Microorganisms

23 pages, 4569 KiB

Open AccessArticle

Multi-Omics Analysis Provides New Insights into the Interplay Between Gut Microbiota, Fatty Acid Metabolism, and Immune Response in Cultured and Wild Coilia nasus from the Yangtze River Area in China

by Chang Yang, Kai Liu, Yanmin Deng, Qianhui Wang, Shiqian Cao and Qunlan Zhou

Microorganisms 2025, 13(7), 1711; https://doi.org/10.3390/microorganisms13071711 - 21 Jul 2025

Viewed by 439

Abstract

To elucidate the interactions among fatty acid metabolism, immune status, and gut microbiota, both cultured and wild Coilia nasus from the Yangtze River were examined in China. The results demonstrated that wild C. nasus exhibited markedly higher lipid and docosahexaenoic acid (DHA) contents, [...] Read more.

To elucidate the interactions among fatty acid metabolism, immune status, and gut microbiota, both cultured and wild Coilia nasus from the Yangtze River were examined in China. The results demonstrated that wild C. nasus exhibited markedly higher lipid and docosahexaenoic acid (DHA) contents, a greater ratio of total ω-3 PUFAs to total ω-6 PUFAs, and more active antioxidant enzymes compared to cultured C. nasus. However, the shear force, water-holding capacity, and total n-6 PUFA content were lower in wild C. nasus. Transcriptome analysis revealed distinct gene expression patterns: wild C. nasus upregulated immune-related genes, while cultured C. nasus downregulated genes related to fatty acid metabolism. Significant differences were observed in alpha and beta diversity between cultured and wild groups. LEfSe analysis identified Clostridium_T, Escherichia, and Glutamicibacter as biomarkers for cultured C. nasus, while eight genera, including Pseudomonas_E and Sphingomonas_L, were predominant in wild C. nasus. Modular analysis identified five modules linked to immune functions and fatty acid metabolism. Clostridium_T, Sphingomonas_L, and Pseudomonas_E were dominant in the first two modules, with Pseudomonas_E and Clostridium_T as key regulators of fatty acid metabolism and immune processes. These differences, likely due to gut microbiota variations, provide insights for C. nasus nutritional studies. Full article

(This article belongs to the Special Issue Microbiome in Fish and Their Living Environment)

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16 pages, 7371 KiB

Open AccessArticle

Effects of Salinity Fluctuation on Antimicrobial Resistance and Virulence Factor Genes of Low and High Nucleic Acid-Content Bacteria in a Marine Environment

by Wei Hu, Xinzhu Zhou, Yu Liu, Yadi Zhang and Yingying Wang

Microorganisms 2025, 13(7), 1710; https://doi.org/10.3390/microorganisms13071710 - 21 Jul 2025

Viewed by 398

Abstract

Salinity, as one of the critical environmental factors in marine ecosystems, has complex and wide-ranging biological effects. However, the effects of salinity fluctuation on antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in the marine environment are not well understood. In this [...] Read more.

Salinity, as one of the critical environmental factors in marine ecosystems, has complex and wide-ranging biological effects. However, the effects of salinity fluctuation on antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in the marine environment are not well understood. In this study, metagenomic sequencing analysis was used to reveal the response of ARGs and VFGs, hosted by low and high nucleic acid-content bacteria (HNA and LNA bacteria), to salinity, as it decreased from 26‰ to 16‰. The results showed that a total of 27 ARG types and 13 VFG types in HNA and LNA bacteria were found. Salinity changes had significant effects on the ARGs’ and VFGs’ composition and their hosts’ composition. In the network topology relationship, the complexity of the network between the ARGs and their host as well as the VFGs and their host differed with the decrease in salinity. The abundance of most genera of HNA and LNA bacteria was significantly corrected with the abundance of ARGs and VFGs, respectively. Overall, this study demonstrates the effects of salinity on ARGs and VFGs hosted by HNA and LNA bacteria in the marine environment and suggests the importance of salinity in regulating HNA and LNA bacterial communities and functions. Full article

(This article belongs to the Special Issue Advances in Genomics and Ecology of Environmental Microorganisms)

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17 pages, 4465 KiB

Open AccessArticle

Lactobacillus murinus Reduces Susceptibility to Secondary MRSA Infection in IAV-Infected Mice Through Promoting a T Cell-Independent IgA Response

by Qichao Chen, Yanfeng Lin, Kaiying Wang, Jinhui Li, Peng Li and Hongbin Song

Microorganisms 2025, 13(7), 1709; https://doi.org/10.3390/microorganisms13071709 - 21 Jul 2025

Viewed by 325

Abstract

Secondary methicillin-resistant Staphylococcus aureus (MRSA) infection causes high mortality in patients with influenza A virus (IAV). Our previous study observed that the relative abundance of Lactobacillus murinus (L. murinus) was significantly reduced in both the respiratory tract and gut of IAV-infected [...] Read more.

Secondary methicillin-resistant Staphylococcus aureus (MRSA) infection causes high mortality in patients with influenza A virus (IAV). Our previous study observed that the relative abundance of Lactobacillus murinus (L. murinus) was significantly reduced in both the respiratory tract and gut of IAV-infected mice and negatively correlated with the severity of IAV–MRSA coinfection pneumonia, but the role of L. murinus remains unclear. Here, we supplemented the respiratory tract and gut of IAV-infected mice with live L. murinus and performed a secondary MRSA infection challenge to investigate the effects and potential mechanisms further. Data showed that L. murinus supplementation significantly reduced mortality and pathogen loads in IAV–MRSA coinfected mice and upregulated the lung T cell-independent (TI) IgA response in IAV-infected mice. The 16S rRNA gene sequencing results showed that L. murinus supplementation ameliorated microbiota composition disorder and regulated metabolic dysfunction in the gut of IAV-infected mice. The correlation analysis and antibiotic cocktail treatment experiment showed that the TI IgA response in lungs is dependent on gut microbiota. These findings demonstrated that L. murinus supplementation reduces susceptibility to secondary MRSA infection in IAV-infected mice by promoting the TI IgA response, and provide a new perspective on the use of probiotics to prevent secondary bacterial infection following IAV infection. Full article

(This article belongs to the Special Issue Advances in Host-Gut Microbiota)

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19 pages, 1387 KiB

Open AccessReview

Enhancing Agricultural Sustainability by Improving the Efficiency of Lignocellulosic Biomass Utilization in the Ruminant Diet via Solid-State Fermentation with White-Rot Fungi: A Review

by Qi Yan, Osmond Datsomor, Wenhao Zhao, Wenjie Chen, Caixiang Wei, Deshuang Wei, Xin Gao, Chenghuan Qin, Qichao Gu, Caixia Zou and Bo Lin

Microorganisms 2025, 13(7), 1708; https://doi.org/10.3390/microorganisms13071708 - 21 Jul 2025

Viewed by 479

Abstract

Against the backdrop of the green circular economy, the exploration of reliable and sustainable applications of lignocellulosic biomass (LCBM) has emerged as a critical research frontier. The utilization of LCBM as a ruminant roughage source offers a promising strategy to address two pressing [...] Read more.

Against the backdrop of the green circular economy, the exploration of reliable and sustainable applications of lignocellulosic biomass (LCBM) has emerged as a critical research frontier. The utilization of LCBM as a ruminant roughage source offers a promising strategy to address two pressing issues: the “human-animal competition for food” dilemma and the environmental degradation resulting from improper LCBM disposal. However, the high degree of lignification in LCBM significantly restricts its utilization efficiency in ruminant diets. In recent years, microbial pretreatment has gained considerable attention as a viable approach to reduce lignification prior to LCBM application as ruminant feed. White-rot fungi (WRF) have emerged as particularly noteworthy among various microbial agents due to their environmentally benign characteristics and unique lignin degradation selectivity. WRF demonstrates remarkable efficacy in enzymatically breaking down the rigid lignocellulosic matrix (comprising lignin, cellulose, and hemicellulose) within LCBM cell walls, thereby reducing lignin content—a largely indigestible component for ruminants—while simultaneously enhancing the nutritional profile through increased protein availability and improved digestibility. Solid-state fermentation mediated by WRF enhances LCBM utilization rates and optimizes its nutritional value for ruminant consumption, thereby contributing to the advancement of sustainable livestock production, agroforestry systems, and global environmental conservation efforts. This review systematically examines recent technological advancements in WRF-mediated solid-state fermentation of LCBM, evaluates its outcomes of nutritional enhancement and animal utilization efficiency, and critically assesses current limitations and future prospects of this innovative approach within the framework of circular bioeconomy principles. Full article

(This article belongs to the Special Issue Fungal Metabolites: Powering Pharmacological and Agricultural Frontiers)

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11 pages, 1123 KiB

Open AccessArticle

Biodiversity of Yeast Species Isolated During Spontaneous Fermentation: Influence of Grape Origin, Vinification Conditions, and Year of Study

by Ana Benito-Castellanos, Beatriz Larreina, María Teresa Calvo de La Banda, Pilar Santamaría, Lucía González-Arenzana and Ana Rosa Gutiérrez

Microorganisms 2025, 13(7), 1707; https://doi.org/10.3390/microorganisms13071707 - 21 Jul 2025

Viewed by 435

Abstract

Winemaking involves a microbial ecosystem where yeast diversity, shaped by terroir and winemaking conditions, determines wine characteristics. Understanding the microbial diversity of vineyards and spontaneous fermentation is crucial for explaining a winery’s typical wine profile. Studying and inoculating indigenous strains make it possible [...] Read more.

Winemaking involves a microbial ecosystem where yeast diversity, shaped by terroir and winemaking conditions, determines wine characteristics. Understanding the microbial diversity of vineyards and spontaneous fermentation is crucial for explaining a winery’s typical wine profile. Studying and inoculating indigenous strains make it possible to produce high quality wines, reflecting the production environment. This study analyzes the yeast species involved in 16 spontaneous fermentations (8 in 2022 and 8 in 2023) from grapes of four distinct vineyards under two sets of winemaking conditions. A total of 1100 yeast colonies were identified by MALDI-TOF and DNA sequencing techniques. Saccharomyces (S.) cerevisiae and Hanseniaspora uvarum were the most prevalent species, alongside significant populations of non-Saccharomyces yeasts such as Lachancea thermotolerans and Metchnikowia pulcherrima, which were the most abundant ones. Minor yeast species, including Aureobasidium pullulans, Starmerella bacillaris, Kazachstania servazzi, and other Hanseniaspora spp., were also detected. The results demonstrated that yeast diversity in spontaneous fermentations varied according to vineyard origin and winemaking conditions. Differences between the two vintages studied indicated that annual climatic conditions significantly influenced yeast diversity, especially among non-Saccharomyces species. This substantial diversity represents a valuable source of indigenous yeasts for preserving the typicity of a winery’s wines under controlled conditions. Full article

(This article belongs to the Special Issue Wine Fermentation Microorganisms)

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19 pages, 5087 KiB

Open AccessReview

Biosensors in Microbial Ecology: Revolutionizing Food Safety and Quality

by Gajanan A. Bodkhe, Vishal Kumar, Xingjie Li, Shichun Pei, Long Ma and Myunghee Kim

Microorganisms 2025, 13(7), 1706; https://doi.org/10.3390/microorganisms13071706 - 21 Jul 2025

Viewed by 655

Abstract

Microorganisms play a crucial role in food processes, safety, and quality through their dynamic interactions with other organisms. In recent years, biosensors have become essential tools for monitoring these processes in the dairy, meat, and fresh produce industries. This review highlights how microbial [...] Read more.

Microorganisms play a crucial role in food processes, safety, and quality through their dynamic interactions with other organisms. In recent years, biosensors have become essential tools for monitoring these processes in the dairy, meat, and fresh produce industries. This review highlights how microbial diversity, starter cultures, and interactions, such as competition and quorum sensing, shape food ecosystems. Diverse biosensor platforms, including electrochemical, optical, piezoelectric, thermal, field-effect transistor-based, and lateral flow assays, offer distinct advantages tailored to specific food matrices and microbial targets, enabling rapid and sensitive detection. Biosensors have been developed for detecting pathogens in real-time monitoring of fermentation and tracking spoilage. Control strategies, including bacteriocins, probiotics, and biofilm management, support food safety, while decontamination methods provide an additional layer of protection. The integration of new techniques, such as nanotechnology, CRISPR, and artificial intelligence, into Internet of Things systems is enhancing precision, particularly in addressing regional food safety challenges. However, their adoption is still hindered by complex food matrices, high costs, and the growing challenge of antimicrobial resistance. Looking ahead, intelligent systems and wearable sensors may help overcome these barriers. Although gaps in standardization and accessibility remain, biosensors are well-positioned to revolutionize food microbiology, linking ecological insights to practical solutions and paving the way for safer, high-quality food worldwide. Full article

(This article belongs to the Special Issue Feature Papers in Food Microbiology)

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13 pages, 1849 KiB

Open AccessArticle

HMOs Induce Butyrate Production of Faecalibacterium prausnitzii via Cross-Feeding by Bifidobacterium bifidum with Different Mechanisms for HMO Types

by Haruka Onodera, Yohei Sato, Yosuke Komatsu, Makoto Yamashita, Yuta Watanabe and Takeshi Kokubo

Microorganisms 2025, 13(7), 1705; https://doi.org/10.3390/microorganisms13071705 - 21 Jul 2025

Viewed by 576

Abstract

Human milk oligosaccharides (HMOs) have garnered significant attention as one of the bioactive components in human milk, with growing applications in infant formula and food products. HMOs enhance butyrate production, which is produced by butyrate-producing bacteria such as Faecalibacterium prausnitzii and contributes to [...] Read more.

Human milk oligosaccharides (HMOs) have garnered significant attention as one of the bioactive components in human milk, with growing applications in infant formula and food products. HMOs enhance butyrate production, which is produced by butyrate-producing bacteria such as Faecalibacterium prausnitzii and contributes to gut health through its diverse biological functions. However, the specific mechanisms by which individual HMOs promote butyrate production remain unclear. In this study, we conducted in vitro co-culture experiments of F. prausnitzii and Bifidobacterium bifidum, examining their relative abundance, fatty acid production, residual sugar levels, and gene expression. Our results revealed that B. bifidum utilizes HMOs and provides the constituent sugars to F. prausnitzii, thereby promoting butyrate production by F. prausnitzii. Furthermore, we found that the underlying mechanisms vary depending on the structure of the HMOs. Specifically, 2′-fucosyllactose and 3′-sialyllactose enhance the butyrate production efficiency of F. prausnitzii, while 6′-sialyllactose primarily promotes the growth of F. prausnitzii. These findings not only deepen our understanding of how HMOs influence infant gut health but also suggest new directions for developing nutritional products that leverage the distinct functional properties of each HMO. Full article

(This article belongs to the Special Issue Gut Microbiota, Diet, and Gastrointestinal Cancer)

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18 pages, 2565 KiB

Open AccessArticle

Effects of Intracellular Polysaccharides and Proteins of Auxenochlorella pyrenoidosa on Water Quality, Floc Formation, and Microbial Composition in a Biofloc System

by Mengsha Lou, Yuhan Zhang, Manman Zhang, Hangxian Zhou, Yixiang Zhang, Qiang Sheng, Jianhua Zhao, Qiyou Xu and Rongfei Zhang

Microorganisms 2025, 13(7), 1704; https://doi.org/10.3390/microorganisms13071704 - 21 Jul 2025

Viewed by 361

Abstract

The use of Auxenochlorella pyrenoidosa (formerly Chlorella pyrenoidosa) and its intracellular substances (ISs) to promote biofloc development has been extensively studied. To identify the key components of the ISs of A. pyrenoidosa that drive biofloc formation, algal-extracted polysaccharides (AEPSs) and algal-extracted proteins [...] Read more.

The use of Auxenochlorella pyrenoidosa (formerly Chlorella pyrenoidosa) and its intracellular substances (ISs) to promote biofloc development has been extensively studied. To identify the key components of the ISs of A. pyrenoidosa that drive biofloc formation, algal-extracted polysaccharides (AEPSs) and algal-extracted proteins (AEPTs) were isolated from the ISs. In this study, we established four groups: ISs, AEPSs, AEPTs, and tap water (TW, control), to investigate the effects of AEPSs and AEPTs on biofloc formation dynamics, water quality parameters, and microbial community composition. The results indicated no significant differences were observed between the ISs and AEPSs groups during the cultivation period. AEPSs significantly enhanced flocculation efficiency, achieving a final floc volume of 60 mL/L. This enhancement was attributed to the selective promotion of floc-forming microbial taxa, such as Comamonas, which can secrete procoagulants like EPS, and Pseudomonas and Enterobacter, which have denitrification capabilities. Water quality monitoring revealed that both AEPSs and AEPTs achieved nitrogen removal efficiencies exceeding 50% in the biofloc system, with AEPSs outperforming AEPTs. This is closely related to the fact that the microorganisms with increased flocculation contain numerous nitrifying and denitrifying bacteria. So, the intracellular polysaccharides were the key component of the ISs of A. pyrenoidosa that drive biofloc formation. These findings provide critical insights into the functional roles of algal-derived macromolecules in biofloc dynamics and their potential applications in wastewater treatment. Full article

(This article belongs to the Special Issue Microbes, Society and Sustainable Solutions)

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12 pages, 1076 KiB

Open AccessArticle

Impact of Sugarcane–Pumpkin Intercropping on Soil Microbial Diversity

by Xianglei Chen, Zhikui Cheng, Liwen Su, Xialei Huang, Yan Deng, Wenhui Bai, Zhihao Chen, Baoshan Chen, Peng Wang, Hongguang Pang and Zhengguo Liu

Microorganisms 2025, 13(7), 1703; https://doi.org/10.3390/microorganisms13071703 - 20 Jul 2025

Viewed by 571

Abstract

Intercropping has been widely proven to boost agricultural yields and control diseases. This study examined the impact of sugarcane monoculture (SM) and sugarcane–pumpkin intercropping (IP) systems on soil physicochemical characteristics and microbial community dynamics. Compared to monoculture, intercropping significantly increased soil pH by [...] Read more.

Intercropping has been widely proven to boost agricultural yields and control diseases. This study examined the impact of sugarcane monoculture (SM) and sugarcane–pumpkin intercropping (IP) systems on soil physicochemical characteristics and microbial community dynamics. Compared to monoculture, intercropping significantly increased soil pH by 8.82% and total potassium (TK) by 17.92%, while reducing soil organic matter (SOM) by 25.56%. Bacterial communities under intercropping exhibited significantly higher alpha and beta diversity, whereas fungal community diversity remained unaffected. Notably, the relative abundances of certain taxa with known roles in plant growth promotion and pathogen suppression—such as Anaeromyxobacter, Nitrospira, and Massilia—were enriched. Canonical correlation analysis revealed that bacterial community composition was strongly associated with TK, while fungal community structure correlated with variations in soil available nitrogen (AN). These findings indicate that sugarcane–pumpkin intercropping reshapes soil microbial communities and contributes to some improvement in soil nutrient availability. Full article

(This article belongs to the Section Environmental Microbiology)

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13 pages, 1593 KiB

Open AccessReview

Airborne Algae and Cyanobacteria Originating from Lakes: Formation Mechanisms, Influencing Factors, and Potential Health Risks

by Xiaoming Liu, Tingfu Li, Yuqi Qiu, Changliang Nie, Xiaoling Nie and Xueyun Geng

Microorganisms 2025, 13(7), 1702; https://doi.org/10.3390/microorganisms13071702 - 20 Jul 2025

Viewed by 494

Abstract

Algal and cyanobacterial blooms are anticipated to increase in frequency, duration, and geographic extent as a result of environmental changes, including climate warming, elevated nutrient concentrations, and increased runoff in both marine and freshwater ecosystems. The eutrophication of aquatic environments represents a substantial [...] Read more.

Algal and cyanobacterial blooms are anticipated to increase in frequency, duration, and geographic extent as a result of environmental changes, including climate warming, elevated nutrient concentrations, and increased runoff in both marine and freshwater ecosystems. The eutrophication of aquatic environments represents a substantial threat to human health. As eutrophication progresses, airborne algae and cyanobacteria, particularly harmful genera originating from aquatic environments, are released into the atmosphere and may pose potential risks to human health. Furthermore, respiratory distress has been documented in individuals exposed to aerosols containing harmful algal bloom (HAB) toxins. This review investigates the generation of aerosolised harmful algal blooms, their responses to environmental factors, and their associated health risks. Evidence suggests that airborne algae, cyanobacteria, and their toxins are widespread. When these are aerosolised into micrometre-sized particles, they become susceptible to atmospheric processing, which may degrade the HAB toxins and produce byproducts with differing potencies compared to the parent compounds. Inhalation of aerosolised HAB toxins, especially when combined with co-morbid factors such as exposure to air pollutants, could present a significant health risk to a considerable proportion of the global population. A more comprehensive understanding of the chemical transformations of these toxins and the composition of harmful algal and cyanobacterial communities can improve public safety. Full article

(This article belongs to the Special Issue Research on Airborne Microbial Communities)

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17 pages, 2234 KiB

Open AccessArticle

Impact of Live Ligilactobacillus salivarius CCFM1332 and Its Postbiotics on Porphyromonas gingivalis Colonization, Alveolar Bone Resorption and Inflammation in a Rat Model of Periodontitis

by Qing Hong, Yu Ren, Xin Tang, Bingyong Mao, Qiuxiang Zhang, Jianxin Zhao, Shumao Cui and Zhenmin Liu

Microorganisms 2025, 13(7), 1701; https://doi.org/10.3390/microorganisms13071701 - 20 Jul 2025

Viewed by 497

Abstract

Periodontitis is a chronic inflammatory disease caused by periodontopathic bacteria such as Porphyromonas gingivalis (P. gingivalis), which leads to alveolar bone destruction and systemic inflammation. Emerging evidence suggests that probiotics may mitigate periodontal pathology. To systematically evaluate the alleviative effects and [...] Read more.

Periodontitis is a chronic inflammatory disease caused by periodontopathic bacteria such as Porphyromonas gingivalis (P. gingivalis), which leads to alveolar bone destruction and systemic inflammation. Emerging evidence suggests that probiotics may mitigate periodontal pathology. To systematically evaluate the alleviative effects and mechanisms of different forms of probiotics, including live bacteria and postbiotics, on periodontitis, we first screened and identified Ligilactobacillus salivarius CCFM1332 (L. salivarius CCFM1332) through in vitro antibacterial and anti-biofilm activity assays. Subsequently, we investigated its therapeutic potential in a rat model of experimental periodontitis. The results demonstrated that both live L. salivarius CCFM1332 (PL) and its postbiotics (PP) significantly reduced the gingival index (GI) and probing depth (PD) in rats, while suppressing oral colonization of P. gingivalis. Serum pro-inflammatory cytokine levels were differentially modulated: the PL group exhibited reductions in interleukin-17A (IL-17A), interleukin-6 (IL-6), and interleukin-1β (IL-1β) by 39.31% (p < 0.01), 17.26% (p < 0.05), and 14.74% (p < 0.05), respectively, whereas the PP group showed decreases of 34.79% (p < 0.05), 29.85% (p < 0.01), and 19.74% (p < 0.05). Micro-computed tomography (Micro-CT) analysis demonstrated that compared to the periodontitis model group (PM), the PL group significantly reduced alveolar bone loss (ABL) by 30.1% (p < 0.05) and increased bone volume fraction (BV/TV) by 49.5% (p < 0.01). In contrast, while the PP group similarly decreased ABL by 32.7% (p < 0.05), it resulted in a 40.4% improvement in BV/TV (p > 0.05). Histological assessments via hematoxylin and eosin (H&E) and tartrate-resistant acid phosphatase (TRAP) staining confirmed that both the PL group and the PP group alleviated structural damage to alveolar bone-supporting tissues and reduced osteoclast-positive cell counts. This study suggests that live L. salivarius CCFM1332 and its postbiotics reduce alveolar bone resorption and attachment loss in rats through antibacterial and anti-inflammatory pathways, thereby alleviating periodontal inflammation in rats. Full article

(This article belongs to the Section Medical Microbiology)

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24 pages, 3946 KiB

Open AccessArticle

Frog Density and Growth Stage of Rice Impact Paddy Field and Gut Microbial Communities in Rice–Frog Co-Cropping Models

by Zhangyan Zhu, Ran Li, Yunshuang Ma, Anran Yu and Rongquan Zheng

Microorganisms 2025, 13(7), 1700; https://doi.org/10.3390/microorganisms13071700 - 20 Jul 2025

Viewed by 598

Abstract

The black-spotted frog (Pelophylax nigromaculatus) is a common economic species in the rice–frog ecological cropping mode. The present study investigated microbial community structures in paddy water and black-spotted frog’s guts across rice monoculture and low-/high-density rice–frog co-cropping systems at four rice [...] Read more.

The black-spotted frog (Pelophylax nigromaculatus) is a common economic species in the rice–frog ecological cropping mode. The present study investigated microbial community structures in paddy water and black-spotted frog’s guts across rice monoculture and low-/high-density rice–frog co-cropping systems at four rice growth stages. Proteobacteria dominate in paddy water, while frog guts are enriched in Firmicutes and Actinobacteriota. The frog density shows no impact on the α-diversity, but rice growth stages significantly alter the Shannon, Simpson, and Pielou_e indices (p < 0.01). Co-cropping may promote amino acid synthesis, elemental cycling, and stress tolerance in paddy water microbiota, which are more diverse than gut microbiota. Strong correlations exist between paddy water and gut microbiotas, with Limnohabitans being linked to gut diversity (p < 0.05). Low-density co-cropping enhances Xenorhabdus, which is beneficial for pest control and stabilizes gut microbiota. The results of this study offer insights for managing rice–frog systems based on rice growth stages. Full article

(This article belongs to the Section Gut Microbiota)

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18 pages, 2887 KiB

Open AccessArticle

Effects of Natural Ingredient Xanthohumol on the Intestinal Microbiota, Metabolic Profiles and Disease Resistance to Streptococcus agalactiae in Tilapia Oreochromis niloticus

by Aiguo Huang, Yanqin Wei, Jialong Huang, Songlin Luo, Tingyu Wei, Jing Guo, Fali Zhang and Yinghui Wang

Microorganisms 2025, 13(7), 1699; https://doi.org/10.3390/microorganisms13071699 - 20 Jul 2025

Viewed by 432

Abstract

Streptococcus agalactiae (SA) is a severe prevalent pathogen, resulting in high morbidity and mortality in the global tilapia industry. With increasing bacterial resistance to antibiotics, alternative strategies are urgently needed. This study aims to investigate the antibacterial activity and the underlying mechanisms of [...] Read more.

Streptococcus agalactiae (SA) is a severe prevalent pathogen, resulting in high morbidity and mortality in the global tilapia industry. With increasing bacterial resistance to antibiotics, alternative strategies are urgently needed. This study aims to investigate the antibacterial activity and the underlying mechanisms of the natural product xanthohumol (XN) against SA infection in tilapia (Oreochromis niloticus). The results showed that XN could significantly reduce the bacterial loads of SA in different tissues (liver, spleen and brain) after treatment with different tested concentrations of XN (12.5, 25.0 and 50.0 mg/kg). Moreover, XN could improve the survival rate of SA-infected tilapia. 16S rRNA gene sequencing demonstrated that the alpha-diversity index (Chao1 and Shannon_e) was significantly increased in the XN-treated group (MX group) compared to the SA-infected group (CG group) (p < 0.05), and the Simpson diversity index significantly decreased. The Bray–Curtis similarity analysis of non-metric multidimensional scaling (NMDS) and principal coordinate analysis (PCA) showed that there were significant differences in microbial composition among groups. At the phylum level, the relative abundance of the phyla Actinobacteria, Proteobacteria and Bacteroidetes decreased in the MX group compared to the CG group, while the relative abundance of the phyla Fusobacteria, Firmicutes and Verrucomicrobia increased. Differences were also observed at the genus level; the relative abundance of Mycobacterium decreased in the MX group, but the abundance of Cetobacterium and Clostridium_sensu_stricto_1 increased. Metabolomics analysis revealed that XN changed the metabolic profile of the liver and significantly enriched aspartate metabolism, glycine and serine metabolism, phosphatidylcholine biosynthesis, arginine and proline metabolism, glutamate metabolism, urea cycle, purine metabolism, methionine metabolism, betaine metabolism, and carnitine synthesis. Correlation analysis indicated an association between the intestinal microbiota and metabolites. In conclusion, XN may be a potential drug for the prevention and treatment of SA infection in tilapia, and its mechanism of action may be related to the regulation of the intestinal microbiota and liver metabolism. Full article

(This article belongs to the Special Issue Advanced Research on Antimicrobial Activity of Natural Products)

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19 pages, 2271 KiB

Open AccessArticle

Possible Use in Soil Bioremediation of the Bacterial Strain Bacillus Sphaericus NM-1 Capable of Simultaneously Degrading Promethrin and Acetochlor

by Yue Cheng, Qian Fu, Junjia Xu, Xinhua Niu, Lin Liu, Jiaqi Wang, Jingwen Quan, Qingyue Yu, Baoyan Chi, Haitao Li and Rongmei Liu

Microorganisms 2025, 13(7), 1698; https://doi.org/10.3390/microorganisms13071698 - 19 Jul 2025

Viewed by 345

Abstract

Prometryn and acetochlor are herbicides used to control weeds in farmlands and other areas. They enter the soil through direct application, residual accumulation in crops, and atmospheric deposition. The pollution of their residues in the environment has attracted people’s attention. Bioremediation is one [...] Read more.

Prometryn and acetochlor are herbicides used to control weeds in farmlands and other areas. They enter the soil through direct application, residual accumulation in crops, and atmospheric deposition. The pollution of their residues in the environment has attracted people’s attention. Bioremediation is one of the main methods to solve such problems. In this study, the effects of prometryn and acetochlor-degrading strain NM-1 on soil enzymes, soil microbial communities, and physiological indexes of soybean seedlings during soil remediation were studied, and the relationship between them was discussed. The results showed that 81.54% of prometryn (50 mg·L⁻¹) and 89.47% of acetochlor (50 mg·L⁻¹) were degraded within 15 days after NM-1 inoculation in soil. NM-1 positively affected soil enzyme activities and soil microbial communities, and the abundance of beneficial bacteria in soil increased. More importantly, the inoculation of strain NM-1 under prometryn and acetochlor stress significantly increased plant height, root length, root volume, water content, chlorophyll concentration, and root activity of soybean. The results of these studies showed that the NM-1 strain showed significant potential in bioremediation in order to provide technical support for solving the problem of prometryn and acetochlor pollution. Full article

(This article belongs to the Section Environmental Microbiology)

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26 pages, 477 KiB

Open AccessReview

Global Epidemiology and Antimicrobial Resistance of Klebsiella Pneumoniae Carbapenemase (KPC)-Producing Gram-Negative Clinical Isolates: A Review

by Matthew E. Falagas, Christina-Maria Asimotou, Maria Zidrou, Dimitrios S. Kontogiannis and Charalampos Filippou

Microorganisms 2025, 13(7), 1697; https://doi.org/10.3390/microorganisms13071697 - 19 Jul 2025

Viewed by 807

Abstract

Klebsiella pneumoniae carbapenemases (KPCs) are a group of class A β-lactamases of Gram-negative bacteria leading to difficult-to-treat infections. We evaluated the global epidemiology of KPC-producing Gram-negative clinical isolates. A systematic search of six databases (Cochrane Library, Embase, Google Scholar, PubMed, Scopus, and Web [...] Read more.

Klebsiella pneumoniae carbapenemases (KPCs) are a group of class A β-lactamases of Gram-negative bacteria leading to difficult-to-treat infections. We evaluated the global epidemiology of KPC-producing Gram-negative clinical isolates. A systematic search of six databases (Cochrane Library, Embase, Google Scholar, PubMed, Scopus, and Web of Science) was conducted. Extracted data were tabulated and evaluated. After screening 1993 articles, 119 were included in the study. The included studies originated from Asia (n = 49), Europe (n = 29), North America (n = 14), South America (n = 11), and Africa (n = 3); 13 studies were multicontinental. The most commonly reported KPC-producing species were Klebsiella pneumoniae (96 studies) and Escherichia coli (52 studies), followed by Enterobacter cloacae (31), Citrobacter spp. (24), Klebsiella oxytoca (23), Serratia spp. (15), Enterobacter spp. (15), Acinetobacter baumannii complex (13), Providencia spp. (11), Morganella spp. (11), Klebsiella aerogenes (9), Pseudomonas aeruginosa (8), Raoultella spp. (8), Proteus spp. (8), and Enterobacter aerogenes (6). Among the studies with specific bla_KPC gene detection, 52/57 (91%) reported the isolation of bla_KPC-2 and 26/57 (46%) reported bla_KPC-3. The antimicrobial resistance of the studied KPC-producing isolates was the lowest for ceftazidime–avibactam (0–4%). Resistance to polymyxins, tigecycline, and trimethoprim–sulfamethoxazole in the evaluated studies was 4–80%, 0–73%, and 5.6–100%, respectively. Conclusions: The findings presented in this work indicate that KPC-producing Gram-negative bacteria have spread globally across all continents. Implementing proper infection control measures, antimicrobial stewardship programs, and enhanced surveillance is crucial. Full article

(This article belongs to the Special Issue ß-Lactamases, 3rd Edition)

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15 pages, 2714 KiB

Open AccessArticle

Bibliometric and Visualized Analysis of Gut Microbiota and Hypertension Interaction Research Published from 2001 to 2024

by Jianhui Mo, Wanghong Su, Jiale Qin, Jiayu Feng, Rong Yu, Shaoru Li, Jia Lv, Rui Dong, Yue Cheng and Bei Han

Microorganisms 2025, 13(7), 1696; https://doi.org/10.3390/microorganisms13071696 - 18 Jul 2025

Viewed by 669

Abstract

A comprehensive bibliometric analysis of literature is imperative to elucidate current research landscapes and hotspots in the interplay between gut microbiota and hypertension, identify knowledge gaps, and establish theoretical foundations for the future. We used publications retrieved from the Web of Science Core [...] Read more.

A comprehensive bibliometric analysis of literature is imperative to elucidate current research landscapes and hotspots in the interplay between gut microbiota and hypertension, identify knowledge gaps, and establish theoretical foundations for the future. We used publications retrieved from the Web of Science Core Collection (WoSCC) and SCOPUS databases (January 2001–December 2024) to analyze the annual publication trends with GraphPad Prism 9.5.1, to evaluate co-authorship, keywords clusters, and co-citation patterns with VOSviewer 1.6.20, and conducted keyword burst detection and keyword co-occurrence utilizing CiteSpace v6.4.1. We have retrieved 2485 relevant publications published over the past 24 years. A 481-fold increase in global annual publications in this field was observed. China was identified as the most productive country, while the United States demonstrated the highest research impact. For the contributor, Yang Tao (University of Toledo, USA) and the University of Florida (USA) have emerged as the most influential contributors. Among journals, the highest number of articles was published in Nutrients (n = 135), which also achieved the highest citation count (n = 5397). The emergence of novel research hotspots was indicated by high-frequency keywords, mainly “hypertensive disorders of pregnancy”, “mendelian randomization”, “gut-heart axis”, and “hepatitis B virus”. “Trimethylamine N-oxide (TMAO)” and “receptor” may represent promising new research frontiers in the gut microbiota–hypertension nexus. The current research trends are shifting from exploring the factors influencing gut microbiota and hypertension to understanding the underlying mechanisms of these factors and the potential therapeutic applications of microbial modulation for hypertension management. Full article

(This article belongs to the Special Issue Effects of Diet and Nutrition on Gut Microbiota)

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12 pages, 2399 KiB

Open AccessCase Report

Chronic Leptospirosis in a Breeding Bull: A Case Report

by Gabrita De Zan, Antonio Carminato, Monia Cocchi, Giacomo Catarin, Irene Pascuci, Laura Lucchese, Laura Bellinati, Letizia Ceglie, Elisa Mazzotta, Mario D’Incau, Martina Ustulin, Laura Grassi and Alda Natale

Microorganisms 2025, 13(7), 1695; https://doi.org/10.3390/microorganisms13071695 - 18 Jul 2025

Viewed by 413

Abstract

Leptospirosis is a (re-)emerging and global zoonotic disease. Given the complex host-pathogen interaction and the numerous environmental risk factors related to the transmission, a One Health approach to both disease prevention and control is needed. Occurring at the human–cattle–environment interfaces, bovine leptospirosis represents [...] Read more.

Leptospirosis is a (re-)emerging and global zoonotic disease. Given the complex host-pathogen interaction and the numerous environmental risk factors related to the transmission, a One Health approach to both disease prevention and control is needed. Occurring at the human–cattle–environment interfaces, bovine leptospirosis represents a zoonotic risk for the professionals in the field, besides being a potential cause of significant economic losses due to the bovine reproductive disorders. Although climatic change is a potential factor in exacerbating the risk of leptospirosis in Europe, this disease remains largely neglected, with several knowledge gaps in research, investigations, and diagnosis of bovine genital leptospirosis syndrome across the continent. The present report describes the results of the diagnostic investigations on a case of chronic bovine leptospirosis in a breeding bull. Following the seroconversion to Leptospira Sejroe var Hardjo after the arrival of the animal in a quarantine facility, a monitoring plan including both serological/molecular analyses and a therapeutic protocol was undertaken. The bull exhibited a persistent seroconversion and a repeated positivity for Leptospira to real-time PCR in urine samples, indicative of a chronic shedder pattern. This report emphasizes the diagnostic and management challenges in the context of such a complex but frequently overlooked disease. Full article

(This article belongs to the Special Issue Advances in the Research on Leptospira and Leptospirosis)

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30 pages, 8115 KiB

Open AccessArticle

Effects of Italian Mediterranean Organic Diet on the Gut Microbiota: A Pilot Comparative Study with Conventional Products and Free Diet

by Laura Di Renzo, Giulia Frank, Barbara Pala, Rossella Cianci, Giada La Placa, Glauco Raffaelli, Roselisa Palma, Daniele Peluso, Antonino De Lorenzo, Paola Gualtieri and on behalf of Clinical Nutrition and Nutrigenomics Project Group

Microorganisms 2025, 13(7), 1694; https://doi.org/10.3390/microorganisms13071694 - 18 Jul 2025

Viewed by 559

Abstract

The human exposome, including dietary exposures such as pesticides, additives, and environmental contaminants, plays a critical role in shaping the gut microbiota (GM) and long-term health outcomes. While the Mediterranean Diet is known for its health-promoting effects, the role of food quality, specifically [...] Read more.

The human exposome, including dietary exposures such as pesticides, additives, and environmental contaminants, plays a critical role in shaping the gut microbiota (GM) and long-term health outcomes. While the Mediterranean Diet is known for its health-promoting effects, the role of food quality, specifically organic vs. conventional products, in modulating GM within this dietary pattern remains underexplored. The aim of this study was to evaluate (1) whether an Italian Mediterranean Organic Diet (IMOD) confers additional benefits compared to an Italian Mediterranean non-Organic Diet (IMnOD), and (2) the impact of IMOD and IMnOD versus a free diet (No Diet) on GM and anthropometric parameters. A randomized, controlled trial was conducted on 39 healthy subjects. Eligible subjects were divided into the following groups: (1) 4 weeks No Diet, (2) 4 weeks IMOD, and (3) 4 weeks IMnOD. Microbiota profiling (16S rRNA sequencing), body composition (BIA), and dietary adherence (MEDAS, FFQ) were evaluated. Distinct microbial shifts following both IMOD and IMnOD compared to No Diet were revealed. Several taxa previously associated with short-chain fatty acid (SCFA) biosynthesis (i.e., Anaerobutyricum hallii, Anaerostipes hadrus, and Dorea longicatena) were increased after both Mediterranean Diet interventions, while Parabacteroides distasonis showed a specific increase in the IMOD group. No significant changes in body weight or composition were observed. These findings suggest that adherence to a Mediterranean Diet, regardless of food source, reshapes the gut microbiota, while organic food intake may influence specific microbial trajectories. Our results support the relevance of food quality in dietary interventions. Full article

(This article belongs to the Special Issue Discovering the Human Holobiont: How the Microbiome Affects Human Health)

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12 pages, 2374 KiB

Open AccessArticle

The Complete Genomes of Microcystis ichthyoblabe Kützing and Microcystis protocystis (Crow) Komárek & Anagnostidis Reveal the Complexity and Plasticity of Microcystis Genomes

by Jina Kim, Hyaekang Kim, Jaeduk Goh, Seung Won Nam, Eu Jin Chung, Miyoung Shin, Donghyeok Seol, Ki Hwan Kim and Woori Kwak

Microorganisms 2025, 13(7), 1693; https://doi.org/10.3390/microorganisms13071693 - 18 Jul 2025

Viewed by 553

Abstract

Microcystis is a genus of cyanobacteria responsible for harmful algal blooms (HABs) in freshwater ecosystems, posing significant ecological and public health risks. Despite its importance, current genomic resources are heavily biased toward Microcystis aeruginosa, limiting comprehensive understanding of genomic diversity within the [...] Read more.

Microcystis is a genus of cyanobacteria responsible for harmful algal blooms (HABs) in freshwater ecosystems, posing significant ecological and public health risks. Despite its importance, current genomic resources are heavily biased toward Microcystis aeruginosa, limiting comprehensive understanding of genomic diversity within the genus. In this study, we present the first complete genome sequences of two morphospecies, M. ichthyoblabe FBCC-A1114 and M. protocystis FBCC-A270. Using long-read sequencing, both genomes were assembled into single circular chromosomes of 5.84 Mb and 5.76 Mb, respectively. Phylogenetic analyses placed both strains within genospecies G, alongside M. aeruginosa and M. viridis. Comparative analysis of biosynthetic gene clusters revealed that, while most genospecies G members harbor aeruginosin, cyanobactin, and microviridin gene clusters, the two newly sequenced strains lack cyanobactin and microcystin clusters but retain the microginin cluster. Synteny analysis demonstrated high structural conservation between the two genomes, while notable structural variations were observed when compared with M. aeruginosa NIES-298. These findings reveal both functional and structural plasticity within the genospecies, suggesting ecotype diversification driven by environmental adaptation. The newly assembled genomes provide critical resources to refine classification frameworks and advance our understanding of Microcystis genomic diversity. Full article

(This article belongs to the Section Environmental Microbiology)

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15 pages, 4791 KiB

Open AccessArticle

Diversity and Metabolic Potential of Gut Bacteria in Dorcus hopei (Coleoptera: Lucanidae): Influence of Fungus and Rotten Wood Diets

by Pan Wang, Xiaoyan Bin, Xingjia Xiang and Xia Wan

Microorganisms 2025, 13(7), 1692; https://doi.org/10.3390/microorganisms13071692 - 18 Jul 2025

Viewed by 403

Abstract

Stag beetles are saproxylic insects, essential for decomposing rotten wood and maintaining the carbon cycle. Their gut bacteria contribute significantly to nutrient digestion and energy acquisition, making them crucial for understanding host-microbe interactions. Despite the fungivorous behavior of stag beetle larvae, research on [...] Read more.

Stag beetles are saproxylic insects, essential for decomposing rotten wood and maintaining the carbon cycle. Their gut bacteria contribute significantly to nutrient digestion and energy acquisition, making them crucial for understanding host-microbe interactions. Despite the fungivorous behavior of stag beetle larvae, research on how diet influences gut bacterial diversity remains scarce. Therefore, this study was conducted to compare the diversity and metabolic functions of gut bacteria in Dorcus hopei larvae fed on fungus (Pleurotus geesteranus) and rotten wood diets using high-throughput sequencing technology. Significant differences (p < 0.05) were observed in gut bacterial community composition between two diets, highlighting diet as a key factor shaping bacterial diversity. Additionally, gut bacterial communities varied across larval developmental stages (p < 0.05), indicating the influence of host age. Dominant bacterial phyla included Firmicutes, Bacteroidetes, and Proteobacteria. Bacteroidetes were more abundant in rotten-wood-fed larvae (7.61%) than fungus-fed larvae (0.15%), while Proteobacteria were more abundant in fungus-fed larvae. Functional analysis revealed that rotten-wood-fed larvae were primarily related to carbohydrate and amino acid metabolism, whereas fungus-fed larvae exhibited enhanced membrane transport function. This study enhances the understanding of gut bacterial diversity and functions in stag beetles, providing a theoretical foundation for their conservation and sustainable utilization. Full article

(This article belongs to the Section Gut Microbiota)

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19 pages, 746 KiB

Open AccessReview

Endophytic Bioactive Compounds for Wound Healing: A Review of Biological Activities and Therapeutic Potential

by Octavio Calvo-Gomez, Farkhod Eshboev, Kamilla Mullaiarova and Dilfuza Egamberdieva

Microorganisms 2025, 13(7), 1691; https://doi.org/10.3390/microorganisms13071691 - 18 Jul 2025

Viewed by 987

Abstract

Endophytic microorganisms inhabiting plant tissues constitute a unique and largely untapped reservoir of bioactive metabolites, including phenolics, terpenoids, alkaloids, polysaccharides, and anthraquinones, among others. This review focuses on the potential of these compounds to modulate the complex processes of wound repair, such as [...] Read more.

Endophytic microorganisms inhabiting plant tissues constitute a unique and largely untapped reservoir of bioactive metabolites, including phenolics, terpenoids, alkaloids, polysaccharides, and anthraquinones, among others. This review focuses on the potential of these compounds to modulate the complex processes of wound repair, such as hemostasis, inflammation, proliferation, and remodeling. Uniquely, this review delineates the specific mechanisms supported not only by indirect evidence but by primary research directly linking endophytic metabolites to wound repair. We synthesized and evaluated evidence from 18 studies, of which over 75% directly assessed wound healing effects through in vitro and in vivo models. Metabolites from endophytic microorganisms promoted wound contraction, suppressed biofilm formation by key pathogens (e.g., MRSA, P. aeruginosa), and accelerated tissue re-epithelialization in animal models. Other compounds demonstrated >99% wound closure in rats, while several extracts showed anti-inflammatory and cytocompatible profiles. Nevertheless, the majority of studies applied unstandardized methods and used crude extracts, hindering precise structure–activity assessment. The originality of this review lies in drawing attention to direct evidence for wound healing from diverse endophytic sources and systematically identifying gaps between preclinical promise and clinical translation, positioning endophytes as a sustainable platform for next-generation wound therapeutics. Full article

(This article belongs to the Section Medical Microbiology)

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12 pages, 225 KiB

Open AccessArticle

Microbiological Sampling in Total Knee Arthroplasty After Post-Traumatic Osteoarthritis: Rate of Periprosthetic Joint Infection and the Debate Around Sampling Unremarkable Tissue

by Felix Erne, Leonard Grünwald, Tina Histing and Philipp Hemmann

Microorganisms 2025, 13(7), 1690; https://doi.org/10.3390/microorganisms13071690 - 18 Jul 2025

Viewed by 313

Abstract

Background: Proximal tibial fractures can lead to post-traumatic osteoarthritis (PTOA), and subsequent total knee arthroplasty (TKA) in such patients is associated with elevated complication rates. A two-stage approach, involving the elective removal of osteosynthetic hardware prior to TKA, is recommended. The utility of [...] Read more.

Background: Proximal tibial fractures can lead to post-traumatic osteoarthritis (PTOA), and subsequent total knee arthroplasty (TKA) in such patients is associated with elevated complication rates. A two-stage approach, involving the elective removal of osteosynthetic hardware prior to TKA, is recommended. The utility of microbiological sampling from macroscopically unremarkable tissue during TKA implantation remains controversial. Objective: To retrospectively evaluate the rate of periprosthetic joint infection (PJI) following TKA after PTOA and to assess the potential benefit of intraoperative microbiological sampling. The secondary objective was to evaluate the presence of prior colonization in osteosynthetic hardware among the affected cases. Patients and Methods: A retrospective screening of the hospital database was conducted between 2008 and 2022, including only AO/OTA type 41-B and 41-C fractures. Patients were assigned to a sampling group (with microbiological sampling during TKA) or a control group (without sampling). All patients received structured follow-up to assess postoperative complications. Results: A total of 40 patients met the screening criteria. In the sampling group (n = 29), 17.24% required surgical revision, and the rate of PJI was 3.45%. In the control group (n = 11), 18.14% underwent revision surgery, with a PJI rate of 9.09%. The average follow-up period was 4.35 years (range 2–11.6 years). Discussion: TKA in patients with PTOA is associated with a heightened risk of complications. A noteworthy possible correlation between systematic microbiological sampling and reduced PJI incidence was observed. While the small sample size limits definitive conclusions regarding causality, the findings support the potential value of consistent intraoperative sampling. Full article

(This article belongs to the Collection Device-Related Infections and Bacterial Biofilms)

15 pages, 4647 KiB

Open AccessArticle

Adaptability and Sensitivity of Trichoderma spp. Isolates to Environmental Factors and Fungicides

by Allinny Luzia Alves Cavalcante, Andréia Mitsa Paiva Negreiros, Naama Jéssica de Assis Melo, Fernanda Jéssica Queiroz Santos, Carla Sonale Azevêdo Soares Silva, Pedro Sidarque Lima Pinto, Sabir Khan, Inês Maria Mendes Sales and Rui Sales Júnior

Microorganisms 2025, 13(7), 1689; https://doi.org/10.3390/microorganisms13071689 - 18 Jul 2025

Viewed by 428

Abstract

Biological control employs beneficial microorganisms to suppress phytopathogens and mitigate the incidence of associated plant diseases. This study investigated the in vitro development and survival of Trichoderma spp. isolates derived from commercial formulations under different temperatures, pH levels, and sodium chloride (NaCl) concentrations [...] Read more.

Biological control employs beneficial microorganisms to suppress phytopathogens and mitigate the incidence of associated plant diseases. This study investigated the in vitro development and survival of Trichoderma spp. isolates derived from commercial formulations under different temperatures, pH levels, and sodium chloride (NaCl) concentrations and with synthetic fungicides with distinct modes of action. Three isolates were analyzed: URM-5911 and TRA-0048 (T. asperellum) and TRL-0102 (T. longibrachiatum). The results revealed substantial variability among the isolates, with the optimal mycelial growth temperatures ranging from 24.56 to 29.42 °C. All the isolates exhibited broad tolerance to the tested pH (5–9) and salinity levels (250–1000 mM), with TRL-0102 demonstrating the highest salt resistance. The fungicide treatments negatively affected mycelial growth across all the isolates, with Azoxystrobin + Difenoconazole and Boscalid causing growth reductions of up to 50%. Notably, Boscalid enhanced conidial production more compared to the control (126.0% for URM-5911, 13.7% for TRA-0048, and 148.5% for TRL-0102) and decreased the percentage of inactive conidia to less than 10% in all the isolates. These results provide strategic information for the application of Trichoderma spp. in agricultural systems, supporting the selection of more adapted and suitable isolates for integrated disease management programs. Full article

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

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10 pages, 558 KiB

Open AccessCommunication

Carbon Sink Potential of Sulfur-Oxidizing Bacteria in Groundwater at Petroleum-Contaminated Sites

by Pingping Cai, Zhuo Ning and Min Zhang

Microorganisms 2025, 13(7), 1688; https://doi.org/10.3390/microorganisms13071688 - 18 Jul 2025

Viewed by 306

Abstract

Groundwater at petroleum-contaminated sites typically exhibits elevated dissolved inorganic carbon (DIC) levels due to hydrocarbon biodegradation; however, our prior field investigations revealed an enigmatic DIC depletion anomaly that starkly contradicts this global pattern and points to an unrecognized carbon sink. In a breakthrough [...] Read more.

Groundwater at petroleum-contaminated sites typically exhibits elevated dissolved inorganic carbon (DIC) levels due to hydrocarbon biodegradation; however, our prior field investigations revealed an enigmatic DIC depletion anomaly that starkly contradicts this global pattern and points to an unrecognized carbon sink. In a breakthrough demonstration, this study provides the first experimental confirmation that sulfur-oxidizing bacteria (SOB) drive substantial carbon sequestration via a coupled sulfur oxidation autotrophic assimilation process. Through integrated hydrochemical monitoring and 16S rRNA sequencing in an enrichment culture system, we captured the complete DIC transformation trajectory: heterotrophic acetate degradation initially increased DIC to 370 mg/L, but subsequent autotrophic assimilation by SOB dramatically reduced DIC to 270 mg/L, yielding a net consumption of 85 mg/L. The distinctive pH dynamics (initial alkalization followed by acidification) further corroborated microbial regulation of carbon cycling. Critically, Pseudomonas stutzeri and P. alcaliphila were identified as the dominant carbon-fixing agents. These findings definitively establish that chemolithoautotrophic SOB convert DIC into organic carbon through a “sulfur oxidation-carbon fixation” coupling mechanism, overturning the conventional paradigm of petroleum-contaminated sites as perpetual carbon sources. The study fundamentally redefines natural attenuation frameworks by introducing microbial carbon sink potential as an essential assessment metric for environmental sustainability. Full article

(This article belongs to the Section Environmental Microbiology)

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24 pages, 3099 KiB

Open AccessArticle

Comprehensive Assessment of Health Risks Associated with Gram-Negative Bacterial Contamination on Healthcare Personnel Gowns in Clinical Settings

by Daniela Moreno-Torres, Carlos Alberto Jiménez-Zamarripa, Sandy Mariel Munguía-Mogo, Claudia Camelia Calzada-Mendoza, Clemente Cruz-Cruz, Emilio Mariano Durán-Manuel, Antonio Gutiérrez-Ramírez, Graciela Castro-Escarpulli, Madeleine Edith Vélez-Cruz, Oscar Sosa-Hernández, Araceli Rojas-Bernabé, Beatriz Leal-Escobar, Omar Agni García-Hernández, Enzo Vásquez-Jiménez, Gustavo Esteban Lugo-Zamudio, María Concepción Tamayo-Ordóñez, Yahaira de Jesús Tamayo-Ordóñez, Dulce Milagros Razo Blanco-Hernández, Benito Hernández-Castellanos, Julio César Castañeda-Ortega, Marianela Paredes-Mendoza, Miguel Ángel Loyola-Cruz and Juan Manuel Bello-López Show full author list Hide full author list

Microorganisms 2025, 13(7), 1687; https://doi.org/10.3390/microorganisms13071687 - 18 Jul 2025

Viewed by 915

Abstract

Microbiological contamination of healthcare workers’ gowns represents a critical risk for the transmission of healthcare-associated infections (HAIs). Despite their use as protective equipment, gowns can act as reservoirs of antibiotic-resistant bacteria, favouring the spread of pathogens between healthcare workers and patients. The presence [...] Read more.

Microbiological contamination of healthcare workers’ gowns represents a critical risk for the transmission of healthcare-associated infections (HAIs). Despite their use as protective equipment, gowns can act as reservoirs of antibiotic-resistant bacteria, favouring the spread of pathogens between healthcare workers and patients. The presence of these resistant bacteria on healthcare workers’ gowns highlights the urgent need to address this risk as part of infection control strategies. The aim of this work was to assess the microbiological risks associated with the contamination of healthcare staff gowns with Gram-negative bacteria, including the ESKAPE group, and their relationship with antimicrobial resistance. An observational, cross-sectional, prospective study was conducted in 321 hospital workers. The imprinting technique was used to quantify the bacterial load on the gowns, followed by bacterial identification by MALDI-TOF mass spectrometry. In addition, antimicrobial resistance profiles were analysed, and tests for carbapenemases and BLEE production were performed. The ERIC-PCR technique was also used for molecular analysis of Pantoea eucrina clones. Several Gram-negative bacteria were identified, including bacteria of the ESKAPE group. The rate of microbiological contamination of the gowns was 61.05% with no association with the sex of the healthcare personnel. It was observed that critical areas of the hospital, such as intensive care units and operating theatres, showed contamination by medically important bacteria. In addition, some strains of P. eucrina showed resistance to carbapenemics and cephalosporins. ERIC-PCR analysis of P. eucrina isolates showed genetic heterogeneity, indicating absence of clonal dissemination. Healthcare personnel gowns are a significant reservoir of pathogenic bacteria, especially in critical areas of Hospital Juárez de México. It is essential to implement infection control strategies that include improving the cleaning and laundering of gowns and ideally eliminating them from clothing to reduce the risk of transmission of nosocomial infections. Full article

(This article belongs to the Section Medical Microbiology)

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11 pages, 798 KiB

Open AccessArticle

Endophytic Bacteria with Potential Antimicrobial Activity Isolated from Theobroma cacao in Brazilian Amazon

by Lívia Freitas da Silva Pinto, Taynara Cristina Santos Tavares, Oscar Victor Cardenas-Alegria, Elaine Maria Silva Guedes Lobato, Cristina Paiva de Sousa and Adriana Ribeiro Carneiro Nunes

Microorganisms 2025, 13(7), 1686; https://doi.org/10.3390/microorganisms13071686 - 18 Jul 2025

Viewed by 424

Abstract

Endophytic bacteria inhabit plant tissues without damaging them and have specialized adaptation capabilities that allow them to establish themselves in this ecological niche. Endophytes produce numerous secondary metabolites with antimicrobial, anticancer, and pesticide properties, among others. In this study, endophytic bacteria were isolated [...] Read more.

Endophytic bacteria inhabit plant tissues without damaging them and have specialized adaptation capabilities that allow them to establish themselves in this ecological niche. Endophytes produce numerous secondary metabolites with antimicrobial, anticancer, and pesticide properties, among others. In this study, endophytic bacteria were isolated and characterized from cocoa plants in a Brazilian municipality, with the view to evaluate their potential antagonistic activity on clinical bacterial strains. The isolates were identified through phenotypic analysis and molecular characterization. After bacterial isolation, it was possible to verify the presence of 11 different endophytic strains, with a bacterial load of up to 6.3 × 10³ CFU/g in each plant. The morphological and biochemical profile of the isolates varied. At the taxonomic level, these bacteria showed 99% similarity with the genera Microbacterium, Curtobacterium, Pseudomonas, Bacillus, Ralstonia, and Methylobacterium. The strains of the phylum Actinobacteria, which are known for producing natural bioactive compounds with high biotechnological potential, were effective in inhibiting Staphylococcus aureus ATCC and multidrug-resistant clinical strains. This work aims to expand knowledge about endophytes, with the aim of applying them in other sectors, such as the production of compounds against resistant human pathogens. Full article

(This article belongs to the Special Issue Microbial Biotechnology: The Biodiversity, Properties and Benefits of Microorganisms in Medical, Clinical, Food and Environmental Fields)

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15 pages, 5000 KiB

Open AccessArticle

High-Resolution Core Gene-Associated Multiple Nucleotide Polymorphism (cgMNP) Markers for Strain Identification in the Wine Cap Mushroom Stropharia rugosoannulata

by Fei Liu, Bin Cao, Hongmei Dai, Guojie Li, Shoumian Li, Wei Gao and Ruilin Zhao

Microorganisms 2025, 13(7), 1685; https://doi.org/10.3390/microorganisms13071685 - 17 Jul 2025

Viewed by 358

Abstract

Stropharia rugosoannulata, an ecologically valuable and economically important edible mushroom, faces challenges in strain-level identification and breeding due to limited genomic resources and the lack of high-resolution molecular markers. In this study, we generated high-quality genomic data for 105 S. rugosoannulata strains [...] Read more.

Stropharia rugosoannulata, an ecologically valuable and economically important edible mushroom, faces challenges in strain-level identification and breeding due to limited genomic resources and the lack of high-resolution molecular markers. In this study, we generated high-quality genomic data for 105 S. rugosoannulata strains and identified over 2.7 million SNPs, unveiling substantial genetic diversity within the species. Using core gene-associated multiple nucleotide polymorphism (cgMNP) markers, we developed an efficient and transferable framework for strain discrimination. The analysis revealed pronounced genetic differentiation among cultivars, clustering them into two distinct phylogenetic groups. Nucleotide diversity (π) across 83 core genes varied significantly, highlighting both highly conserved loci under purifying selection and highly variable loci potentially associated with adaptive evolution. Phylogenetic analysis of the most variable gene, Phosphatidate cytidylyltransferase mitochondrial, identified 865 SNPs, enabling precise differentiation of all 85 cultivars. Our findings underscore the utility of cgMNP markers in addressing challenges posed by horizontal gene transfer and phylogenetic noise, demonstrating their robustness in cross-species applications. By providing insights into genetic diversity, evolutionary dynamics, and marker utility, this study establishes a foundation for advancing breeding programs, conservation strategies, and functional genomics in S. rugosoannulata. Furthermore, the adaptability of cgMNP markers offers a universal tool for high-resolution strain identification across diverse fungal taxa, contributing to broader fungal phylogenomics and applied mycology. Full article

(This article belongs to the Special Issue Fungal Biology and Interactions—3rd Edition)

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11 pages, 263 KiB

Open AccessArticle

Prevalence and Diagnostic Comparison of Helicobacter pylori and Non-Helicobacter pylori Helicobacter Infections in Patients Undergoing Upper Gastrointestinal Endoscopy with Gastric Biopsy in Algarve, Portugal

by Francisco Cortez Nunes, Teresa Letra Mateus, Catarina Aguieiras, Ricardo Louro, Bruno Peixe, Mauro Calhindro, Patrícia Queirós and Pedro Castelo-Branco

Microorganisms 2025, 13(7), 1684; https://doi.org/10.3390/microorganisms13071684 - 17 Jul 2025

Cited by 1 | Viewed by 1157

Abstract

H. pylori infects over half of the global population and is associated with various gastric and extra-gastric diseases. Other species, such as zoonotic non-Helicobacter pylori Helicobacters (NHPHs), have shown similar associations with gastritis and MALT lymphoma and H. pylori-negative cases with [...] Read more.

H. pylori infects over half of the global population and is associated with various gastric and extra-gastric diseases. Other species, such as zoonotic non-Helicobacter pylori Helicobacters (NHPHs), have shown similar associations with gastritis and MALT lymphoma and H. pylori-negative cases with gastric disease have been identified, including gastric MALT lymphoma, chronic gastritis, and gastroduodenal ulcers. Accurate identification of these species is of great relevance but remains challenging using conventional diagnostic methods. This cross-sectional study aimed to determine the prevalence of H. pylori and NHPH infections, comparing standard histological protocols with molecular techniques. Between December 2024 and February 2025, 54 adult patients undergoing upper gastrointestinal endoscopy (UGE) with gastric biopsy in three hospitals in Algarve, Portugal were recruited. Endoscopic assessment was performed, and gastric biopsies were collected for histological and molecular analysis. DNA was extracted from antral biopsies and analyzed by conventional PCR to detect H. pylori and NHPH. H. pylori diagnostic techniques were compared, descriptive plus statistical analysis was performed, and p-values < 0.05 were considered to be statistically significant. Fifty-four patients were included in the study, with 51.9% of them presenting symptoms. Endoscopic gastritis was observed in 66.7% of patients, while histological gastritis was present in 88.9%, with statistically significant differences between the two diagnostic techniques (p = 0.004). Helicobacter spp. were identified in 44.4% (24/54) of the patients. H. pylori was detected in 42.6% of the patients by Modified Giemsa stain and in 33.3% by PCR. H. bizzozeronii was found in 35.9% of the patients, with 22.2% showing mixed infections. This study reveals a significant prevalence of Helicobacter spp. in patients from the Algarve region, with both H. pylori and zoonotic H. bizzozeronii detected. This is the first report of H. bizzozeronii DNA detection in gastric biopsies via PCR from patients undergoing UGE in Portugal, highlighting the need to consider NHPH in clinical diagnosis. It is important to include molecular methods in routine diagnostics and the need for broader studies to assess regional and national trends in Helicobacter infections besides H. pylori. Full article

(This article belongs to the Section Public Health Microbiology)

18 pages, 3226 KiB

Open AccessArticle

Isolation, Identification, and Antibiotic Resistance, CRISPR System Analysis of Escherichia coli from Forest Musk Deer in Western China

by Kaiwei Yang, Xi Wu, Hui Ding, Bingcun Ma, Zengting Li, Yin Wang, Zexiao Yang, Xueping Yao and Yan Luo

Microorganisms 2025, 13(7), 1683; https://doi.org/10.3390/microorganisms13071683 - 17 Jul 2025

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Abstract

Escherichia coli (E. coli) is an opportunistic pathogen widely distributed in nature, and multi-drug resistance (MDR) E. coli has been widely recognized as a critical reservoir of resistance genes, posing severe health threats to humans and animals. A total of 288 [...] Read more.

Escherichia coli (E. coli) is an opportunistic pathogen widely distributed in nature, and multi-drug resistance (MDR) E. coli has been widely recognized as a critical reservoir of resistance genes, posing severe health threats to humans and animals. A total of 288 E. coli strains were isolated and purified from fresh fecal samples of forest musk deer collected from farms in Sichuan, Shaanxi, and Yunnan Provinces of China between 2013 and 2023. This study aimed to conduct antibiotic susceptibility testing and resistance gene detection on the isolated forest musk deer-derived E. coli, analyze the correlations between them, investigate the presence of CRISPR systems within the strains, and perform bioinformatics analysis on the CRISPR systems carried by the strains. Results showed that 138 out of 288 E. coli strains were MDR, with the highest resistance to tetracycline (48.3%), cefalexin (45.1%), and doxycycline (41.7%). Prevalent genes were tetA (41.0%), sul2 (30.2%), blaTEM (27.1%), with 29 gene–phenotype pairs correlated. CRISPR system-negative strains had higher resistance rates to 16 antibiotics and lower detection rates only for aac (6′)-Ib-cr, qnrA, and qnrB compared to CRISPR system-positive strains. Regional analysis showed that the problem of drug resistance in Sichuan and Shaanxi was more serious, and that the detection rate of antibiotic resistance genes was relatively high. This study guides E. coli infection control in forest musk deer and enriches resistance research data. Full article

(This article belongs to the Special Issue Bacterial Infections and Antimicrobial Resistance in Animal Populations)

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Open AccessArticle

Initial Analysis of Plant Soil for Evidence of Pathogens Associated with a Disease of Seedling Ocotea monteverdensis

by William D. Eaton, Debra A. Hamilton, Alexander Lemenze and Patricia Soteropoulos

Microorganisms 2025, 13(7), 1682; https://doi.org/10.3390/microorganisms13071682 - 17 Jul 2025

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Abstract

Seedlings of the ecologically important, critically endangered tree Ocotea monteverdensisis experience high mortality in the Monteverde, Costa Rica, cloud forests at the onset of the wet season, yet there are no studies suggesting the disease etiology. Here, healthy and diseased plant root and [...] Read more.

Seedlings of the ecologically important, critically endangered tree Ocotea monteverdensisis experience high mortality in the Monteverde, Costa Rica, cloud forests at the onset of the wet season, yet there are no studies suggesting the disease etiology. Here, healthy and diseased plant root and bulk soils were analyzed for various carbon and nitrogen (N) metrics and respiration levels, and DNA sequence-based bacterial and fungal community compositions. All nitrogen metric levels were greater in diseased vs. healthy plant root soils, which could enhance pathogen growth and pathogenic mechanisms. Greater DNA percentages from several potential pathogens were found in diseased vs. healthy plant root soils, suggesting this disease may be associated with a root pathogen. The DNA of the fungus Mycosphaerella was at greater levels in diseased vs. healthy plant root soils than other potential pathogens. Mycosphaerella causes similar diseases in other plants, including coffee, after onset of the wet season. The O. monteverdensis disease also occurs in seedlings planted within or near former coffee plantations at wet season onset. Distance-based linear model analyses indicated that NO₃⁻ levels best predicted the pattern of fungal pathogens in the soils, and Mycosphaerella and Tremella best predicted the patterns of the different N metrics in the soils, supporting their possible roles in this disease. Full article

(This article belongs to the Special Issue Plant–Microbe Interactions Revisited: Emerging Concepts and Biotechnological Innovations)

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