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In Utero Exposure to 2,3,7,8-Tetrachlorodibenzo-p-dioxin Impairs the Ability of Mice to Clear a Pseudomonas aeruginosa Infection in Adulthood
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Nematophagous Fungi Occurrence: Prediction Using Bioclimatic Variables
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Genomic Insights into Plant Growth-Promoting Traits of Lysinibacillus fusiformis and Bacillus cereus from Rice Fields in Panama
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Tick Dispersal and Borrelia Species in Ticks from Migratory Birds: Insights from the Asinara National Park, Sardinia, Italy
Journal Description
Microbiology Research
Microbiology Research
is an international, scientific, peer-reviewed open access journal published monthly online by MDPI (from Volume 11 Issue 2-2020).
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, ESCI (Web of Science), Embase, and other databases.
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 20.7 days after submission; acceptance to publication is undertaken in 2.9 days (median values for papers published in this journal in the first half of 2025).
- Recognition of Reviewers: APC discount vouchers, optional signed peer review, and reviewer names published annually in the journal.
Impact Factor:
2.2 (2024);
5-Year Impact Factor:
2.1 (2024)
Latest Articles
The Nosocomial Transmission of Carbapenem-Resistant Gram-Negative Bacteria in a Hospital in Baoding City, China
Microbiol. Res. 2025, 16(7), 147; https://doi.org/10.3390/microbiolres16070147 (registering DOI) - 2 Jul 2025
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Background: The global rise of multidrug-resistant Gram-negative bacteria, particularly non-fermenting species and carbapenemase-producing Enterobacteriaceae, poses a significant challenge to hospital infection control. Methods: In this study, a total of 89 Acinetobacter spp. isolates, 14 Pseudomonas aeruginosa, and 14 carbapenem-resistant Enterobacteriaceae isolates were
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Background: The global rise of multidrug-resistant Gram-negative bacteria, particularly non-fermenting species and carbapenemase-producing Enterobacteriaceae, poses a significant challenge to hospital infection control. Methods: In this study, a total of 89 Acinetobacter spp. isolates, 14 Pseudomonas aeruginosa, and 14 carbapenem-resistant Enterobacteriaceae isolates were collected from patients in a tertiary hospital. Whole-genome sequencing and antimicrobial susceptibility testing were conducted. Resistance mechanisms and evolutionary relationships were analyzed using phylogenetic analysis and genetic context mapping. Results: Among the non-fermenting isolates, A. baumannii exhibited high resistance to carbapenems, clustering into distinct clonal groups enriched with genes associated with biofilm formation and virulence genes. P. aeruginosa isolates harbored fewer resistance genes but carried notable mutations in the efflux pump systems and the oprD gene. In Enterobacteriaceae, four blaNDM alleles were identified within a conservative structural sequence, while blaKPC-2 was located in a non-Tn4401 structure flanked by IS481- and IS1182-like insertion sequences. Phylogenetic analysis revealed that blaNDM-positive E. coli strains were closely related to susceptible lineages, indicating horizontal gene transfer. Conversely, K. pneumoniae isolates harboring blaKPC-2 formed a tight clonal cluster, suggesting clonal expansion. Conclusions: The study reveals distinct transmission patterns between resistance genes: horizontal dissemination of blaNDM and clonal expansion of blaKPC-2 in K. pneumoniae. These findings emphasize the need for resistance-gene-specific genomic surveillance and infection control strategies to prevent further nosocomial dissemination.
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Open AccessCommunication
Transcriptomic Analysis of Macrophages Infected with Mycobacterium smegmatis
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Hong Sun, Yue Hou, Wenzhao Xu, Wenjing Wang, Na Tian, Dingyi Liu and Zhaogang Sun
Microbiol. Res. 2025, 16(7), 146; https://doi.org/10.3390/microbiolres16070146 (registering DOI) - 2 Jul 2025
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Mycobacterium tuberculosis (MTB) can cause serious infectious diseases. MTB is retained in the macrophages of an organism, activating the immune response or evading the immune response through other mechanisms. Mycobacterium smegmatis (M. smeg) has the advantage of high safety and maneuverability
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Mycobacterium tuberculosis (MTB) can cause serious infectious diseases. MTB is retained in the macrophages of an organism, activating the immune response or evading the immune response through other mechanisms. Mycobacterium smegmatis (M. smeg) has the advantage of high safety and maneuverability as an alternative to MTB. M. smeg has physiological functions similar to those of MTB. It is mainly used to study the molecular mechanism of the interaction between the modified M. smeg carrying MTB-related components and cells. There are few studies on the interaction between the unmodified M. smeg and macrophages. Transcriptomics is an emerging research tool in recent years, which can deeply explore the relevant molecules inside a cell and explore the possible regulatory mechanisms more comprehensively. In this study, we first constructed an in vitro model of M. smeg-infected macrophages, collected RNA extracted from the infected cells, performed transcriptome sequencing using the Illunima platform, and verified the expression levels of the main markers related to phenotypic or functional changes in macrophages by qPCR and ELISA. In this study, through the transcriptomic analysis of M. smeg-infected macrophages, we found that M. smeg can regulate multiple cell signaling pathways in macrophages dominated by immune responses and activate the production of the cytokines IL-6 and TNF-α, which are mainly involved in the immune response in macrophages. This study suggests that M. smeg and MTB have similar physiological functions in activating the immune response of macrophages. Meanwhile, the interaction between M. smeg and macrophages also indicates the primary position and significant role of immune regulation in cellular signaling pathways. Therefore, studying the interaction mechanism between macrophages and M. smeg through transcriptomics is conducive to a comprehensive understanding of the related physiological functions of M. smeg in regulating immune responses or immune escape, providing strong evidence for its use as a model alternative bacteria for MTB in the future research on MTB immunity and related physiological functions.
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Open AccessArticle
Occurrence of Philaenus spumarius in Xylella fastidiosa Demarcated Zones of Northern Portugal
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Talita Loureiro, Luís Serra, Ângela Martins, Isabel Cortez and Patrícia Poeta
Microbiol. Res. 2025, 16(7), 145; https://doi.org/10.3390/microbiolres16070145 - 2 Jul 2025
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The introduction of non-native species like Xylella fastidiosa to new environments can lead to potentially catastrophic ecological and economic repercussions. This work comprehended the prospection phase (insect sampling and submission of samples to the laboratory) from X. fastidiosa demarcated zones of Área Metropolitana
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The introduction of non-native species like Xylella fastidiosa to new environments can lead to potentially catastrophic ecological and economic repercussions. This work comprehended the prospection phase (insect sampling and submission of samples to the laboratory) from X. fastidiosa demarcated zones of Área Metropolitana do Porto; Sabrosa; Alijó; Baião; Mirandela; Mirandela II; and Bougado and the research phase (collecting and organizing data and statistical treatment). The results of this study showed the presence of the bacterium in some tested spittlebugs species captured in DZ of Área Metropolitana do Porto, which highlights the role of the vector in mediating the disease’s propagation. Most insects were found in public gardens and in nurseries/gardens where there is a diverse array of food sources, shelter, mating locations, and suitable substrates for egg laying that serve as ideal conditions for the population of Philaenus spumarius. We observed that most insects were found in the first trimester (36.5%), followed by the third trimester (23.2%). Finally, it was shown that, in our study, the most frequent host plants where insects were found included Lavandula dentata, Ulex minor, Ulex europaeus, Quercus suber, Plantago lanceolata. Our findings imply a robust connection between plant communities, ecological conditions, and insect populations with the occurrence of Xylella fastidiosa, particularly within the examined climatic context.
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Open AccessArticle
Microbial Changes in Hand Skin During COVID-19: A Longitudinal Study in Majorca, Spain
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Cristina Turpín and Antonio Doménech-Sánchez
Microbiol. Res. 2025, 16(7), 144; https://doi.org/10.3390/microbiolres16070144 - 2 Jul 2025
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The COVID-19 pandemic prompted widespread adoption of intensified hand hygiene practices, raising concerns about their medium-term impact on the skin microbiome. This study investigates alterations in the hand microbiome of healthy adults during the pandemic compared to pre-pandemic periods in Majorca, Spain. A
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The COVID-19 pandemic prompted widespread adoption of intensified hand hygiene practices, raising concerns about their medium-term impact on the skin microbiome. This study investigates alterations in the hand microbiome of healthy adults during the pandemic compared to pre-pandemic periods in Majorca, Spain. A total of 30 volunteers (16 women, 14 men; mean age 44.1 ± 8.8 years) were sampled between 2014 and 2021. Palm swabs were collected following WHO guidelines, alongside measurements of skin pH, temperature, and handwashing frequency. Bacterial DNA was extracted and analyzed via 16S rRNA (V3-V4) metagenomic sequencing to assess microbial diversity and composition. Results revealed a significant decline in microbial diversity during the COVID-19 period, accompanied by a marked shift in the community structure. The Firmicutes phylum dominated, with Bacillales increasing from 30.7% to 84.1%, primarily driven by a surge in Staphylococcus species (e.g., S. pasteuri). Conversely, S. hominis and Actinomycetales nearly disappeared. No significant associations were observed with gender or handwashing frequency. The skin temperature increased during the pandemic, while the pH remained stable. The Staphylococcus/Bacillus ratio shifted significantly, favoring Staphylococcus dominance. These findings, derived from a geographically limited population in Majorca, Spain, demonstrate that stringent hygiene measures during COVID-19 reduced microbial diversity and restructured hand microbiome composition. The study underscores the necessity for balanced hygiene strategies that mitigate pathogen transmission while preserving beneficial microbial communities critical to skin health.
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Open AccessArticle
The TOR Regulatory Mechanism Controls the Metabolism of Nitrate and the Fermentation Activity in the Yeast Dekkera bruxellensis GDB 248
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Karolini Miranda, Beatriz Câmara de Melo, Gilberto Henriques Teles, Irina Charlot Peña-Moreno, Rafael Barros de Souza and Marcos Antonio de Morais, Jr.
Microbiol. Res. 2025, 16(7), 143; https://doi.org/10.3390/microbiolres16070143 - 1 Jul 2025
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Dekkera bruxellensis is already known for its great biotechnological potential, part of this due to the ability to assimilate nitrate during fermentation. Despite the previous works on nitrogen metabolism in this yeast, especially regarding nitrate assimilation, the relation between this metabolism and the
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Dekkera bruxellensis is already known for its great biotechnological potential, part of this due to the ability to assimilate nitrate during fermentation. Despite the previous works on nitrogen metabolism in this yeast, especially regarding nitrate assimilation, the relation between this metabolism and the TOR (Target of Rapamycin) regulatory mechanism remains unexplored. This connection may reveal key regulatory mechanisms to maximize its fermentative performance and biotechnological use. Herein, we evaluated the physiological, metabolic, and gene expression profile of D. bruxellensis GDB 248 cultivated in ammonium and nitrate as nitrogen sources in the presence of TOR complex 1 (TORC1) inhibitor rapamycin. Our results showed that inhibition of the TORC1 significantly reduces cell growth and fermentative capacity, especially in nitrate media. Gene expression analysis revealed that TORC1 plays a central role in regulating genes involved in nitrate assimilation and the adaptive performance of D. bruxellensis in fermentative environments. Therefore, the regulation of nitrate assimilatory genes YNTI, YNRI, and YNI1 responds to a nitrate-dependent mechanism as well as to a TOR-dependent mechanism. These findings expand the understanding of the regulation of nitrogen metabolism in D. bruxellensis, providing valuable information that may aid in the development of future strategies for its use as an industrial yeast.
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Open AccessArticle
Microbiological Profile and Resistance Patterns in Periprosthetic Joint Infections: A Regional Multicenter Study in Spain
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Lucia Henriquez, Ander Uribarri, Iñaki Beguiristain, Ignacio Sancho, Carmen Ezpeleta Baquedano and Maria Eugenia Portillo
Microbiol. Res. 2025, 16(7), 142; https://doi.org/10.3390/microbiolres16070142 - 1 Jul 2025
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Due to the significant number of microbiologically negative periprosthetic joint infections (PJIs), understanding the trend in etiology and resistance patterns is essential for the correct management of these infections. Currently, few studies have been published in Spain. In this study, we analyzed the
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Due to the significant number of microbiologically negative periprosthetic joint infections (PJIs), understanding the trend in etiology and resistance patterns is essential for the correct management of these infections. Currently, few studies have been published in Spain. In this study, we analyzed the incidence, clinical characteristics, etiology, and antibiotic resistance in patients with PJIs over the last 5 years in Navarra. In this multicentric and retrospective study, all patients diagnosed with PJIs in Navarra from 2019 to 2023 were included. Of the total 156 PJIs, 23% had negative cultures and 56% of these patients had been treated with antibiotics prior to sampling. Staphylococcus epidermidis with methicillin resistance was the predominant etiological agent, followed by Staphylococcus aureus and Cutibacterium acnes. Forty percent of the Gram-positive cocci (GPC) and 35% of the Gram-negative bacilli (GNB) were multidrug-resistant organisms (MDROs). Quinolone resistance was 46% for staphylococci and 18% for Gram-negatives. In addition, 9% of staphylococci were resistant to rifampicin. Antibiotic therapy administration prior to sampling is one of the main problems for microbiological diagnosis and is present more frequently in culture-negative PJIs (56%). New sequencing techniques could improve this difficulty. The high percentage of resistance in the microorganisms causing PJI leads us to reconsider the empirical treatment for suspected PJI, with the use of different therapeutic approaches depending on the time of infection and the possible use of new non-antibiotic therapies.
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Open AccessArticle
Endophytic Microbiome Is a Unique Repository of Bio-Foes Against Toxigenic Fungi Harming Peanut Productivity
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Nagwa I. M. Helal, Mona H. Badawi, Abeer M. El-Hadidy, Mohamed K. M. Agha, Ahmed Abou-Shady and Mohamed Fayez
Microbiol. Res. 2025, 16(7), 141; https://doi.org/10.3390/microbiolres16070141 - 1 Jul 2025
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The major objective was to investigate the protective capabilities of endophytic bacterial strains isolated from a number of medicinal plant species towards Aspergillus spp. secured from the internal tissues of fungi-infected peanuts. Among 32 fungal isolates surveyed for mycotoxin production in various culture
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The major objective was to investigate the protective capabilities of endophytic bacterial strains isolated from a number of medicinal plant species towards Aspergillus spp. secured from the internal tissues of fungi-infected peanuts. Among 32 fungal isolates surveyed for mycotoxin production in various culture media (PDA, RBCA, YES, CA), 10 isolates qualitatively producing AFB1, besides 10 OTA-producers, were assayed by HPLC for quantitative toxin production. Aspergillus spp. isolate Be 13 produced an extraordinary quantity of 1859.18 μg mL−1 AFB1, against the lowest toxin level of 280.40 μg mL−1 produced by the fungus isolate IS 4. The estimated amounts of OTA were considerably lower and fell in the range 0.88–6.00 μg mL−1; isolate Sa 1 was superior, while isolate Be 7 seemed inferior. Based on ITS gene sequencing, the highly toxigenic Aspergillus spp. isolates Be 13 and Sa 1 matched the description of A. novoparasiticus and A. ochraceus, respectively, ochraceus, respectively, which are present in GenBank with identity exceeding 99%. According to 16S rRNA gene sequencing, these antagonists labeled Ar6, Ma27 and So34 showed the typical characteristics of Pseudomonas aeruginosa, Bacillus subtilis and Bacillus velezensis, respectively, with similarity percentages of 99–100. The plant growth-promoting activity measurements of the identified endophytes indicated the production of 16.96–80.00 μg/100 mL culture medium of IAA. Phosphate-solubilizing capacity varied among endophytes from 2.50 to 21.38 μg/100 mL. The polysaccharide production pool of bacterial strains ranged between 2.74 and 6.57 mg mL−1. P. aeruginosa Ar6 and B. velezensis successfully produced HCN, but B. subtilis failed. The in vitro mycotoxin biodegradation potential of tested bacterial endophytes indicated the superiority of B. velezensis in degrading both mycotoxins (AFB1-OTA) with average percentage of 88.7; B. subtilis ranked thereafter (85.6%). The 30-day old peanut (cv. Giza 6) seedlings grown in gnotobiotic system severely injured due to infection with AFB1/OTA-producing fungi, an effect expressed in significant reductions in shoot and root growth traits. Simultaneous treatment with the endophytic antagonists greatly diminished the harmful impact of the pathogens; B. velezensis was the pioneer, not P. aeruginosa Ar6. In conclusion, these findings proved that several endophytic bacterial species have the potential as alternative tools to chemical fungicides for protecting agricultural commodities against mycotoxin-producing fungi.
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Open AccessArticle
Insights into the Thriving of Bacillus megaterium and Rhodotorula mucilaginosa in Mining Areas: Their Adaptation and Tolerance Under Extreme Levels of Cu and Mn
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Alfonso Álvarez-Villa, Maribel Plascencia-Jatomea, Kadiya Calderón, Katiushka Arévalo-Niño, Guadalupe López-Avilés and Francisco Javier Almendariz-Tapia
Microbiol. Res. 2025, 16(7), 140; https://doi.org/10.3390/microbiolres16070140 - 1 Jul 2025
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Understanding microbial adaptation and tolerance based on the cellular concentration and biosorption capacity provides critical insights for evaluating microbial performance under heavy metal stress, which is essential for selecting efficient strains or consortia for bioremediation applications. In this study, the adaptation and tolerance
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Understanding microbial adaptation and tolerance based on the cellular concentration and biosorption capacity provides critical insights for evaluating microbial performance under heavy metal stress, which is essential for selecting efficient strains or consortia for bioremediation applications. In this study, the adaptation and tolerance of Bacillus megaterium and Rhodotorula mucilaginosa to elevated concentrations of copper (Cu) and manganese (Mn) were investigated by introducing the maximum adaptation concentration (MAC) alongside the maximum tolerable concentration (MTC) and the minimum inhibitory concentration (MIC). A Gaussian model was fitted to the relative growth responses to estimate the MACs, MTCs, and MICs. B. megaterium exhibited MACs of 4.6 ppm Cu and 393.9 ppm Mn, while R. mucilaginosa showed MACs of 59.6 ppm Cu and 64.4 ppm Mn, corresponding to concentrations that stimulated their maximum cell density. A biosorption analysis revealed average capacities of 6.3 ± 5.3 mg Cu/g biomass and 28.6 ± 17.2 mg Mn/g biomass, positively correlated with the MTCs, indicating enhanced metal uptake under sublethal stress. The co-culture assays demonstrated dynamic microbial interactions shaped by the type and concentration of metal, including coexistence, competitive substitution, and dominance by tolerance. These findings support the use of MACs as indicators of growth stimulation and MTCs as thresholds for enhanced metal uptake, providing a dual-parameter framework for selecting metallotolerant microorganisms for metal recovery strategies.
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Open AccessArticle
Characterization and Expression Analysis of the Sterol C-5 Desaturase Gene PcERG3 in the Mycobiont of the Lichen Peltigera canina Under Abiotic Stresses
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Moatasem A. Swid, Milana V. Koulintchenko, Alfred O. Onele, Ilya Y. Leksin, Daniya F. Rakhmatullina, Ekaterina I. Galeeva, Julia N. Valitova, Farida V. Minibayeva and Richard P. Beckett
Microbiol. Res. 2025, 16(7), 139; https://doi.org/10.3390/microbiolres16070139 - 1 Jul 2025
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Lichens, symbiotic organisms with a high tolerance to harsh environments, possess a greater diversity of sterols than other organisms. Sterols are involved in maintaining membrane integrity, hormone biosynthesis, and signal transduction. (1) Background: A characteristic feature of lichen sterols is a high degree
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Lichens, symbiotic organisms with a high tolerance to harsh environments, possess a greater diversity of sterols than other organisms. Sterols are involved in maintaining membrane integrity, hormone biosynthesis, and signal transduction. (1) Background: A characteristic feature of lichen sterols is a high degree of unsaturation, which influences membrane properties. Desaturases play an important role in the synthesis of unsaturated sterols, in particular, sterol C-5 desaturase (ERG3), which controls the conversion of episterol to ergosterol. Earlier, we demonstrated that the treatment of the lichen Peltigera canina with low and elevated temperatures results in changes in the levels of episterol and ergosterol. (2) Methods: Here, for the first time, we identified ERG3 in P. canina and, using an in silico analysis, we showed that PcERG3 belongs to the superfamily of fatty acid hydrolyases. A phylogenetic analysis was conducted to determine the evolutionary relationships of PcERG3. (3) Results: A phylogenetic analysis showed that PcERG3 clusters with ERG3 from other Peltigeralian and non-Peltigeralian lichens and also with ERG3 from free-living fungi. This suggests that PcERG3 has an ancient evolutionary origin and is related to fungi with lichenized ancestors, e.g., Penicillium. The differential expression of PcERG3 in response to temperature stress, a dehydration/rehydration cycle, and heavy metal exposure suggests that it plays a crucial role in maintaining the balance between more and less saturated sterols and, more generally, in membrane functioning. The multifaceted response of P. canina to abiotic stresses was documented by simultaneously measuring changes in the expression of PcERG3, as well as the genes encoding the heat shock proteins, PcHSP20 and PcHSP98, and PcSOD1, which encodes the antioxidant enzyme superoxide dismutase. (4) Conclusions: These findings suggest that PcERG3 is similar to the sterol C-5 desaturases from related and free-living fungi and plays important roles in the molecular mechanisms underlying the tolerance of lichens to environmental stress.
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Open AccessArticle
Antibacterial In Vitro Properties of Silver Sulfadiazine in Combination with Tris-EDTA and N-Acetylcysteine Against Pseudomonas aeruginosa Isolates from Dogs with Suppurative Otitis
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Ioanna Papadogiannaki, Rosario Cerundolo, Jennifer Plant, Elizabeth Villiers, Jenny Littler, Anika Wisniewska and Panagiotis Sgardelis
Microbiol. Res. 2025, 16(7), 138; https://doi.org/10.3390/microbiolres16070138 - 1 Jul 2025
Abstract
Pseudomonas aeruginosa otitis is common in dogs and antibiotic-resistant strains are often isolated. We are unaware of reports evaluating the combination of silver sulfadiazine (SSD) with a biofilm disruptor solution containing Tris-EDTA (tromethamine-ethylenediaminetetraacetic acid) and N-acetylcysteine (Tris-NAC). Forty-eight P. aeruginosa strains from dogs
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Pseudomonas aeruginosa otitis is common in dogs and antibiotic-resistant strains are often isolated. We are unaware of reports evaluating the combination of silver sulfadiazine (SSD) with a biofilm disruptor solution containing Tris-EDTA (tromethamine-ethylenediaminetetraacetic acid) and N-acetylcysteine (Tris-NAC). Forty-eight P. aeruginosa strains from dogs with suppurative otitis were analysed using the agar well diffusion method. A volume of 70 μL of Tris-NAC, a water solution of 10% SSD and their combination in equal amount was pipetted into the designated wells. After incubation, the diameter of the inhibition zone was measured. A synergy experiment using the checkerboard assay was performed to look at any potential synergistic effects of SSD and Tris-NAC against only 10 randomly selected isolates of P. aeruginosa. The samples tested with Tris-NAC + 10% SSD solution, compared with the samples tested with 10% SSD alone, demonstrated significantly higher inhibition zones against P. aeruginosa, p < 0.00001. The checkerboard assay results showed an additive effect between the two compounds. The use of 10% SSD could be evaluated as a therapeutic tool against strains of P. aeruginosa if combined with Tris-NAC.
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(This article belongs to the Special Issue Veterinary Microbiology and Diagnostics)
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Open AccessArticle
Investigating Antibiotic Susceptibility of Pathogenic Micro-Organisms in Groundwater from Boreholes and Shallow Wells in T/A Makhwira, Chikwawa
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Baleke Vinjeru Banda, Harold Wilson Tumwitike Mapoma and Bernard Thole
Microbiol. Res. 2025, 16(7), 137; https://doi.org/10.3390/microbiolres16070137 - 30 Jun 2025
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Many rural communities in Malawi use groundwater from boreholes and shallow wells for drinking and cooking with limited or no treatment because it is considered as a safe source of water. The contamination of groundwater sources by antimicrobial resistant bacteria renders the water
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Many rural communities in Malawi use groundwater from boreholes and shallow wells for drinking and cooking with limited or no treatment because it is considered as a safe source of water. The contamination of groundwater sources by antimicrobial resistant bacteria renders the water unsafe to use. This study investigated the antibiotic susceptibility of pathogenic micro-organisms isolated from groundwater sources in T/A Makhwira, Chikwawa. Water samples were collected from 13 boreholes and 7 protected shallow wells from T/A Makhwira, Chikwawa. E. coli, Salmonella enterica ssp. Arizona, K. pneumoniae, ESBL E. coli, and ESBL K. pneumoniae were detected in some water samples. Antibiotic susceptibility tests showed that the isolates had a high resistance to Ampicillin (42%), followed by Trimethoprim-sulfamethoxazole (26%), Ciprofloxacin (21%), Doxycycline, and Amoxicillin/clavulanic acid (16%). The isolates had a very high sensitivity to Gentamicin (89%). The study revealed that the water from some boreholes and shallow wells in T/A Makhwira is highly contaminated and needs to be treated before consumption. Drinking untreated water from these sources could transfer antibiotic-resistant bacteria to humans because the groundwater may act as a vehicle for the transmission of these antibiotic-resistant bacteria.
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Open AccessArticle
Beneficial Cecal Microbiome Modulation in Turkeys Exposed to Probiotics and Vaccine After Multidrug-Resistant Salmonella Heidelberg Challenge
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Dhananjai Muringattu Prabhakaran, Anup Kollanoor Johny, Divek V. T. Nair, Shijinaraj Manjankattil, Timothy J. Johnson, Sally Noll and Kent M. Reed
Microbiol. Res. 2025, 16(7), 136; https://doi.org/10.3390/microbiolres16070136 - 25 Jun 2025
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Salmonella Heidelberg (SH) is a major serotype of foodborne Salmonella associated with turkeys. Understanding the effect of antibiotic alternatives (AAs) on the cecal microbiome of turkeys challenged with Salmonella could inform the development of microbiome-based strategies on farms. This study examined the effects
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Salmonella Heidelberg (SH) is a major serotype of foodborne Salmonella associated with turkeys. Understanding the effect of antibiotic alternatives (AAs) on the cecal microbiome of turkeys challenged with Salmonella could inform the development of microbiome-based strategies on farms. This study examined the effects of multiple AAs, such as probiotics, Lactobacillus and Propionibacterium, and a Salmonella Typhimurium vaccine, on the turkey cecal microbiome exposed to multidrug-resistant (MDR) SH. Microbial DNA was extracted from the cecal contents of 12-week-old commercial turkeys grown in five treatments for shotgun metagenomic sequencing and analysis: NC—Negative Control; PC—Salmonella Control; LAB—Lactobacillus treatment; PF—P. freudenreichii treatment; and VAC—vaccine treatment. Except for the NC, turkeys were challenged with MDR SH (108 CFU/turkey) on the 11th week. Differential abundance tests at the species level found that all AA treatments resulted in an increased abundance of multiple lactic acid-producing bacteria in the cecum compared to PC. In addition, multiple metabolic pathways were differentially abundant in AA treatments compared to PC. This study highlights the importance of AA strategies producing an increased abundance of lactic acid bacteria and critical metabolic pathways, indicating the potential of AAs to improve the gut health of turkeys during the Salmonella challenge.
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Open AccessReview
New Antibiotics for Lower Respiratory Tract Infections
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Despoina Papageorgiou, Maria Gavatha, Dimitrios Efthymiou, Eleni Polyzou, Aristotelis Tsiakalos and Karolina Akinosoglou
Microbiol. Res. 2025, 16(7), 135; https://doi.org/10.3390/microbiolres16070135 - 23 Jun 2025
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Respiratory tract infections are frequently encountered in clinical practice. The growing incidence of antimicrobial resistance among the causative pathogens exerts sustained pressure on the existing therapeutic options. The emergence of antimicrobial resistance limits the treatment options and often leads to unfavorable patient outcomes.
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Respiratory tract infections are frequently encountered in clinical practice. The growing incidence of antimicrobial resistance among the causative pathogens exerts sustained pressure on the existing therapeutic options. The emergence of antimicrobial resistance limits the treatment options and often leads to unfavorable patient outcomes. However, in the past few years, newly developed antibiotics have become available, providing viable choices for antibiotic-resistant infections. New β-lactam/β-lactamase combinations, such as ceftazidime/avibactam, meropenem/vaborbactam, and imipenem/relebactam, are effective against carbapenem-resistant Enterobacterales. Several new drugs including ceftolozane/tazobactam are active against multi-drug-resistant Pseudomonas aeruginosa, while sulbactam/durlobactam and cefiderocol have potent activity against Acinetobacter baumannii. A number of new options, such as lefamulin, omadacycline, and delafloxacin, have also emerged for pathogens commonly associated with community acquired pneumonia. This article aims to review the characteristics of newly approved antibiotics for the treatment of respiratory tract infections, as well as to discuss some investigational agents that are currently under development.
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Open AccessArticle
In Vitro Evaluation of a Gel Formulation with Postbiotics and Prebiotics Against Pathogenic Microorganisms Present in the Microbiota of Psoriatic Skin
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Nadine Gonçalves Mascarenhas, Vânia Rodrigues Leite-Silva, Márcio Adriano Andréo, Newton Andréo-Filho and Patricia Santos Lopes
Microbiol. Res. 2025, 16(7), 134; https://doi.org/10.3390/microbiolres16070134 - 23 Jun 2025
Abstract
Psoriasis is a chronic, non-contagious, immune-mediated inflammatory skin disease. Although current treatments help manage the condition, many present limitations that affect patient adherence, particularly topical therapies. Given that the skin microbiota represents a promising therapeutic target, this study investigated the potential of prebiotics
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Psoriasis is a chronic, non-contagious, immune-mediated inflammatory skin disease. Although current treatments help manage the condition, many present limitations that affect patient adherence, particularly topical therapies. Given that the skin microbiota represents a promising therapeutic target, this study investigated the potential of prebiotics derived from β-glucans and postbiotics produced by Lactobacillus paracasei and Saccharomyces cerevisiae to modulate microbial balance; the in vitro activity was evaluated against Staphylococcus aureus and Malassezia furfur, both as isolated compounds and within topical formulations. Extracts were characterized by HPLC, and antimicrobial activity was assessed using broth microdilution and agar diffusion methods. Postbiotic extracts at 500 mg/mL inhibited microbial growth by 90–97%. Oat-derived β-glucan at 0.5% inhibited over 97% of microbial growth, while yeast-derived β-glucan showed approximately 60% inhibition. In agar diffusion tests, the active ingredients reduced the growth of both microorganisms, except for the yeast-derived β-glucan. These findings are promising and suggest that these bioactive compounds could support the rebalancing of skin microbiota in dermatological conditions. Further research is needed to identify the molecules produced by probiotics and assess the most suitable vehicle for incorporating the active compounds.
Full article
(This article belongs to the Topic Microbiota Diversity and Its Broader Biological Implications Across Human and Animal Health)
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Open AccessArticle
Emergence, Spread of Antimicrobial-Resistant Bacteria and Phylogenetic Relationships in Coastal Ecosystems—Gastropod Phorcus lineatus as a Bioindicator
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Dércia Santos, Ana Rita Pinto, Rita Barata, Conceição Fernandes, Hugo Guedes, Gonçalo Almeida, Edna Cabecinha, Sandra M. Monteiro, Simone Varandas and Maria José Saavedra
Microbiol. Res. 2025, 16(6), 133; https://doi.org/10.3390/microbiolres16060133 - 19 Jun 2025
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Coastal environments have been recognized as key reservoirs for antibiotic-resistant bacteria. The present study evaluated marine gastropods, Phorcus lineatus, as potential bioindicators to assess the spread of antibiotic-resistant bacteria. P. lineatus was sampled in four sites, with different anthropogenic pressures, along the
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Coastal environments have been recognized as key reservoirs for antibiotic-resistant bacteria. The present study evaluated marine gastropods, Phorcus lineatus, as potential bioindicators to assess the spread of antibiotic-resistant bacteria. P. lineatus was sampled in four sites, with different anthropogenic pressures, along the northwest Portuguese coastal area. From these specimens, bacteria were isolated and tested for their antimicrobial susceptibility, followed by their phylogenetic and pathotypic determination. All the Escherichia coli isolates showed resistance to at least one antimicrobial agent. The highest levels of multidrug resistance (25%) were observed in E. coli isolates obtained from SITE 2, which is impacted by the city of Porto and industrial settlements, while nearly 17% of these isolates showed a multiple antibiotic resistance (MAR) index higher than 0.2. Among the isolates, phylogroups A and B2 were the most prevalent, followed by phylogroup B1. The isolates of phylogroup A showed a higher prevalence of antimicrobial resistance. This study offers valuable insights into the antibiotic resistance risks posed to marine ecosystems and underscores the need for microbiological monitoring and the development of effective management strategies. The findings suggest P. lineatus as a potential bioindicator of antibiotic-resistant bacteria in marine environments.
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Open AccessArticle
Anti-Influenza A Virus Activity of Rhododendron brachycarpum Extract and Identification of Hyperoside as the Active Constituent
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Yung Hun Park, Soo Yong Shin, Hayeong Choi, Jae Hyeok Lee, You Jin Kim, Seong Ji Woo, Wonkyun Ronny Im and Sung Ho Jeon
Microbiol. Res. 2025, 16(6), 132; https://doi.org/10.3390/microbiolres16060132 - 18 Jun 2025
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Influenza A virus (IAV) poses significant public health challenges due to its rapid mutation and drug resistance, necessitating novel antiviral strategies. Rhododendron brachycarpum, traditionally employed in folk medicine to treat inflammatory conditions, contains bioactive flavonoids with potential antiviral effects. In this study,
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Influenza A virus (IAV) poses significant public health challenges due to its rapid mutation and drug resistance, necessitating novel antiviral strategies. Rhododendron brachycarpum, traditionally employed in folk medicine to treat inflammatory conditions, contains bioactive flavonoids with potential antiviral effects. In this study, we investigated the anti-influenza activity of R. brachycarpum leaf extract and identified hyperoside (quercetin-3-O-galactoside) as the active constituent. The crude extract and its n-butanol fraction markedly reduced IAV replication in Madin–Darby canine kidney (MDCK) cells, with IC50/CC50 values of 74.51/201.09 μg/mL and 24.5/113.1 μg/mL, respectively. Hyperoside, purified via bioactivity-guided fractionation and HPLC analysis, demonstrated potent antiviral activity, with an IC50 of 66.59 μM (30.92 μg/mL) and a CC50 of 318.9 μM (148.1 μg/mL), indicating a favorable selectivity index. It significantly suppressed viral mRNA and protein expression in infected cells. Time-of-addition and hemagglutination inhibition assays suggested that hyperoside exerts antiviral effects during early infection stages, likely interfering with viral entry. In silico molecular docking analysis further supported this mechanism, revealing that hyperoside binds strongly to the receptor-binding domain of hemagglutinin (−11.5 kcal/mol), potentially blocking viral attachment. These findings reveal that hyperoside is a major antiviral component of R. brachycarpum and underscore its therapeutic potential as a natural antiviral candidate against IAV infections.
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Open AccessArticle
Genotypic Characterisation and Risk Assessment of Virulent ESBL-Producing E. coli in Chicken Meat in Tunisia: Insights from Multi-Omics Machine Learning Perspective
by
Khaled Abdallah, Ghassan Tayh, Elaa Maamar, Amine Mosbah, Omar Abbes, Ismail Fliss and Lilia Messadi
Microbiol. Res. 2025, 16(6), 131; https://doi.org/10.3390/microbiolres16060131 - 18 Jun 2025
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Antibiotics are frequently used in the poultry industry, which has led to the emergence of bacterial strains that are resistant to antimicrobial treatments. The main objectives of this research were to conduct a multimodal risk assessment, to determine the extent of contamination of
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Antibiotics are frequently used in the poultry industry, which has led to the emergence of bacterial strains that are resistant to antimicrobial treatments. The main objectives of this research were to conduct a multimodal risk assessment, to determine the extent of contamination of chicken meat with Escherichia coli, assess the prevalence of strains resistant to extended-spectrum cephalosporins (ESC), and characterise the genes associated with resistance and virulence. A standardised procedure involving enrichment in buffered peptone water and isolation of E. coli on MacConkey agar was carried out on 100 chicken carcasses. Subsequently, the sensitivity of the strains was tested against 21 antibiotic discs. Additionally, ESBL production was detected using a double synergy test. Specific PCRs were employed to identify resistance to critical antibiotics in human medicine (such as cephalosporins, carbapenems, fluoroquinolones, and colistin), as well as the presence of virulence genes. The contamination rate of chicken meat with E. coli was 82%. The prevalence of ESC-resistant isolates was 91.2%. Furthermore, 76.5% of the isolates exhibited ESBL production, with the different beta-lactamase genes (blaCTXM, blaTEM, and blaSHV). The mcr-1 gene, associated with colistin resistance, was detected in four strains (5.9%). Some isolates also carried resistance genes such as sul1, sul2, sul3, tetA, tetB, qnrB, and qnrS. In addition, several virulence genes were detected. In our study, we were able to link the expression of AMR to the iron metabolic regulatory elements using a multimodal machine learning approach; this mechanism could be targeted to mitigate the bacteria virulence and resistance. The high prevalence of ESBL-producing and multi-resistant E. coli strains in poultry presents significant human health risks, with the focus on antibiotic-resistant uropathogenic strains since poultry meat could be an important source of uropathogenic strains, underscoring the danger of hard-to-treat urinary tract infections, stressing the need for controlled antibiotic use and thorough monitoring.
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Open AccessArticle
Native Strains T. longibrachiatum UCF17-M4 and Trichoderma sp. UCPF2 Reduce Cd Uptake in Cacao CCN51 Under Controlled Conditions
by
Rozana Yanina Malca-Cerna, Cortez-Lazaro Anthony Apolinario, Chavez-Castillo Jeremy Israel, Arce-Inga Marielita and Cumpa-Velasquez Liz Marjory
Microbiol. Res. 2025, 16(6), 130; https://doi.org/10.3390/microbiolres16060130 - 17 Jun 2025
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The cacao trade and export industry has been impacted by cadmium (Cd2+) accumulation in soils, as the metal is absorbed by plants and transferred to the tissues. Consequently, cacao beans and their derivatives can become contaminated, sometimes exceeding permissible limits. In
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The cacao trade and export industry has been impacted by cadmium (Cd2+) accumulation in soils, as the metal is absorbed by plants and transferred to the tissues. Consequently, cacao beans and their derivatives can become contaminated, sometimes exceeding permissible limits. In this study, the capacity of native Trichoderma strains to reduce Cd accumulation in cacao was evaluated. Twelve Trichoderma strains were analyzed to assess their cadmium removal capacity through in vitro assays and their ability to reduce Cd concentration in cacao plants under controlled in vivo conditions. The in vitro results showed that several Trichoderma strains could remove cadmium and accumulate it in their biomass. However, this process is complex as it depends on metal concentration and environmental conditions. Notably, T. afroharzianum UCF18-M1 and CP24-6 exhibited high removal efficiencies at 100 ppm (61.79 ± 2.98% and 57.93 ± 4.14%, respectively). In contrast, the in vivo assays revealed that, contrary to expectations, some strains—including those with the highest removal efficiency—stimulated Cd uptake in plants, even at toxic levels, such as T. orientale BLPF1-C1. However, T. longibrachiatum UCF17-M4 and Trichoderma sp. UCPF2-C1 significantly reduced Cd accumulation in the stem. These findings highlight the potential of these strains to mitigate Cd contamination in cacao.
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Open AccessArticle
Therapeutic Potential of Clerodendrum glabrum and Gardenia volkensii Acetone Extracts: Antioxidant, Antibacterial, and Anti-Virulence Activities
by
Ndzalama Sithole, Mashilo Mash Matotoka and Peter Masoko
Microbiol. Res. 2025, 16(6), 129; https://doi.org/10.3390/microbiolres16060129 - 16 Jun 2025
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Background/Objectives: Antibiotic-resistant bacteria pose a global health threat, driving the need for alternative treatments. Medicinal plants such as Clerodendrum glabrum and Gardenia volkensii are promising sources of bioactive compounds. This study evaluated the antioxidant, antibacterial, and anti-virulence activities of their acetone extracts, comparing
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Background/Objectives: Antibiotic-resistant bacteria pose a global health threat, driving the need for alternative treatments. Medicinal plants such as Clerodendrum glabrum and Gardenia volkensii are promising sources of bioactive compounds. This study evaluated the antioxidant, antibacterial, and anti-virulence activities of their acetone extracts, comparing sonication and conventional shaking extraction methods. Methods: Colorimetric methods assessed total polyphenol content. Antioxidant activity was measured using 2,2-Diphenyl-1-picrylhydrazyl (DPPH) radical scavenging and hydrogen peroxide (H2O2) assays. Antibacterial effects against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Streptococcus pyogenes were analysed through broth microdilution, total activity, growth kinetics, and combinational studies. Anti-virulence activity was assessed via biofilm biomass inhibition, metabolic activity and anti-swarming assays. Results: Phenolics were the most abundant phytochemicals, followed by flavonols. C. glabrum exhibited strong antioxidant activity in both DPPH and H2O2 assays. MIC values ranged from 0.16 to 2.5 mg/mL, with the shaken G. volkensii leaf extract showing the highest total activity (575 mL/g) against E. coli. A combination of G. volkensii leaf extract and gentamicin resulted in an additive antibacterial effect. All extracts prevented the formation of biofilm biomass in all tested microorganisms (inhibition > 50%) except for extracts obtained by sonication. The sonicated leaf extract of C. glabrum inhibited initial E. coli attachment. Additionally, the sonicated leaf extract of C. glabrum inhibited P. aeruginosa motility. Conclusions: These findings suggested that a targeted approach based on plant species and extraction methods could improve treatment outcomes against biofilm-associated pathogens. Notably, acetone extracts derived from C. glabrum and G. volkensii exhibit considerable potential as natural sources of antioxidant, antibacterial, and anti-virulence agents effective against nosocomial infections.
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Open AccessArticle
Microbial Contamination in Commercial Honey: Insights for Food Safety and Quality Control
by
Felipe Bruxel, Ana Maria Geller, Andrei Giacchetto Felice, Jeferson Aloísio Ströher, Anderson Santos de Freitas, Angela Balen, Maria Beatriz Prior Pinto Oliveira and Wemerson de Castro Oliveira
Microbiol. Res. 2025, 16(6), 128; https://doi.org/10.3390/microbiolres16060128 - 13 Jun 2025
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Honey is a sugar-rich product produced by Apis mellifera bees, with significant variability in properties due to the influence of geographic and climatic conditions and the predominant flora in the production region. Economically, beekeeping is an activity that generates profit and fulfills environmental
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Honey is a sugar-rich product produced by Apis mellifera bees, with significant variability in properties due to the influence of geographic and climatic conditions and the predominant flora in the production region. Economically, beekeeping is an activity that generates profit and fulfills environmental and social functions, reinforcing the pillars of sustainability. This study aimed to characterize samples of honey sold in southern Brazil, including physicochemical analyses, the detection of microbiological contaminants with potential impact on human health, and the detailed identification of bacterial composition through the Next-Generation Sequencing (NGS). The present study was divided into five main stages: (1) sample collection; (2) sample fractionation; (3) physicochemical analysis; (4) microbiological analysis; (5) 16S metataxonomy analysis. The physicochemical analyses agreed with the regulated values, indicating the good quality of the honey and the absence of adulteration. The microbiological analyses indicated the absence of Salmonella spp., in addition to a low count of total coliforms. The limits for molds and yeasts were exceeded in three samples, indicating non-compliance with current MERCOSUR legislation. Metabarcoding analysis identified a total of 15,736 OTUs divided into three different genera: Bacillus (41.54%), Lysinnibacillus, and Rossellomorea, all belonging to the Bacillaceae family. Some pathogenic species were identified, namely the Bacillus cereus group and Bacillus pumilus. Our results point to an increased need for surveillance, as honey contamination can lead to public health problems, requiring improvements in legislation and control parameters.
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