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Search Results (1,172)

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27 pages, 5575 KB  
Article
Changes in Soil Bacteriobiome in Response to Organic Amendments and Cd2+ Stress
by Agata Borowik, Jadwiga Wyszkowska, Magdalena Zaborowska and Jan Kucharski
Int. J. Mol. Sci. 2026, 27(13), 5783; https://doi.org/10.3390/ijms27135783 - 26 Jun 2026
Viewed by 145
Abstract
Cadmium contamination of soils poses a global threat to food security and ecosystem stability. Soil bacteria play a key role in mitigating Cd-induced stress, and their adaptive capabilities can be modulated by the application of organic amendments such as compost, fermented bark, or [...] Read more.
Cadmium contamination of soils poses a global threat to food security and ecosystem stability. Soil bacteria play a key role in mitigating Cd-induced stress, and their adaptive capabilities can be modulated by the application of organic amendments such as compost, fermented bark, or preparations containing humic acid. This article presents the results of studies on soil bacterial communities using culture-dependent and next-generation sequencing approaches. Based on the obtained data, colony development indices and ecophysiological diversity indices were determined for organotrophic bacteria and actinobacteria. Alpha and beta diversity of bacteria were also assessed, common and unique genera occurring in the studied soils were identified, and the predicted metabolic functions of microorganisms were determined. It was found that cadmium reduced the abundance of organotrophic bacteria and actinobacteria by 54.5% and 12.9%, respectively, compared to the control, resulting in a shift in the bacterial community structure from r-strategists toward K-strategists. Humic acid increased the abundance of organotrophic bacteria and actinobacteria by 42.8% and 57.3%. Compost most effectively mitigated cadmium effects by stabilizing the colony development index and bacterial ecophysiological diversity. Cadmium strongly altered the soil bacterial microbiome, reducing the abundance of Actinomycetota while increasing that of Pseudomonadota and Bacteroidota. The application of organic amendments influenced the bacterial response to Cd2+-induced stress. Fermented bark was associated with an increased abundance of Sphingomonas, whereas compost was associated with an increased abundance of Cellulosimicrobium. Although none of the organic amendments affected the overall diversity index under these conditions, compost improved the evenness and ecological stability of the bacterial community. The dominance of aerobic chemoheterotrophs involved in the carbon cycle and the degradation of organic compounds was demonstrated. Compost most effectively supported biogeochemical processes. Full article
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23 pages, 12628 KB  
Article
Bioinformatics-Based Data Mining of GenBank and Diversity Patterns of Soil Fungal Sequences
by Željko Savković, Miloš Stupar, Andrija Finka, Slaven Zjalić and Jelena Lončar
Forests 2026, 17(7), 731; https://doi.org/10.3390/f17070731 - 24 Jun 2026
Viewed by 313
Abstract
Soil fungi are key drivers of terrestrial ecosystem functioning, contributing to organic matter decomposition, nutrient cycling, and plant–microorganism interactions. Despite their importance, the global distribution and structural biases of public sequence records for soil fungi remain incompletely characterized. In this study, we analyzed [...] Read more.
Soil fungi are key drivers of terrestrial ecosystem functioning, contributing to organic matter decomposition, nutrient cycling, and plant–microorganism interactions. Despite their importance, the global distribution and structural biases of public sequence records for soil fungi remain incompletely characterized. In this study, we analyzed soil-associated fungal DNA sequences retrieved from the NCBI GenBank database using a custom R-based bioinformatics pipeline. Following filtering and metadata standardization, 544,554 filtered sequence records were obtained. The taxonomic composition of the dataset consisted primarily of Ascomycota (69.62%), followed by Basidiomycota, Glomeromycota, and Mucoromycota, with Trichoderma, Penicillium, and Aspergillus representing the most frequent genera. The geographic distribution revealed strong sampling bias, with China and the United States accounting for over one-third of all records. Ecological metadata indicated that rhizospheric and forest soils were the most common sources of the deposited sequences. At the same time, gene marker analyses confirmed the widespread use of the ITS region as the primary fungal barcode. Sequence diversity analyses revealed continental variation, with Europe and Asia showing higher medians, while the ordination highlighted clustering of sequence profiles, particularly among records from extreme environments. This study demonstrates the potential of public sequence databases for large-scale biodiversity assessments while highlighting the influence of sampling bias and the limitations of metadata. Full article
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18 pages, 3721 KB  
Review
Functional Food Containing Probiotics–Differences in Health Benefits Among Men and Women
by Barbara Sionek and Piotr Szymański
Appl. Sci. 2026, 16(12), 6120; https://doi.org/10.3390/app16126120 - 17 Jun 2026
Viewed by 305
Abstract
The consumption of functional foods, especially enriched by probiotics, is appreciated by a growing group of consumers. In this comprehensive review, the comparison of food probiotics’ health advantages between adult healthy women and healthy men was demonstrated with the aim of indicating the [...] Read more.
The consumption of functional foods, especially enriched by probiotics, is appreciated by a growing group of consumers. In this comprehensive review, the comparison of food probiotics’ health advantages between adult healthy women and healthy men was demonstrated with the aim of indicating the target group of consumers. Based on clinical studies and meta-analyses, in the context of sex differences, the impact of functional foods with probiotics on selected disease development and disease course, as well as on the potential health benefits, was discussed. Significantly population-related and most common health abnormalities, such as obesity, metabolic disorders, hypertension, irritable bowel syndrome, and functional gastrointestinal disorders, were analysed. There is a sex-dependent variety of gut microorganisms, and a greater diversity of the gut microbiome is found in women. The major differences between men and women considered in the study included higher prevalence of irritable bowel syndrome and obesity in women, a different lipid profile, and different age-related hypertension occurrence in both groups. Life expectancy has also been taken into account. According to the statistical data, women live longer, experience more health problems in the course of life, and therefore will probably more frequently seek functional food. In general, consumption of functional foods should be supported and recommended for the entire population. The open questions that need to be clarified are if the sex-dependent strategy is justified for choosing specified functional foods and probiotic strains. Full article
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20 pages, 1869 KB  
Article
Microbially Induced Corrosion of Carbon Steel in Oilfield Waters from the Romashkino Oilfield (Republic of Tatarstan): Immersion Corrosion Testing
by Elvira E. Ziganshina and Ayrat M. Ziganshin
Corros. Mater. Degrad. 2026, 7(2), 36; https://doi.org/10.3390/cmd7020036 - 11 Jun 2026
Viewed by 375
Abstract
Microbially induced corrosion is a common problem in the petroleum industry. In this study, weight loss and surface analysis of grade 20 carbon steel corrosion witness samples were used to evaluate biocorrosion in produced fluids from different wells (Romashkino oilfield, Republic of Tatarstan, [...] Read more.
Microbially induced corrosion is a common problem in the petroleum industry. In this study, weight loss and surface analysis of grade 20 carbon steel corrosion witness samples were used to evaluate biocorrosion in produced fluids from different wells (Romashkino oilfield, Republic of Tatarstan, Russia). The structure of the resulting microbial communities in the systems with high corrosion indicators was elucidated. The addition of acetate/lactate, yeast extract, and sulfate was found to promote the growth of individual microorganisms in the designed systems and to increase the corrosion rate in several samples (to an average of 0.12 mm year−1). The results of 16S rRNA gene sequence analysis showed that water from different wells from the Romashkino oilfield had distinct microbial compositions. The main genera in the analyzed waters were Oleidesulfovibrio, Halanaerobium, Proteiniphilum, Acetobacterium, Fusibacter, and Methanocrinis, but their relative abundances depended on the water itself and the type of stimulation. Acetogenic bacteria of the genera Fusibacter, Proteiniphilum, Acetobacterium, and acetoclastic methanogenic archaea Methanocrinis became dominant in the microbial community structure in the acetate-enriched systems in water from one of the studied wells. Electron donors, generated by various bacteria and artificially introduced ones, facilitated active dissimilatory sulfate reduction by Oleidesulfovibrio, Desulfotignum, Desulfocurvus, and Pseudodesulfovibrio in water from another production well. The obtained results are important for identifying the causes of premature failures of oilfield equipment, particularly in areas where microbial enhanced oil recovery is used. Full article
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16 pages, 1808 KB  
Article
The Effect of Microplastics on Soil Microbial Activity, Biomass, and Microbial Community Structure in Three Types of Temperate Forest
by Beata Klimek, Maciej Choczyński and Maria Niklińska
Forests 2026, 17(6), 686; https://doi.org/10.3390/f17060686 - 9 Jun 2026
Viewed by 396
Abstract
Microplastic pollution is a problem of global concern, but its effects on forest soils are largely overlooked. This study is based on a laboratory experiment where the effects of soil-added polyethylene microplastic particles (MP-) of two sizes (60 μm and 140 μm) (Cospheric [...] Read more.
Microplastic pollution is a problem of global concern, but its effects on forest soils are largely overlooked. This study is based on a laboratory experiment where the effects of soil-added polyethylene microplastic particles (MP-) of two sizes (60 μm and 140 μm) (Cospheric LLC, USA) were measured to examine their effects on three types of temperate forest: dry pine forest, beech-dominated forest, and ash-dominated riparian forest that differ greatly in several physicochemical and biological soil properties. The addition of MP- did not significantly alter the respiration rate of any of the forest soils studied (p = 0.6303), as shown by ANOVA. Soil microbial biomass, as measured by the phospholipid fatty acid (PLFA) method, decreased under 60 µm MP treatment but not under 140 µm MP treatment (p = 0.0094). MP- did affect microbial community structure, especially increasing the proportion of bacteria in the community under 60 µm MP treatment (p = 0.0023). MP- affected the PLFA pattern, as shown by PERMANOVA analysis along with NMDS ordination; the effect was similar in the three studied forest types. As shown by SIMPER analysis, there was a relative decrease in fatty acid 16:1ω7 and a simultaneous increase in 16:0 and 18:0 under both MP treatments. This may potentially serve as an indication of MP pollution in temperate forest soils. Our results suggest that forest soil bacteria, as a group, may benefit from MPs at the expense of fungi, which provides a new perspective on how soil microorganisms interact under globally common MP pollution. Full article
(This article belongs to the Special Issue The Role of Soil Fauna and Microbial Communities in Forests)
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30 pages, 4834 KB  
Article
Valorization of Lemon Processing By-Products Through Multi-Strain Fermentation: Strain-Specific Changes in Flavonoids, Limonoids, and Antioxidant Capacity
by Ching I Lin, Chih Hsuan Fan, Shu Hsien Tsai, Chia Hsin Chang, Chiao Min Yang, Bao Hong Shi, Ying Hsuan Tsai and Ming Yi Lee
Antioxidants 2026, 15(6), 730; https://doi.org/10.3390/antiox15060730 - 9 Jun 2026
Viewed by 308
Abstract
Lemon processing by-products are rich in flavonoids, limonoids, and phenolic acids, but their direct utilization is limited by glycoside-dominant flavonoid profiles, bitterness-associated limonoids, and insufficiently defined valorization strategies. This study compared eight food-relevant microorganisms, including lactic acid bacteria, Bacillus, yeast, and filamentous [...] Read more.
Lemon processing by-products are rich in flavonoids, limonoids, and phenolic acids, but their direct utilization is limited by glycoside-dominant flavonoid profiles, bitterness-associated limonoids, and insufficiently defined valorization strategies. This study compared eight food-relevant microorganisms, including lactic acid bacteria, Bacillus, yeast, and filamentous fungi, using a common aerobic submerged fermentation framework for lemon by-products. Rather than evaluating fermentation as a single uniform process, the study aimed to determine whether different microbial groups could redirect the same substrate toward distinct functional remodeling profiles. Targeted HPLC analysis of flavonoids, limonoids, and phenolic acids, together with DPPH and ABTS radical-scavenging assays, revealed clear strain-dependent differences in metabolite remodeling and antioxidant outcomes. L. plantarum showed the most consistent antioxidant enhancement profile, characterized by increased hesperetin and phenolic acid responses together with low DPPH and ABTS IC50 values. L. pentosus promoted flavonoid remodeling but showed a more timing-sensitive antioxidant response. S. cerevisiae tended to preserve glycosylated flavonoids and showed a release-oriented phenolic acid profile with strong early ABTS activity. R. stolonifer exhibited the most pronounced limonoid remodeling, including marked limonin reduction and obacunone accumulation, suggesting potential relevance for bitterness-oriented applications. These findings demonstrate that different microorganisms can be functionally classified according to their dominant remodeling tendencies, including antioxidant enhancement, flavonoid conversion, glycosylated flavonoid preservation, phenolic acid release, and limonoid-associated debittering. This functional classification provides a practical basis for selecting microorganisms according to the intended application of lemon by-product valorization. Full article
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14 pages, 30002 KB  
Article
A Comprehensive In Vitro Assessment of Broad-Spectrum Antimicrobial Efficacy of Organo-Selenium-Incorporated Urinary Catheter in Comparison to a Zwitterionic Surface Catheter
by Harry May, Md Abid Afridi, Phat L. Tran, Hannah Seo, Eric Tran, Wei Li, Ted W. Reid and Werner T. W. de Riese
Antibiotics 2026, 15(6), 574; https://doi.org/10.3390/antibiotics15060574 - 4 Jun 2026
Viewed by 406
Abstract
Background/Objectives: Catheter-associated urinary tract infections (CAUTIs) are one of the most common healthcare-related morbidities. Also, severe clinical outcomes derived from CAUTIs demand an urgent need for the development of novel antimicrobial catheter materials. Since CAUTIs are primarily driven by a wide range [...] Read more.
Background/Objectives: Catheter-associated urinary tract infections (CAUTIs) are one of the most common healthcare-related morbidities. Also, severe clinical outcomes derived from CAUTIs demand an urgent need for the development of novel antimicrobial catheter materials. Since CAUTIs are primarily driven by a wide range of microorganisms causing biofilm formation on the surfaces of catheters, evaluating the effectiveness of innovative antimicrobial materials against a broad spectrum of known uropathogens is warranted. We aim (1) to demonstrate the ability of incorporated organo-selenium versus that of an FDA-cleared antimicrobial catheter and (2) to show that the results of the study are consistent against the most common microorganisms causing urinary tract infections in humans. Methods: Based on encouraging preliminary studies, three percent of organo-selenium (weight-based), as a novel antimicrobial catheter material, was incorporated into thermoplastic polyurethane (TPU). This was compared in vitro with plain polyurethane catheters and the SILQ ClearTract catheter with a zwitterionic coating (FDA-cleared for its antimicrobial properties in December 2022). The antimicrobial activity was studied against Candida albicans, Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa, Staphylococcus aureus, MRSA, and Staphylococcus epidermidis by assessment of colony-forming unit counts along with visual confirmation using Scanning Electron Microscopy (SEM). Results: Plain polyurethane catheters (control group) showed 7- to 8-log of in vitro growth for all tested microbes, whereas the antimicrobial zwitterionic SILQ ClearTract catheters still showed 6- to 7-log of microbial growth. In contrast, organo-selenium-incorporated catheters demonstrated no detectable in vitro growth for all tested microbes (C. albicans, E. coli, K. pneumoniae, P. mirabilis, P. aeruginosa, S. aureus, MRSA, and S. epidermidis). SEM analysis also validated the findings. Conclusions: Potentially non-leaching organo-selenium, as a novel urinary catheter material, significantly inhibited microbial attachment, growth, and biofilm formation across a wide spectrum of common uropathogenic organisms compared to a zwitterionic catheter, providing a strong foundation for further detailed in vivo and clinical studies. Full article
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24 pages, 3453 KB  
Article
Scale of Concern: Efficacy of Commercially Available Topical Carp Care Formulations for Recreational Application in Carp
by Eleanor Makin, Georgina Shilton, Olivia Brotherhood, Amaara Rassool-Amin, Kyle Gordon, Harini Satkunarasa, Paula Reynolds, Ian Wellby, Jessica Locker, Omar Qutachi and Chris Young
Aquac. J. 2026, 6(2), 19; https://doi.org/10.3390/aquacj6020019 - 31 May 2026
Viewed by 7690
Abstract
Opportunistic bacterial and fungal infections from surface wounds remain a persistent threat to aquaculture, resulting in significant economic losses and reduced stock welfare. Topical wound sealants are widely employed in recreational aquaculture applications, yet no market regulation or efficacy data exist to support [...] Read more.
Opportunistic bacterial and fungal infections from surface wounds remain a persistent threat to aquaculture, resulting in significant economic losses and reduced stock welfare. Topical wound sealants are widely employed in recreational aquaculture applications, yet no market regulation or efficacy data exist to support their usage. The broader biological/environmental impacts of these products also remain poorly characterized. This study provides the first quantitative assessment of the antibacterial, antifungal and cellular toxicity of a panel of commercially available topical ‘carp care’ formulations. Our data highlights highly variable to no functional growth inhibition or killing of microbial pathogens, significant inherent cyprinid cellular toxicity, and lack of submerged wet adhesion in all products tested. We show for the first time that commercial propolis solutions are ineffective against the four main pathogenic microorganisms affecting carp. Propolis formulations were also found to induce apoptosis and ROS generation in cyprinid cells in vitro, and permeabilise intact carp skin, questioning the foundation of propolis formulations in topical wound-care treatments for carp rearing/angling. We show improved efficacies can be attained through natural compound implementation, with increased antibacterial and antifungal effects, inherent regenerative benefits to cyprinid fibroblasts, and improved human and environmental safety profiles. This research demonstrates the widespread lack of efficacy in currently commercially available wound sealants for carp; of those tested here, many popular formulations are in fact inherently toxic to carp cells, and also have a permeabilizing effect on intact carp skin due to carrier solvent effects, providing a route for secondary infection; most show no activity against any common carp pathogens; and all uniformly lacked wet adhesion. This work provides a framework standard for the future development of topical wound-care formulations for carp and highlights the need for better dialogue between trade and academia when designing novel wound-care products. Full article
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18 pages, 683 KB  
Article
Comprehensive Evaluation of Uropathogens’ AMR in a Romanian Tertiary Center: Male vs. Female Comparison
by Răzvan-Ionuț Popescu, Cristian Toma, Răzvan-Cosmin Petca, Cristian Mareș, Leonard Ostafi, Aida Petca and Viorel Jinga
Microorganisms 2026, 14(6), 1236; https://doi.org/10.3390/microorganisms14061236 - 30 May 2026
Viewed by 436
Abstract
Introduction: Urinary tract infections (UTIs) represent a growing concern in both clinical practice and public health, affecting hospitalized and outpatient populations across all ages and genders. This study aims to evaluate the prevalence of uropathogens and their antimicrobial resistance profiles in male and [...] Read more.
Introduction: Urinary tract infections (UTIs) represent a growing concern in both clinical practice and public health, affecting hospitalized and outpatient populations across all ages and genders. This study aims to evaluate the prevalence of uropathogens and their antimicrobial resistance profiles in male and female patients comparatively at a tertiary urological center. Materials and Methods: A retrospective descriptive analysis was conducted, covering three identical 6-month periods—September 1 to February 28—in three consecutive years from 2023 to 2025. The study included 2270 male patients (2270. 57.06%) and 1708 female patients (1708. 42.94%), all with at least one positive urine culture (>105 CFU/mL). Data on age, gender, bacterial species, and antimicrobial agents were collected and analyzed. Results: A higher prevalence of Gram-negative bacteria was observed compared to Gram-positive bacteria in both male (1752; 77.18% vs. 518; 22.82%) and female (1369; 80.15% vs. 339; 19.85%) groups. The most common microorganisms were Escherichia coli, followed by Klebsiella and Enterococcus. Klebsiella showed high rates of antimicrobial resistance, especially in males, across various antibiotic classes such as amoxicillin-clavulanic acid (60.6% vs. 43.25%), levofloxacin (40.18% vs. 27.91%), aztreonam (37.4% vs. 27.27%), and ceftazidime (36.23% vs. 24.03%). High resistance levels, although not statistically significant, were also noted for trimethoprim/sulfamethoxazole (43.64%) and nitrofurantoin (65.69%). In males, E. coli exhibited higher resistance rates to trimethoprim/sulfamethoxazole (44.65% vs. 32.89%), levofloxacin (43.27% vs. 30.78%), and amoxicillin-clavulanic acid (40.18% vs. 27.19%). Carbapenems remained highly susceptible in both groups. Enterococcus showed similar resistance patterns in both cohorts, primarily resistant to penicillin and levofloxacin. Conclusion: This study highlights higher resistance rates among Gram-negative bacteria in males to commonly used antibiotics such as fluoroquinolones, trimethoprim/sulfamethoxazole, and β-lactams. Resistance patterns in Gram-positive bacteria remained stable across both populations, with high susceptibility to fosfomycin, nitrofurantoin, linezolid, and carbapenems. Differences between sexes emphasize the need for more detailed analysis of local and sex-specific resistance patterns. Full article
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13 pages, 988 KB  
Article
Linking Groundwater Contamination to Microbial Community Shifts Around Rare Earth Tailing Ponds: A Correlational Study Using Microbiological Indices
by Tinglin Chen, Yan Wei, Yuner Liu and Minjie Chen
Diversity 2026, 18(6), 315; https://doi.org/10.3390/d18060315 - 25 May 2026
Viewed by 776
Abstract
Pollutants often exist in tailings and surrounding areas as complex mixtures, and the resulting combined effects make it difficult to identify the primary target pollutants, particularly common inorganic anions. To address this, high-throughput 16S rRNA gene sequencing was used to characterize the microbial [...] Read more.
Pollutants often exist in tailings and surrounding areas as complex mixtures, and the resulting combined effects make it difficult to identify the primary target pollutants, particularly common inorganic anions. To address this, high-throughput 16S rRNA gene sequencing was used to characterize the microbial community structure in groundwater around rare earth tailing ponds, and multivariate statistical analyses were applied to link community patterns to specific environmental variables. A total of 14 groundwater samples were collected from seven sites (two spatial replicates per site) along a contamination gradient. The results showed distinct differences in microbial community composition between the control site and the tailing-pond-impacted sites. Nitrosomonas was the dominant genus at highly contaminated sites, while halotolerant genera such as Seohaeicola, Pusillimonas, and Oceanibaculum also showed elevated relative abundances. Redundancy analysis (RDA) with forward selection identified the co-occurring elevated concentrations of NH4+ and SO42− (originating from tailing pond leachate) as the environmental variables most strongly associated with microbial community structure (p < 0.05). In contrast, the microbial community at the control site WLJ-5, located farthest from the tailing pond, was markedly different. These findings suggest that shifts in microbial community composition and the prevalence of specific microorganisms may serve as potential bioindicators to assist in identifying the dominant contaminant types in groundwater around rare earth tailing ponds. Full article
(This article belongs to the Section Microbial Diversity and Culture Collections)
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21 pages, 1112 KB  
Article
Assessment of the Impacts of Common Morel (Morchella sextelata) Cultivation on Soil Physicochemical Properties and Microbial Communities in Different Environments
by Zhongyan Tang, Chen Chen, Li Dong, Liuyuan Bao, Chengcui Yang, Xiaodan Wang, Xiaoling Chen, Xiaokun Li, Fajun Xiang and Shunqiang Yang
Microorganisms 2026, 14(5), 1115; https://doi.org/10.3390/microorganisms14051115 - 14 May 2026
Viewed by 375
Abstract
Morchella sextelata a species of high nutritional and economic value, is widely cultivated. To investigate how different cultivation environments affect the soil physicochemical properties and microbial communities associated with common morel, this study established cultivation plots under three distinct settings: apple orchard canopies, [...] Read more.
Morchella sextelata a species of high nutritional and economic value, is widely cultivated. To investigate how different cultivation environments affect the soil physicochemical properties and microbial communities associated with common morel, this study established cultivation plots under three distinct settings: apple orchard canopies, dry upland fields, and paddy fields. The objective was to compare the differential impacts of common morel cultivation on soil environmental conditions across these habitats. The results indicate that cultivating common morel effectively enhances soil fertility. Across all environments, soil hydrolyzable nitrogen (HN), available potassium (AK), and organic matter content were higher than in the control. In apple orchard and dryland soils, total phosphorus (TP), total potassium (TK), available phosphorus (AP), and pH values were also elevated compared to the control, with most differences reaching significant levels. Solid Sucrase (S-SC) activity increased in all environments compared to the control, with values of 17.52 mg/d/g in PG, 17.39 mg/d/g in HD, and 21.68 mg/d/g in DT soils. Soil Amylase (S-AL) activity was higher in PG (451.28 μg/h/g) and HD (475.38 μg/h/g) soils. In contrast, Soil-acid phosphatase (S-ACP) activity was significantly elevated in DT soil (2922.08 nmol/h/g). PG soil exhibited significantly higher activities of Solid-Catalase (S-CAT), Solid polyphenol oxidase (S-PPO), and Solid Urease (S-UE), with S-CAT reaching 952.5 μmol/h/g. Following common morel cultivation, bacterial richness and diversity decreased across all conditions, while fungal richness increased but diversity declined. At the phylum level, Proteobacteria remained the dominant bacterial group, accounting for 26.78% in PG, 28.27% in HD, and 20.05% in DT soils. Ascomycota was the predominant fungal phylum, comprising 68.03% in PG, 72.16% in HD, and 68.94% in DT soils. Predicted bacterial functional pathways were primarily associated with metabolism, genetic information processing, environmental information processing, and cellular processes. Key metabolic pathways included carbohydrate metabolism, amino acid metabolism, and metabolism of cofactors and vitamins. fungal functional guilds were mainly classified as pathotrophic, pathotrophic–saprotrophic, pathotrophic–saprotrophic–symbiotrophic, and saprotrophic. Among these, saprotrophic and pathotrophic guilds showed higher abundance compared to the control. This shift is characterized by a reduction in both the diversity and abundance of beneficial microorganisms, alongside an increase in the richness of harmful microbial taxa. The combined effect of these factors disrupts the soil microbial equilibrium. The findings of this study provide a theoretical foundation for the cultivation of common morel and the management of associated soils. Full article
(This article belongs to the Section Environmental Microbiology)
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20 pages, 4432 KB  
Article
Comparative Metagenomic Studies Reveal Different Evolutionary Directions of Synthetic Indoor Microbial Communities Under Different Nutritional Conditions
by Xinyi Zhang, Lin Cai, Yukun Bai and Fang Peng
Int. J. Mol. Sci. 2026, 27(10), 4238; https://doi.org/10.3390/ijms27104238 - 10 May 2026
Viewed by 329
Abstract
The relationship between microorganisms and human health is inseparable. In today’s increasingly urbanized world, the relationship between indoor microbial communities and human health is particularly close. Studies have shown that the composition of indoor microbial communities is influenced by various factors, including temperature, [...] Read more.
The relationship between microorganisms and human health is inseparable. In today’s increasingly urbanized world, the relationship between indoor microbial communities and human health is particularly close. Studies have shown that the composition of indoor microbial communities is influenced by various factors, including temperature, humidity, and nutrient conditions. However, research on how to alter indoor microbial community structures by adjusting nutrient components to improve human health is still limited. In this work, we constructed artificial microbial communities composed of common indoor microorganisms, and analyzed the species composition, metabolic capabilities, antibiotic resistance, and virulence of the microbial communities before and after cultivation using metagenomic sequencing technologies and metatranscriptomic sequencing technologies. We then assessed their community characteristics and evolutionary direction under different nutrient conditions. Overall, when the nutrient conditions were altered and reduced, the evolutionary direction of indoor microbial communities changed significantly. Specifically, this evolutionary direction was manifested in a taxonomic succession of community composition, with marked shifts in the relative abundances of constituent species, as well as in a significant alteration of the community-level metabolic functions. In-depth research in this field can help improve the composition of indoor microbial communities, thereby benefiting human health and public health construction in urbanized environments. Full article
(This article belongs to the Section Molecular Microbiology)
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14 pages, 638 KB  
Article
Diagnostic Accuracy of Synovial Calprotectin in Megaprosthetic Reconstructions: A Prospective Cohort Study from a Tertiary Sarcoma Center
by Panayiotis Gavriil, Pavlos Altsitzioglou, Ioannis Trikoupis, Efthalia Maleka, Panagiotis Briassoulis, Jendrik Hardes, Panayiotis Papagelopoulos and Vasileios Kontogeorgakos
Cancers 2026, 18(10), 1511; https://doi.org/10.3390/cancers18101511 - 8 May 2026
Viewed by 498
Abstract
Background/Objectives: Diagnosing periprosthetic joint infection (PJI) after megaprosthetic reconstruction may be difficult due to altered inflammatory responses, extensive prior surgery, and the limited performance of conventional criteria such as the 2018 ICM score. Synovial calprotectin is a rapid neutrophil-derived biomarker that may improve [...] Read more.
Background/Objectives: Diagnosing periprosthetic joint infection (PJI) after megaprosthetic reconstruction may be difficult due to altered inflammatory responses, extensive prior surgery, and the limited performance of conventional criteria such as the 2018 ICM score. Synovial calprotectin is a rapid neutrophil-derived biomarker that may improve diagnostic accuracy in this challenging setting. The primary aim of this study was to evaluate the diagnostic performance of synovial calprotectin in detecting periprosthetic infection in patients treated with tumor megaprostheses; secondary aims included comparison with ICM classification, assessment in infection classification-inconclusive cases, and exploratory performance in patients with low CRP. Methods: This prospective study included 20 consecutive megaprosthesis patients evaluated for suspected PJI at ATTIKON University Hospital, Athens, with a minimum follow-up of 1 year after biomarker testing. Synovial calprotectin was measured using a lateral-flow assay (positive ≥ 50 mg/L) and compared with a predefined infection reference standard. ICM final status (0 = aseptic, 1 = inconclusive, 2 = infected) was recorded for all cases. Other synovial biomarkers (α-defensin, leukocyte esterase, synovial D-dimer) were not routinely available. The cohort had a mean age of 52.9 ± 22.5 years, 70% were male, and reconstructions involved the knee (80%), hip (15%), and humerus (5%). Preoperative cultures were positive in 40%, the median systemic WBC was 7100/μL, and the median time from last surgery to testing was 1.0 years (IQR 0.46–2.0). Among infected cases, the most common microorganisms were coagulase-negative staphylococci (61.5%) and Staphylococcus aureus (23.1%), with 30.8% demonstrating polymicrobial infection. Results: Thirteen of 20 patients (65%) were classified as infected. Using the ≥50 mg/L threshold, synovial calprotectin demonstrated high apparent diagnostic accuracy in this exploratory cohort, and no false positives, yielding a sensitivity of 92.3%, specificity of 100%, PPV of 100%, NPV of 87.5%, LR+ = ∞, and LR− = 0.08. The AUC for continuous values was 1.00. Agreement with the ICM final classification was substantial (κ = 0.76), with no directional discordance (McNemar p = 1.00). Among the three ICM-inconclusive cases, calprotectin correctly reclassified two (66.7%). In patients with low CRP (<10 mg/L), a clinically difficult subgroup, calprotectin maintained strong performance (sensitivity 75%, specificity 100%, NPV 85.7%). Conclusion: Synovial calprotectin demonstrated promising diagnostic performance for PJI in megaprosthesis patients, with high sensitivity and specificity, and substantial agreement with the 2018 ICM criteria. It successfully clarified most ICM-inconclusive cases and remained reliable even in patients with low CRP. These findings support calprotectin as a valuable adjunctive biomarker in the complex diagnostic environment of megaprosthetic reconstruction and justify further validation in larger cohorts. Full article
(This article belongs to the Special Issue Sarcoma Management in Orthopaedic Oncology)
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18 pages, 8664 KB  
Article
Metagenomic Profiling Reveals Extensive Bacterial Diversity in Chicken Manure and Associated Contaminated Wastewater
by Sadir Zaman, Nawab Ali, Waheed Ullah, Nadia Taimur, Noor ul Akbar, Aiman Waheed, Niaz Muhammad and Muhammad Saeed Khan
Int. J. Mol. Sci. 2026, 27(9), 3741; https://doi.org/10.3390/ijms27093741 - 23 Apr 2026
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Abstract
Chicken manure and its potential to contaminate water systems through the dispersal of pathogenic bacteria are major concerns in environmental and public health. In this study, a metagenomic analysis was employed to systematically identify and compare bacterial assemblages in chicken manure (CM) and [...] Read more.
Chicken manure and its potential to contaminate water systems through the dispersal of pathogenic bacteria are major concerns in environmental and public health. In this study, a metagenomic analysis was employed to systematically identify and compare bacterial assemblages in chicken manure (CM) and in a contaminated sample of chicken manure wastewater (CMW). Whole DNA was extracted from CM and CMW, followed by whole-genome shotgun sequencing; data analysis was done using online Galaxy software (ver. 26.0.1.dev1). Metagenomic analysis reveals a complex One Health challenge. Data showed that CM and CMW are different in their microbiota, as indicated by a distinct separation of beta diversity values and limited overlapping of species between sample types. In the current study, we found a greatly significant common functional set of adapted bacterial masses, including major pathogenic bacterial groups as well as opportunistic and environmental bacterial species, indicative of a direct contamination from CM and CMW. Notably, in both CM and CMW, a plethora of opportunistic, enteric, and environmental pathogens like Escherichia coli, Salmonella enterica, and Acinetobacter baumannii were found, coupled with an indication of a direct functional flow between both ecosystems as tangled reservoirs. Chicken manure samples showed differences in taxonomic composition and inferred functional profiles at the time of sampling: CM1 was pathogen-enriched, CM2 exhibited strong nitrogen-supportive metabolism, CM3 was dominated by fiber-degrading decomposers, and CM4 showed high methane-producing potential with environmental risk. Such findings underscore the raising of chickens as a potential source of harmful bacteria for the environment. It is important to note that this study represents a preliminary investigation with certain limitations, including the absence of biological replicates, lack of temporal sampling, and limited capacity to infer dynamic ecological interactions. Yet this metagenomic report is more about describing the taxonomy and functional potential of the bacteria, rather than discussing the actual ecological processes of these microorganisms in the environment. Future studies will be required to explore these aspects. Full article
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16 pages, 1194 KB  
Article
A Multiplex One-Tube Nested Real-Time PCR Assay for the Point-of-Care Testing of Infectious Meningitis
by Duoxiao Zhang, Jie Wang, Zijin Zhao, Yanqing Tie, Jianing Wu, Shihao Jiao, Xingyu Liu, Yuxin Wang, Shijue Gao, Mengchuan Zhao, Pei Zhao, Zhiqiang Han, Xiaona Lyu, Xinxin Shen, Xuejun Ma and Zhishan Feng
Pathogens 2026, 15(5), 456; https://doi.org/10.3390/pathogens15050456 - 22 Apr 2026
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Abstract
In this study, we developed a multiplex one-tube nested real-time fluorescent quantitative PCR (mONRT-PCR) assay integrated with a portable, fully automated nucleic acid point-of-care testing (POCT) platform for the detection of Haemophilus influenzae (H. influenzae), Listeria monocytogenes (L. monocytogenes), [...] Read more.
In this study, we developed a multiplex one-tube nested real-time fluorescent quantitative PCR (mONRT-PCR) assay integrated with a portable, fully automated nucleic acid point-of-care testing (POCT) platform for the detection of Haemophilus influenzae (H. influenzae), Listeria monocytogenes (L. monocytogenes), and Cryptococcus neoformans (C. neoformans) in cerebrospinal fluid (CSF). The assay enables nested amplification within a closed system using conventional primers and probes, thereby reducing operational complexity and minimizing contamination risk. Analytical evaluation demonstrated limits of detection of 100 copies/μL for H. influenzae and L. monocytogenes, and 101 copies/μL for C. neoformans using recombinant plasmids, as well as 10−7 to 10−6 ng/μL using genomic DNA. No cross-reactivity was observed when tested against a panel of 17 common non-target microorganisms encountered in clinical microbiology laboratories. In simulated CSF samples, the assay maintained detectable amplification at low pathogen concentrations. When implemented on the POCT platform, detection limits reached 5, 10, and 50 CFU/mL for the three pathogens, respectively. Clinical evaluation using 43 CSF samples showed almost perfect agreement with conventional qPCR (κ = 0.861, p < 0.001). Notably, additional C. neoformans detections were observed by mONRT-PCR-POCT compared with qPCR, suggesting improved sensitivity under clinical conditions. The assay yielded results within approximately 1 h and 47 min. These findings indicate that the proposed assay provides a rapid, sensitive, and integrated approach for meningitis pathogen detection, while maintaining a practical balance between analytical performance and operational simplicity. Further validation in larger cohorts is warranted. Full article
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