Microorganisms

13 pages, 1082 KiB

Open AccessArticle

Control of Methicillin-Resistant Staphylococcus aureus Using Photodynamic Therapy in Synergy with Staphylococcus epidermidis: Role of Mixed Cultures in Developing Strategies to Inhibit Infections

by Rebeca Vieira de Lima, Kate Cristina Blanco and Vanderlei Salvador Bagnato

Microorganisms 2025, 13(6), 1196; https://doi.org/10.3390/microorganisms13061196 (registering DOI) - 23 May 2025

Abstract

Staphylococcus aureus is a Gram-positive bacterium living abundantly on our skin and mucous membranes. When there is an imbalance in microbiota, they are the main protagonists of various infections, such as soft tissue infections and bacteremia. However, Staphylococcus epidermidis also colonizes this microbiome, [...] Read more.

Staphylococcus aureus is a Gram-positive bacterium living abundantly on our skin and mucous membranes. When there is an imbalance in microbiota, they are the main protagonists of various infections, such as soft tissue infections and bacteremia. However, Staphylococcus epidermidis also colonizes this microbiome, is able to compete with pathogenic bacteria, including methicillin-resistant Staphylococcus aureus (MRSA), and can contribute to treatments such as photodynamic inactivation (PDI) by inhibiting infection progression and restoring a healthy microbiota. In vitro photodynamic inactivation experiments were carried out using synthetic curcumin at a concentration of 5 μM as a photosensitizer and varying light doses (1, 2 and 5 J/cm²) at a wavelength of 450 nm, on pure cultures (S. aureus, S. epidermidis and MRSA) and mixed cultures, in which bacteria were placed together proportionally. This study revealed that pure cultures of these bacteria obtained statistically significant results with varying light doses of 2 and 5 J/cm². In addition, in an attempt to bring infections closer to reality, experiments were carried out on mixed cultures. The results were not only significant but also increased reduction of bacteria, including resistant bacteria. Study offers new perspectives on the importance of themicrobiota for treatment of infections caused by the Staphylococcus genus. Full article

(This article belongs to the Topic Microbiota Diversity and Its Broader Biological Implications Across Human and Animal Health)

16 pages, 1474 KiB

Open AccessArticle

Genomic Insights into Carbapenem-Resistant Organisms Producing New Delhi Metallo-β-Lactamase in Live Poultry Markets

by Xueqiang Xin, Yi Yin, Jiayong Kong, Mianzhi Wang, Zhiqiang Wang and Ruichao Li

Microorganisms 2025, 13(6), 1195; https://doi.org/10.3390/microorganisms13061195 - 23 May 2025

Abstract

New Delhi metallo-β-lactamase (NDM) is an enzyme that can degrade a wide range of β-lactam antibiotics. The widespread dissemination of the bla_NDM gene, which encodes NDM, in animal-derived settings poses a threat to public health security. Live poultry markets represent critical nodes [...] Read more.

New Delhi metallo-β-lactamase (NDM) is an enzyme that can degrade a wide range of β-lactam antibiotics. The widespread dissemination of the bla_NDM gene, which encodes NDM, in animal-derived settings poses a threat to public health security. Live poultry markets represent critical nodes in public health surveillance. However, there is currently limited reporting on the spread of the bla_NDM gene within these markets under the One Health approach. This study investigated the prevalence of the bla_NDM gene in live poultry markets and, by integrating newly sequenced genomes with publicly available database entries, performed an in-depth analysis of its association networks with other genetic elements across species. A total of 233 bla_NDM-positive strains, comprising 218 Escherichia coli strains, 4 Enterobacter cloacae strains, 7 Klebsiella pneumoniae, 2 Klebsiella aerogenes, 1 Providencia rettgeri, and 1 Proteus mirabilis were isolated from two live poultry markets in Jiangsu, China. Among the bla_NDM-positive strains, multiple variants were identified, primarily bla_NDM-5, followed by bla_NDM-1, bla_NDM-13, bla_NDM-27, and bla_NDM-39. The coexistence of bla_NDM-5 and mcr-1 was detected in five E. coli strains. Additionally, we found one E. coli strain in which bla_NDM-5 coexisted with estT and tet(X4), and another E. coli strain where bla_NDM-5 coexisted with estT. Spearman correlation analysis of publicly available genomes revealed that the genetic element preferences of bla_NDM variants vary significantly across species (|R| > 0.3, p < 0.05). The element preferences of E. coli strains carrying bla_NDM-5 are similar to those of Klebsiella pneumoniae harboring bla_NDM-1. In Klebsiella aerogenes, Enterobacter cloacae, and Proteus mirabilis, strains carrying bla_NDM-1, have opposite genetic element preferences when compared with strains harboring bla_NDM-5 or bla_NDM-7. Notably, we report the first evidence of the bla_NDM-1 gene transfer mediated by ISKpn13, ISSpu2, and MITEKpn1. The findings highlight that live poultry markets are important transmission hotspots of AMR and thus require continuous surveillance. Full article

(This article belongs to the Special Issue Antimicrobial Resistance (AMR) Diagnostics and Genomic/Molecular Epidemiology of Multidrug-Resistant Isolates)

22 pages, 4689 KiB

Open AccessArticle

Seasonal Dynamics of Sediment Microbial Communities at Different Distances from Artificial Reef Units

by Meiling Zhu and Yanli Tang

Microorganisms 2025, 13(6), 1194; https://doi.org/10.3390/microorganisms13061194 - 23 May 2025

Abstract

Artificial reefs (ARs) are important for habitat restoration and exhibit clear spatial gradient effects. However, most studies focus on AR groups, neglecting the ecological functions and mechanisms of individual AR units at a local scale. This limits a deeper understanding and optimization of [...] Read more.

Artificial reefs (ARs) are important for habitat restoration and exhibit clear spatial gradient effects. However, most studies focus on AR groups, neglecting the ecological functions and mechanisms of individual AR units at a local scale. This limits a deeper understanding and optimization of the ecological effects of ARs. This study employed high-throughput sequencing to examine the seasonal and spatial variations in sediment microbial communities surrounding AR units. The results showed that microbial community distributions in sediments varied significantly with seasons, reef distance, and reef structure. The community structure varied significantly across seasons at different reef distances, with the most unique structure observed at 3 m (1.5-times the reef height). In May, microbial community spatial changes were mainly driven by sediment organic matter (OM), while in November and February, although the spatial enrichment patterns of microbial groups changed seasonally, they were not strongly affected by functional types (aerobic or anaerobic). The Neutral Community Model (NCM) showed lower levels of R² and Nm at 0 m and 3 m, which are relatively consistent with the flow field effects (upwelling and reverse eddy currents). Key environmental factors and their regulatory effects vary with distance from the reef. Full article

(This article belongs to the Section Environmental Microbiology)

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18 pages, 5429 KiB

Open AccessArticle

Different Emergency Response Strategies to Oil Spills in Rivers Lead to Divergent Contamination Compositions and Microbial Community Response Characteristics

by Xinyu Wen, An Fan, Jinsong Wang, Yulin Xia, Sili Chen and Yuyin Yang

Microorganisms 2025, 13(6), 1193; https://doi.org/10.3390/microorganisms13061193 - 23 May 2025

Abstract

Oil spills in inland rivers pose a significant threat to the surrounding environment, and the emergency response differs greatly from that in ocean or coastal areas. In this study, we focused on several commonly used emergency water treatment strategies in China’s inland oil [...] Read more.

Oil spills in inland rivers pose a significant threat to the surrounding environment, and the emergency response differs greatly from that in ocean or coastal areas. In this study, we focused on several commonly used emergency water treatment strategies in China’s inland oil spills, as well as the spilled washing oil in a serious accident case. We investigated the changes in oil-related chemical components before and after water treatment using GCxGC-TOF MS (Comprehensive Two-dimensional Gas Chromatography Time of Flight Mass Spectrometer). We tracked the shifts of microbial communities in the microcosms incubated with clean river water, simulated oil-contaminated water, and the treatment effluent. The results revealed that typical components, especially nitrogen-containing heterocyclic compounds, had different removal efficiencies among treatments. The diversity, composition, and potential functions of microbial communities responded differently to the treatments, and could be related to various substances, including PAHs (polycyclic aromatic hydrocarbons) and heterocyclic compounds. A few genera, such as SC-I-84, exhibited a high correlation with washing oil-related components and could serve as an indicator in such an oil spill emergency response. Our findings indicated that simply using petroleum oil or PAHs to evaluate oil spills was likely to underestimate the ecological impact, especially when the spilled substances were coal chemical products widely used in China. This will provide an important scientific basis for decision-making and strategy evaluation in emergency responses to inland oil spills. Full article

(This article belongs to the Special Issue Microorganisms: A Way Forward for Sustainable Development?)

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16 pages, 1663 KiB

Open AccessArticle

Matrine Attenuates Streptococcus agalactiae Virulence by Suppressing Capsular Polysaccharide Synthesis and Host Adhesion Pathways

by Shijiao Guo, Kaiming Wang, Hua Zhang, Chaochao Luo, Zixuan Zhao and Jinjin Tong

Microorganisms 2025, 13(6), 1192; https://doi.org/10.3390/microorganisms13061192 - 23 May 2025

Abstract

Streptococcus agalactiae (GBS) is a major pathogen causing mastitis in dairy cows while causing oxidative stress. Matrine is an alkaloid compound extracted from the roots of Sophora flavescens, a plant used in traditional Chinese medicine. It possesses antioxidant, immunomodulatory, anti-inflammatory, and pro-apoptotic [...] Read more.

Streptococcus agalactiae (GBS) is a major pathogen causing mastitis in dairy cows while causing oxidative stress. Matrine is an alkaloid compound extracted from the roots of Sophora flavescens, a plant used in traditional Chinese medicine. It possesses antioxidant, immunomodulatory, anti-inflammatory, and pro-apoptotic properties. The aim of this study was to investigate the regulatory effects of matrine on the virulence of the ATCC strain (ATCC13813) and clinical GBS strains by transcriptome analysis and qRT-PCR validation. The results showed that the ABC transporter, peptidoglycan biosynthesis, and quorum-sensing pathways were significantly altered in ATCC (4 mg/mL) and GBS (12 mg/mL) strains after matrine treatment at MIC concentrations. Additionally, genes related to invasion and immune escape, including CylE, CAMP, ScpB, and CpsA, and genes related to the expression of adhesion and virulence factors, such as Bac, Lmb, PI2a, and PI2b, were significantly downregulated (p < 0.05). Overall, these data suggest that matrine effectively inhibits the virulence genes of GBS, thereby reducing immune evasion and infection by decreasing the synthesis of capsular polysaccharides and host cell adhesion. Full article

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

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20 pages, 1434 KiB

Open AccessArticle

Gut Microbiome Development in Rock Pigeons: Effects of Food Restriction Early in Life

by Maurine W. Dietz, Bin-Yan Hsu, Marco van der Velde and B. Irene Tieleman

Microorganisms 2025, 13(6), 1191; https://doi.org/10.3390/microorganisms13061191 - 23 May 2025

Abstract

The developmental period is a critical phase in birds, influencing even lifetime reproductive success. The gut microbiome (GM) is important herein, affecting digestive capacity and immune function. Diet impacts the GM, but wild nestlings may experience resource limitations, which may also affect the [...] Read more.

The developmental period is a critical phase in birds, influencing even lifetime reproductive success. The gut microbiome (GM) is important herein, affecting digestive capacity and immune function. Diet impacts the GM, but wild nestlings may experience resource limitations, which may also affect the GM. We investigated the effects of a week of food restriction early in life on the GM in captive rock pigeon nestlings (Columba livia). We sampled the GM at 0, 2, 4, 7, 8, 12, 20, 27, and 38 days and in foster parents. Alpha diversity varied only with age. However, differences in alpha diversity between nestlings and adults were larger during food restriction. Beta diversity varied with age, food treatment, and their interaction term. Four of the eleven major genera varied with age, while four others did not vary with age or food treatment. Major genera that contained potential pathogens (Escherichia-Shigella and Clostridium sensu stricto 1) were more abundant under food restriction. Food restriction thus affected GM development. The increase in alpha diversity and potential pathogens suggest that suppressed immune function may mediate the impact of food restriction on the GM. The effect diminished when food restriction was ended, suggesting that in wild nestlings, the impact of food restriction on the GM may be short-term. Full article

(This article belongs to the Special Issue Gut Microbiota: Metagenomics to Study Ecology, 2nd Edition)

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24 pages, 2046 KiB

Open AccessArticle

A Bifidobacterium Strain with Antibacterial Activity, Its Antibacterial Characteristics and In Vitro Probiotics Studies

by Jing Ji, Tiange Li, Baoying Ma and Runzhong Wang

Microorganisms 2025, 13(6), 1190; https://doi.org/10.3390/microorganisms13061190 - 23 May 2025

Abstract

The search for natural antimicrobials has intensified with rising food safety demands. This study evaluated 23 probiotic strains, identifying Bifidobacterium sp. strain TF04 as a potent inhibitor against pathogens, with inhibition zone diameters of 12.85 ± 0.12 mm (Escherichia coli), 14.85 [...] Read more.

The search for natural antimicrobials has intensified with rising food safety demands. This study evaluated 23 probiotic strains, identifying Bifidobacterium sp. strain TF04 as a potent inhibitor against pathogens, with inhibition zone diameters of 12.85 ± 0.12 mm (Escherichia coli), 14.85 ± 0.10 mm (Staphylococcus aureus), and 17.50 ± 0.23 mm (Staphylococcus epidermidis). Preliminary analysis shows that the main antibacterial compounds produced by TF04 in the process of bacterial growth inhibition are antibacterial active proteins. TF04 exhibits optimal bacteriostatic activity within the pH range of 2–4, with a notable decline in effectiveness as the pH value increases. At the same time, the bacteriostat produced by TF04 showed strong thermal stability and ultraviolet stability. TF04 demonstrated excellent probiotic potential: surviving acidic (pH 2.0, >45% viability) and bile conditions (3% bile salts, >55% survival). It showed strong auto-aggregation (40.10%) and hydrophobicity (>30%), indicating gut colonization potential, along with notable antioxidant capacity. Safety was confirmed by absent hemolytic and gelatinase activities. These properties position TF04 as a promising multifunctional candidate for food preservation, combining antimicrobial efficacy with probiotic benefits. Further studies will purify its bioactive compounds and validate applications in food systems. Full article

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

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20 pages, 1742 KiB

Open AccessArticle

Chlorophyllin-Mediated Photodynamic Inactivation: Dosage and Time Dependency in the Inhibition of Bacillus subtilis

by Sarah Pohland, Jana Vourvoutsiotou, Leah Brandtner, David Geißler, Selina Wiesmeth, Vanessa Scudlo, Peter Richter, Andreas Burkovski and Michael Lebert

Microorganisms 2025, 13(6), 1189; https://doi.org/10.3390/microorganisms13061189 - 23 May 2025

Abstract

Photodynamic inactivation of bacteria offers a promising alternative to counteract the trend towards the development of resistance, which, if left uncontrolled, will lead to the death of 10 million people per year by 2050. Its advantage over antibiotics is the site-specific mode of [...] Read more.

Photodynamic inactivation of bacteria offers a promising alternative to counteract the trend towards the development of resistance, which, if left uncontrolled, will lead to the death of 10 million people per year by 2050. Its advantage over antibiotics is the site-specific mode of action due to the photosensitizer (PS) and the low risk of developing resistance. This is primarily prevented by the damage of the bacteria, which also destroy internal structures such as nucleic acid, proteins, and lipids. A promising and still little-researched PS is chlorophyllin (CHL), a chlorophyll derivative. This study investigated its mode of action on Bacillus subtilis growth using optical density (OD) measurements. It was shown that the PS is highly effective even at low concentrations and short irradiation durations. Here, 1 mg/L and an irradiation duration of 1 min were sufficient to inhibit the growth of the Gram-positive bacterium Bacillus subtilis for several hours. Full article

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

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30 pages, 1026 KiB

Open AccessReview

Impact of Gut Microbiome on Gut Permeability in Liver and Gut Diseases

by Punnag Saha and Phillipp Hartmann

Microorganisms 2025, 13(6), 1188; https://doi.org/10.3390/microorganisms13061188 - 23 May 2025

Abstract

Hepatobiliary and gastrointestinal conditions, including chronic liver diseases and inflammatory bowel disease, are associated with significant morbidity and mortality globally. While the pathophysiology and symptoms vary from one disease to another, aberrations of the gut microbiome with deleterious microbial products affecting the intestinal [...] Read more.

Hepatobiliary and gastrointestinal conditions, including chronic liver diseases and inflammatory bowel disease, are associated with significant morbidity and mortality globally. While the pathophysiology and symptoms vary from one disease to another, aberrations of the gut microbiome with deleterious microbial products affecting the intestinal barrier are common in patients suffering from these diseases. In this review, we summarize changes in the gut microbiome associated with various disease states and detail their role in gut barrier disruption and in modulating disease progression. Further, we discuss therapeutic interventions and precision medicine approaches targeting the microbiome, which have shown promise in alleviating these chronic illnesses in mouse models and patients. Full article

(This article belongs to the Special Issue Gut Microbiome in Homeostasis and Disease, 2nd Edition)

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24 pages, 6849 KiB

Open AccessArticle

Efficiency, Microbial Communities, and Nitrogen Metabolism in Denitrification Biological Filter: Insights into Varied Pore Ceramsite Media

by Jiajun Song, Na Yu, Cui Zhao, Yufeng Lv and Jifu Yang

Microorganisms 2025, 13(6), 1187; https://doi.org/10.3390/microorganisms13061187 - 23 May 2025

Abstract

This study presented an investigation into the role of ceramsite pore structures in optimizing DNBFs for nitrate-contaminated water treatment. Through systematic comparison of three ceramsite media (CE1, CE2, CE3) with distinct pore structures, we elucidated the microbial mechanisms underlying nitrate removal efficiency by [...] Read more.

This study presented an investigation into the role of ceramsite pore structures in optimizing DNBFs for nitrate-contaminated water treatment. Through systematic comparison of three ceramsite media (CE1, CE2, CE3) with distinct pore structures, we elucidated the microbial mechanisms underlying nitrate removal efficiency by analyzing denitrification performance, biomass accumulation, EPS, microbial community structure, and nitrogen metabolic function. Results demonstrated that the CE2 medium, characterized by an effective porosity (pore size > 0.5 μm) of 55.8% and an optimal porosity (pore size 0.5–25 μm) percentage of 83.1%, achieved superior nitrate removal efficiency (87.8%) with an R_vd of 0.82 kg TN/(m³·d) at HRT = 1.5 h, outperforming CE1 (0.74 kg TN/(m³·d)) and CE3 (0.68 kg TN/(m³·d)). Enhanced performance was mechanistically linked to CE2’s higher biomass accumulation (8.5 vs. 7.8 mg/m² in CE1 and 6.9 mg/m² in CE3) and greater EPS production (48.5 vs. 44.7 in CE1 and 35.4 mg/g in CE3), which facilitated biofilm resilience under hydraulic stress. Microbial analysis revealed CE2’s unique enrichment of a higher relative abundance of Proteobacteria (90.1% vs. 67.2% in CE1 and 47.4% in CE3) and denitrifying taxa (unclassified_f_Comamonadaceae: 42.7%, unclassified_f_Enterobacteriaceae: 35.3%). PICRUST2 showed 1.2- and 1.4-fold higher abundance of denitrification genes (narGHI, nosZ) compared to CE1 and CE3, respectively. These findings establish that optimizing ceramsite pore structure, particularly increasing the optimal porosity ratio (pore size 0.5–25 μm) can enhance denitrification efficiency, offering a scalable strategy for cost-effective groundwater remediation. This work provides actionable criteria for designing high-performance DNBFs, with immediate relevance to industrial and municipal wastewater treatment systems facing stringent nitrate discharge limits. Full article

(This article belongs to the Section Microbial Biotechnology)

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15 pages, 1820 KiB

Open AccessArticle

Assess the Variability and Robustness of an Aluminum-Based Adsorption–Precipitation Method for Virus Detection in Wastewater Samples

by Lorena Casado-Martín, Marta Hernández, José M. Eiros, Antonio Valero and David Rodríguez-Lázaro

Microorganisms 2025, 13(6), 1186; https://doi.org/10.3390/microorganisms13061186 - 23 May 2025

Abstract

Wastewater-based molecular epidemiology enables the surveillance of both symptomatic and asymptomatic individuals in a non-invasive, cost-effective, rapid, and early-detection manner. The use of wastewater analysis to monitor the prevalence of viral pathogens in a given population has increased significantly since the COVID-19 pandemic. [...] Read more.

Wastewater-based molecular epidemiology enables the surveillance of both symptomatic and asymptomatic individuals in a non-invasive, cost-effective, rapid, and early-detection manner. The use of wastewater analysis to monitor the prevalence of viral pathogens in a given population has increased significantly since the COVID-19 pandemic. These studies typically involve three main steps: viral concentration, nucleic acid extraction, and DNA/RNA quantification. However, the absence of a standardized methodology remains a major limitation, hindering result comparability across studies. Among the available viral concentration techniques, aluminum-based adsorption–precipitation is one of the most commonly used due to its simplicity, efficiency, and low cost. This study evaluates the robustness and variability of the viral concentration and nucleic acid extraction steps by implementing different process controls in wastewater samples across 122 independent experiments. Additionally, correlations between viral recovery efficiencies and relevant physicochemical parameters were also analyzed (n = 600). The results indicate that, despite the overall robustness of the method, the concentration step exhibits the highest variability (CV = 53.82%), which accounted for 53.73% of the overall variability. In addition, our results show that, on average, 0.65 logarithmic units were lost during the viral concentration step. Furthermore, viral recovery rates were influenced by seasonality and sample characteristics, while no significant correlation was observed with pH or conductivity. These findings highlight the importance of process controls, confirming the robustness of the methodology, and identifying key parameters that should be considered in future studies for improved data interpretation. Full article

(This article belongs to the Special Issue The Molecular Epidemiology of Infectious Diseases)

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24 pages, 1148 KiB

Open AccessArticle

In-Feed vs. In-Water Chlortetracycline Administration on the Fecal Prevalence of Virulence Genes and Pathotypes of Escherichia coli Involved in Enteric Colibacillosis in Piglets

by Ramya Kalam, Raghavendra G. Amachawadi, Xiaorong Shi, Jianfa Bai, Mina Abbasi, Mike D. Tokach and Tiruvoor G. Nagaraja

Microorganisms 2025, 13(6), 1185; https://doi.org/10.3390/microorganisms13061185 - 22 May 2025

Abstract

Colibacillosis in nursery pigs, caused by Escherichia coli (ETEC, EPEC, and STEC pathotypes), remains a major economic concern in the swine industry. This study evaluated the effects of in-feed or in-water chlortetracycline (CTC) administration on the fecal prevalence of virulence genes and pathotypes [...] Read more.

Colibacillosis in nursery pigs, caused by Escherichia coli (ETEC, EPEC, and STEC pathotypes), remains a major economic concern in the swine industry. This study evaluated the effects of in-feed or in-water chlortetracycline (CTC) administration on the fecal prevalence of virulence genes and pathotypes associated with colibacillosis. A total of 1296 weaned piglets (21 days old) were allocated to 48 pens (16 pens/treatment; 27 piglets/pen) and assigned randomly to no CTC, in-feed CTC, or in-water CTC groups. CTC was administered from days 0 to 14. Fecal samples from five piglets per pen on days 0, 14, and 28 were enriched, screened by 11-plex PCR, cultured for pathotypes, and tested for CTC susceptibility and tetracycline resistance genes. None of the 360 fecal samples or 3267 E. coli isolates were positive for bfpA or aggA. Prevalence of estB (96.9%) and astA (92.8%) was highest. ETEC was the dominant pathotype (41.2%), with astA (29%) and estB (21.9%) as predominant enterotoxin genes. CTC administration had no significant effect on fecal prevalence of virulence genes or pathotypes (p > 0.05). stx2 and STEC were detected only at day 28, all harboring stx2e. All pathotypes were CTC-resistant, with tetA as the predominant resistance gene. Full article

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

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15 pages, 1803 KiB

Open AccessArticle

Vegetation-Driven Changes in Soil Salinity Ions and Microbial Communities Across Tidal Flat Reclamation

by Shumei Cai, Sixin Xu, Deshan Zhang, Yun Liang and Haitao Zhu

Microorganisms 2025, 13(6), 1184; https://doi.org/10.3390/microorganisms13061184 - 22 May 2025

Abstract

Soil microbes play a vital role in tidal flat ecosystems but are highly susceptible to disturbances from land reclamation. This study investigated the dynamics of bacterial communities and their environmental drivers across a 50-year reclamation chronosequence under three vegetation types (bare flats, reed [...] Read more.

Soil microbes play a vital role in tidal flat ecosystems but are highly susceptible to disturbances from land reclamation. This study investigated the dynamics of bacterial communities and their environmental drivers across a 50-year reclamation chronosequence under three vegetation types (bare flats, reed beds, and rice fields). The results showed that, after 50 years of reclamation, total dissolved salts decreased significantly in vegetated zones, particularly in rice fields, where Cl⁻ dropped by 54.71% and nutrients (SOC, TN, TP) increased substantially. Key ions, including HCO₃⁻, Cl⁻, and K⁺, were the primary drivers of microbial community structure, exerting more influence than total salinity (TDS) or pH. Bacterial abundance and diversity increased over time, with rice fields showing the highest values after 50 years. Actinobacteriota and Proteobacteria were positively correlated with HCO₃⁻ and K⁺, while Cl⁻ negatively affected Acidobacteriota. Genus-level analyses revealed that specific taxa, such as Sphingomonas and Gaiella, exhibited ion responses diverging from broader phylum-level patterns, exemplifying niche-specific adaptations to salinity regimes. These findings underscore the pivotal role of vegetation type and individual salinity ions in driving microbial succession during tidal flat reclamation. A phased vegetation strategy, starting with reed colonization and followed by rice cultivation, can enhance soil quality and microbial diversity. This research provides important insights for optimizing vegetation management and ion monitoring in sustainable tidal flat reclamation. Full article

(This article belongs to the Special Issue Microorganisms from Terrestrial Extreme Environments: Exploration and Exploitation Towards Sustainable Plant Production)

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3 pages, 229 KiB

Open AccessEditorial

Insights into Plant–Soil–Microbe Interactions

by Wajid Zaman

Microorganisms 2025, 13(6), 1183; https://doi.org/10.3390/microorganisms13061183 - 22 May 2025

Abstract

The interactions between plants, soil, and microorganisms play a pivotal role in shaping ecosystem health, biodiversity, and agricultural productivity [...] Full article

(This article belongs to the Special Issue Insights into Plant–Soil–Microbe Interactions)

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11 pages, 1773 KiB

Open AccessArticle

First Molecular Identification of Zoonotic Babesia odocoilei in Ticks from Romania

by Ioan Cristian Dreghiciu, Diana Hoffman, Simona Dumitru, Ion Oprescu, Mirela Imre, Tiana Florea, Anamaria Plesko, Vlad Iorgoni, Sorin Morariu, Gheorghe Dărăbuș and Marius Stelian Ilie

Microorganisms 2025, 13(6), 1182; https://doi.org/10.3390/microorganisms13061182 - 22 May 2025

Abstract

Babesia odocoilei is an emerging zoonotic protozoan parasite primarily associated with cervids, with growing recognition among non-cervid hosts and in terms of potential public health implications. While this species has been documented in North America and parts of Europe, data on its presence [...] Read more.

Babesia odocoilei is an emerging zoonotic protozoan parasite primarily associated with cervids, with growing recognition among non-cervid hosts and in terms of potential public health implications. While this species has been documented in North America and parts of Europe, data on its presence in Romania remain scarce. This study aimed to investigate the presence of Babesia spp. in ticks collected from Romania, providing new information on the existing species and their distribution, as well as their potential epidemiologic significance. A total of 41 Ixodidae ticks were collected from 184 wild boars across six counties from Western and Central Romania. Ticks were identified using morphological assessments, and DNA was extracted from the samples using a standardized protocol. The presence of Babesia spp. was assessed using real-time PCR with primers and a Taq Man probe targeting 116 bp fragments of 18S rRNA genes. Molecular analysis was used to detect Babesia spp. DNA from a single tick sample (1/41, 2.43%), identified as Dermacentor marginatus, from Timiș County. The resulting amplicons were sequenced and compared with reference sequences in GenBank for species confirmation. This finding represents the first molecular identification of B. odocoilei in questing ticks from Romania. The expanding host range and geographic distribution of B. odocoilei raise concerns regarding its zoonotic potential. The presence of this pathogen in Dermacentor marginatus ticks suggests a broader vector competence than previously recognized, and future research should focus on host reservoirs, vector competence, and potential zoonotic transmission, with an emphasis on public health implications, including potential implications for veterinary diagnostics, vector control policies, and public health awareness regarding emerging tick-borne pathogens. Full article

(This article belongs to the Special Issue Ticks and Threats: Insights on Tick-Borne Diseases)

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18 pages, 1141 KiB

Open AccessArticle

Associations Between Candida and Staphylococcus aureus, Pseudomonas aeruginosa, and Acinetobacter Species as Ventilator-Associated Pneumonia Isolates in 84 Cohorts of ICU Patients

by James Hurley

Microorganisms 2025, 13(6), 1181; https://doi.org/10.3390/microorganisms13061181 - 22 May 2025

Abstract

Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter species, and Candida species are common ventilator-associated pneumonia (VAP) isolates. Whilst the clinical significance of Candida as a VAP isolate is unclear, evidence is emerging that Candida interacts with bacteria, contributing to colonization susceptibility. Indirectly, VAP isolate [...] Read more.

Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter species, and Candida species are common ventilator-associated pneumonia (VAP) isolates. Whilst the clinical significance of Candida as a VAP isolate is unclear, evidence is emerging that Candida interacts with bacteria, contributing to colonization susceptibility. Indirectly, VAP isolate data reflect patient colonization within cohorts. The objective here is to estimate the association between these three bacteria and Candida as VAP isolates. ICU cohorts were obtained by searching the literature for mechanically ventilated (MV) patient cohorts in which Candida was listed as an isolate among patients with VAP. Regression models of the associated VAP incidence per 100 MV patients, using random effects methods, incorporated group-level factors such as the year of publication, mode of VAP diagnosis, and ICU stay length. The median VAP incidence proportions for Staphylococcus aureus, Pseudomonas aeruginosa, and Acinetobacter species were 3.3 (IQR: 1.2–6.9), 3.6 (IQR: 1.8–5.7), and 1.2 (IQR: 0.4–4.1), respectively. Among 84 cohorts from 67 publications, Staphylococcus aureus (correlation coefficient = 0.759) and Pseudomonas aeruginosa (0.749), and less so Acinetobacter species (0.53), each show correlation with the isolation of Candida species among these ICU populations. These associations may underlie the poor prognosis with Candida colonization. Full article

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

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15 pages, 1742 KiB

Open AccessArticle

Genomic Diversity of the tet(X)-Positive Myroides Species

by Chong Chen, Taotao Wu, Jing Liu and Yilin Lv

Microorganisms 2025, 13(6), 1180; https://doi.org/10.3390/microorganisms13061180 - 22 May 2025

Abstract

The rapid spread of tet(X) genes capable of inactivating tigecycline represents a critical challenge to global public health. This study aims to explore the distribution, genetic diversity, and transferability of tet(X) genes in Myroides, a genus of Gram-negative bacteria increasingly [...] Read more.

The rapid spread of tet(X) genes capable of inactivating tigecycline represents a critical challenge to global public health. This study aims to explore the distribution, genetic diversity, and transferability of tet(X) genes in Myroides, a genus of Gram-negative bacteria increasingly implicated in multidrug-resistant (MDR) bacterial infections. From 2021 to 2024, 646 samples of chicken, sheep, soil, and water were randomly collected, yielding nine chicken-derived tet(X)-positive Myroides sp. strains in Shandong, China. All of them were MDR to tetracycline, ceftazidime, gentamicin, amikacin, colistin, ciprofloxacin, gatifloxacin, and trimethoprim-sulfamethoxazole, with elevated minimum inhibitory concentrations (MICs) for tigecycline, florfenicol, and macrolides, but exhibited susceptibility to meropenem (100%), ampicillin-sulbactam (66.7%), and cefotaxime (33.3%). A genomic analysis of the isolates and 86 public tet(X)-positive Myroides genomes revealed the widespread distribution of tet(X) and macrolide-inactivating estT genes across 12 Myroides species, including 7 novel species. Eight tet(X) and eight estT variants were identified, half of which were novel. The phylogenetic analysis highlighted interspecies transmission risks, with ISCR2-mediated transposons of tet(X6) and estT-2 across Myroides, Riemerella, Empedobacter, Providencia, Acinetobacter, and Proteus species. These findings illuminate the genomic diversity driving antibiotic resistance in understudied bacterial taxa, with implications for global One Health strategies. Full article

(This article belongs to the Special Issue Antibiotic and Resistance Gene Pollution in the Environment)

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13 pages, 3591 KiB

Open AccessArticle

Synergistic Engineering of the Twin-Arginine Translocation (Tat) Pathway and Membrane Capacity Enhances Extracellular Production of Amylosucrase in Bacillus licheniformis

by Caizhe Wang, Dandan Niu, Yongqing Zhou, Hui Liu, Nokuthula Peace Mchunu, Meng Zhang, Suren Singh and Zhengxiang Wang

Microorganisms 2025, 13(6), 1179; https://doi.org/10.3390/microorganisms13061179 - 22 May 2025

Abstract

Amylosucrase (AS) is a highly versatile enzyme with significant potential for industrial applications, including functional food production and glycosylation of bioactive compounds. However, its large-scale production is hampered by low secretion efficiency in microbial hosts. This study focuses on engineering the twin-arginine translocation [...] Read more.

Amylosucrase (AS) is a highly versatile enzyme with significant potential for industrial applications, including functional food production and glycosylation of bioactive compounds. However, its large-scale production is hampered by low secretion efficiency in microbial hosts. This study focuses on engineering the twin-arginine translocation (TAT) pathway and optimizing membrane resource allocation in Bacillus licheniformis to enhance the extracellular production of Neisseria polysaccharea amylosucrase (NpAS). The investigation integrates three targeted strategies: optimizing the hydrophobic region adjacent to the TAT signal peptide, modifying TAT translocases via site-directed mutagenesis, and improving inter-pathway membrane resource redistribution by deleting non-essential Sec pathway components. Among the engineered strains, BLΔDF93S-2.0AS1 achieved an extracellular enzyme activity of 706.10 U/L, equating to a 2.01-fold improvement over the parental strain. These results emphasize the potential of combining multifaceted engineering strategies to optimize heterologous protein secretion systems. Full article

(This article belongs to the Special Issue Advances in Microbial Cell Factories, 3rd Edition)

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14 pages, 1720 KiB

Open AccessArticle

Effects of the Addition of Microbial Agents After Dazomet Fumigation on the Microbial Community Structure in Soils with Continuous Cropping of Strawberry (Fragaria × Ananassa Duch.)

by Ran Wu, Yan Li, Jian Meng and Jiangwei Han

Microorganisms 2025, 13(6), 1178; https://doi.org/10.3390/microorganisms13061178 - 22 May 2025

Abstract

To study the effects of different microbial agents on the microbial community structure of continuously cropped strawberry soil after soil fumigation, seven treatments were applied: T1 (Trichoderma harzianum + Bacillus subtilis + actinomycetes), T2 (Trichoderma harzianum + Bacillus subtilis), [...] Read more.

To study the effects of different microbial agents on the microbial community structure of continuously cropped strawberry soil after soil fumigation, seven treatments were applied: T1 (Trichoderma harzianum + Bacillus subtilis + actinomycetes), T2 (Trichoderma harzianum + Bacillus subtilis), T3 (Trichoderma harzianum + actinomycetes), T4 (CK) (water control), T5 (Bacillus subtilis), T6 (actinomycetes) and T7 (Trichoderma harzianum). A high-throughput sequencing platform (Illumina HiSeq 2500) was used to analyze the soil bacterial and fungal communities and their compositions. Compared with the T4 (CK) treatment, the application of microbial agents increased the richness and diversity of soil bacteria and fungi, and the effects of single microbial agents and compound microbial agents differed. The richness, diversity indices and population sizes of bacteria and fungi in the T6 treatment were the highest. The Chao1, observed species and Shannon indices of bacteria were 22.51%, 23.56% and 5.61% greater, respectively, than those of T4 (CK). The Chao1, observed species, Shannon and Simpson indices of fungi were 41.28%, 41.83%, 128.02% and 88.65% higher, respectively, than those of T4 (CK). At the genus level, the bacterial community compositions of T2 and T6 were the most similar, and the fungal community compositions of T1 and T5 were the most similar. Analysis of the genera in the dominant communities revealed that the application of microbial agents after dazomet fumigation increased the numbers and recovery rates of soil bacteria and fungi, especially the beneficial fungal genera, Lecanicillium, Cladosporium, Saccharomyces and Aspergillus. An investigation of strawberry growth and yield-related indicators revealed that the T6 treatment resulted in the lowest seedling mortality and the highest yield. In summary, adding microbial agents to soil with continuous cropping of strawberry after fumigation with dazomet is a scientifically sound and effective method for reconstructing the balance of the soil microbial flora and overcoming the obstacles associated with continuous cropping. In this study, the T6 (actinomycetes) treatment presented the best performance. Full article

(This article belongs to the Section Plant Microbe Interactions)

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