Microorganisms

23 pages, 1429 KiB

Open AccessArticle

L-Arabinose Alters the E. coli Transcriptome to Favor Biofilm Growth and Enhances Survival During Fluoroquinolone Stress

by Katherine M. Austin, Jenna K. Frizzell, Audrey A. Neighmond, Isabella J. Moppel and Lisa M. Ryno

Microorganisms 2025, 13(7), 1665; https://doi.org/10.3390/microorganisms13071665 (registering DOI) - 15 Jul 2025

Abstract

Environmental conditions, including nutrient composition and temperature, influence biofilm formation and antibiotic resistance in Escherichia coli. Understanding how specific metabolites modulate these processes is critical for improving antimicrobial strategies. Here, we investigated the growth and composition of Escherichia coli in both planktonic [...] Read more.

Environmental conditions, including nutrient composition and temperature, influence biofilm formation and antibiotic resistance in Escherichia coli. Understanding how specific metabolites modulate these processes is critical for improving antimicrobial strategies. Here, we investigated the growth and composition of Escherichia coli in both planktonic and biofilm states in the presence of L-arabinose, with and without exposure to the fluoroquinolone antibiotic levofloxacin, at two temperatures: 28 and 37 °C. At both temperatures, L-arabinose increased the growth rate of planktonic E. coli but resulted in reduced total growth; concurrently, it enhanced biofilm growth at 37 °C. L-arabinose reduced the efficacy of levofloxacin and promoted growth in sub-minimum inhibitory concentrations (25 ng/mL). Transcriptomic analyses provided insight into the molecular basis of arabinose-mediated reduced susceptibility of E. coli to levofloxacin. We found that L-arabinose had a temperature- and state-dependent impact on the transcriptome. Using gene ontology overrepresentation analyses, we found that L-arabinose modulated the expression of many critical antibiotic resistance genes, including efflux pumps (ydeA, mdtH, mdtM), transporters (proVWX), and biofilm-related genes for external structures like pili (fimA) and curli (csgA, csgB). This study demonstrates a previously uncharacterized role for L-arabinose in modulating antibiotic resistance and biofilm-associated gene expression in E. coli and provides a foundation for additional exploration of sugar-mediated antibiotic sensitivity in bacterial biofilms. Full article

(This article belongs to the Section Biofilm)

24 pages, 2320 KiB

Open AccessArticle

Glucoselipid Biosurfactant Biosynthesis Operon of Rouxiella badensis DSM 100043^T: Screening, Identification, and Heterologous Expression in Escherichia coli

by Andre Fahriz Perdana Harahap, Chantal Treinen, Leonardo Joaquim Van Zyl, Wesley Trevor Williams, Jürgen Conrad, Jens Pfannstiel, Iris Klaiber, Jakob Grether, Eric Hiller, Maliheh Vahidinasab, Elvio Henrique Benatto Perino, Lars Lilge, Anita Burger, Marla Trindade and Rudolf Hausmann

Microorganisms 2025, 13(7), 1664; https://doi.org/10.3390/microorganisms13071664 (registering DOI) - 15 Jul 2025

Abstract

Rouxiella badensis DSM 100043^T had been previously proven to produce a novel glucoselipid biosurfactant which has a very low critical micelle concentration (CMC) as well as very good stability against a wide range of pH, temperature, and salinity. In this study, we [...] Read more.

Rouxiella badensis DSM 100043^T had been previously proven to produce a novel glucoselipid biosurfactant which has a very low critical micelle concentration (CMC) as well as very good stability against a wide range of pH, temperature, and salinity. In this study, we performed a function-based library screening from a R. badensis DSM 100043^T genome library to identify responsible genes for biosynthesis of this glucoselipid. The identified open reading frames (ORFs) were cloned into several constructs in Escherichia coli for gene permutation analysis and the individual products were analyzed using high-performance thin-layer chromatography (HPTLC). Products of interest from positive expression strains were purified and analyzed by liquid chromatography/electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) and nuclear magnetic resonance (NMR) for further structure elucidation. Function-based screening of 5400 clones led to the identification of an operon containing three ORFs encoding acetyltransferase GlcA (ORF1), acyltransferase GlcB (ORF2), and phosphatase/HAD GlcC (ORF3). E. coli pCAT2, with all three ORFs, resulted in the production of identical R. badensis DSM 100043^T glucosedilipid with Glu-C_10:0-C_12:1 as the main congener. ORF2-deletion strain E. coli pAFP1 primarily produced glucosemonolipids, with Glu-C_10:0,3OH and Glu-C_12:0 as the major congeners, predominantly esterified at the C-2 position of the glucose moiety. Furthermore, fed-batch bioreactor cultivation of E. coli pCAT2 using glucose as the carbon source yielded a maximum glucosedilipid titer of 2.34 g/L after 25 h of fermentation, which is 55-fold higher than that produced by batch cultivation of R. badensis DSM 100043^T in the previous study. Full article

(This article belongs to the Special Issue Advances in Microbial Surfactants: Production and Applications (2nd Edition))

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22 pages, 9507 KiB

Open AccessArticle

Essential Oils as an Antifungal Alternative to Control Several Species of Fungi Isolated from Musa paradisiaca: Part III

by Maritza D. Ruiz Medina and Jenny Ruales

Microorganisms 2025, 13(7), 1663; https://doi.org/10.3390/microorganisms13071663 (registering DOI) - 15 Jul 2025

Abstract

Essential oils (EOs) are widely recognized for their antifungal properties, but their efficacy against specific phytopathogenic fungi associated with banana (Musa paradisiaca) rot remains underexplored. This study aimed to evaluate the antifungal potential of EOs from Origanum vulgare, Salvia rosmarinus [...] Read more.

Essential oils (EOs) are widely recognized for their antifungal properties, but their efficacy against specific phytopathogenic fungi associated with banana (Musa paradisiaca) rot remains underexplored. This study aimed to evaluate the antifungal potential of EOs from Origanum vulgare, Salvia rosmarinus, Syzygium aromaticum, Thymus vulgaris, Cinnamomum verum, and Ocimum basilicum against five fungal species isolated from infected banana peels. Fungal isolates were obtained using PDA medium supplemented with chloramphenicol and were purified by weekly subculturing. Morphological and microscopic characterization was complemented by molecular identification based on ITS sequencing and phylogenetic reconstruction using Neighbor-Joining and UPGMA methods in MEGA v11. In vitro and ex vivo antifungal assays were performed at EO concentrations ranging from 200 to 1000 ppm. Thyme oil exhibited the strongest inhibitory effect, with complete growth suppression at 1000 ppm. Cinnamon and oregano also demonstrated effective inhibition at 600 ppm, while clove, rosemary, and basil were markedly less effective. Statistical analysis confirmed significant effects of EO type and concentration on fungal growth (p < 0.001). Molecular results showed strong phylogenetic support for isolate identification, with bootstrap values above 93% in most clades. These findings support the selective use of specific EOs as sustainable alternatives to synthetic fungicides in the postharvest management of banana diseases and provide a molecularly supported basis for their targeted application in integrated control strategies. Full article

(This article belongs to the Special Issue Current Pattern in Epidemiology and Antifungal Resistance)

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11 pages, 1235 KiB

Open AccessArticle

Foodborne Botulism Caused by Clostridium botulinum Subtype A5(b3) by Self-Packaged Vacuum Spicy Rabbit Heads

by Wen Cui, Chuanmin Ma, Ming Liu, Yan Li, Lin Zhou, Yuwen Shi, Xuefang Xu and Hui Liu

Microorganisms 2025, 13(7), 1662; https://doi.org/10.3390/microorganisms13071662 (registering DOI) - 15 Jul 2025

Abstract

Botulism is a severe muscle paralysis disease mediated by the botulinum toxin. Here, we reported a foodborne botulism case caused by Clostridium botulinum subtype A5(b3) from self-packaged vacuum spicy rabbit heads. Treatment for this case was delayed due to misdiagnosis and insufficient diagnostic [...] Read more.

Botulism is a severe muscle paralysis disease mediated by the botulinum toxin. Here, we reported a foodborne botulism case caused by Clostridium botulinum subtype A5(b3) from self-packaged vacuum spicy rabbit heads. Treatment for this case was delayed due to misdiagnosis and insufficient diagnostic capacity in three hospitals, which resulted in progressive clinical deterioration, and eventually, the patient was transferred to Shandong Public Health Clinical Center for specialized therapy. The case was suspected as foodborne botulism by the Qilu Medical-Prevention Innovation Integration pathway and multi-disciplinary consultation. An epidemiological investigation and laboratory confirmation revealed that the botulinum neurotoxin originated from vacuum-packaged spicy rabbit heads distributed via interprovincial cold chain logistics. After treatment with botulism antiserum, the patient’s condition significantly improved, and they were discharged after recovery. We revealed that this foodborne botulism outbreak was caused by the Clostridium botulinum A5(b3) subtype from food by whole-genome sequencing and SNP typing. All the strains belonged to Group I carrying the botulinum neurotoxin gene classified as the ha cluster. Toxin A was confirmed by MBA and other methods, while toxin B was non-functional due to the truncated bont/B gene. Other virulence genes and antibiotic resistance genes were also detected. Our findings indicate that self-packaged vacuum meat products represent an emerging risk factor for botulism transmission when stored improperly. Importantly, the recurrent misdiagnosis in this case underscored the urgent need to enhance the training of healthcare professionals in medical institutions to improve the diagnostic accuracy and clinical management of botulism. Full article

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

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17 pages, 2846 KiB

Open AccessArticle

IL-24 Is a Promising Molecular Adjuvant for Enhancing Protective Immunity Induced by DNA Vaccination Against Toxoplasma gondii

by Bohuai Xu, Xiuqiang Zhang, Yaowen Wang and Jia Chen

Microorganisms 2025, 13(7), 1661; https://doi.org/10.3390/microorganisms13071661 (registering DOI) - 14 Jul 2025

Abstract

Toxoplasma gondii, a parasitic protozoan, causes zoonotic infections with severe health impacts in humans and warm-blooded animals, underscoring the urgent need for effective vaccines to control these infections. In this study, a DNA vaccine encoding TgROP5, TgROP18, TgGRA7, TgGRA15, and TgMIC6 was [...] Read more.

Toxoplasma gondii, a parasitic protozoan, causes zoonotic infections with severe health impacts in humans and warm-blooded animals, underscoring the urgent need for effective vaccines to control these infections. In this study, a DNA vaccine encoding TgROP5, TgROP18, TgGRA7, TgGRA15, and TgMIC6 was formulated using the eukaryotic expression vector pVAX I. IL-24 was delivered as a molecular adjuvant using plasmid pVAX-IL-24. BALB/c, C57BL/6, and Kunming mouse strains received the DNA immunization, after which antibody levels, cytokine production, and lymphocyte surface markers were analyzed to assess immune responses. Additionally, survival rates and brain cyst counts were measured 1 to 2 months post-vaccination in experimental models of toxoplasmosis. As a result, compared to controls, the DNA vaccine cocktail significantly increased serum IgG levels, Th1 cytokine production, and proportions of CD4+/CD8+ T cells, leading to extended survival and reduced brain cyst counts post-challenge with T. gondii ME49. Furthermore, the five-gene DNA vaccine cocktail conferred greater protection compared to single-gene immunizations. Co-administration of IL-24 significantly enhanced the immune efficacy of the multi-gene DNA vaccination. Our findings suggest that IL-24 is an effective molecular adjuvant, enhancing the protective immunity of DNA vaccines against T. gondii, supporting its potential role in vaccine strategies targeting other apicomplexan parasites. Full article

(This article belongs to the Topic Advances in Infectious and Parasitic Diseases of Animals)

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18 pages, 2892 KiB

Open AccessArticle

Risk of Secondary Bacterial Infections Revealed by Changes in Trachinotus ovatus Skin and Gill Microbiota During a Cryptocaryon irritans Infection Cycle

by Naiqi Liang, Li Zhu, Shifeng Wang, Weihao Zhang, Xinlei Lin, Yongcan Zhou, Haizhu Ke, Shanheng Yuan, Meijing Li and Yan Cai

Microorganisms 2025, 13(7), 1660; https://doi.org/10.3390/microorganisms13071660 (registering DOI) - 14 Jul 2025

Abstract

This study aims to investigate the response of surface bacterial communities in Trachinotus ovatus to Cryptocaryon irritans infection at different stages of a single infection cycle (0~168 h). These samples were analyzed using high-throughput 16S rRNA sequencing. Alpha diversity analysis showed a reduction [...] Read more.

This study aims to investigate the response of surface bacterial communities in Trachinotus ovatus to Cryptocaryon irritans infection at different stages of a single infection cycle (0~168 h). These samples were analyzed using high-throughput 16S rRNA sequencing. Alpha diversity analysis showed a reduction in the richness and diversity of skin microbiota during infection, with partial recovery post-detachment. Beta diversity analysis revealed distinct structural shifts in skin microbiota at early (24 h) and post-detachment (168 h) stages compared to other phases, while gill microbiota remained stable except during detachment. At the phylum level, Proteobacteria, Actinobacteriota, Bacteroidetes, and Firmicutes were dominant on the skin at different stages, whereas the gill microbiota was predominantly Proteobacteria (>90%). At the genus level, opportunistic pathogens, such as Vibrio and Nautella, increased in relative abundance on the skin with the infection progression, while gill microbiota composition barely changed. The hepatic bacterial load continued to increase with infection duration. These findings indicate that C. irritans alters microbiota composition on skin, facilitating pathogen invasion, thereby elevating the risk of secondary bacterial infections in T. ovatus. Full article

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

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15 pages, 809 KiB

Open AccessArticle

Fermentation of Microalgae as a Platform for Naturally Encapsulated Oil Powders: Characterization of a High-Oleic Algal Powder Ingredient

by Walter Rakitsky, Leon Parker, Kevin Ward, Thomas Pilarski, James Price, Mona Correa, Roberta Miller, Veronica Benites, Dino Athanasiadis, Bryce Doherty, Lucy Edy, Jon Wittenberg, Gener Eliares, Daniel Gates, Manuel Oliveira, Frédéric Destaillats and Scott Franklin

Microorganisms 2025, 13(7), 1659; https://doi.org/10.3390/microorganisms13071659 (registering DOI) - 14 Jul 2025

Abstract

Powdered oil ingredients are widely used across food, nutrition, and personal care industries, but they are typically produced through encapsulation technologies that involve multiple additives and stabilizers. These systems can compromise oxidative stability, clean-label compliance, and functional performance. Here, we present the development [...] Read more.

Powdered oil ingredients are widely used across food, nutrition, and personal care industries, but they are typically produced through encapsulation technologies that involve multiple additives and stabilizers. These systems can compromise oxidative stability, clean-label compliance, and functional performance. Here, we present the development and characterization of a novel high-oleic algal powder (HOAP) produced from a heterotrophically fermented microalgae. The production strain was developed through classical mutagenesis to enhance oleic acid and lipid accumulation. Three independent fermentation batches at a 20 L scale demonstrated strong reproducibility in key metrics, including dried-cell weight (210.0 g per L on average, CV% = 0.7), oil content (62.0% of DCW on average, CV% = 2.0), and oleic acid (88.8% of total fatty acids on average, CV% = 0.1). HOAP exhibited a favorable nutritional profile (e.g., high monounsaturated fat and fiber, low sugar and moisture) and good oxidative stability under ambient and accelerated storage conditions. Microbiological analyses confirmed compliance with food-grade standards, and in silico allergenicity screening revealed no clinically relevant homologs. Unlike traditional oil powders, HOAP does not require encapsulation and retains oil within a natural protein–fiber matrix, offering both functional and clean-labeling advantages. Its compositional attributes and stability profile support potential use in food, nutrition, and the delivery of bioactive nutrients. These findings establish HOAP as a next generation of oil powder ingredients with broad application potential. Full article

(This article belongs to the Special Issue Microalgal Biotechnology: Innovations and Applications)

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18 pages, 4199 KiB

Open AccessArticle

Effects of Antibiotic Residues on Fecal Microbiota Composition and Antimicrobial Resistance Gene Profiles in Cattle from Northwestern China

by Wei He, Xiaoming Wang, Yuying Cao, Cong Liu, Zihui Qin, Yang Zuo, Yiming Li, Fang Tang, Jianjun Dai, Shaolin Wang and Feng Xue

Microorganisms 2025, 13(7), 1658; https://doi.org/10.3390/microorganisms13071658 - 14 Jul 2025

Abstract

Grazing is a free-range farming model commonly practiced in low-external-input agricultural systems. The widespread use of veterinary antibiotics in livestock farming has led to significant environmental accumulation of antibiotic residues and antibiotic resistance genes (ARGs), posing global health risks. This study investigated the [...] Read more.

Grazing is a free-range farming model commonly practiced in low-external-input agricultural systems. The widespread use of veterinary antibiotics in livestock farming has led to significant environmental accumulation of antibiotic residues and antibiotic resistance genes (ARGs), posing global health risks. This study investigated the antibiotic residues, bacterial community, ARG profiles, and mobile genetic elements (MGEs) in cattle feces from three provinces in western China (Ningxia, Xinjiang, and Inner Mongolia) under grazing modes. The HPLC-MS detection showed that the concentration of tetracycline antibiotics was the highest in all three provinces. Correlation analysis revealed a significant negative correlation between antibiotic residues and the diversity and population abundance of intestinal microbiota. However, the abundance of ARGs was directly proportional to antibiotic residues. Then, the Sankey analysis revealed that the ARGs in the cattle fecal samples were concentrated in 15 human pathogenic bacteria (HPB) species, with 9 of these species harboring multiple drug resistance genes. Metagenomic sequencing revealed that carbapenemase-resistant genes (bla_KPC and bla_VIM) were also present in considerable abundance, accounting for about 10% of the total ARGs detected in three provinces. Notably, Klebsiella pneumoniae strains carrying bla_CTX-M-55 were detected, which had a possibility of IncFII plasmids harboring transposons and IS19, indicating the risk of horizontal transfer of ARGs. This study significantly advances the understanding of the impact of antibiotic residues on the fecal microbiota composition and ARG profiles in grazing cattle from northwestern China. Furthermore, it provides critical insights for the development of rational antibiotic usage strategies and comprehensive public health risk assessments. Full article

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

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16 pages, 5800 KiB

Open AccessArticle

Healthy Ageing and Gut Microbiota: A Study on Longevity in Adults

by Lihua Deng, Jun Xu, Qian Xue, Yanan Wei and Jingtong Wang

Microorganisms 2025, 13(7), 1657; https://doi.org/10.3390/microorganisms13071657 - 14 Jul 2025

Abstract

Many studies have focused on ageing and gut microbiota, but the correlation between gut microbiota and physical function in older adults, especially those with longevity, remains obscure and deserves further exploration. In this study we investigated changes in the gut microbiota and the [...] Read more.

Many studies have focused on ageing and gut microbiota, but the correlation between gut microbiota and physical function in older adults, especially those with longevity, remains obscure and deserves further exploration. In this study we investigated changes in the gut microbiota and the association between gut microbiota and physical function in adults with longevity. This is a prospective observational study. Fifty-one older adults aged ≥ 60 years (including 27 participants aged 90 years and above) were enrolled. Information on clinical data, physical function including intrinsic capacity by Integrated Care for Older People (ICOPE) tool, and dietary habits of participants was collected and analysed. Gut microbiota structure and functional pathways were analysed by Metagenomics. Intrinsic capacity (measured as ICOPE scores) of adults’ longevity (aged 90–98, longe group) was significantly lower than older adults aged 60–89 years (CON group) (5.44 ± 2.15 vs. 6.71 ± 1.46, p = 0.017). Gut microbiota of the longe group is enriched in Akkermansia and Bifidobacterium, which may be beneficial to health. Gut microbiota was closely related to daily milk (including plain milk, flavoured milk with a content of cow’s milk or reconstituted milk of ≥80%, or reconstituted milk or fermented milk with a content of cow’s milk or milk powder of ≥80%) consumption, anxiety, and physical function including grip strength by the Short Physical Performance Battery (SPPB). Bacteroides plebeius and Bacteroides eggerthii were increased in long-living adults with better physical function. Escherichia coli was more abundant in frail young-old adults. Grip strength is positively correlated with the abundance of Roseburia hominis, Eubacterium rectale, Eubacterium eligens, and Roseburia intestinalis (p < 0.05). Pathways related to amino acid synthesis that include L-isoleucine, L-valine, and L-threonine were over-presented in long-living adults of better physical function. Adults with longevity showed comparable gut microbiota abundance to younger elderly individuals. The gut microbiota of long-living adults showed higher abundance of potentially beneficial bacteria, and the altered bacteria are closely associated with physical function. Changes in the gut microbiota may precede clinical indicators during the process of ageing. Gut microbiota may be a potential biomarker for longevity and healthy ageing. Nutrition and emotional state can be important influencing factors. Full article

(This article belongs to the Section Gut Microbiota)

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14 pages, 869 KiB

Open AccessArticle

Subgingival Microbiome Profiles in Bulgarian Children Aged 10–14 with Gingival Inflammation and Healthy Periodontium: A Targeted PCR Study

by Hristina Tankova and Nadezhda Mitova

Microorganisms 2025, 13(7), 1656; https://doi.org/10.3390/microorganisms13071656 - 14 Jul 2025

Abstract

The subgingival microbiome is a critical component of the oral microbiota and plays a central role in pediatric periodontology. This study investigated differences in periodontopathogen profiles in children with gingival inflammation compared to healthy controls using real-time PCR, with a focus on the [...] Read more.

The subgingival microbiome is a critical component of the oral microbiota and plays a central role in pediatric periodontology. This study investigated differences in periodontopathogen profiles in children with gingival inflammation compared to healthy controls using real-time PCR, with a focus on the microbial complexes defined by Socransky. A total of 73 children (ages 10–14) underwent comprehensive periodontal assessment, including assessments of general health status, the O’Leary hygiene index (HI), gingival condition, and the papillary bleeding index (PBI). Subgingival plaque samples were analyzed using real-time PCR to identify key bacterial species associated with gingival health and disease. Highly pathogenic periodontopathogens such as Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Treponema denticola, and Eubacterium nodatum were absent in healthy subjects. In contrast, Tannerella forsythia was significantly more frequently detected in children with gingival inflammation (p < 0.05). The most abundant species in the inflammation group were Prevotella intermedia and Capnocytophaga gingivalis. Children with gingival inflammation exhibit a distinct subgingival microbiome profile characterized by an increased presence of specific periodontopathogens, including a higher prevalence of red complex species as defined by Socransky. However, the cross-sectional nature of this study limits the ability to establish causal relationships. Full article

(This article belongs to the Section Medical Microbiology)

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16 pages, 1767 KiB

Open AccessArticle

Population Structure, Genomic Features, and Antibiotic Resistance of Avian Pathogenic Escherichia coli in Shandong Province and Adjacent Regions, China (2008–2023)

by Shikai Song, Yao Wang, Zhihai Liu, Rongling Zhang, Kaiyuan Li, Bin Yin, Zunxiang Yan, Shifa Yang, Shuqian Lin and Yunpeng Yi

Microorganisms 2025, 13(7), 1655; https://doi.org/10.3390/microorganisms13071655 - 13 Jul 2025

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Abstract

Avian pathogenic Escherichia coli (APEC) poses a global threat to poultry health and public safety due to its high lethality, limited treatment options, and potential for zoonotic transmission via the food chain. However, long-term genomic surveillance remains limited, especially in countries like China [...] Read more.

Avian pathogenic Escherichia coli (APEC) poses a global threat to poultry health and public safety due to its high lethality, limited treatment options, and potential for zoonotic transmission via the food chain. However, long-term genomic surveillance remains limited, especially in countries like China where poultry farming is highly intensive. This study aimed to characterize the population structure, virulence traits, and antimicrobial resistance of 81 APEC isolates from diseased chickens collected over 16 years from Shandong and neighboring provinces in eastern China. The isolates were grouped into seven Clermont phylogroups, with A and B1 being dominant. MLST revealed 27 STs, and serotyping identified 29 O and 16 H antigens, showing high genetic diversity. The minor phylogroups (B2, C, D, E, G) encoded more virulence genes and had higher virulence-plasmid ColV carriage, with enrichment for iron-uptake, protectins, and extraintestinal toxins. In contrast, the dominant phylogroups A and B1 primarily carried adhesin and enterotoxin genes. Antimicrobial resistance was widespread: 76.5% of isolates were multidrug-resistant. The minor phylogroups exhibited higher tetracycline resistance (mediated by tet(A)), whereas the major phylogroups showed increased resistance to third- and fourth-generation cephalosporins (due to bla_CTX-M-type ESBL genes). These findings offer crucial data for APEC prevention and control, safeguarding the poultry industry and public health. Full article

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

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14 pages, 1496 KiB

Open AccessArticle

Tetanus in Romania—Trends and Challenges

by Andreea Marilena Păuna, Ștefan Eduard Mîinea, Bianca Georgiana Enciu, Daniela Pițigoi, Anca Mirela Sîrbu, Rodica Popescu, Carmen Daniela Chivu, Carmen-Cristina Vasile and Maria Dorina Crăciun

Microorganisms 2025, 13(7), 1654; https://doi.org/10.3390/microorganisms13071654 - 12 Jul 2025

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Abstract

Tetanus is a life-threatening, vaccine-preventable disease caused by tetanospasmin and tetanolysin, which are potent neurotoxins produced by Clostridium tetani, an anaerobic, spore-forming bacterium. Due to the widespread presence of spores in the environment, the disease cannot be eradicated. However, global tetanus prevention [...] Read more.

Tetanus is a life-threatening, vaccine-preventable disease caused by tetanospasmin and tetanolysin, which are potent neurotoxins produced by Clostridium tetani, an anaerobic, spore-forming bacterium. Due to the widespread presence of spores in the environment, the disease cannot be eradicated. However, global tetanus prevention initiatives have contributed to a significant decline in tetanus incidence worldwide. Aiming to present the tetanus trends in Romania, we conducted a retrospective analysis of the tetanus surveillance data. During the study period (2010–2023), 97 cases of tetanus were reported in Romania (median: 6.5; IQR: 5–7) with an average incidence rate of 0.03 per 100,000 inhabitants (95% CI: 0.02–0.04; range: 0.01–0.09). The highest incidence rates were recorded among people aged 1 to 14 years old (0.09 per 100,000 inhabitants, 95% CI: 0.06–0.13; range: 0.00–0.20), male (0.05 per 100,000 inhabitants; 95% CI: 0.03–0.06; range: 0.03–0.12), and from rural areas (0.05 per 100,000 inhabitants; 95% CI: 0.03–0.08; range: 0.01–0.17). A decline in the number of tetanus cases of 7% by year was observed, which is supported by the statistical analysis showing a p-value of 0.005 (IRR: 0.93; 95% CI: 0.88–0.98). However, the same decline in tetanus incidence was not supported by the statistical analysis (IRR: 0.93; 95% CI: 0.44–1.98; p = 0.9). Forty-seven tetanus deaths were recorded, with an average case fatality ratio of 42% (95% CI: 25.62–57.92; range: 0–100), showing a decreasing trend of 9% by year (IRR: 0.91; 95% CI: 0.89–0.93). Although the annual number of tetanus cases in Romania has shown a slight downwards trend, its situation has remained relatively stable, as shown by the tetanus incidence. Moreover, the case fatality rate continues to be high. Therefore, our study emphasizes the importance of achieving high vaccination uptake among children and adolescents, raising awareness of the importance of booster doses in adults, and improving the management of tetanus-prone wounds. Full article

(This article belongs to the Special Issue Infectious Disease Surveillance in Romania)

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18 pages, 2705 KiB

Open AccessArticle

Irrigation of Suaeda salsa with Saline Wastewater and Microalgae: Improving Saline–Alkali Soil and Revealing the Composition and Function of Rhizosphere Bacteria

by Qiaoyun Yan, Yitong Zhang, Zhenting Xu, Wenying Qu, Junfeng Li, Wenhao Li, Chun Zhao and Hongbo Ling

Microorganisms 2025, 13(7), 1653; https://doi.org/10.3390/microorganisms13071653 - 12 Jul 2025

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Abstract

Limited research has been conducted on the potential and mechanisms of irrigating Suaeda salsa with wastewater and microalgae to improve saline–alkali land. This study used three irrigation treatments (freshwater, saline wastewater, and saline wastewater with microalgae) to irrigate S. salsa, and microalgae [...] Read more.

Limited research has been conducted on the potential and mechanisms of irrigating Suaeda salsa with wastewater and microalgae to improve saline–alkali land. This study used three irrigation treatments (freshwater, saline wastewater, and saline wastewater with microalgae) to irrigate S. salsa, and microalgae promoted the growth of S. salsa and increased soil nutrient content, increasing available nitrogen (4.85%), available phosphorus (44.51%), and organic carbon (24.05%) while alleviating salt stress through reduced soil salinity (13.52%) and electrical conductivity (21.62%). These changes promoted eutrophic bacteria while inhibiting oligotrophic bacteria. Bacterial community composition exhibited significant variations, primarily driven by soil pH, total nitrogen, and organic carbon content. Notably, rhizosphere bacteria showed enhanced functional capabilities, with increased abundance of salt stress resistance and nitrogen metabolism-related genes compared to original soil, particularly under saline irrigation conditions. Furthermore, microalgae addition enriched nitrogen metabolism-related gene abundance. These findings revealed the potential role of key bacteria in enhancing plant growth and the soil environment and highlighted the potential of applying S. salsa, wastewater, and microalgae for the synergistic improvement of saline–alkali land. Full article

(This article belongs to the Special Issue New Advances in Microalgae Biotechnology—Increasing Productivity Towards Achieving a More Profitable Production Chain)

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17 pages, 4334 KiB

Open AccessArticle

Responses of Different Temperature-Acclimated Diatom Species, Smaller Thalassiosira pseudonana and Larger Thalassiosira rotula, to Increased Ambient Temperature

by Wei Zhao, Jihua Liu, Hui Song, Bokun Chen, Hongli Ji, Xue Yang and Gang Li

Microorganisms 2025, 13(7), 1652; https://doi.org/10.3390/microorganisms13071652 - 12 Jul 2025

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Abstract

The acute rise in temperature due to marine heatwaves has a strong impact on marine phytoplankton. To determine whether these effects depend on ambient temperature and cell size, we acclimated two diatom species, smaller Thalassiosira pseudonana (Hasle and Heimdal, 1970) and larger Thalassiosira [...] Read more.

The acute rise in temperature due to marine heatwaves has a strong impact on marine phytoplankton. To determine whether these effects depend on ambient temperature and cell size, we acclimated two diatom species, smaller Thalassiosira pseudonana (Hasle and Heimdal, 1970) and larger Thalassiosira rotula (Meunier, 1910), at low (LAT), medium (MAT) and high ambient temperatures (HAT) and examined their physiochemical and transcriptional responses to temperature rise (AT + 6 °C). The specific growth rate (µ) of smaller cells was increased by 32% due to temperature rise at LAT, but decreased by 13% at HAT, with the stimulatory and inhibitory extent being ~50% less than that of larger cells. At LAT, chlorophyll a (Chl a), carotenoid (Car) and carbon (POC) contents were increased in smaller cells due to temperature rise, but were decreased in larger cells; at HAT, Chl a and Car were increased in both smaller and larger cells and POC was increased in only smaller cells. At LAT, temperature rise led to a disproportionate increase in photosynthesis and dark respiration, resulting in an increase in carbon utilization efficiency (CUE) in smaller cells and a decrease in CUE in larger cells; at HAT, there was a decrease in CUE in both the smaller and larger cells, but to a lesser extent in the former than in the latter. Our results also show that smaller cells cope with the acute temperature rise mainly by strengthening their enzyme activity (e.g., the antioxidant system) and conservatively regulating their metabolism, while larger cells mainly regulate their photosynthetic and central carbon metabolism. Moreover, larger cells can outperform their smaller counterparts when the temperature rise occurs at lower ambient temperature. Full article

(This article belongs to the Section Environmental Microbiology)

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19 pages, 3395 KiB

Open AccessArticle

Hybrid Whole Genomes of Brucella melitensis from Tunisian Animal Isolates: Virulence Factors, Antimicrobial Susceptibility, and Phylogeny

by Ibtihel Ben Abdallah, Germán Kopprio, Awatef Béjaoui, Susanne Köhler, Kaouther Guesmi, Sana Kalthoum, Jacob Gatz, Amel Arfaoui, Monia Lachtar, Haikel Hajlaoui, Mohamed Naceur Baccar, Holger Scholz and Abderrazak Maaroufi

Microorganisms 2025, 13(7), 1651; https://doi.org/10.3390/microorganisms13071651 - 12 Jul 2025

Viewed by 176

Abstract

Brucellosis remains endemic in Tunisia, causing abortions in small ruminants, and represents a public health threat through occupational exposure and the consumption of contaminated animal products. The aims of this study are to assess the antibiotic susceptibility of two Brucella melitensis isolates (TATA [...] Read more.

Brucellosis remains endemic in Tunisia, causing abortions in small ruminants, and represents a public health threat through occupational exposure and the consumption of contaminated animal products. The aims of this study are to assess the antibiotic susceptibility of two Brucella melitensis isolates (TATA and SBZ) from aborted sheep, to analyze their genomes using hybrid whole-genome sequencing, and to investigate their antimicrobial resistance (AMR), potential virulence factors (VFs), and phylogenetic relationships. Both isolates were phenotypically confirmed to be susceptible to doxycycline, gentamicin, rifampicin, streptomycin, and trimethoprim–sulfamethoxazole, and no corresponding classical AMR genes were identified. However, several potential AMR-related genes (mprF, bepCDEFG, qacG, and adeF) and a mutation in the parC gene were detected. The analysis of the genotypes revealed 74 potential virulence genes, primarily involved in lipopolysaccharide synthesis and type IV secretion systems. Genomic comparison showed over 99% nucleotide identity between the Tunisian strains, B. melitensis bv. 1 16M and B. melitensis bv. 3 Ether. Five gene clusters, including three hypothetical proteins with 100% identity, were detected exclusively in the TATA and SBZ strains. Additionally, two unique gene clusters were identified in SBZ: a rhodocoxin reductase and another hypothetical protein. Both isolates were assigned to sequence types ST11 and ST89. Core-genome-based phylogenetic analysis clustered both strains with biovar 3 and ordered the Tunisian strains into two distinct groups: TATA within Tunisian Cluster 1 is closely related to strains from Egypt and Italy, while SBZ near MST Cluster 4 is more related to isolates from Austria and two outliers from Italy and Tunisia. This study provides the first genomic characterization of B. melitensis from aborted sheep in Tunisia and offers valuable insights into AMR, virulence, and phylogenetic distribution. Full article

(This article belongs to the Special Issue Epidemiology and Control Strategies for Brucellosis)

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13 pages, 2979 KiB

Open AccessArticle

Taxon-Dependent Community Assembly of Bacteria and Protists in River Ecosystems: A Case Study from the Yujiang River

by Yusen Li, Wenjian Chen, Yaoquan Han, Jianjun Lei, Bo Huang, Youjie Qin, Feng Lin, Caijin Li, Dapeng Wang and Lei Zhou

Microorganisms 2025, 13(7), 1650; https://doi.org/10.3390/microorganisms13071650 - 12 Jul 2025

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Abstract

Understanding the processes that drive microbial community assembly is a fundamental question in ecology, with important implications for predicting community responses to environmental disturbances. River ecosystems are under growing pressure from human disturbances, jeopardizing their ecological functions. Here, we investigated bacterial and protistan [...] Read more.

Understanding the processes that drive microbial community assembly is a fundamental question in ecology, with important implications for predicting community responses to environmental disturbances. River ecosystems are under growing pressure from human disturbances, jeopardizing their ecological functions. Here, we investigated bacterial and protistan communities along the Yujiang River using environmental DNA metabarcoding. Bacterial communities exhibited significantly greater alpha diversity and broader habitat niches compared to protists. Additionally, a negative correlation was found between alpha diversity and niche breadth for both groups. Protistan communities exhibited significantly higher beta diversity (Bray–Curtis distance) than bacterial communities, with species turnover being the principal factor driving the variations in both communities. Null model results indicated that heterogeneous selection primarily structured bacterial communities, while stochastic processes (drift) mainly governed protist communities. Redundancy analysis and Mantel tests showed significant associations between environmental factors (e.g., temperature and pH) and bacterial community composition. Moreover, the longitude of sampling sites was linked to spatial variations in both bacterial and protistan communities. Further analyses, including distance-decay patterns, variation partitioning, and multiple regression on distance matrices, demonstrated that bacterial communities were driven by both environmental and spatial factors, while protist communities exhibited a stronger response to spatial factors. These results enhance our understanding of microbial community assembly in river ecosystems and provide valuable insights for the conservation and sustainable management of freshwater systems. Full article

(This article belongs to the Section Environmental Microbiology)

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13 pages, 1764 KiB

Open AccessArticle

Surface Display of Avian H5 and H9 Hemagglutinin Antigens on Non-Genetically Modified Lactobacillus Cells for Bivalent Oral AIV Vaccine Development

by Fuyi Liu, Jingbo Chang, Jingqi Huang, Yuping Liao, Xiaonan Deng, Tingting Guo, Jian Kong and Wentao Kong

Microorganisms 2025, 13(7), 1649; https://doi.org/10.3390/microorganisms13071649 - 11 Jul 2025

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Abstract

A novel bivalent oral vaccine candidate against H5N1 and H9N2 avian influenza virus (AIV) was developed using Lactobacillus surface display technology without genetic modification. The hemagglutinin subunit 1 (HA1) antigens from both subtypes were fused to the surface layer-binding domain of Lactobacillus crispatus [...] Read more.

A novel bivalent oral vaccine candidate against H5N1 and H9N2 avian influenza virus (AIV) was developed using Lactobacillus surface display technology without genetic modification. The hemagglutinin subunit 1 (HA1) antigens from both subtypes were fused to the surface layer-binding domain of Lactobacillus crispatus K313, expressed in Escherichia coli, and purified. Wild-type Lactobacillus johnsonii H31, isolated from chicken intestine, served as a delivery vehicle by adsorbing and stably displaying the HA1 proteins on its surface. This approach eliminates the need for bacterial engineering while utilizing lactobacilli’s natural capacity to protect surface-displayed antigens, as evidenced by HA1’s protease resistance. Mouse immunization studies demonstrated induction of strong systemic IgG and mucosal IgA responses against both H5N1 and H9N2 HA1. The system offers several advantages, including safety through non-GMO probiotics, potential for multivalent vaccine expansion, and intrinsic antigen protection by lactobacilli. These findings suggest this platform could enable development of cost-effective, multivalent AIV vaccines. Full article

(This article belongs to the Section Food Microbiology)

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19 pages, 2862 KiB

Open AccessArticle

Characterization of Soil Bacterial Communities in Different Vegetation Types on the Lava Plateau of Jingpo Lake

by Yanli Zhang, Jiaxing Huang, Jiaxin Xue, Kaining Zhang, Xintong Chen, Jianhui Jia and Qingyang Huang

Microorganisms 2025, 13(7), 1648; https://doi.org/10.3390/microorganisms13071648 - 11 Jul 2025

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Abstract

To explore the interactions within the vegetation–soil–microorganism continuum on the Jingpo Lake lava platform, five vegetation types—grassland (GL), shrubland (SL), deciduous broad-leaved forest (DB), coniferous and broad-leaved mixed forest (CB), and coniferous forest (CF)—were examined. Significant differences in the soil physical and chemical [...] Read more.

To explore the interactions within the vegetation–soil–microorganism continuum on the Jingpo Lake lava platform, five vegetation types—grassland (GL), shrubland (SL), deciduous broad-leaved forest (DB), coniferous and broad-leaved mixed forest (CB), and coniferous forest (CF)—were examined. Significant differences in the soil physical and chemical properties were identified among these types (p < 0.05). The soil bacterial community structures also varied significantly (p < 0.05), with Actinobacteriota, Proteobacteria, and Acidobacteria as the dominant phyla, exhibiting notable genus-level differences (p < 0.05). The soil organic matter (SOM), available nitrogen (AN), total nitrogen (TN), and soil water content (SWC) were significantly correlated with the bacterial community structure (p < 0.05 or p < 0.01), acting as key determinants of the microbial community structure and function. PICRUSt2 functional predictions revealed significant variations in the metabolic functions of the soil bacterial communities across vegetation types, indicating distinct functional specializations. In conclusion, the Jingpo Lake lava plateau harbors abundant bacterial resources. When devising vegetation adaptation strategies, it is essential to take into account variations in the rhizosphere soil bacteria across different vegetation types. Furthermore, prioritizing the implementation of forest vegetation is crucial in the adaptive management of the lava plateau. This approach holds significant implications for studying the bacterial diversity in the lava plateau and exploring the cultivation and application of functional bacteria in extreme environments. Full article

(This article belongs to the Special Issue Microbial Communities in Soil: Drivers of Terrestrial Ecosystem Processes)

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10 pages, 1272 KiB

Open AccessCommunication

Antibiotic Resistance in Bifidobacterium animalis subsp. lactis and Bifidobacterium longum: Definition of Sensitivity/Resistance Profiles at the Species Level

by Mario Terlizzi, Barbara Speranza, Milena Sinigaglia, Maria Rosaria Corbo and Antonio Bevilacqua

Microorganisms 2025, 13(7), 1647; https://doi.org/10.3390/microorganisms13071647 - 11 Jul 2025

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Abstract

Antimicrobial resistance is a threat to probiotic microorganisms due to their potential role in harboring and transmitting resistance genes. This study focuses on two Bifidobacterium species (B. animalis subsp. lactis and B. longum) by analyzing 657 Minimal Inhibitory Concentration (MIC) values [...] Read more.

Antimicrobial resistance is a threat to probiotic microorganisms due to their potential role in harboring and transmitting resistance genes. This study focuses on two Bifidobacterium species (B. animalis subsp. lactis and B. longum) by analyzing 657 Minimal Inhibitory Concentration (MIC) values extracted from research articles indexed in Scopus, PubMed, and Web of Science, published since 2014, and considering 17 different antibiotics. MIC values were used for descriptive statistical analysis (boxplots and violin plots) to evaluate both inter- and intraspecies distributions. The results showed an overall increase in MIC values compared to historical data, with B. longum exhibiting high resistance to tetracyclines and streptomycin—approximately 25% to 50% of the strains had MIC values > EFSA cut-offs. The violin plots revealed the presence of resistant subpopulations, particularly within B. longum. These findings support the relevance of longitudinal MIC analysis as a tool for detecting early shifts in antimicrobial susceptibility and highlight the importance of data-driven approaches for microbiological risk assessment in probiotic applications. Full article

(This article belongs to the Section Food Microbiology)

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19 pages, 1297 KiB

Open AccessReview

Biology and Application of Chaetomium globosum as a Biocontrol Agent: Current Status and Future Prospects

by Shailja Sharma, Saurabh Pandey, Sourabh Kulshreshtha and Mukesh Dubey

Microorganisms 2025, 13(7), 1646; https://doi.org/10.3390/microorganisms13071646 - 11 Jul 2025

Viewed by 432

Abstract

Chaetomium globosum is a widely distributed fungal species recognized for its ability to produce a range of secondary metabolites. This fungus plays a significant ecological role by degrading organic matter and contributing to nutrient cycling in diverse ecosystems. In recent years, C. globosum [...] Read more.

Chaetomium globosum is a widely distributed fungal species recognized for its ability to produce a range of secondary metabolites. This fungus plays a significant ecological role by degrading organic matter and contributing to nutrient cycling in diverse ecosystems. In recent years, C. globosum has attracted considerable scientific interest due to its potential as a biocontrol agent [BCA] against a wide array of diseases in numerous plant species. While the precise mechanisms of C. globosum as a BCA remain poorly understood, interference competition through antibiosis is one of the key mechanisms. Moreover, C. globosum can enhance plant health by promoting nutrient availability, manipulating the rhizosphere microbiome, and inducing plant defense responses. The formulation of C. globosum for agricultural applications has been reported, which can significantly improve stability and efficacy under field conditions. However, despite significant advancements in omics and molecular biology technologies, the biology of C. globosum is understudied. Enhanced research into the genetics and functional genomics of C. globosum could pave the way for its applications in sustainable agriculture. This review summarizes the role of C. globosum as a BCA, focusing on its underlying mechanisms such as genomics and transcriptomics, and the effects of C. globosum application on soil health and the rhizosphere microbiome. Full article

(This article belongs to the Section Plant Microbe Interactions)

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13 pages, 13698 KiB

Open AccessArticle

Gut Microbiota Diversity in 16 Stingless Bee Species (Hymenoptera: Apidae: Meliponini)

by María de Lourdes Ramírez-Ahuja, Kenzy I. Peña-Carrillo, Mayra A. Gómez-Govea, Mariana Lizbeth Jiménez-Martínez, Gerardo de Jesús Trujillo-Rodríguez, Marisol Espinoza-Ruiz, Antonio Guzmán Velasco, Adriana E. Flores, José Ignacio González-Rojas, Diana Reséndez-Pérez and Iram Pablo Rodríguez-Sánchez

Microorganisms 2025, 13(7), 1645; https://doi.org/10.3390/microorganisms13071645 - 11 Jul 2025

Viewed by 133

Abstract

Bacterial symbionts play an important role in insect survival by contributing to key metabolic and defensive functions. While stingless bees are known to harbor diverse microbial communities, their core bacterial symbionts remain poorly characterized. In this study, we analyzed the gut microbiota of [...] Read more.

Bacterial symbionts play an important role in insect survival by contributing to key metabolic and defensive functions. While stingless bees are known to harbor diverse microbial communities, their core bacterial symbionts remain poorly characterized. In this study, we analyzed the gut microbiota of sixteen stingless bee species collected from different regions of Mexico using 16S rRNA gene sequencing on the Illumina^® MiSeq™ platform. Our results revealed that Proteobacteria, Firmicutes, and Actinobacteria are the most abundant bacterial phyla across species. Among the dominant genera, lactic acid bacteria, such as Lactobacillus spp., Bifidobacterium, and Fructobacillus spp., were the most prevalent. These bacteria are responsible for developing biochemical functions in metabolic processes like lactic fermentation and the biotransformation of complex organic compounds into molecules that are more easily assimilated by bees. This study offers a novel perspective on the diversity and predicted composition of gut microbiota in Mexican stingless bees. By highlighting differences in microbial communities among species with different feeding habits, our results emphasize the importance of preserving microbial biodiversity in these pollinators. Full article

(This article belongs to the Section Gut Microbiota)

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18 pages, 5258 KiB

Open AccessArticle

Fusobacterium nucleatum Is Associated with Tumor Characteristics, Immune Microenvironment, and Survival in Appendiceal Cancer

by Christopher Sherry, Neda Dadgar, Hyun Park, Chelsea Knotts, Erin Grayhack, Rose Blodgett, Kunhong Xiao, Ashten N. Omstead, Albert D. Donnenberg, David L. Bartlett, Vera Donnenberg, Ajay Goel, Ali H. Zaidi and Patrick L. Wagner

Microorganisms 2025, 13(7), 1644; https://doi.org/10.3390/microorganisms13071644 - 11 Jul 2025

Viewed by 107

Abstract

Emerging evidence highlights the role of the tumor microbiome, including Fusobacterium nucleatum (Fn), in a wide range of gastrointestinal cancers. Fn purportedly contributes to tumorigenesis by activating oncogenic pathways and modulating immune responses. Although the prevalence and impact of Fn has been extensively [...] Read more.

Emerging evidence highlights the role of the tumor microbiome, including Fusobacterium nucleatum (Fn), in a wide range of gastrointestinal cancers. Fn purportedly contributes to tumorigenesis by activating oncogenic pathways and modulating immune responses. Although the prevalence and impact of Fn has been extensively studied in colorectal cancer, no previous systematic or in situ studies have been performed in appendiceal cancer (AC). The aim of this study was to evaluate the prevalence and association of Fn density in AC with clinical factors and oncologic outcomes. Archival tissue from 54 patients with AC was assessed for Fn density using RNA in situ hybridization. Clinicopathological variables were obtained for each case through electronic medical record review, and the immune microenvironment was characterized in each case using immunohistochemistry to quantify CD3+ and CD8+ T lymphocytes and M1-/M2-like tumor-associated macrophages. In AC, Fn density was associated with patient age, tumor grade, and histologic subtype. Fn was negatively associated with CD3+ and CD8+ T lymphocytes and positively associated with M2-like TAMs in low-grade AC. Interestingly, tumor Fn content was associated with better overall and progression-free survival, even when controlling for tumor grade. In this exploratory study, we found that Fn is prevalent in AC. Fn is associated with a number of clinical, pathologic, immunologic, and prognostic variables in AC that are distinct from the corresponding observed associations in colorectal cancer. Further research is warranted to validate these findings and explore the mechanistic contributions of Fn to AC pathogenesis or immune response. Full article

(This article belongs to the Special Issue The Microbiome in Ecosystems)

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19 pages, 2510 KiB

Open AccessArticle

In Vitro Evaluation of the Probiotic Properties and Whole Genome Sequencing of Lacticaseibacillus rhamnosus J3205 Isolated from Home-Made Fermented Sauce

by Yiming Chen, Lingchao Ma, Weiye Chen, Yiwen Chen, Zile Cheng, Yongzhang Zhu, Min Li, Yan Zhang, Xiaokui Guo and Chang Liu

Microorganisms 2025, 13(7), 1643; https://doi.org/10.3390/microorganisms13071643 - 11 Jul 2025

Viewed by 113

Abstract

Lacticaseibacillus rhamnosus J3205 was isolated from traditional fermented sauces and demonstrated potential probiotic properties. The strain exhibited high tolerance to simulated saliva (93.24% survival) and gastrointestinal conditions (69.95% gastric and 50.44% intestinal survival), along with strong adhesion capacity (58.25%) to intestinal epithelial cells. [...] Read more.

Lacticaseibacillus rhamnosus J3205 was isolated from traditional fermented sauces and demonstrated potential probiotic properties. The strain exhibited high tolerance to simulated saliva (93.24% survival) and gastrointestinal conditions (69.95% gastric and 50.44% intestinal survival), along with strong adhesion capacity (58.25%) to intestinal epithelial cells. Safety assessments confirmed the absence of virulence and antibiotic resistance genes. Genomic analysis revealed stress-response genes and 34 insertion sequence (IS) elements, while proteomic profiling identified Pgk as a key enzyme in lactic acid production and SecY in oxidative stress resistance. Functionally, J3205 significantly reduces pro-inflammatory cytokines (TNF-α, IL-6, IL-1β) and enhances antioxidant markers (SOD, GSH) in vitro. These results position L. rhamnosus J3205 as a promising candidate for gut-health foods, anti-inflammatory nutraceuticals, and oxidative-stress therapeutics, warranting further in vivo validation. Full article

(This article belongs to the Section Food Microbiology)

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16 pages, 528 KiB

Open AccessArticle

Elixhauser Comorbidity Measure and Charlson Comorbidity Index in Predicting the Death of Spanish Inpatients with Diabetes and Invasive Pneumococcal Disease

by Enrique Gea-Izquierdo, Rossana Ruiz-Urbaez, Valentín Hernández-Barrera and Ángel Gil-de-Miguel

Microorganisms 2025, 13(7), 1642; https://doi.org/10.3390/microorganisms13071642 - 11 Jul 2025

Viewed by 142

Abstract

Invasive pneumococcal disease (IPD) is a serious infection caused by the bacterium Streptococcus pneumoniae (pneumococcus) that can produce a wide spectrum of clinical manifestations. The aim of this study was to analyze the comorbidity factors that influenced the mortality in patients with diabetes [...] Read more.

Invasive pneumococcal disease (IPD) is a serious infection caused by the bacterium Streptococcus pneumoniae (pneumococcus) that can produce a wide spectrum of clinical manifestations. The aim of this study was to analyze the comorbidity factors that influenced the mortality in patients with diabetes (D) according to IPD. A retrospective study to analyze patients with D and IPD was carried out. Based on the discharge reports from the Spanish Minimum Basic Data Set (MBDS) from 1997 to 2022, the Elixhauser Comorbidity Index (ECI) and the Charlson Comorbidity Index (CCI) were calculated to predict in-hospital mortality (IHM) in Spain. A total of 12,994,304 patients with D were included, and 84,601 cases of IPD were identified. The average age for men was 70.23 years and for women 73.94 years. In all years, ECI and CCI were larger for type 2 D than for type 1 D, with men having a higher mean than women. An association was found between risk factors ECI, age, type 1 D, COVID-19, IPD (OR = 1.31; 95% CI: 1.29–1.35; p < 0.001); CCI, age, type 1 D, COVID-19, IPD (OR = 1.45; 95% CI: 1.42–1.49; p < 0.001), and increased mortality. The IHM increased steadily with the number of comorbidities and index scores from 1997 to 2022. D remains a relevant cause of hospitalization in Spain. Comorbidities reflected a great impact on patients with D and IPD, which would mean a higher risk of mortality. Predicting mortality events and length of stay by comparing indices showed that CCI outperforms ECI in predicting inpatient death after IPD. Full article

(This article belongs to the Section Public Health Microbiology)

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13 pages, 1938 KiB

Open AccessArticle

Encapsulation of Fresh Spirulina Biomass in Alginate Spheres for Yogurt Fortification

by Domenico Siclari, Maria Rosaria Panuccio and Rossana Sidari

Microorganisms 2025, 13(7), 1641; https://doi.org/10.3390/microorganisms13071641 - 11 Jul 2025

Viewed by 198

Abstract

A new spherification of Spirulina (Arthrospira platensis) was developed for its use as a food supplement. The novelty of this study is the incorporation of fresh Spirulina biomass into alginate spheres formulated with 3% sodium alginate and 1.5% calcium lactate and [...] Read more.

A new spherification of Spirulina (Arthrospira platensis) was developed for its use as a food supplement. The novelty of this study is the incorporation of fresh Spirulina biomass into alginate spheres formulated with 3% sodium alginate and 1.5% calcium lactate and its addition into yogurt. The spheres and the fortified yogurt were stored at 4 °C for 15 days. The viability of Spirulina, either in contact with the yogurt or not, was evaluated both by OD_550nm measurements and microscopic observations. Furthermore, the effect of Spirulina spheres on Streptococcus thermophilus and Lactobacillus bulgaricus was evaluated by enumerating them in standard media. Spirulina retained its viability for up to 15 days when stored separately from the yogurt matrix. Spirulina had a stimulating effect on the lactic acid bacteria: after 15 days, L. bulgaricus and S. thermophilus showed a load increase of 2.66% and 1.64%, respectively, compared to the load detected in the unfortified yogurt. Our study has demonstrated the technical feasibility of producing fresh Spirulina spheres, which can be used alone or added to food preparation. Nevertheless, additional investigations—including quantitative assessment of bioactive compounds and comprehensive sensory analysis—are essential to validate the methodology and support its scalability. Full article

(This article belongs to the Special Issue Microorganisms in Functional Foods: 2nd Edition)

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18 pages, 437 KiB

Open AccessArticle

Validation of a Real-Time PCR Assay for Fully Automated Detection of Bacillus cereus in Donor Human Milk

by Gemma Aran, Vanessa Pleguezuelos, Margarita Blanco, Cristina Garcia, Mariama Jallow, Mar López, Sara Monge, Natalia Casamitjana, Eva Alonso-Nogués and Gloria Soria

Microorganisms 2025, 13(7), 1640; https://doi.org/10.3390/microorganisms13071640 - 11 Jul 2025

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Abstract

Donor human milk (DHM) can harbor microbial contaminants that cause serious infections in premature infants. Bacillus cereus is a pathogen frequently found in DHM, capable of forming spores that can resist Holder pasteurization (62.5 °C, 30 min). Since no microbial growth is acceptable [...] Read more.

Donor human milk (DHM) can harbor microbial contaminants that cause serious infections in premature infants. Bacillus cereus is a pathogen frequently found in DHM, capable of forming spores that can resist Holder pasteurization (62.5 °C, 30 min). Since no microbial growth is acceptable in post-pasteurized DHM, microbiological testing of pre-pasteurized DHM provides information about its contamination level to determine if it should be accepted for pasteurization. Culture is the gold standard in microbiological control but it requires 24–48 h to provide results. In this study we developed and validated a non-commercial real-time PCR assay for the detection of Bacillus cereus (BC test) in DHM specimens on a fully automated high-throughput platform, the cobas^® 6800 system. The BC test showed excellent sensitivity and specificity, repeatability and linearity over an 8-log range and a low limit of detection in milk specimens, as well as good agreement with selective culture methods. BC test was then used to systematically control all milk donations (3439) over a 24-month period. Bacillus cereus was detected in 14.2% of DHM, with monthly rates ranging from 6 to 29% and a significantly higher incidence in warmer months. Incorporating this assay into our laboratory workflow improved efficiency and reduced turnaround time. Full article

(This article belongs to the Section Food Microbiology)

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16 pages, 1265 KiB

Open AccessReview

Novel Treatments for Diabetic Foot Osteomyelitis: A Narrative Review

by Crystal Jing, Julia E. Ralph, Jamie Lim, Jackson M. Cathey, Conor N. O'Neill and Albert T. Anastasio

Microorganisms 2025, 13(7), 1639; https://doi.org/10.3390/microorganisms13071639 - 11 Jul 2025

Viewed by 212

Abstract

Diabetic foot osteomyelitis (DFO) is a severe complication of diabetes mellitus and a leading cause of non-traumatic lower extremity amputation. Treatment remains clinically challenging with high recurrence rates despite standard antibiotic therapy and surgical debridement. This narrative review synthesizes current evidence on novel [...] Read more.

Diabetic foot osteomyelitis (DFO) is a severe complication of diabetes mellitus and a leading cause of non-traumatic lower extremity amputation. Treatment remains clinically challenging with high recurrence rates despite standard antibiotic therapy and surgical debridement. This narrative review synthesizes current evidence on novel operative and nonoperative therapies for DFO, focusing on emerging biomaterials, local antibiotic delivery systems, innovative surgical techniques, and adjunctive topical agents. Studies examining bioabsorbable and nonabsorbable antibiotic carriers, such as calcium sulfate beads, collagen sponges, and bioactive glass, demonstrate promising infection resolution rates and a potential to reduce the surgical burden, though most are limited by small cohorts and observational designs. Similarly, alternative surgical approaches (i.e., cancelloplasty, conservative bone excision, and tibial cortex distraction) have shown early success in limb preservation. Nonoperative strategies, including adjunct antimicrobials, antimicrobial peptides, and topical oxygen, offer additional options, particularly for patients unfit for surgery. While initial outcomes are encouraging, the supporting evidence is heterogeneous and primarily limited to case series and small, noncomparative trials. Overall, these novel therapies show potential as adjuncts to established DFO management, but further prospective research is indicated to define their long-term efficacy, safety, and role in clinical practice. Full article

(This article belongs to the Section Medical Microbiology)

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20 pages, 2279 KiB

Open AccessArticle

Enhancing Soil Health and Corn Productivity with a Co-Fermented Microbial Inoculant (CFMI-8): A Field-Based Evaluation

by Raul De Jesus Cano, Judith M. Daniels, Martha Carlin and Don Huber

Microorganisms 2025, 13(7), 1638; https://doi.org/10.3390/microorganisms13071638 - 11 Jul 2025

Viewed by 243

Abstract

Soil degradation and declining fertility threaten sustainable agriculture and crop productivity. This study evaluates the effects of CFMI-8, a co-fermented microbial inoculant comprising eight bacterial strains selected through genomic and metabolic modeling, on soil health, nutrient availability, and corn performance. Conducted in a [...] Read more.

Soil degradation and declining fertility threaten sustainable agriculture and crop productivity. This study evaluates the effects of CFMI-8, a co-fermented microbial inoculant comprising eight bacterial strains selected through genomic and metabolic modeling, on soil health, nutrient availability, and corn performance. Conducted in a randomized complete block design at Findlay Farm, Wisconsin, the field trial assessed soil biological activity, nutrient cycling, and crop yield responses to CFMI-8 treatment. Treated soils exhibited significant increases in microbial organic carbon (+224.1%) and CO₂ respiration (+167.1%), indicating enhanced microbial activity and organic matter decomposition. Improvements in nitrate nitrogen (+20.2%), cation exchange capacity (+23.1%), and potassium (+27.3%) were also observed. Corn yield increased by 28.6%, with corresponding gains in silage yield (+9.6%) and nutritional quality. Leaf micronutrient concentrations, particularly iron, manganese, boron, and zinc, were significantly higher in treated plants. Correlation and Random Forest analyses identified microbial activity and nitrogen availability as key predictors of yield and nutrient uptake. These results demonstrate CFMI-8’s potential to enhance soil fertility, promote nutrient cycling, and improve crop productivity under field conditions. The findings support microbial inoculants as viable tools for regenerative agriculture and emphasize the need for long-term studies to assess sustainability impacts. Full article

(This article belongs to the Section Plant Microbe Interactions)

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14 pages, 6052 KiB

Open AccessArticle

Comparative Analysis of Soil Microbial Community Structures in Rhizosphere of Two Texture-Differentiated Lotus Root Varieties

by Xinni Li, Qiyue Liang, Meiping Gao, Yangxiu Ou, Yifeng Hu, Wen Jiang, Huiping Jiang and Shangdong Yang

Microorganisms 2025, 13(7), 1637; https://doi.org/10.3390/microorganisms13071637 - 10 Jul 2025

Viewed by 155

Abstract

To investigate the relationship between the rhizosphere microbial community structure and lotus root texture, the biological properties, and the rhizosphere microbial composition of mealy (ML) and crunchy lotus (CL) varieties were all analyzed using traditional and high-throughput sequencing technologies. The results showed that [...] Read more.

To investigate the relationship between the rhizosphere microbial community structure and lotus root texture, the biological properties, and the rhizosphere microbial composition of mealy (ML) and crunchy lotus (CL) varieties were all analyzed using traditional and high-throughput sequencing technologies. The results showed that the ML varieties exhibited significantly lower moisture but higher starch contents than those of CL. Meanwhile, the rhizosphere fungal richness of ML was also significantly higher than that of CL. Moreover, the relative abundances of bacterial phyla and genera, such as Nitrospirota, Bacteroidota, Proteobacteria, and Bacillus, alongside fungal phyla and genera, i.e., Ascomycota and Emericellopsis, were enriched in rhizosphere of ML compared to CL. Functional prediction also revealed that elevated nitrogen cycling, polysaccharide degradation and cellulose breakdown functions could be detected in ML, potentially driving starch accumulation and cell wall modification. These results suggest that rhizosphere microbial composition, particularly nitrogen-cycling bacteria and lignocellulose-degrading fungi, may contribute to texture formation between texture-differentiated lotus root varieties. Full article

(This article belongs to the Section Plant Microbe Interactions)

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15 pages, 6783 KiB

Open AccessArticle

Disruptive DNA Intercalation Is the Mode of Interaction Behind Niacinamide Antimicrobial Activity

by Michal Rasis, Noa Ziklo and Paul Salama

Microorganisms 2025, 13(7), 1636; https://doi.org/10.3390/microorganisms13071636 - 10 Jul 2025

Viewed by 171

Abstract

Niacinamide was recently shown to directly interact with bacterial DNA and interfere with cell replication; niacinamide mode of interaction and efficacy as a natural anti-microbial molecule were also described. The aim of this study is to elucidate the exact binding mechanism of niacinamide [...] Read more.

Niacinamide was recently shown to directly interact with bacterial DNA and interfere with cell replication; niacinamide mode of interaction and efficacy as a natural anti-microbial molecule were also described. The aim of this study is to elucidate the exact binding mechanism of niacinamide to microbial DNA. Intercalation is a binding mode where a small planar molecule, such as niacinamide, is inserted between base pairs, causing structural changes in the DNA. Melting curve analysis with various intercalating dyes demonstrated that niacinamide interaction with bacterial DNA reduces its melting temperature in a linear dose-dependent manner. Niacinamide’s effect on the melting temperature was found to be % GC-dependent, while purine stretches were also found to influence the binding kinetics. Finally, fluorescent intercalator displacement (FID) assays demonstrated that niacinamide strongly reduces SYBR Safe signal in a dose-dependent manner. Interestingly, competition assays with a minor groove binder also reduced Hoechst signal but in a non-linear manner, which can be attributed to strand lengthening and unwinding following niacinamide intercalation. Taken altogether; our results suggest a “disruptive intercalation” as the mode of interaction of niacinamide with bacterial DNA. Formation of locally destabilized DNA portions by niacinamide might interfere with protein–DNA interaction and potentially affect several crucial bacterial cellular processes, e.g., DNA repair and replication, subsequently leading to cell death. Full article

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

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Microorganisms, Volume 13, Issue 7 (July 2025) – 232 articles

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