterization of Bacillus safensis BSF-4, a halophilic bacterium derived from saline-alkali [...] Read more.

Microbial reduction in hexavalent chromium (Cr(VI)) is a well characterized bioremediation strategy, yet the mechanistic diversity among bacterial taxa necessitates detailed investigations into strain-specific pathways. Here, we report the isolation and characterization of Bacillus safensis BSF-4, a halophilic bacterium derived from saline-alkali soil, which demonstrates efficient Cr(VI) reduction capacity. Physiological assays showed that BSF-4 achieved 89.15% reduction of 20 mg/L Cr(VI) within 72 h, with Cr(III) identified as the primary extracellular end product. Resting cell assays and subcellular fractionation analyses confirmed that Cr(VI) reduction predominantly occurs in the extracellular milieu. X-ray photoelectron spectroscopy (XPS) further revealed soluble Cr(III) complexed with extracellular polymeric substances (EPS). Transcriptomic profiling indicated upregulation of membrane-associated transport systems (facilitating Cr(VI) exclusion) and quorum sensing (QS) pathways (mediating adaptive stress responses). These findings highlight a dual mechanism: (1) extracellular enzymatic reduction mediated by EPS-bound redox proteins, and (2) intracellular detoxification via QS-regulated defense pathways. Collectively, Bacillus safensis BSF-4 exhibits robust Cr(VI) reduction capacity under saline conditions, positioning it as a promising candidate for bioremediation of Cr(VI)-contaminated saline soils and aquatic ecosystems. Full article

(This article belongs to the Section Environmental Microbiology)

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22 pages, 1055 KiB

Open AccessReview

Advanced Strategies in Phage Research: Innovations, Applications, and Challenges

by Pengfei Wu, Wanwu Li, Wenlu Zhang, Shasha Li, Bo Deng, Shanghui Xu and Zhongjie Li

Microorganisms 2025, 13(8), 1960; https://doi.org/10.3390/microorganisms13081960 - 21 Aug 2025

Abstract

The escalating global threat of antimicrobial resistance (AMR) underscores the urgent need for innovative therapeutics. Bacteriophages (phages), natural bacterial predators, offer promising solutions, especially when harnessed through advances in artificial intelligence (AI). This review explores how AI-driven innovations are transforming phage biology, with [...] Read more.

The escalating global threat of antimicrobial resistance (AMR) underscores the urgent need for innovative therapeutics. Bacteriophages (phages), natural bacterial predators, offer promising solutions, especially when harnessed through advances in artificial intelligence (AI). This review explores how AI-driven innovations are transforming phage biology, with an emphasis on three pivotal areas: (1) AI-enhanced structural prediction (e.g., AlphaFold); (2) deep learning functional annotation; (3) bioengineering strategies, including CRISPR-Cas. We further discuss applications extending to medical therapy, biosensing, agricultural biocontrol, and environmental remediation. Despite progress, critical challenges persist—including high false-positive rates, difficulties in modeling disordered protein regions, and biosafety concerns remain. Overcoming these requires experimental validation, robust computational frameworks, and global regulatory oversight. AI integration in phage research is accelerating the development of next-generation therapeutics to combat AMR and advance engineered living therapeutics. Full article

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

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25 pages, 7381 KiB

Open AccessArticle

Noctiluca scintillans Bloom Reshapes Microbial Community Structure, Interaction Networks, and Metabolism Patterns in Qinhuangdao Coastal Waters, China

by Yibo Wang, Min Zhou, Xinru Yue, Yang Chen, Du Su and Zhiliang Liu

Microorganisms 2025, 13(8), 1959; https://doi.org/10.3390/microorganisms13081959 - 21 Aug 2025

Abstract

The coastal waters of Qinhuangdao are a major hotspot for harmful algal blooms (HABs) in the Bohai Sea, with Noctiluca scintillans being one of the primary algal species responsible for these events. A comprehensive understanding of the microbial community structure and functional responses [...] Read more.

The coastal waters of Qinhuangdao are a major hotspot for harmful algal blooms (HABs) in the Bohai Sea, with Noctiluca scintillans being one of the primary algal species responsible for these events. A comprehensive understanding of the microbial community structure and functional responses to N. scintillans bloom events is crucial for elucidating their underlying mechanisms and ecological impacts. This study investigated the microbial community dynamics, metabolic shifts, and the environmental drivers associated with a N. scintillans bloom in the coastal waters of Qinhuangdao, China, using high-throughput sequencing of 16S and 18S rRNA genes, co-occurrence network analysis, and metabolic pathway prediction. The results revealed that the proliferation of autotrophic phytoplankton, such as Minutocellus spp., likely provided a nutritional foundation and favorable conditions for the N. scintillans bloom. The bloom significantly altered the community structures of prokaryotes and microeukaryotes, resulting in significantly lower α-diversity indices in the blooming region (BR) compared to the non-blooming region (NR). Co-occurrence network analyses demonstrated reduced network complexity and stability in the BR, with keystone taxa primarily belonging to Flavobacteriaceae and Rhodobacteraceae. Furthermore, the community structures of both prokaryotes and microeukaryotes correlated with multiple environmental factors, particularly elevated levels of NH₄⁺-N and PO₄³⁻-P. Metabolic predictions indicated enhanced anaerobic respiration, fatty acid degradation, and nitrogen assimilation pathways, suggesting microbial adaptation to bloom-induced localized hypoxia and high organic matter. Notably, ammonia assimilation was upregulated, likely as a detoxification strategy. Additionally, carbon flux was redirected through the methylmalonyl-CoA pathway and pyruvate-malate shuttle to compensate for partial TCA cycle downregulation, maintaining energy balance under oxygen-limited conditions. This study elucidates the interplay between N. scintillans blooms, microbial interactions, and functional adaptations, providing insights for HAB prediction and management in coastal ecosystems. Full article

(This article belongs to the Section Environmental Microbiology)

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25 pages, 14023 KiB

Open AccessArticle

Seasonal Variation in In Hospite but Not Free-Living, Symbiodiniaceae Communities Around Hainan Island, China

by Tinghan Yang, Zhao Qi, Haihua Wang, Pengfei Zheng, Shuh-Ji Kao and Xiaoping Diao

Microorganisms 2025, 13(8), 1958; https://doi.org/10.3390/microorganisms13081958 - 21 Aug 2025

Abstract

Coral reefs are increasingly threatened by global climate change, and mass bleaching and mortality events caused by elevated seawater temperature have led to coral loss worldwide. Hainan Island hosts extensive coral reef ecosystems in China, yet seasonal variation in Symbiodiniaceae communities within this [...] Read more.

Coral reefs are increasingly threatened by global climate change, and mass bleaching and mortality events caused by elevated seawater temperature have led to coral loss worldwide. Hainan Island hosts extensive coral reef ecosystems in China, yet seasonal variation in Symbiodiniaceae communities within this region remains insufficiently understood. We aimed to investigate the temperature-driven adaptability regulation of the symbiotic Symbiodiniaceae community in reef-building corals, focusing on the environmental adaptive changes in its community structure in coral reefs between cold (23.6–24.6 °C) and warm (28.2–30.6 °C) months. Symbiodiniaceae shuffling and rare genotype turnover were discovered in adaptability variations in the symbiotic Symbiodiniaceae community between two months. Symbiodiniaceae genetic diversity increased during warm months, primarily due to temporal turnover of rare genotypes within the Cladocopium and Durusdinium genera. Coral Favites, Galaxea, and Porites exhibited the shuffling of Symbiodiniaceae between tolerant Durusdinium and sensitive Cladocopium. Symbiodiniaceae interactions in G. fascicularis and P. lutea exhibited the highest levels of stability with the increase in temperature, whereas the interactions in A. digitifera and P. damicornis showed the lowest levels of stability. Rare genotypes functioned as central hubs and important roles within Symbiodiniaceae communities, exhibiting minimal responsiveness to temperature fluctuations while maintaining community structural stability. The temperature-driven adaptability regulation of symbiotic Symbiodiniaceae could be achieved by Symbiodiniaceae shuffling and rare genotype turnover. The process might be aggravated by concurrent adverse factors, including elevated salinity, pollution, and anthropogenic disturbance. These findings provide insights into how the Symbiodiniaceae community influences the adaptation and resilience of coral hosts to temperature fluctuations in coral reefs. Furthermore, they may contribute to assessing the reef-building coral’s capacity to withstand environmental stressors associated with global climate change. Full article

(This article belongs to the Special Issue Microbes in Aquaculture)

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23 pages, 7223 KiB

Open AccessArticle

Microbial and Geochemical Diversity of Laguna Timone, an Extreme Hypersaline Crater Lake in Patagonia (52° S)

by Carolina Henríquez, José M. Pérez-Donoso, Nicolás Bruna, Mauricio Calderón, Leonardo Fadel Cury, Paulo Quezada, Gustavo Athayde, Poldie Oyarzún and Anelize Bahniuk

Microorganisms 2025, 13(8), 1957; https://doi.org/10.3390/microorganisms13081957 - 21 Aug 2025

Abstract

Extreme environments, such as hypersaline habitats, hot springs, deep-sea hydrothermal vents, glaciers, and permafrost, provide diverse ecological niches for studying microbial evolution. However, knowledge of microbial communities in extreme environments at high southern latitudes remains limited, aside from Antarctica. Laguna Timone is a [...] Read more.

Extreme environments, such as hypersaline habitats, hot springs, deep-sea hydrothermal vents, glaciers, and permafrost, provide diverse ecological niches for studying microbial evolution. However, knowledge of microbial communities in extreme environments at high southern latitudes remains limited, aside from Antarctica. Laguna Timone is a hypersaline crater lake located in a Pleistocene maar of the Pali Aike Volcanic Field, southern Patagonia; the lake was formed during basaltic eruptions in a periglacial setting. Here, we report the first integrative characterization of microbial communities from biofilms and microbial mats in this lake using high-throughput 16S rRNA and ITS gene sequencing, along with mineralogical and hydrochemical analyses of water, sediments, and carbonates. Bacterial communities were dominated by the genera Enterobacterales ASV1, Pseudomonas, Oscillatoria, Nodularia, and Belliella, with site-specific assemblages. Fungal communities included Laetinaevia, Ilyonectria, Thelebolus, Plectosphaerella, and Acrostalagmus, each showing distinct distribution patterns. These baseline data contribute to understanding microbial dynamics in hypersaline maar environments and support future investigations. This integrative approach highlights key microbe–mineral relationships and underscores the potential of Laguna Timone as a natural laboratory for exploring biosignature formation and microbial adaptation in chemically extreme environments, both on early Earth and potentially beyond. Full article

(This article belongs to the Section Environmental Microbiology)

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29 pages, 2219 KiB

Open AccessReview

Fecal Microbiota Transplantation in Alzheimer’s Disease: Mechanistic Insights Through the Microbiota–Gut–Brain Axis and Therapeutic Prospects

by Jiayu Ren, Qinwen Wang, Hang Hong and Chunlan Tang

Microorganisms 2025, 13(8), 1956; https://doi.org/10.3390/microorganisms13081956 - 21 Aug 2025

Abstract

Alzheimer’s disease (AD), a prevalent neurodegenerative disorder in the aging population, remains without definitive therapeutic solutions. Emerging insights into the gut microbiota (GM) and its bidirectional communication with the central nervous system(CNS) through the microbiota–gut–brain axis (MGBA) have unveiled potential correlative mechanisms that [...] Read more.

Alzheimer’s disease (AD), a prevalent neurodegenerative disorder in the aging population, remains without definitive therapeutic solutions. Emerging insights into the gut microbiota (GM) and its bidirectional communication with the central nervous system(CNS) through the microbiota–gut–brain axis (MGBA) have unveiled potential correlative mechanisms that may contribute to AD pathogenesis, though causal evidence remains limited. Dysregulation of GM composition (dysbiosis) exacerbates AD progression via neuroinflammation, amyloid-β (Aβ) deposition, and tau hyperphosphorylation (p-tau), while restoring microbial homeostasis presents a promising therapeutic strategy. Fecal microbiota transplantation (FMT), a technique to reconstitute gut ecology by transferring processed fecal matter from healthy donors, has demonstrated efficacy in ameliorating cognitive deficits and neuropathology in AD animal models. Preclinical studies reveal that FMT reduces Aβ plaques, normalizes tau phosphorylation, suppresses inflammasome activation, and restores microglial homeostasis through modulation of microbial metabolites and immune pathways. Although clinical evidence remains limited to case reports and small-scale trials showing potential therapeutic effect, safety concerns regarding long-term effects and protocol standardization necessitate further investigation. This review synthesizes current knowledge on GM–AD interactions, evaluates FMT’s mechanistic potential, and discusses challenges in translating this ancient practice into a cutting-edge AD therapy. Rigorous randomized controlled trials and personalized microbiota-based interventions are imperative to advance FMT from bench to bedside. Full article

(This article belongs to the Special Issue Effects of Gut Microbiota on Human Health and Disease, 2nd Edition)

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15 pages, 601 KiB

Open AccessSystematic Review

Association of Helicobacter pylori as an Extragastric Reservoir in the Oral Cavity with Oral Diseases in Patients with and Without Gastritis—A Systematic Review

by Eber Cuba, María C. Sánchez, María J. Ciudad and Luis Collado

Microorganisms 2025, 13(8), 1955; https://doi.org/10.3390/microorganisms13081955 - 21 Aug 2025

Abstract

This systematic review aimed to evaluate the association between Helicobacter pylori in the oral cavity as an extragastric reservoir and oral diseases in patients with or without gastritis. Following the PRISMA guidelines, a comprehensive search was conducted on the PubMed, Scopus, Cochrane Central, [...] Read more.

This systematic review aimed to evaluate the association between Helicobacter pylori in the oral cavity as an extragastric reservoir and oral diseases in patients with or without gastritis. Following the PRISMA guidelines, a comprehensive search was conducted on the PubMed, Scopus, Cochrane Central, and Embase databases (2010–2025) using MeSH terms and keywords related to H. pylori, the oral cavity, and oral diseases. Inclusion criteria included observational studies, clinical trials, and case–control studies. Data extraction and quality assessment were performed using the Newcastle–Ottawa Scale (NOS). Of the 298 records initially identified, 22 studies met the inclusion criteria. The presence of H. pylori in the oral cavity (plaque, saliva) was variably associated with gastritis, periodontitis, dental caries, and halitosis. Detection rates varied widely (0–100%), influenced by methodological differences (PCR, culture, antigen tests). Some studies reported an improvement in oral health after eradication therapy, while others found no significant association. The oral cavity may serve as a reservoir for H. pylori, with implications for oral and systemic health. Standardized diagnostic methods and integrated treatment approaches (combining gastric eradication and oral hygiene) are needed to clarify their role and optimize clinical outcomes. Further research is warranted to establish causal relationships and therapeutic strategies. Full article

(This article belongs to the Section Medical Microbiology)

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14 pages, 1191 KiB

Open AccessArticle

Biodegradation of Zearalenone by a Novel Bacillus Strain X13 Isolated from Volcanic Rock Soil Using the Mycotoxin as the Sole Carbon Source

by Di Meng, Kaizhong Xu, Jinbin Liu and Xiangru Liao

Microorganisms 2025, 13(8), 1954; https://doi.org/10.3390/microorganisms13081954 - 21 Aug 2025

Abstract

Zearalenone (ZEN) is a widespread estrogenic mycotoxin that poses serious health risks to both humans and animals through the contamination of cereals and feeds. In this study, a novel Bacillus strain X13 was isolated from volcanic rock soil and demonstrated the unique ability [...] Read more.

Zearalenone (ZEN) is a widespread estrogenic mycotoxin that poses serious health risks to both humans and animals through the contamination of cereals and feeds. In this study, a novel Bacillus strain X13 was isolated from volcanic rock soil and demonstrated the unique ability to utilize ZEN as the sole carbon source for growth and metabolism. Under optimized conditions (37 °C, pH 8.0, and 5% inoculum in M9 minimal medium), strain X13 achieved a ZEN degradation efficiency of 98.57%. LC-MS analysis identified 1-(3,5-dihydroxyphenyl)-6′-hydroxy-1′-undecen-10′-one as the primary degradation product, indicating enzymatic hydrolysis of the lactone ring. Enzymatic assays revealed that the active components were extracellular, proteinaceous, and metal ion-dependent. Furthermore, the strain reduced ZEN content in mold-contaminated corn flour by 74.6%, effectively lowering toxin levels below regulatory limits. These findings suggest that Bacillus sp. X13 is a promising candidate for the bioremediation of ZEN-contaminated agricultural products, with significant potential for application in food and feed detoxification strategies. The robust degradation performance of strain X13 under simulated environmental conditions, combined with its adaptability to agricultural substrates, positions it as a viable solution for large-scale mycotoxin mitigation in the food industry chain, from pre-harvest field management to post-harvest storage processing. Full article

(This article belongs to the Section Environmental Microbiology)

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16 pages, 6730 KiB

Open AccessArticle

Insights into the Genomic Architecture and Improvement of the Capabilities of Acinetobacter calcoaceticus for the Biodegradation of Petroleum Hydrocarbons

by Yaning Zeng, Mutian Wang, Xiaoyu Chang, Leilei Wang, Xiaowen Fu, Yujie Huang, Fanyong Song, Lei Ji and Jianing Wang

Microorganisms 2025, 13(8), 1953; https://doi.org/10.3390/microorganisms13081953 - 21 Aug 2025

Abstract

Petroleum-contaminated terrestrial ecosystems require effective bioremediation strategies. In this study, genomic analysis revealed key biodegradation genes on the Acinetobacter calcoaceticus 21# chromosome: alkane hydroxylases (alkB, almA, LadA) and aromatic ortho-cleavage pathway genes (catABC). Phylogenetic and multiple sequence [...] Read more.

Petroleum-contaminated terrestrial ecosystems require effective bioremediation strategies. In this study, genomic analysis revealed key biodegradation genes on the Acinetobacter calcoaceticus 21# chromosome: alkane hydroxylases (alkB, almA, LadA) and aromatic ortho-cleavage pathway genes (catABC). Phylogenetic and multiple sequence alignment analyses of the almA gene in strain 21# revealed the presence of signature motifs characteristic of Baeyer–Villiger monooxygenase. Functional annotation analysis demonstrated stronger phylogenetic affinity of this protein to previously characterized BVMOs than to hydroxylases. Therefore, it is suggested that the AlmA protein in 21# exhibits BVMO activity and participates in the subterminal oxidation pathway of alkane degradation. Wild-type 21# degraded both n-Octacosane (24.47%) and pyrene (34.03%). Engineered 21#-A3 showed significantly enhanced n-Octacosane degradation (28.68%). To validate AlmA function and assess impacts of exogenous gene integration, we expressed the almA gene from A. vivianii KJ-1 via pET-28a(+)-av-almA-BH vector. Enzymatic assays demonstrated no activity toward long-chain alkanes but high activity for 2-decanone (0.39 U/mg) and 2-dodecanone (0.37 U/mg). Metabolite analysis confirmed recombinant AlmA functions through subterminal oxidation. This study establishes a foundational framework for advancing the optimization of petroleum-degrading bacteria. To engineer more efficient hydrocarbon-degrading strains, future research should integrate meta-cleavage pathways to expand their substrate utilization range for polycyclic aromatic hydrocarbons. Full article

(This article belongs to the Section Environmental Microbiology)

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14 pages, 2710 KiB

Open AccessArticle

vapD Mutation Shows Impairment in the Persistence of Helicobacter pylori Within AGS Cells

by Rosario Morales-Espinosa, Gabriela Delgado, Carlos A. Santiago, Alejandro Flores-Alanis, Rafael Diaz-Mendez, Alberto Gonzalez-Pedraza, José L. Méndez and Alejandro Cravioto

Microorganisms 2025, 13(8), 1952; https://doi.org/10.3390/microorganisms13081952 - 21 Aug 2025

Abstract

The Helicobacter pylori vapD gene is transcribed and expressed when the bacteria are within the gastric cell. In this current study, we investigated how vapD knockout affects the survival of H. pylori inside human gastric adenocarcinoma cells. We constructed an H. pylori 26695 [...] Read more.

The Helicobacter pylori vapD gene is transcribed and expressed when the bacteria are within the gastric cell. In this current study, we investigated how vapD knockout affects the survival of H. pylori inside human gastric adenocarcinoma cells. We constructed an H. pylori 26695 vapD (Hp ΔvapD) mutant strain. H. pylori 26695 wt and Hp ΔvapD strains were grown in synthetic media and were co-cultured with AGS cells. From the start, the growth curve, total protein concentration and colony-forming units (CFUs) of each strain were measured. From each co-culture, CFUs and total RNA were obtained, and transcript levels of GAPDH, vapD, vacA, ureA, and 16s Hp were measured by qRT-PCR. Hp ΔvapD did not affect the growth rate of the strain in synthetic media, showing that the vapD gene is not necessary when the bacteria grow outside eukaryote cells. However, in the intracellular environment, the number of CFUs recovered from the Hp ΔvapD strain from AGS cells decreased after 36 h. Transcription levels of the vacA gene from the Hp ΔvapD strain were 10,000-fold lower than those of H. pylori wt, to the point of being undetectable. The results suggest that the vapD gene contributed to maintaining H. pylori inside gastric cells. Full article

(This article belongs to the Special Issue Bacterial Pathogenesis and Host Immune Responses)

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