Microbiology Research

10 pages, 1938 KB

Open AccessArticle

Fungi from the Depths: A Preliminary Survey Using Hybrid Underwater Robotics in the Bathypelagic Zone off the Coast of Toulon (SE France)

by Michael De Benedetto, Grazia Cecchi, Laura Cutroneo, Simone Di Piazza, Vincent Bertin, Marco Capello and Mirca Zotti

Microbiol. Res. 2026, 17(2), 45; https://doi.org/10.3390/microbiolres17020045 - 20 Feb 2026

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Abstract

The deep sea is characterized by unique and extreme habitats. The absence of light, high salinity, hydrostatic pressure, low temperature, and high competition led to the evolution of physiological and biochemical adaptations necessary for survival. Marine fungi represent a significant part of deep-sea [...] Read more.

The deep sea is characterized by unique and extreme habitats. The absence of light, high salinity, hydrostatic pressure, low temperature, and high competition led to the evolution of physiological and biochemical adaptations necessary for survival. Marine fungi represent a significant part of deep-sea microbial communities. Studying bathypelagic sediment fungi helps us to understand their little-known communities and ecology, as well as their metabolic potential and ecophysiological properties, which have applications in pharmaceutical biotechnologies and bioremediation protocols. During an oceanographic campaign off the coast of Toulon (France, northwest Mediterranean Sea) in October 2021, as part of the KM3NeT Project, the Hybrid Remotely Operated Vehicle (HROV) Ariane collected a composite sediment sample at a depth of 2417 m. The sediment was physically, geochemically and mycologically characterized. Culturable fungi were isolated, and vital fungal strains were identified morphologically and molecularly. A total of 17 strains were isolated and identified in pure culture. The major taxa belonged to the Penicillium, Aspergillus, and Cladosporium genera, but widespread species such as Wallemia sebi were also found. This study also paves the way for further research into the advantages and disadvantages of using HROV technology for mycological cultural investigations at prohibitive depths. Full article

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9 pages, 12341 KB

Open AccessCommunication

Anomalous Emergence of D614 Reverse Mutations in the Delta and Omicron BA.2 Variants

by Hideki Kakeya and Yoshihisa Matsumoto

Microbiol. Res. 2026, 17(2), 44; https://doi.org/10.3390/microbiolres17020044 - 20 Feb 2026

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Abstract

Background: The spike D614G substitution became globally dominant early in the COVID-19 pandemic, and reversion to ancestral D614 is expected to be rare once D614G is fixed. SARS-CoV-2 sequences lacking D614G detected later raise questions about the origin of these reversions. Methods: We [...] Read more.

Background: The spike D614G substitution became globally dominant early in the COVID-19 pandemic, and reversion to ancestral D614 is expected to be rare once D614G is fixed. SARS-CoV-2 sequences lacking D614G detected later raise questions about the origin of these reversions. Methods: We analyzed spike protein amino-acid sequences from 22 SARS-CoV-2 Variants of Concern (VOCs) deposited in the NCBI GenBank database, screening for sequences carrying ancestral D614 and comparing their distributions across VOCs. Results: D614 reversions (reverse mutations of D614G) were not evenly distributed across VOCs but were strongly enriched in Delta (B.1.617.2) and Omicron BA.2, reaching levels statistically inconsistent with other VOCs. In both lineages, D614-containing sequences showed limited mutational diversity and pronounced geographic clustering within specific U.S. regions. Conclusions: These non-random patterns are difficult to reconcile with spontaneous reverse mutation arising and spreading through typical community transmission and are more consistent with localized reintroduction of an older genetic background. Further investigation is warranted to assess whether laboratory-associated events could be involved. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)

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16 pages, 2707 KB

Open AccessArticle

Study of the Relationship Between Natural Mating Expression and Intestinal Resistance Genes in Captive Adult Giant Pandas

by Ming-Yue Zhang, Xiao-Hui Zhang, Xue-Ying Wang, Jun-Hui An, Dong-Hui Wang, Rong Hou and Yu-Liang Liu

Microbiol. Res. 2026, 17(2), 43; https://doi.org/10.3390/microbiolres17020043 - 18 Feb 2026

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Abstract

A growing body of evidence indicates that the gut microbiota has a role in the mating preference process in mammals. This likely occurs through the modulation of various mating signals induced by symbiotic bacteria, thereby leading to variations in mating behavior. Given that [...] Read more.

A growing body of evidence indicates that the gut microbiota has a role in the mating preference process in mammals. This likely occurs through the modulation of various mating signals induced by symbiotic bacteria, thereby leading to variations in mating behavior. Given that giant pandas are solitary wild animals that rely on chemical signals for mate selection, it is relevant to explore whether the mating behavior of giant pandas is also affected by the gut microbiota. We hypothesize that antibiotic treatment-induced residual antibiotic resistance genes in captive giant pandas may disrupt intestinal microbiota homeostasis, diminish the abundance of beneficial microorganisms involved in short-chain fatty acid synthesis, and consequently impair nervous system function via the gut–brain axis. The ensuing physiological stress is likely to suppress innate mating behavior and compromise pheromone synthesis, thereby reducing an individual’s attractiveness to potential mates. To answer this question, we utilize fecal metagenomics technology to analyze the differences in gut microbes and antibiotic resistance genes (ARGs) between captive male adult giant pandas displaying natural versus non-natural mating behavior. The research findings suggest that, when compared with captive adult male giant pandas demonstrating natural mating behavior, those with non-natural mating behavior exhibit a significantly reduction in the abundance of beneficial gut microorganisms (s_Clostridium sp. and f_Ruminococcaceae) (p < 0.05). Concurrently, there is a significantly increase in the observed resistance genes tetO and mgtA, which are mainly associated with macrolide and tetracycline resistance (p < 0.05). Furthermore, Kegg functional analysis reveals a significant up-regulation of metabolic pathways related to sensory systems, such as taste and olfactory transduction, in the intestines of captive adult male giant pandas showing natural mating behavior. These results imply that changes in the abundance of gut microbiota and ARGs are correlated with the manifestation of natural mating behavior in captive adult male giant pandas. Consequently, to improve the success rate of natural reproduction within the male giant panda populations in captive environments, it is advisable to administer antibiotics judiciously and closely monitor the composition of beneficial bacteria in their gut microbiota. The findings of this study provide novel perspectives on the mechanisms by which captive conditions affect the decline in natural mating behavior observed in adult male giant pandas. Full article

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12 pages, 386 KB

Open AccessArticle

Hierarchical Risk Profiles in Tuberculosis Treatment Outcomes: The Role of Drug Resistance, Age, and Socio-Economic Factors

by Nande Ndamase, Lindiwe Modest Faye, Ntandazo Dlatu, Teke Apalata and Mojisola Clara Hosu

Microbiol. Res. 2026, 17(2), 42; https://doi.org/10.3390/microbiolres17020042 - 14 Feb 2026

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Abstract

Background: Tuberculosis (TB) outcomes remain suboptimal in high-burden, resource-constrained settings. Clinical and socio-economic factors contribute to loss to follow-up, failure, and mortality, yet their relative importance remains underexplored. Methods: We analyzed a retrospective cohort of patients treated for pulmonary TB in the Eastern [...] Read more.

Background: Tuberculosis (TB) outcomes remain suboptimal in high-burden, resource-constrained settings. Clinical and socio-economic factors contribute to loss to follow-up, failure, and mortality, yet their relative importance remains underexplored. Methods: We analyzed a retrospective cohort of patients treated for pulmonary TB in the Eastern Cape, South Africa. Treatment outcomes were dichotomized as success (cured or treatment completed) versus unsuccessful (loss to follow-up, failure, or death), excluding transfers and patients still on treatment. Predictors included age, gender, income, occupation, comorbidities, HIV status, previous treatment history, patient category, and drug resistance status. Regularized logistic regression was used to estimate odds ratios, while the best decision tree model was applied to identify hierarchical risk profiles. Results: Logistic regression demonstrated high accuracy (86%) and identified drug susceptibility, age, income stability, and comorbidity burden as the strongest predictors of treatment success. The decision tree achieved lower accuracy (65%) but improved detection of unsuccessful outcomes, highlighting a clear hierarchy of risk: (1) drug resistance status, (2) age, (3) income source, and (4) comorbidities. Patients with drug-resistant TB, older age, no income or reliance on grants, and coexisting conditions were at the highest risk of poor outcomes. Conclusions: Drug resistance, age, income, and comorbidity burden shape a hierarchical risk profile for TB treatment outcomes in rural South Africa. Logistic regression offered robust overall classification, while the decision tree provided transparent stratification of at-risk groups. These findings underscore the need for integrated clinical and socio-economic support strategies to improve outcomes in high-burden settings. Full article

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17 pages, 1281 KB

Open AccessArticle

Alginate-Based Emulsion with Oregano Essential Oil for the Preservation of Frozen–Thawed Ready-to-Cook Hake Fillets as a Model System

by Sebastiano Rosati, Martina Cofelice, Nicolaia Iaffaldano, Francesco Lopez, Giuseppe Cinelli, Alessandra Mazzeo, Emanuele Antenucci, Lucia Maiuro and Elena Sorrentino

Microbiol. Res. 2026, 17(2), 41; https://doi.org/10.3390/microbiolres17020041 - 14 Feb 2026

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Abstract

Fish are nutritionally valuable foods but are also highly perishable, representing a major research focus for the development of effective preservation strategies to delay spoilage while maintaining microbiological acceptability. In this context, edible coatings have gained increasing attention as clean-label tools to extend [...] Read more.

Fish are nutritionally valuable foods but are also highly perishable, representing a major research focus for the development of effective preservation strategies to delay spoilage while maintaining microbiological acceptability. In this context, edible coatings have gained increasing attention as clean-label tools to extend the shelf life of perishable foods. In this study, an alginate-based emulsion containing oregano essential oil (OEO) was applied to commercial frozen–thawed ready-to-cook (RTC) hake fillets, intentionally selected as a reproducible model system to evaluate coating performance under refrigerated conditions. Coated and uncoated fillets, stored at 4 °C for up to 7 days, were monitored over time for microbiological and physicochemical parameters, including microbial loads, pH, weight loss, and lipid oxidation (TBARS). Compared to uncoated samples, fillets treated with the alginate–OEO emulsion exhibited a marked delay in spoilage-related microbial growth, with a consistent inhibition of Pseudomonas spp. throughout the experimental period, while maintaining microbiological acceptability. Emulsion-based coated fillets also exhibited reduced lipid oxidation, a more uniform surface appearance with only minor visible color changes, and the absence of unpleasant off odors during the refrigerated storage. Overall, the results demonstrate that the alginate–OEO coating could represent an effective strategy for improving the microbiological and oxidative stability of RTC fish fillets under refrigerated conditions, with potential implications for extended shelf life and a reduction in food waste. Full article

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23 pages, 3349 KB

Open AccessArticle

Dynamics of Antimicrobial Resistance and Antimicrobial Consumption in a Secondary-Care Hospital in Serbia, 2019–2022: A Retrospective Observational Study

by Milena Branković, Miroslava Jordović Pavlović, Ana Tomic, Natasa Opavski and Ina Gajić

Microbiol. Res. 2026, 17(2), 40; https://doi.org/10.3390/microbiolres17020040 - 14 Feb 2026

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Abstract

Antimicrobial resistance (AMR) is accelerating and driven by antimicrobial use. Hospital consumption and resistance data remain scarce in Serbia. This retrospective study assessed the prevalence of infectious agents among hospitalized patients (2019–2022), distribution and AMR rates of Escherichia coli and Klebsiella pneumoniae, [...] Read more.

Antimicrobial resistance (AMR) is accelerating and driven by antimicrobial use. Hospital consumption and resistance data remain scarce in Serbia. This retrospective study assessed the prevalence of infectious agents among hospitalized patients (2019–2022), distribution and AMR rates of Escherichia coli and Klebsiella pneumoniae, antimicrobial consumption, and associations between AMR and antibiotic use (Spearman’s correlation). All bacterial isolates were included for species-frequency analyses. For AMR and specimen distribution, repeat isolates of E. coli and K. pneumoniae per patient were excluded. Among 10,780 isolates, E. coli remained most frequent (24.7% in 2019; 24.3% in 2022), whereas K. pneumoniae increased from 7.7% to 16.9% (p < 0.001). E. coli resistance to cephalosporins, fluoroquinolones, and piperacillin/tazobactam increased significantly from 2019 to 2022 (p < 0.05). K. pneumoniae resistance increased to most agents (p < 0.001), with meropenem resistance rising from 11.7% to 52.0%. Multidrug resistance rose from 27.3% to 35.4% for E. coli (2020–2022; p = 0.006) and from 62.4% to 82.9% for K. pneumoniae (2019–2022; p < 0.001). Total hospital antibiotic consumption nearly doubled from 57 to 111.8 Defined Daily Doses per 100 bed days (2019–2021) and decreased to 52.0 (2022). Temporal concurrence of increased antimicrobial use during COVID-19 and escalating resistance underscores the need for strengthened surveillance and stewardship. Full article

(This article belongs to the Special Issue Klebsiella pneumoniae: Resistance, Virulence, and Epidemiology in Healthcare and Community Settings)

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12 pages, 2435 KB

Open AccessCommunication

Whole-Genome Assembly and Antimicrobial Properties of Bacillus atrophaeus R7PjV2-12 from Spruce Picea jezoensis

by Alexey A. Ananev, Olga A. Aleynova, Nikolay N. Nityagovsky, Alina A. Dneprovskaya, Alexandra S. Dubrovina, Haiping Xin and Konstantin V. Kiselev

Microbiol. Res. 2026, 17(2), 39; https://doi.org/10.3390/microbiolres17020039 - 11 Feb 2026

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Abstract

The search for antagonistic microorganisms as alternatives to chemical pesticides is an urgent priority in sustainable agriculture. Previously, we isolated several bacterial isolates from spruce plants, and one of them, identified as Bacillus atrophaeus R7PjV2-12, showed strong antagonistic properties against plant pathogens such [...] Read more.

The search for antagonistic microorganisms as alternatives to chemical pesticides is an urgent priority in sustainable agriculture. Previously, we isolated several bacterial isolates from spruce plants, and one of them, identified as Bacillus atrophaeus R7PjV2-12, showed strong antagonistic properties against plant pathogens such as Magnaporthe oryzae, Fusarium avenaceum, and Erwinia billingiae. Given its strong fungicidal properties, we decided to sequence the complete genome of this bacterium to determine how it can inhibit fungal growth. The whole genome size of B. atrophaeus R7PjV2-12 was 4,127,644 bp with 4032 open reading frames. B. atrophaeus R7PjV2-12 genome possessed clusters of secondary metabolites with a complete set of genes with 100% similarity representing clusters of biosynthesis of bacillin, bacillibactin, subtilosin A, and fungicin, which indicates the studied strain’s ability to synthesize these substances. Thus, this paper has shown and discussed the potential importance of B. atrophaeus R7PjV2-12 for biocontrol of pathogenic microorganisms in agriculture. Full article

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15 pages, 1885 KB

Open AccessArticle

Identification and Characterization of Two Antibacterial Compounds Extracted from Thuja arborvitae

by Tory M. Johnson, Quanbo Xiong and Zhengxin Wang

Microbiol. Res. 2026, 17(2), 38; https://doi.org/10.3390/microbiolres17020038 - 10 Feb 2026

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Abstract

Thuja arborvitae are widely grown in North America and East Asia for their ornamental value, and their leaf oil extracts have been used to treat bacterial infections. This study aimed to identify antibacterial compounds from Thuja leaves. The methanol extract of Thuja leaves [...] Read more.

Thuja arborvitae are widely grown in North America and East Asia for their ornamental value, and their leaf oil extracts have been used to treat bacterial infections. This study aimed to identify antibacterial compounds from Thuja leaves. The methanol extract of Thuja leaves exhibited strong antibacterial activity against Gram-positive (Staphylococcus aureus and Streptococcus mutans) and Gram-negative (Acinetobacter baumannii, Pseudomonas aeruginosa) bacteria. The major compounds in the active fractions were isolated and identified as apigenin-7-di-p-coumarylglucoside and eicosapentaenoic acid. The identified compounds showed potent antibacterial activity against the four tested microorganisms with IC50 values of 10 to 50 µg/mL. More importantly, these compounds showed potent inhibitory activity (IC50: 10 μg/mL) against the multidrug-resistant bacterial strain Acinetobacter baumannii. Two antibacterial compounds are now being reported for the first time in Thuja arborvitae, and they may have potential for the treatment of bacterial infections. Full article

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15 pages, 1152 KB

Open AccessCommunication

Genomic Insights into Bombiscardovia sp. JNUCC 75 Isolated from the Flowers of Prunus yedoensis

by Kyung-A Hyun, Ji-Hyun Kim, Min Nyeong Ko and Chang-Gu Hyun

Microbiol. Res. 2026, 17(2), 37; https://doi.org/10.3390/microbiolres17020037 - 10 Feb 2026

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Abstract

Bombiscardovia sp. JNUCC 75 (=CH12) was isolated from the flowers of Prunus yedoensis on Jeju Island, representing one of the few known flower-associated members of the Bombiscardovia asteroides group. Whole-genome sequencing revealed a compact 2.28 Mb genome and a functional gene profile enriched [...] Read more.

Bombiscardovia sp. JNUCC 75 (=CH12) was isolated from the flowers of Prunus yedoensis on Jeju Island, representing one of the few known flower-associated members of the Bombiscardovia asteroides group. Whole-genome sequencing revealed a compact 2.28 Mb genome and a functional gene profile enriched in translation, amino-acid metabolism, and DNA repair. Although the strain contains a pseudogene content comparable to other B. asteroides-group members, the overall genomic architecture—together with the presence of stress-response and polyprenyl/terpenoid biosynthetic pathways—suggests adaptation to oxygen-variable, phenolic-rich, and UV-exposed floral environments. Comparative genomic analyses (OrthoANIu 97.16%; dDDH 72.7%) demonstrated that JNUCC 75 is closely related to B. polysaccharolytica yet forms a genetically distinct lineage within the group. Genome mining uncovered two previously unreported terpenoid/polyprenyl biosynthetic gene clusters, indicating a novel isoprenoid-derived metabolic repertoire with potential roles in membrane stabilization and oxidative-stress defense. These genomic features collectively position JNUCC 75 as a bridge between gut-associated and environmental bifidobacteria and highlight its potential as a promising microbial resource for postbiotic, antioxidant, and skin-barrier-enhancing applications. This study expands the ecological range of bifidobacteria and provides a genomic framework for evaluating flower-derived Bombiscardovia strains in cosmeceutical and functional food innovation. Full article

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13 pages, 739 KB

Open AccessArticle

Phytochemical Screening and Dual Antimicrobial–Antibiofilm Activities of Platanus orientalis Linn Methanolic Leaf Extract Against Multidrug-Resistant Salmonella enterica and Shigella flexneri

by Ahmed Najm Abed, Maroua Gdoura Ben Amor and Radhouane Gdoura

Microbiol. Res. 2026, 17(2), 36; https://doi.org/10.3390/microbiolres17020036 - 10 Feb 2026

Viewed by 424

Abstract

Antimicrobial resistance among multidrug-resistant enteric pathogens, such as Salmonella enterica and Shigella flexneri, poses a critical global health challenge, necessitating novel therapeutic strategies from natural sources. This study evaluated the preliminary phytochemical profile and dual antibacterial and antibiofilm activities of methanolic leaf [...] Read more.

Antimicrobial resistance among multidrug-resistant enteric pathogens, such as Salmonella enterica and Shigella flexneri, poses a critical global health challenge, necessitating novel therapeutic strategies from natural sources. This study evaluated the preliminary phytochemical profile and dual antibacterial and antibiofilm activities of methanolic leaf extract from Platanus orientalis Linn. Qualitative and quantitative phytochemical analyses were conducted to assess phenolic and flavonoid contents, while antibacterial activity against multidrug-resistant isolates was determined using broth microdilution to obtain minimum inhibitory concentrations (MICs). Antibiofilm effects were examined at sub-MIC concentrations via the crystal violet assay. The extract was found to be rich in phenolics and flavonoids and exhibited concentration-dependent antibacterial activity, with MICs of 64 µg/mL for S. enterica and 32 µg/mL for S. flexneri. Sub-MIC concentrations significantly reduced biofilm biomass by 60–80%, likely through interference with quorum sensing and extracellular polymeric substance production. These results highlight the extract’s potential as a phytotherapeutic agent targeting both planktonic cells and biofilms, providing insights for the development of natural antimicrobials against resistant enteric pathogens. Overall, the findings underscore the potential of Platanus orientalis methanolic leaf extract as a promising natural antibacterial and antibiofilm agent against multidrug-resistant enteric pathogens and support its further development as an alternative or complementary therapeutic strategy. It should be noted that the phytochemical results are qualitative and indicative, and further LC–MS or NMR analyses are required for definitive compound identification. Full article

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14 pages, 1633 KB

Open AccessArticle

Establishment and Application of a SYBR Green I qPCR Detection Method Based on the CP40 Gene of Corynebacterium pseudotuberculosis Biovar Ovi

by Jingpeng Zhang, Jinxiu Jiang, Dingding Zhang, Yusheng Lin, Chunhe Wan and Yongliang Che

Microbiol. Res. 2026, 17(2), 35; https://doi.org/10.3390/microbiolres17020035 - 6 Feb 2026

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Abstract

Caseous lymphadenitis (CLA), an infectious disease caused by Corynebacterium pseudotuberculosis (C. pseudotuberculosis), poses a significant economic burden to the global small ruminant industry. This study aimed to investigate genetic variations in the CP40 gene of C. pseudotuberculosis and to develop a [...] Read more.

Caseous lymphadenitis (CLA), an infectious disease caused by Corynebacterium pseudotuberculosis (C. pseudotuberculosis), poses a significant economic burden to the global small ruminant industry. This study aimed to investigate genetic variations in the CP40 gene of C. pseudotuberculosis and to develop a rapid detection assay for enhanced pathogen identification. Homology analysis was performed to compare the CP40 gene sequence of the FJ-PN strain with other Corynebacterium species. Specific primers targeting CP40 were designed, and a SYBR Green I-based real-time PCR protocol was optimized. The assay’s specificity, sensitivity, and reproducibility were subsequently validated. The FJ-PN strain exhibited ≥99.65% nucleotide identity and ≥98.94% amino acid identity with C. pseudotuberculosis biovar ovi reference strains, showing 90.18–91.84% nucleotide identity and 88.63–90.77% amino acid identity with C. pseudotuberculosis biovar equi, and ≤82.71% nucleotide identity and ≤78.63% amino acid identity with other Corynebacterium species. The established qPCR assay demonstrated high specificity, the limit of detection was 52 copies/μL, and it demonstrated good reproducibility (intra- and inter-assay CV < 1.0%). Clinical sample testing revealed 18.8% positivity rates in nasal swabs, which was higher than that detected by conventional PCR (16.3%). These results indicate that the CP40 gene is evolutionarily conserved and represents a specific molecular marker for the identification of C. pseudotuberculosis biovar ovis. The developed SYBR Green I real-time PCR assay enables the efficient detection of C. pseudotuberculosis and provides technical support for CLA surveillance and control. Full article

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12 pages, 1897 KB

Open AccessArticle

Genomic Surveillance Reveals Distinct Clonal Lineages and Antibiotic Resistance Patterns in Staphylococcus aureus from Retail Pork in Beijing Versus Copenhagen

by Yuan Gao, Linli Ji, Taya Tang, Jiadi Zhu, Shuyang Yu, Junjie Niu and Heng Li

Microbiol. Res. 2026, 17(2), 34; https://doi.org/10.3390/microbiolres17020034 - 5 Feb 2026

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Abstract

The global rise of multidrug resistance (MDR) across bacterial pathogens poses a severe threat to public health, with the food chain serving as a critical reservoir and transmission route for resistant clones. This study investigated the genomic epidemiology of Staphylococcus aureus in retail [...] Read more.

The global rise of multidrug resistance (MDR) across bacterial pathogens poses a severe threat to public health, with the food chain serving as a critical reservoir and transmission route for resistant clones. This study investigated the genomic epidemiology of Staphylococcus aureus in retail pork from Beijing, China, and Copenhagen, Denmark, with a focus on MDR patterns and associated genetic elements. Among 134 isolates, the livestock-associated clonal complex CC398 was the dominant lineage (24.63%) and exhibited a high burden of MDR (48.48%), carrying resistance genes to β-lactams (blaZ and mecA), tetracyclines (tetM and tetK), and aminoglycosides. Notably, MRSA isolates displayed a significantly higher MDR prevalence (73.53%) compared to MSSA isolates (18.00%), underscoring methicillin resistance as a key marker for broader resistance phenotypes. Phylogenetic analysis revealed the segregation of CC398 into distinct sub-lineages, with the livestock-associated branch consistently linked to a characteristic tetracycline–β-lactam MDR profile. Furthermore, high frequencies of mobile genetic elements, such as the rep16 plasmid, were associated with MDR dissemination in CC398. These findings highlight retail meat as an important reservoir for MDR S. aureus and illustrate how livestock-adapted clones contribute to the environmental burden of antimicrobial resistance. This study underscores the need for integrated One Health surveillance that connects veterinary, food safety, and human health sectors to monitor and contain the spread of MDR bacteria across ecological niches. Full article

(This article belongs to the Topic Multidrug Resistance Across Pathogens: Fungi, Bacteria, Parasites, and Viruses)

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22 pages, 1871 KB

Open AccessArticle

Determining Selenomonas Species Subclusters in Periodontal Samples by FISH

by Monika Gothwal, Flurina Suter, Lamprini Karygianni, Thomas Attin and Thomas Thurnheer

Microbiol. Res. 2026, 17(2), 33; https://doi.org/10.3390/microbiolres17020033 - 3 Feb 2026

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Abstract

The highly destructive pathogenic processes in patients with periodontitis are attributed to the presence of subgingival biofilms comprising key periodontal pathogens, such as Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia, as well as other periodontopathogens including Fusobacterium nucleatum, Selenomonas [...] Read more.

The highly destructive pathogenic processes in patients with periodontitis are attributed to the presence of subgingival biofilms comprising key periodontal pathogens, such as Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia, as well as other periodontopathogens including Fusobacterium nucleatum, Selenomonas spp., Centipeda spp., and Campylobacter spp. Considering the vast microbial diversity in periodontitis, we aimed to analyze the presence of various bacterial species in subgingival dental plaque, with a special focus on Selenomonas spp. We first developed a phylogenetic tree for Selenomonas–Veillonella clusters, using in silico analysis followed by fluorescence in situ hybridization (FISH) on subgingival dental plaque samples from 22 patients with a history of chronic periodontitis, by using specific 16S rRNA oligonucleotide probes. These oligonucleotide probes’ specificity and hybridization conditions were determined on previously characterized bacterial strains. Qualitative and quantitative analysis of FISH slides was carried out by using an epifluorescence microscope. The majority of the patient samples showed high fluorescence signals with the oligonucleotide probes SEL1150, Sspu439, and SEL1469 (specific for Selenomonas spp.), ACI623 (identifying Selenomonas, Veillonella, and Dialister spp.), Tfor127 (T. forsythia) and L-Pgin1006-23 (P. gingivalis). SEL1150 showed specificity for bacterial species in the subclusters A, B, and C, namely S. dianae, S. infelix, S. flueggei, C. periodontii, S. artemidis, S. noxia, and S. sputigena; Sspu439 for S. sputigena; SEL1469 for subclusters A and B, and for S. sputigena; ACI623 for bacterial species in subclusters C and F, namely the S. sputigena and Veillonella species. The experimentally observed specificities of the oligonucleotide probes corresponded with our in silico analysis. Selenomonas spp. may play a role in the subgingival microbiome of periodontitis and contribute to the disease process. Targeting Selenomonas spp. with specific therapeutic strategies could offer new insights into the management of periodontitis. However, further studies are needed to determine a definite functional significance. Full article

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22 pages, 1579 KB

Open AccessArticle

Grape-Associated Yeasts as Promising Antagonists Against Fungal Pathogens

by Tamar Maghradze, Alessandra Di Canito, Carmen Cris De Oliveira Nobre Bezerra, Mathabatha Evodia Setati, Roberto Carmine Foschino, Daniela Fracassetti and Ileana Vigentini

Microbiol. Res. 2026, 17(2), 32; https://doi.org/10.3390/microbiolres17020032 - 2 Feb 2026

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Abstract

Biocontrol, a practice for using living organisms to target plant pathogens, offers a promising, sustainable agricultural strategy. This study involves epiphytic yeasts isolated from Vitis vinifera ssp. sylvestris and ssp. vinifera as natural antagonists against Aspergillus carbonarius, Botrytis cinerea, and Penicillium [...] Read more.

Biocontrol, a practice for using living organisms to target plant pathogens, offers a promising, sustainable agricultural strategy. This study involves epiphytic yeasts isolated from Vitis vinifera ssp. sylvestris and ssp. vinifera as natural antagonists against Aspergillus carbonarius, Botrytis cinerea, and Penicillium expansum. Twenty-one of 37 yeasts were chosen based on the Pathology Intensity (PA) score during preliminary in vivo screening. Following identification, dual-culture assays, VOC production, copper tolerance, and commercial fungicide resistance were assessed. On YPD and GJ medium, Saccharomyces isolates were the strongest antagonists, whereas P. terricola UMY197 inhibited Penicillium and Aspergillus. H. uvarum UMY1473 was notably effective against B. cinerea. VOC analysis confirmed that S. cerevisiae UMY1430 was the most effective against Aspergillus, likely owing to its production of oxalic acid, while S. cerevisiae UMY1438 was a producer of various esters and phenylethyl alcohol. C. intermedia UMY189, M. pulcherrima UMY1472, H. uvarum UMY1473, and S. cerevisiae UMY1436 were the most copper-resistant. Yeast activity on chemical fungicide SWITCH (up to 1 g/L) depended on culture media usage; in fact, a higher viability on YPD than on GJ was observed, where only 4 yeasts were able to grow. Thus, since several yeasts exhibit promising inhibitory activity through various mechanisms and against different molds, the use of synthetic consortia could represent a powerful and essential tool in field trials to limit fungicide use while preventing the emergence of resistance. Full article

(This article belongs to the Special Issue Advances in Plant–Pathogen Interactions)

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15 pages, 1153 KB

Open AccessArticle

Biotechnological Potential of Sweet Sorghum as a Substrate in the Production of Xylanases and Cellulases by Actinobacteria

by Renata Danielle de Souza Bartolomeu, Ederson da Conceição Jesus, Rafael Augusto da Costa Parrella, Ivanildo Evódio Marriel and Maria Lúcia Ferreira Simeone

Microbiol. Res. 2026, 17(2), 31; https://doi.org/10.3390/microbiolres17020031 - 31 Jan 2026

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Abstract

Obtaining enzymes through bioconversion depends on a complex relationship between the microorganisms and the biomass used. Here, we evaluate xylanase production by diverse actinobacterial species, cultivated using xylan as the sole carbon source and complex media containing sorghum as the substrate. Fifty-three actinobacteria [...] Read more.

Obtaining enzymes through bioconversion depends on a complex relationship between the microorganisms and the biomass used. Here, we evaluate xylanase production by diverse actinobacterial species, cultivated using xylan as the sole carbon source and complex media containing sorghum as the substrate. Fifty-three actinobacteria were tested for xylanase production in a solid medium. Seventeen strains produced xylanase and were tested for their ability to produce xylanase, total cellulases (filter paper activity, FPase), and endoglycanase in submerged culture using a defined liquid medium. The best xylanase-producing species was Streptomyces capoamus, yielding 24 IU·mL⁻¹. For FPase, Streptomyces sp. showed the highest yield (1.12 IU·mL⁻¹); for endoglycanase, the best producer was Streptomyces ossamyceticus (0.99 IU·mL⁻¹). When sweet sorghum was used alone, S. curacoi, S. ossamyceticus, and S. capoamus showed xylanase activities of 4.5 IU·mL⁻¹, 4.4 IU·mL⁻¹, and 0.8 IU·mL⁻¹, respectively. However, FPase activity was not detected under the assay conditions. The results showed that there is an intraspecific difference in xylanase, endoglucanase, and FPase production by actinobacteria, with the species S. curacoi, S. ossamyceticus, and S. capoamus able to use sorghum as a carbon source, demonstrating biotechnological potential. Full article

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28 pages, 2242 KB

Open AccessArticle

Multiple Infections, Recombination, and Hypermutation During a 12-Month Prospective Study of Five HIV-1 Infected Individuals

by Fernando M. Rodrigues, Paula Prieto-Oliveira, Jean P. Zukurov, Wagner T. Alkmim, Michel M. Soane, Michelle Camargo, Sabri S. Sanabani, Esper G. Kallas, Maria Cecília Sucupira, Ricardo Sobhie Diaz, Denis Jacob Machado and Luiz Mario Janini

Microbiol. Res. 2026, 17(2), 30; https://doi.org/10.3390/microbiolres17020030 - 27 Jan 2026

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Abstract

The considerable HIV-1 genetic diversity has several implications for viral adaptive and evolutionary capabilities. Its genetic diversity is due to its high mutational rates derived from the error-prone viral reverse transcriptase activity, which generates highly heterogeneous viral populations. Moreover, genetic diversity can also [...] Read more.

The considerable HIV-1 genetic diversity has several implications for viral adaptive and evolutionary capabilities. Its genetic diversity is due to its high mutational rates derived from the error-prone viral reverse transcriptase activity, which generates highly heterogeneous viral populations. Moreover, genetic diversity can also increase due to intra- or intersubtype viral genomic recombination following multiple infections. This study examines HIV-1 intersubtype recombinant viruses and their increased genomic diversity over a 12-month period in five individuals from São Paulo state, Brazil. We collected peripheral blood mononuclear cells once every three months from selected participants at five distinct visits. Molecular clones of 1.15 Kbp fragments of the Pol polyprotein, spanning the protease and a portion of the reverse transcriptase (RT) genes, were generated by bulk PCR. Pol sequences were used for evolutionary analysis, including phylogenetics (using TnT), genetic diversity (using Highlighter), and hypermutation frequency (using Hypermut). Recombination detection experiments were conducted with a jumping profile-hidden Markov model (jpHMM), SimPlot++, and RDP5. We observed great genetic diversity and frequent recombination events in all patients. Furthermore, most of the patients presented hypermutations. These findings highlight the dynamic nature of HIV-1 genetic diversity, driven by frequent recombination and hypermutation, which can accelerate viral adaptation and diversification, underscoring the challenges for treatment, prevention, and disease control. Full article

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12 pages, 268 KB

Open AccessArticle

Use of Daptomycin for the Treatment of Infective Endocarditis Due to Methicillin-Susceptible Staphylococcus aureus (MSSA): A Multicenter Retrospective Study

by Andrea Tommasi, Cesare Bolla, Laura Curci, Serena Penpa, Giovanni Genga, Cristina Sarda, Elisabetta Svizzeretto, Andrea Salvaderi, Giorgia Piceni, Giuseppe Vittorio De Socio, Daniela Francisci, Antonio Maconi, Guido Chichino and Carlo Pallotto

Microbiol. Res. 2026, 17(2), 29; https://doi.org/10.3390/microbiolres17020029 - 23 Jan 2026

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Abstract

Infective endocarditis (IE) due to methicillin-susceptible Staphylococcus aureus (MSSA) still represents a clinical and therapeutic issue. Discrepancies between guidelines, clinical studies and clinical practice have already been highlighted, especially regarding daptomycin use in MSSA cases. The aim of this study was to evaluate [...] Read more.

Infective endocarditis (IE) due to methicillin-susceptible Staphylococcus aureus (MSSA) still represents a clinical and therapeutic issue. Discrepancies between guidelines, clinical studies and clinical practice have already been highlighted, especially regarding daptomycin use in MSSA cases. The aim of this study was to evaluate daptomycin’s impact on outcomes in this setting. This was a retrospective observational study. We enrolled all patients with MSSA IE admitted from 2015 to 2023. Patients were divided into two groups according to daptomycin administration. We enrolled 76 patients, with 49 in group A (standard treatment) and 27 in group B (treated with daptomycin). The in-hospital crude mortality was 14.3% and 29.6% in group A and B, respectively (p = 0.191). Only heart failure was significantly associated with negative outcome in the univariate and multivariate analyses (OR 6.424, 95% CI, 1.680–24.559; p = 0.007). In this study population, daptomycin treatment for IE due to MSSA was not associated with a reduced mortality rate. Heart failure was the only independent risk factor associated with in-hospital mortality. Full article

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Microbiol. Res., Volume 17, Issue 2 (February 2026) – 17 articles

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