Microorganisms

11 pages, 4968 KiB

Open AccessArticle

Genomic Characterization of Carbapenemase-Producing Klebsiella pneumoniae ST895 Isolates from Canine Origins Through Whole-Genome Sequencing Analysis

by Ronglei Huang, Wei Gao, Yue Sun, Yan Ye, Tingting Luo, Yitong Pan, Chengyang Zhang, Ang Zhou, Wenzhi Ren and Chongtao Du

Microorganisms 2025, 13(2), 332; https://doi.org/10.3390/microorganisms13020332 - 3 Feb 2025

Abstract

The widespread application of carbapenems and other broad-spectrum antibiotics has significantly escalated the threat posed by highly drug-resistant Klebsiella pneumoniae to human public health. In this research, we isolated a carbapenem-resistant K. pneumoniae strain from the feces of pet dogs at a veterinary [...] Read more.

The widespread application of carbapenems and other broad-spectrum antibiotics has significantly escalated the threat posed by highly drug-resistant Klebsiella pneumoniae to human public health. In this research, we isolated a carbapenem-resistant K. pneumoniae strain from the feces of pet dogs at a veterinary hospital in Changchun, Jilin Province, China. To gain insights into its genetic makeup and resistance mechanisms, we conducted comprehensive whole-genome sequencing and antimicrobial susceptibility testing on the isolated strain. Our findings revealed the presence of three distinct plasmids within the strain, classified as IncFIB&IncFII, IncR, and IncX3. Notably, the bla_NDM-5 gene, conferring resistance to carbapenems, was uniquely harbored on the IncX3 plasmid, which was devoid of any other resistance genes beyond bla_NDM-5. In contrast, the remaining two plasmids, IncFIB&IncFII and IncR, were found to encode an array of additional drug resistance genes, contributing to the strain’s broad-spectrum resistance phenotype. The IncX3 plasmid, specifically, measures 45,829 bp in length and harbors the IS5D-bla_NDM-5-Ble-MBL-PRAI cassette, which has been closely linked to the dissemination of bla_NDM-5 genes in K. pneumoniae strains. We reported the bla_NDM-5-carrying IncX3 in K. pneumoniae isolates recovered from the pet dog and revealed the molecular characterization. Emphasis should be placed on, and continuous monitoring carried out for, the dissemination of K. pneumoniae harboring the bla_NDM-5 gene among humans, companion animals, and their related environments. Full article

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

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15 pages, 620 KiB

Open AccessArticle

Host Jumps and Pathogenicity of Botryosphaeriaceae Species on Grapevines (Vitis vinifera) in Chile

by Yadira Hernández, Mauricio Lolas, Karina Elfar, Akif Eskalen, Felipe Gainza-Cortés and Gonzalo A. Díaz

Microorganisms 2025, 13(2), 331; https://doi.org/10.3390/microorganisms13020331 - 3 Feb 2025

Abstract

Botryosphaeria dieback disease is a significant grapevine trunk disease (GTD) caused by species of Botryosphaeriaceae in Chile and worldwide. Moreover, Botryosphaeriaceae have been described attacking fruit and nut crops in Chile. However, it remains unknown whether fungal isolates from tree hosts have the [...] Read more.

Botryosphaeria dieback disease is a significant grapevine trunk disease (GTD) caused by species of Botryosphaeriaceae in Chile and worldwide. Moreover, Botryosphaeriaceae have been described attacking fruit and nut crops in Chile. However, it remains unknown whether fungal isolates from tree hosts have the potential to infect grapevines in Chile. The aggressiveness and potential cross infection of species of Botryosphaeriaceae collected from crops (grapevines, apples, blueberries, and walnuts), was assessed on grapevines. Plant materials, including nursery cuttings, lignified canes, and green shoots of grapevine cultivars (Cabernet Sauvignon, Syrah, Sauvignon Blanc, Malbec, Aspirant Bouschet, and Merlot), were inoculated with Diplodia mutila, D. seriata, Dothiorella sarmentorum, Lasiodiplodia theobromae, Neofusicoccum arbuti, and N. parvum, under greenhouse and vineyard conditions. Regardless of the origin of the isolates, most species of Botryosphaeriaceae were pathogenic on plant materials, causing necrotic lesions of mean lengths from 11.9 to 86.2 mm using mycelial suspension and from 24.8 to 253.7 mm with mycelial plugs. Notably, Neofusicoccum species were the most aggressive, regardless of host origin. Other less aggressive species included L. theobromae, D. mutila, and D. seriata isolated from apple and walnut. This study highlights the potential of species of Botryosphaeriaceae from alternative fruit hosts as inoculum sources for grapevines in Chile. Full article

(This article belongs to the Special Issue Plant Pathogens: Monitoring, Identification and Biological Control)

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14 pages, 209 KiB

Open AccessCase Report

Use of Cefiderocol in Management of Resistant Gram-Negative Infections in Patients Admitted to a Burn Center

by Lindey C. Lane, Jonathon K. Walker and David M. Hill

Microorganisms 2025, 13(2), 330; https://doi.org/10.3390/microorganisms13020330 - 3 Feb 2025

Viewed by 174

Abstract

Cefiderocol is a novel cephalosporin antibiotic approved for urinary tract infections and hospital-acquired or ventilator-associated pneumonias caused by difficult-to-treat Gram-negative pathogens. To date, its use in treating difficult-to-treat Gram-negative infections in burn patients has been minimally described in the literature. Our aim was [...] Read more.

Cefiderocol is a novel cephalosporin antibiotic approved for urinary tract infections and hospital-acquired or ventilator-associated pneumonias caused by difficult-to-treat Gram-negative pathogens. To date, its use in treating difficult-to-treat Gram-negative infections in burn patients has been minimally described in the literature. Our aim was to evaluate cefiderocol use in a population of burn patients initiated on cefiderocol for resistant Gram-negative infections. A retrospective chart review of nine patients was conducted. Two patients were treated for pneumonia; five for bacteremia, three of which had coexisting burn wound infections or pneumonia; one was treated for a burn wound infection alone; and one patient was treated for a simultaneous burn wound infection, pneumonia, and bacteremia. The pathogens treated included the following: multidrug-resistant Pseudomonas aeruginosa, carbapenem-resistant Acinetobacter baumannii, and carbapenem-resistant Enterobacterales. Three isolates were confirmed as New Delhi metallo-beta-lactamase (NDM) producers, though this was likely an underestimate as genetic testing is not routinely performed at our institution and not all the isolates were tested. One of the nine patients in this study succumbed to their infection. Of note, the multidrug-resistant Pseudomonas aeruginosa in this patient tested intermediate to cefiderocol. The patients were treated with cefiderocol for a median of 14 days, most commonly in combination with other antimicrobial therapies. Treatment with cefiderocol appeared to be efficacious in this population of burn patients when other antibiotics routinely used for complicated infections caused by multidrug-resistant (MDR) Gram-negative pathogens showed treatment failure or resistance. Full article

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

15 pages, 1030 KiB

Open AccessArticle

Adaptive Resistance of Staphylococcus aureus to Cefquinome Sulfate in an In Vitro Pharmacokinetic Model with Transcriptomic Insights

by Yue Hu, Hao Zhu, Xingbo Zhang, Yuhui Wu, Jingtao Li, Nan Li, Zhanbo Cai and Yuhui Yang

Microorganisms 2025, 13(2), 329; https://doi.org/10.3390/microorganisms13020329 - 2 Feb 2025

Viewed by 373

Abstract

Cefquinome sulfate has a strong killing effect against Staphylococcus aureus (S. aureus), but bacterial resistance has become increasingly widespread. Experiments were conducted to investigate the pattern of adaptive resistance of S. aureus to cefquinome sulfate under different dosage regimens by using [...] Read more.

Cefquinome sulfate has a strong killing effect against Staphylococcus aureus (S. aureus), but bacterial resistance has become increasingly widespread. Experiments were conducted to investigate the pattern of adaptive resistance of S. aureus to cefquinome sulfate under different dosage regimens by using pharmacokinetic-pharmacodynamics (PK-PD) modeling, and the adaptive-resistant bacteria in different states were screened and subjected to transcriptomic sequencing. The results showed that the minimum inhibitory concentration of Staphylococcus aureus under the action of cefquinome sulfate was 0.5 μg/mL, the anti-mutation concentration was 1.6 μg/mL, and the mutation selection window range was 0.5~1.6 μg/mL. In the in vitro pharmacokinetic model to simulate different dosing regimens in the animal body, there are certain rules for the emergence of adaptive drug-resistant bacteria: the intensity of bacterial resistance gradually increased with culture time, and the order of emergence was tolerant bacteria (TO) followed by persistent bacteria (PE) and finally resistant bacteria (RE). The sequence reflected the evolution of adaptive drug resistance. Transcriptome Gene Ontology (GO) analysis revealed that differentially expressed genes were involved in cellular respiration, energy derivation by oxidation of organic compounds, and oxidation–reduction processes. The differentially expressed genes identified functioned in the synthesis of cell membranes, cytoplasm, and intracellular parts. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis found that 65 genes were differentially expressed after cefquinome sulfate treatment, of which 35 genes were significantly upregulated and 30 genes were significantly downregulated. Five genes, sdhB, sdhA, pdhA, lpdA, and sucC, may be involved in network regulation. This study revealed the cross-regulation of multiple metabolic pathway networks and the targets of network regulation of S. aureus to produce adaptive drug resistance. The results will provide guidance for clinical drug use in animals infected with S. aureus. Full article

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

16 pages, 1372 KiB

Open AccessSystematic Review

Post-COVID-19 Small Fiber Neuropathy as a New Emerging Quality of Life-Threatening Disease: A Systematic Review

by Francesca Bandinelli, Marco Di Carlo, Virginia Alba Colantuono, Filippo Nozzoli, Fausto Salaffi, Barbara Chiocchetti, Elena Nucci, Alessandra Mastricci, Eleonora Gherardi and Mirko Manetti

Microorganisms 2025, 13(2), 328; https://doi.org/10.3390/microorganisms13020328 - 2 Feb 2025

Viewed by 912

Abstract

Post-acute sequelae of COVID-19 (PASC) syndrome is considered an emergent and diffuse multidisciplinary problem. Compelling evidence suggests that COVID-19 increases symptoms of pre-existent small fiber neuropathy (SFN) and might trigger de novo onset of SFN. In this systematic review, for the first time, [...] Read more.

Post-acute sequelae of COVID-19 (PASC) syndrome is considered an emergent and diffuse multidisciplinary problem. Compelling evidence suggests that COVID-19 increases symptoms of pre-existent small fiber neuropathy (SFN) and might trigger de novo onset of SFN. In this systematic review, for the first time, we provide a comprehensive overview of the clinical and diagnostic features of PASC-SFN, including the accompanying disorders, disease evolution, and possible treatments, described in the recent literature. Following infection, many patients reported a wide range of symptoms and complications, not self-limiting and independent from previous infection severity. SFN begins more frequently with distal limb burning pain and numbness, which accompany other dysautonomia, cognitive, visual, and osteoarticular disorders involving multiple organ systems. In an initial diagnostic suspicion, some tests might be useful as complementary examinations, such as nerve quantitative sensory testing, electromyography, and optic nerve tomography. Otherwise, definite diagnosis is reached with skin biopsy as the gold standard, along with corneal in vivo microscopy when ocular discomfort is present. Being a long-term condition, multiple and dissimilar symptomatic and disease-modifying drugs were employed for the treatment of this condition with the achievement of partial results, including steroids, pregabalin, gabapentin, duloxetine, vitamins, homotaurine and phosphatidylserine, alpha lipoic acid, immunosuppressants, and intravenous immunoglobulin therapy. PASC-SFN is a complex emerging disease and extremely challenging for physicians. At present, the only feasible management of PASC-SFN is represented by a multidisciplinary tailored approach, with future definitive protocols for diagnosis and treatment deemed essential. Full article

(This article belongs to the Special Issue Microbial Infections and Rheumatic Diseases)

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7 pages, 3914 KiB

Open AccessCommunication

Microbial Changes Occurring During Oronasal Fistula Wound Healing

by Steven L. Goudy, Heath L. Bradley, Camillo Anthony Gacasan, Afra Toma, Keerthi Priya Chinniampalayam Sekar, William M. Wuest, Martin Tomov, Vahid Serpooshan, Ahmet Coskun and Rheinallt M. Jones

Microorganisms 2025, 13(2), 327; https://doi.org/10.3390/microorganisms13020327 - 2 Feb 2025

Viewed by 413

Abstract

The oral microbiome is a complex community that matures with dental development and is recognized as a risk factor for systemic disease. Despite the oral cavity having a substantial microbial burden, healing of superficial oral wounds occurs quickly and with little scarring. By [...] Read more.

The oral microbiome is a complex community that matures with dental development and is recognized as a risk factor for systemic disease. Despite the oral cavity having a substantial microbial burden, healing of superficial oral wounds occurs quickly and with little scarring. By contrast, creation of an oro-nasal fistula (ONF), often occurring after surgery to correct a cleft palate, is a significant wound healing challenge. Methods: In this study, we characterized the changes in the oral microbiome of mice following a freshly inflicted wound in the oral palate that results in an open and unhealed ONF. Results: Creation of an ONF in mice significantly lowered oral microbiome alpha diversity, with concurrent blooms of Enterococcus faecalis, Staphylococcus lentus, and Staphylococcus xylosus in the oral cavity. Treatment with oral antibiotics one week before ONF infliction reduced microbiome alpha diversity and prevented E. faecalis, S. lentus, and S. xylosus blooms, but did not impact ONF healing. Conclusions: An ONF in the murine palate leads to a dysbiotic oral microbiome and a bloom of opportunistic pathogens that may prevent ONF healing. Delivery of therapeutics that accelerate ONF healing might restore oral microbiome diversity and inhibit blooms of opportunistic pathogens. Full article

(This article belongs to the Section Microbiomes)

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15 pages, 3252 KiB

Open AccessArticle

Viral Infections in HSCT Recipients with Post-Transplant Lymphoproliferative Disorder: The Role of Torque Teno Virus as a Marker of Immune Functions

by Martyna Pociupany, Carolina Tarabella, Robert Snoeck, Daan Dierickx and Graciela Andrei

Microorganisms 2025, 13(2), 326; https://doi.org/10.3390/microorganisms13020326 - 2 Feb 2025

Viewed by 392

Abstract

Monitoring immune function in post-transplant patients is crucial to reduce the risk of viral infections (e.g., cytomegalovirus [CMV] or Epstein–Barr virus [EBV]), which can lead to serious complications such as post-transplant lymphoproliferative disorder (PTLD). Recently, Torque Teno virus (TTV) has attracted interest as [...] Read more.

Monitoring immune function in post-transplant patients is crucial to reduce the risk of viral infections (e.g., cytomegalovirus [CMV] or Epstein–Barr virus [EBV]), which can lead to serious complications such as post-transplant lymphoproliferative disorder (PTLD). Recently, Torque Teno virus (TTV) has attracted interest as a marker of immune function. Thus, we studied the kinetics of common post-transplant viral infections (TTV, EBV, CMV, human herpesvirus-6 [HHV-6], and adenovirus [AdV]) and their association with clinical parameters in 23 HSCT recipients who developed PTLD (PTLD-HSCT) and 25 post-HSCT patients without PTLD (Non-PTLD-HSCT) at three different timepoints: at the time of the transplant (T0), 3 months (T1), and 6 months (T2) post-HSCT. Additionally, 25 healthy donors (HD) were used as the control. EBV, CMV, HHV-6, or AdV infections were found in a few samples, while TTV was found in all of our samples. The highest TTV levels (4.61 [T0], 6.24 [T1] and 6.70 [T2] log₁₀ copies/mL) were seen in PTLD-HSCT patients compared to Non-PTLD-HSCT (3.39 [T0], 4.86 [T1], and 3.75 [T2] log₁₀ copies/mL) and HD (2.25 log₁₀ copies/mL) at all timepoints. Higher TTV levels were also seen in patients with a destructive type of PTLD and in surviving PTLD-HSCT patients compared to deceased ones. TTV kinetics in PTLD patients post-HSCT showed that TTV levels increase with the fall in the host immunocompetence and that by monitoring TTV kinetics, the immune status of the patient can be monitored. Full article

(This article belongs to the Section Virology)

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21 pages, 983 KiB

Open AccessReview

Antimicrobial Potential of Cannabinoids: A Scoping Review of the Past 5 Years

by Maria João Coelho, Maria Duarte Araújo, Márcia Carvalho, Inês Lopes Cardoso, Maria Conceição Manso and Cristina Pina

Microorganisms 2025, 13(2), 325; https://doi.org/10.3390/microorganisms13020325 - 2 Feb 2025

Viewed by 532

Abstract

In the scenario of fighting bacterial resistance to antibiotics, natural products have been extensively investigated for their potential antibacterial activities. Among these, cannabinoids—bioactive compounds derived from cannabis—have garnered attention for their diverse biological activities, including anxiolytic, anti-inflammatory, analgesic, antioxidant, and neuroprotective properties. Emerging [...] Read more.

In the scenario of fighting bacterial resistance to antibiotics, natural products have been extensively investigated for their potential antibacterial activities. Among these, cannabinoids—bioactive compounds derived from cannabis—have garnered attention for their diverse biological activities, including anxiolytic, anti-inflammatory, analgesic, antioxidant, and neuroprotective properties. Emerging evidence suggests that cannabinoids may also possess significant antimicrobial properties, with potential applications in enhancing the efficacy of conventional antimicrobial agents. Therefore, this review examines evidence from the past five years on the antimicrobial properties of cannabinoids, focusing on underlying mechanisms such as microbial membrane disruption, immune response modulation, and interference with microbial virulence factors. In addition, their synergistic potential, when used alongside standard therapies, underscores their promise as a novel strategy to address drug resistance, although further research and clinical trials are needed to validate their therapeutic use. Overall, cannabinoids offer a promising avenue for the development of innovative treatments to combat drug-resistant infections and reduce the reliance on traditional antimicrobial agents. Full article

(This article belongs to the Special Issue Antimicrobial Effects of Bioactive Compounds: Phytoproducts-Based Fight against Pathogens)

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24 pages, 2047 KiB

Open AccessArticle

Engineering the Marine Pseudoalteromonas haloplanktis TAC125 via the pMEGA Plasmid Targeted Curing Using PTasRNA Technology

by Angelica Severino, Concetta Lauro, Marzia Calvanese, Christopher Riccardi, Andrea Colarusso, Marco Fondi, Ermenegilda Parrilli and Maria Luisa Tutino

Microorganisms 2025, 13(2), 324; https://doi.org/10.3390/microorganisms13020324 - 2 Feb 2025

Viewed by 290

Abstract

Marine bacteria that have adapted to thrive in extreme environments, such as Pseudoalteromonas haloplanktis TAC125 (PhTAC125), offer a unique biotechnological potential. The discovery of an endogenous megaplasmid (pMEGA) raises questions about its metabolic impact and functional role in that strain. This [...] Read more.

Marine bacteria that have adapted to thrive in extreme environments, such as Pseudoalteromonas haloplanktis TAC125 (PhTAC125), offer a unique biotechnological potential. The discovery of an endogenous megaplasmid (pMEGA) raises questions about its metabolic impact and functional role in that strain. This study aimed at streamlining the host genetic background by curing PhTAC125 of the pMEGA plasmid using a sequential genetic approach. We combined homologous recombination by exploiting a suicide vector, with the PTasRNA gene-silencing technology interfering with pMEGA replication machinery. This approach led to the construction of the novel PhTAC125 KrPL² strain, cured of the pMEGA plasmid, which exhibited no significant differences in growth behavior, though showcasing enhanced resistance to oxidative stress and a reduced capacity for biofilm formation. These findings represent a significant achievement in developing our understanding of the role of the pMEGA plasmid and the biotechnological applications of PhTAC125 in recombinant protein production. This opens up the possibility of exploiting valuable pMEGA genetic elements and further advancing the genetic tools for PhTAC125. Full article

(This article belongs to the Special Issue Cold-Adapted Bacteria and Marine Bacteria)

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10 pages, 598 KiB

Open AccessReview

Balancing Nature and Nurture: The Role of Biocontrol Agents in Shaping Plant Microbiomes for Sustainable Agriculture

by Suzana Moussa and Lilach Iasur Kruh

Microorganisms 2025, 13(2), 323; https://doi.org/10.3390/microorganisms13020323 - 2 Feb 2025

Viewed by 201

Abstract

Microbial communities in the plant environment are highly dynamic, with bacterial populations rapidly responding to changes. Numerous studies have examined how both inherent plant characteristics and environmental factors shape plant-associated microbiota. These factors determine which bacterial communities thrive and how they interact with [...] Read more.

Microbial communities in the plant environment are highly dynamic, with bacterial populations rapidly responding to changes. Numerous studies have examined how both inherent plant characteristics and environmental factors shape plant-associated microbiota. These factors determine which bacterial communities thrive and how they interact with plants; certain conditions favor beneficial bacteria, and others support pathogens. In this mini-review, we focus on an additional factor influencing plant microbiomes and their surrounding environments: the use of biocontrol agents. The increasing application of microbial inoculants and their metabolites as biocontrol strategies in agriculture has created a critical knowledge gap about the effects of introducing non-native bacterial species into natural plant ecosystems. The inoculation of plants and their environments with exogenous biocontrol microorganisms has the potential to alter microbial community diversity and composition, presenting both opportunities and challenges for sustainable agricultural practices. Full article

(This article belongs to the Special Issue Effect of Microbial Communities for Environmental Protection and Development of Agriculture)

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19 pages, 11266 KiB

Open AccessArticle

Molecular Evolutionary Analyses of the RNA-Dependent RNA Polymerase (RdRp) Region and VP1 Gene in Sapovirus GI.1 and GI.2

by Fuminori Mizukoshi, Ryusuke Kimura, Tatsuya Shirai, Asumi Hirata-Saito, Eri Hiraishi, Kosuke Murakami, Yen Hai Doan, Hiroyuki Tsukagoshi, Nobuhiro Saruki, Takeshi Tsugawa, Kana Kidera, Yoshiyuki Suzuki, Naomi Sakon, Kazuhiko Katayama, Tsutomu Kageyama, Akihide Ryo and Hirokazu Kimura

Microorganisms 2025, 13(2), 322; https://doi.org/10.3390/microorganisms13020322 - 1 Feb 2025

Viewed by 338

Abstract

Human sapovirus (HuSaV) is a significant cause of gastroenteritis. This study aims to analyze the evolutionary dynamics of the RNA-dependent RNA polymerase (RdRp) and capsid (VP1) genes of the HuSaV GI.1 and GI.2 genotypes between 1976 and 2020. Using [...] Read more.

Human sapovirus (HuSaV) is a significant cause of gastroenteritis. This study aims to analyze the evolutionary dynamics of the RNA-dependent RNA polymerase (RdRp) and capsid (VP1) genes of the HuSaV GI.1 and GI.2 genotypes between 1976 and 2020. Using bioinformatics tools such as the Bayesian phylogenetics software BEAST 2 package (v.2.7.6), we constructed time-scale evolutionary trees based on the gene sequences. Most of the recent common ancestors (MRCAs) of the RdRp region and VP1 gene in the present HuSaV GI.1 diverged around 1930 and 1933, respectively. The trees of the HuSaV GI.1 RdRp region and VP1 gene were divided into two clusters. Further, the MRCAs of the RdRp region and VP1 gene in HuSaV GI.2 diverged in 1960 and 1943, respectively. The evolutionary rates were higher for VP1 gene in HuSaV GI.1 than that in HuSaV GI.2, furthermore, were higher in GI.1 Cluster B than GI.1 Cluster A. In addition, a steep increase was observed in the time-scaled genome population size of the HuSaV GI.1 Cluster B. These results indicate that the HuSaV GI.1 Cluster B may be evolving more actively than other genotypes. The conformational B-cell epitopes were predicted with a higher probability in RdRp for GI.1 and in VP1 for GI.2, respectively. These results suggest that the RdRp region and VP1 gene in HuSaV GI.1 and GI.2 evolved uniquely. These findings suggest unique evolutionary patterns in the RdRp region and VP1 gene of HuSaV GI.1 and GI.2, emphasizing the need for a ‘One Health’ approach to better understand and combat this pathogen. Full article

(This article belongs to the Special Issue Microbial Evolutionary Genomics and Bioinformatics)

15 pages, 3603 KiB

Open AccessArticle

Drug Resistance Mutations (DRMs) for Long-Acting Injectable Cabotegravir and Rilpivirine (CAB/RPV LAI) in the HIV-1 Subtype A6 Epidemic in Poland

by Andrzej Załęski, Agnieszka Lembas, Tomasz Dyda, Joanna Osińska, Joanna Jabłońska, Justyna Stempkowska-Rejek, Justyna Orzechowska and Alicja Wiercińska-Drapało

Microorganisms 2025, 13(2), 321; https://doi.org/10.3390/microorganisms13020321 - 1 Feb 2025

Viewed by 420

Abstract

HIV subtype A6 with the L74I polymorphism, which increases the risk of cabotegravir/rilpivirine treatment failure, causes more and more infections in Poland. In this multicenter, observational, cross-sectional study (2023–2024), we analyzed viral subtypes and drug-resistance mutations to drugs used for long-acting injectable antiretroviral [...] Read more.

HIV subtype A6 with the L74I polymorphism, which increases the risk of cabotegravir/rilpivirine treatment failure, causes more and more infections in Poland. In this multicenter, observational, cross-sectional study (2023–2024), we analyzed viral subtypes and drug-resistance mutations to drugs used for long-acting injectable antiretroviral treatment and pre-exposure prophylaxis. Among 357 people with HIV, 247 (69%) were Polish nationals, and 102 (29%) were from former Soviet Union countries. Of the 357 people included, 159 (45%) had subtype B, and 177 (50%) had subtype A6 infections, with 165 (87%) of the latter characterized by the L74I polymorphism. Subtype A6 was more frequent in women (66% vs. 46% in men, p < 0.05) and among people from former Soviet countries (77% vs. 39% in Polish nationals, p < 0.05). About 40% of people had either drug-resistance mutations for cabotegravir/rilpivirine or HIV A6 subtype with the L74I polymorphism; 4.5% had both of these conditions. Compared to subtype B infections, subtype A6 infections were characterized by more frequent major transmitted drug-resistance mutations for non-nucleoside reverse transcriptase inhibitors (8.5% vs. 1.9%, p = 0.007) and rilpivirine (5.1% vs. 0.6%, p = 0.016). Due to the frequent occurrence of the L74I polymorphism and drug-resistance mutations in HIV A6 subtype infection, about 40% of people with HIV in Poland may be at risk of long-acting injectable treatment failure. Full article

(This article belongs to the Special Issue Genomics and Epidemiology of Clinical Microorganisms)

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12 pages, 1942 KiB

Open AccessArticle

Association of Longitudinal Oral Microbiome Activity and Pediatric Concussion Recovery

by Justin Ceasar, Deepika Pugalenthi Saravanan, Brennen A. Harding and Steven D. Hicks

Microorganisms 2025, 13(2), 320; https://doi.org/10.3390/microorganisms13020320 - 1 Feb 2025

Viewed by 309

Abstract

Mild traumatic brain injury (mTBI) results in a constellation of symptoms commonly referred to as a concussion. It is unclear why certain individuals experience persistent symptoms. Given the growing evidence linking the microbiome with cognition and inflammation, we examined whether longitudinal microbiome patterns [...] Read more.

Mild traumatic brain injury (mTBI) results in a constellation of symptoms commonly referred to as a concussion. It is unclear why certain individuals experience persistent symptoms. Given the growing evidence linking the microbiome with cognition and inflammation, we examined whether longitudinal microbiome patterns were associated with concussion symptoms. A cohort study of 118 children (aged 7–21 years) was conducted. Symptoms were assessed at three timepoints post-injury (4, 11, and 30 days) using the Post-Concussion Symptom Inventory. Saliva microbial activity was measured at each timepoint using RNA sequencing. A linear mixed model assessed the relationship between microbial activity and symptom burden while controlling for age, sex, and days post-mTBI. The participants’ mean age was 16 (±3) years. The symptom burden decreased across all three timepoints (25 ± 22, 13 ± 17, and 5 ± 12). The longitudinal symptom burden was associated with elevated activity of Lactobacillus (F = 5.47; adj. p = 0.020) and Saccharomyces (F = 6.79; adj. p = 0.020) and reduced activity of Micrococcus (F = 7.94, adj. p = 0.015). These results do not establish a causative relationship, or support the use of microbial measures as a concussion test. Further studies are needed to explore the role of the gut–brain axis in mTBI. Full article

(This article belongs to the Special Issue Oral Microbes and Human Health)

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19 pages, 8414 KiB

Open AccessArticle

Mechanisms Driving Seasonal Succession and Community Assembly in Sediment Microbial Communities Across the Dali River Basin, the Loess Plateau, China

by Xin Chen, Jing Li, Guoce Xu, Kang Fang, Shun Wan, Bin Wang and Fengyou Gu

Microorganisms 2025, 13(2), 319; https://doi.org/10.3390/microorganisms13020319 - 1 Feb 2025

Viewed by 279

Abstract

Microorganisms are instrumental in river ecosystems and participate in biogeochemical cycles. It is thought that dynamic hydrological processes in rivers influence microbial community assembly, but the seasonal succession and community assembly of river sediments on the Loess Plateau remain unclear. This study used [...] Read more.

Microorganisms are instrumental in river ecosystems and participate in biogeochemical cycles. It is thought that dynamic hydrological processes in rivers influence microbial community assembly, but the seasonal succession and community assembly of river sediments on the Loess Plateau remain unclear. This study used high-throughput sequencing technology (16S and ITS) and the neutral community model to analyze seasonal succession and the assembly processes associated with microbial communities in the Dali River, a tributary of the Yellow River on the Loess Plateau. The results showed that sediment bacterial and fungal community diversity indexes in non-flood season were 1.03–3.15 times greater than those in flood season. There were obvious variations between non-flood and flood seasons in sediment microorganisms. The similarities among all, abundant, and rare microbial communities decreased as geographical distance increased. Proteobacteria (52.5–99.6%) and Ascomycota (22.0–34.2%) were the primary microbial phyla in all, abundant, and rare microbial communities. Sediment ammonia nitrogen, water temperature, and sediment organic carbon significantly affected (p < 0.05) the structure of all, abundant, and rare sediment microorganism communities. The ecological networks for the bacterial community of non-flood season and fungal community of flood season had complex topological parameters. The bacterial community in river sediments was driven by deterministic processes, while the fungal community was dominated by stochastic processes. These results expanded understanding about sediment microbial community characteristics in rivers on the Loess Plateau and provided insights into the assembly processes and the factors driving microbial communities in river networks. Full article

(This article belongs to the Section Environmental Microbiology)

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20 pages, 4781 KiB

Open AccessArticle

Molecular Epidemiology of Dengue Viruses in Lao People’s Democratic Republic, 2020–2023

by Cécile Troupin, Kedkeo Intavong, Somphavanh Somlor, Souksakhone Viengphouthong, Sitsana Keosenhom, Thep Aksone Chindavong, Phaithong Bounmany, Longthor Vachouaxiong, Thonglakhone Xaybounsou, Chittaphone Vanhnollat, Phonepadith Khattignavong, Darouny Phonekeo, Bouaphanh Khamphaphongphane, Phonepadith Xangsayarath, Vincent Lacoste, Philippe Buchy and Gary Wong

Microorganisms 2025, 13(2), 318; https://doi.org/10.3390/microorganisms13020318 - 1 Feb 2025

Viewed by 370

Abstract

Dengue fever is a widespread mosquito-borne viral disease caused by infections with dengue virus (DENV). Since its initial detection in 1979, the disease has posed a significant public health threat to the Lao People’s Democratic Republic (Lao PDR). Surveillance is crucial for understanding [...] Read more.

Dengue fever is a widespread mosquito-borne viral disease caused by infections with dengue virus (DENV). Since its initial detection in 1979, the disease has posed a significant public health threat to the Lao People’s Democratic Republic (Lao PDR). Surveillance is crucial for understanding the circulation of DENV in endemic regions and identifying potential hot spots with higher-than-expected case numbers of dengue fever. In this study, we present the results from our surveillance activities in the Lao PDR spanning 2020–2023. While quarantine restrictions from the COVID-19 pandemic posed substantial disruptions to performing DENV surveillance, over 8800 samples were tested during this period, with a positive rate of close to 60%. Cases were reported from all three regions (northern, Central, and southern) of the Lao PDR. Three circulating serotypes (DENV-1, DENV-2, and DENV-4) were detected, with DENV-1 dominant in 2021 and 2022, while DENV-2 was dominant in 2020 and 2023. Phylogenetic analyses suggest that the genotypes of DENV-1, DENV-2, and DENV-4 were closely related to corresponding isolates from neighboring countries. These findings provide an update on the nature of DENV cases detected in the Lao PDR and underscore the critical importance of sustaining a robust surveillance network to track infections. Full article

(This article belongs to the Special Issue Epidemiology of Hemorrhagic Fever Viruses)

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22 pages, 1817 KiB

Open AccessArticle

The Characterization of Lactic Acid Bacteria Strains as Components of a Biopreparation for Chickens for Slaughter

by Daria Zamojska, Justyna Rosicka-Kaczmarek, Ewa Macierzyńska-Piotrowska and Adriana Nowak

Microorganisms 2025, 13(2), 317; https://doi.org/10.3390/microorganisms13020317 - 1 Feb 2025

Viewed by 317

Abstract

Since 2022, the European Union has banned the use of antibiotics in animal production. We conducted studies to characterize Lactiplantibacillus plantarum (47, AN8, and OK-B) and Ligilactobacillus salivarius (AN9) and evaluate their potential to create a biopreparation based on fermented whey for chickens. [...] Read more.

Since 2022, the European Union has banned the use of antibiotics in animal production. We conducted studies to characterize Lactiplantibacillus plantarum (47, AN8, and OK-B) and Ligilactobacillus salivarius (AN9) and evaluate their potential to create a biopreparation based on fermented whey for chickens. The following methods were used: lactic acid bacteria (LAB) culture and storage, crystal violet staining, Koch’s plate method, Caco-2 cell culture, hydrophobicity test, and spectrophotometric measurements. All bacteria showed weak adhesion to polystyrene and collagen, and the L. plantarum species demonstrated weak adhesion to mucus. All bacteria showed strong adhesion to the intestinal epithelial cell line Caco-2. LAB showed strong autoaggregation and coaggregation with E. coli ATCC10536. The highest affinity for xylene was exhibited by L. salivarius AN9 (above 30%) while, for chloroform, the highest affinity was exhibited by L. plantarum OK-B (approx. 95%); the affinity for n-hexadecane for all strains was below 20%. The highest survival in the presence of bile salts (0.3%) was demonstrated by L. plantarum 47 (above 54%). The effect of low pH resulted in decreased viability for all strains. Significant differences were demonstrated in the concentration of lactic acid between MRS and whey medium after culturing LAB. These results will aid in qualifying these strains for further research to create a functional feed for chickens. Full article

(This article belongs to the Special Issue Microorganisms in Functional Foods)

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13 pages, 1418 KiB

Open AccessArticle

QuantiFERON^® Monitor Test as a Potential Tool for Stratifying Patients by Infection Risk and Tailoring Follow-Up Care in Lung Transplant Recipients: A Single-Center Retrospective Experience

by Paolo Solidoro, Antonio Curtoni, Filippo Patrucco, Eleonora Russo, Francesca Sidoti, Giorgia Piccinini, Alessandro Bondi, Paolo Valesella, Mattia Genco, Massimo Boffini, Rocco Francesco Rinaldo and Cristina Costa

Microorganisms 2025, 13(2), 316; https://doi.org/10.3390/microorganisms13020316 - 1 Feb 2025

Viewed by 246

Abstract

Background: Lung transplantation is a life-saving option for patients with end-stage respiratory diseases, but risk of infections remains critical for ensuring long-term organ function. This study aimed to assess immune recovery in lung transplant recipients by measuring IFN-γ levels using the QuantiFERON Monitor [...] Read more.

Background: Lung transplantation is a life-saving option for patients with end-stage respiratory diseases, but risk of infections remains critical for ensuring long-term organ function. This study aimed to assess immune recovery in lung transplant recipients by measuring IFN-γ levels using the QuantiFERON Monitor Test (QFM). Results were correlated with episodes of infection and organ rejection to explore the assay’s predictive potential. Methods: A retrospective study was conducted on 15 lung transplant recipients at the Lung Transplant Centre of Turin (Città della Salute e della Scienza di Torino, Italy) between December 2019 and January 2023. Patients were divided into a High Infection (HI) group (with >3 infections) and Low Infection (LI) group (with ≤3 infections). QFM assays were performed after 18 months post-transplant. Results: HI patients had lower QFM levels compared to LI (68.84 ± 21.98 vs. 380.54 ± 104.64 UI/mL, p = 0.033). A QFM value <89.5 UI/mL was associated with increased infection risk (p < 0.05). Patients with lower QFM levels also exhibited higher rates of MRSA bacteremia during hospitalization (50% HI vs. 0% LI, p = 0.04). No differences were observed in acute or chronic rejection rates, but LI patients showed more frequent alveolar neutrophilia at the fourth month post-transplant (0% HI vs. 55.5% LI, p = 0.04). Conclusion: lower QFM values were associated with higher infection risk, highlighting the assay’s potential for immune monitoring. In this study, a QFM value of 89.5 UI/mL showed good predictive accuracy for infections beyond 18 months. Further studies are needed to refine QFM’s role in post-transplant care. Full article

(This article belongs to the Special Issue Pneumonia: New Diagnostic and Therapeutic Options)

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26 pages, 1303 KiB

Open AccessReview

The Urogenital System Microbiota: Is It a New Gamechanger in Urogenital Cancers?

by Gülfem Ece, Ahmet Aktaş, Ayse Caner, İmran Sağlık, Tuğba Kula Atik, Özlem Ulusan Bağcı, Fulya Bayındır Bilman, Hadiye Demirbakan, Seda Güdül Havuz, Esra Kaya, Özlem Koyuncu Özyurt, Gülay Yetkin and Orçun Zorbozan

Microorganisms 2025, 13(2), 315; https://doi.org/10.3390/microorganisms13020315 - 1 Feb 2025

Viewed by 391

Abstract

The human microbiome, which encompasses microbial communities and their genetic material, significantly influences health and disease, including cancer. The urogenital microbiota, naturally present in the urinary and genital tracts, interact with factors such as age, lifestyle, and health conditions to affect homeostasis and [...] Read more.

The human microbiome, which encompasses microbial communities and their genetic material, significantly influences health and disease, including cancer. The urogenital microbiota, naturally present in the urinary and genital tracts, interact with factors such as age, lifestyle, and health conditions to affect homeostasis and carcinogenesis. Studies suggest that alterations in this microbiota contribute to the development and progression of genitourinary cancers, emphasizing the concept of oncobiome, which refers to microbial genetic contributions to cancer. Similarly, gut microbiota can influence hormone levels and systemic inflammation, impacting cancers such as cervical and prostate cancer. Advanced studies indicate that microbial communities in genitourinary cancers have distinct profiles that may serve as diagnostic biomarkers or therapeutic targets. Dysbiosis of the urinary microbiota correlates with bladder and kidney cancer. Additionally, gut microbiota influence the effectiveness of cancer treatments. However, further research is necessary to clarify causality, the role of microbial metabolites, and hormonal regulation. The aim of this review is to understand that these dynamics present opportunities for innovative cancer diagnostics and therapies, highlighting the need for integration of microbiology, oncology, and genomics to explore the role of microbiota in genitourinary cancers. For this, a comprehensive search of relevant databases was conducted, applying specific inclusion and exclusion criteria to identify studies examining the association between microbiota and urogenital cancers. Research into the mechanisms by which microbiota influence urogenital cancers may pave the way for new diagnostic and therapeutic approaches, ultimately improving patient outcomes. Full article

(This article belongs to the Special Issue Microbiota in Human Health and Disease)

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8 pages, 993 KiB

Open AccessCommunication

Emergence of NDM-7-Producing Klebsiella quasipneumoniae subs. simillipneumoniae ST138 in a Hospital from the Northern Region of Brazil

by Amália R. F. Lobato, Mikhail J. S. Souza, Emanoele S. Pereira, Thalyta B. Cazuza, Artur Silva, Rafael A. Baraúna and Danielle M. Brasiliense

Microorganisms 2025, 13(2), 314; https://doi.org/10.3390/microorganisms13020314 - 1 Feb 2025

Viewed by 283

Abstract

Clinical emergent bacterial pathogens are a great threat to the global health system, chiefly Gram-negative carbapenem-resistant Enterobacterales and the Klebsiella pneumoniae species complex. Here, we present the molecular and phenotypic characterization of Klebsiella quasipneumoniae subs. similipneumoniae IEC57090 strain, belonging to ST138 and showing [...] Read more.

Clinical emergent bacterial pathogens are a great threat to the global health system, chiefly Gram-negative carbapenem-resistant Enterobacterales and the Klebsiella pneumoniae species complex. Here, we present the molecular and phenotypic characterization of Klebsiella quasipneumoniae subs. similipneumoniae IEC57090 strain, belonging to ST138 and showing a multidrug resistance phenotype. The bla_NDM-7 present in one of the two resistance plasmids carried by the isolate, the antibiotic resistance genes fosA, oqxAB, and acrR, and gene mutations on porins ompK36 and ompK37, both associated with cephalosporin and carbapenem resistance, were detected. Virulence factors such as the clusters of type I and III fimbria, type IV pili genes, and genes associated with the K1 capsule, siderophore production, and multiple mobile genetic elements (MGE) were predicted. The emergence of silent pathogens in clinical environments highlights the importance of active research on new threads that may compromise the last resources of antimicrobials, such as carbapenems, specifically on mobile genetic elements containing carbapenemases in emergent pathogens, which can spread these antimicrobial resistance elements. This study reinforces that molecular biology vigilance can prevent outbreaks and help to better understand antimicrobial resistance and pathogens in clinical environment dynamics. Full article

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

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12 pages, 8454 KiB

Open AccessArticle

IL-6–Caspase 3 Axis Plays an Important Role in Enteritis Caused by Legionella pneumophila Pulmonary Infection

by Dahui Zhao, Xuefeng Duan, Li Zhu, Min Fang, Tian Qin and Yuhai Bi

Microorganisms 2025, 13(2), 313; https://doi.org/10.3390/microorganisms13020313 - 1 Feb 2025

Viewed by 257

Abstract

Background: Since Legionella pneumophila (Lp) is widely present in natural and artificial water environments, it has a high potential risk of outbreak. Diarrhea caused by Lp pulmonary infection is an important symptom of Legionnaires’ disease (LD); however, the underlying mechanism of the diarrhea [...] Read more.

Background: Since Legionella pneumophila (Lp) is widely present in natural and artificial water environments, it has a high potential risk of outbreak. Diarrhea caused by Lp pulmonary infection is an important symptom of Legionnaires’ disease (LD); however, the underlying mechanism of the diarrhea has not yet been revealed. This not only has a negative impact on clinical diagnosis and treatment, but may also cause misdiagnosis. Methods: In the present study, a mouse model of enteritis caused by pulmonary infection of Lp was established. By using this mouse model, we explored the underlying mechanisms of the enteritis caused by Lp pulmonary infection. Results: The results indicated that the systemic inflammatory response played a very important role in the enteritis phenotype caused by a strong-virulence strain of Lp. Furthermore, we found that the expression of Bcl-2 was downregulated by IL-6 through the p53 signaling pathway, thereby activating the caspase 3 of intestinal epithelial cells (IECs), causing the apoptosis of IECs, and ultimately leading to the enteritis phenotype. Conclusions: The IL-6–caspase 3 axis plays an important role in enteritis caused by Lp pulmonary infection. Full article

(This article belongs to the Section Medical Microbiology)

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21 pages, 11727 KiB

Open AccessArticle

Production and Bioseparation Applications of Polyhydroxyalkanoate Nano-Granules Functionalized with Streptavidin

by Yuyan Zhang, Jiping Zhao, Hui Guo, Xiaoyun Lu and Dan Tan

Microorganisms 2025, 13(2), 312; https://doi.org/10.3390/microorganisms13020312 - 1 Feb 2025

Viewed by 167

Abstract

Rapidly growing industrial biotechnology and bio-manufacturing require simple and cost-effective bioseparation tools. A novel strategy of bioseparation based on the streptavidin-decorated polyhydroxyalkanoate (PHA) nano-granules was developed in this study. By fusing to the N-terminus of PHA-associated phasin protein, the streptavidin was one-step immobilized [...] Read more.

Rapidly growing industrial biotechnology and bio-manufacturing require simple and cost-effective bioseparation tools. A novel strategy of bioseparation based on the streptavidin-decorated polyhydroxyalkanoate (PHA) nano-granules was developed in this study. By fusing to the N-terminus of PHA-associated phasin protein, the streptavidin was one-step immobilized on the surface of PHA nano-granules simultaneously with the accumulation of PHA in recombinant Escherichia coli. About 1.95 g/L of PHA nano-granules (54.51 wt% of cell dry weight) were produced after 48 h bacterial cultivation. The following qualitative and quantitative characterizations demonstrated that the streptavidin accounted for approximately 6.78% of the total weight of the purified PHA nano-granules and confirmed a considerable biotin affinity of 0.1 ng biotin/μg surface protein. As a proof of concept, the nano-granules were further functionalized with biotinylated oligo(dT) for mRNA isolation and about 1.26 μg of mRNA (occupied 2.59%) was purified from 48.45 μg of total RNA, achieving good integrity and high purity with few DNA and rRNA contaminations. Moreover, the nano-granules retained more than 80% of their initial mRNA recovery efficiency after ten cycles of repeated use. The PHA-SAP nano-granules were also functionalized with biotinylated magnetic beads, allowing magnetic recovery of the PHA nano-granules from cell lysates that still needs optimization. Our study provides a novel and expandable platform of PHA nano-granules that can be further functionalized with various biological groups for bioseparation applications. The functional PHA nano-granules have a great potential to serve as bioseparation resin for large-scale purification processes after suitable optimizations for “bench-to-factory” translation, contributing to scalable and sustainable bioprocessing. Full article

(This article belongs to the Section Microbial Biotechnology)

13 pages, 2716 KiB

Open AccessArticle

Tracing Emergence of SARS-CoV-2 Variants: Insights from Comprehensive Assessment Using Reverse Transcription Polymerase Chain Reaction and Whole Genome Sequencing

by Duyeon Na, Yuna Hong, Chaeyeon Lee and Myungshin Kim

Microorganisms 2025, 13(2), 311; https://doi.org/10.3390/microorganisms13020311 - 31 Jan 2025

Viewed by 360

Abstract

The emergence and evolution of SARS-CoV-2 variants, such as Delta and Omicron, pose significant challenges to pandemic management. This study evaluated the effectiveness of reverse-transcription polymerase chain reaction (RT-PCR) and whole-genome sequencing (WGS) in detecting and characterizing SARS-CoV-2 variants using 624 samples collected [...] Read more.

The emergence and evolution of SARS-CoV-2 variants, such as Delta and Omicron, pose significant challenges to pandemic management. This study evaluated the effectiveness of reverse-transcription polymerase chain reaction (RT-PCR) and whole-genome sequencing (WGS) in detecting and characterizing SARS-CoV-2 variants using 624 samples collected in South Korea from mid-2021 to mid-2022. Two RT-PCR genotyping assays demonstrated a high concordance rate (90.4%) in identifying the Delta variant during its dominance. In contrast, WGS revealed extensive genetic diversity among Omicron sub-lineages, identifying 29 distinct sub-lineages, including two South Korea-specific variants (BA.1.1.5 and BA.2.3.8). Clustering analysis of WGS data highlighted distinct groupings of BA.1, BA.2, and BA.5 sub-lineages, with overlap in shared mutations suggesting evolutionary convergence. Sub-lineage diversity expanded during rapid transmission phases and subsequently consolidated as dominant lineages emerged. These findings highlight the complementary strengths of RT-PCR and WGS and underscore the importance of integrating these methodologies for effective variant monitoring and public health response. Full article

(This article belongs to the Special Issue New Knowledge in the Study of Coronaviruses: Towards One Health and Whole Genome Sequencing Approaches, 2nd Edition)

16 pages, 729 KiB

Open AccessArticle

Impact of Feed Composition on Rumen Microbial Dynamics and Phenotypic Traits in Beef Cattle

by André L. A. Neves, Ricardo Augusto Mendonça Vieira, Einar Vargas-Bello-Pérez, Yanhong Chen, Tim McAllister, Kim H. Ominski, Limei Lin and Le Luo Guan

Microorganisms 2025, 13(2), 310; https://doi.org/10.3390/microorganisms13020310 - 31 Jan 2025

Viewed by 325

Abstract

The rumen microbiome is central to feed digestion and host performance, making it an important target for improving ruminant productivity and sustainability. This study investigated how feed composition influences rumen microbial abundance and phenotypic traits in beef cattle. Fifty-nine Angus bulls were assigned [...] Read more.

The rumen microbiome is central to feed digestion and host performance, making it an important target for improving ruminant productivity and sustainability. This study investigated how feed composition influences rumen microbial abundance and phenotypic traits in beef cattle. Fifty-nine Angus bulls were assigned to forage- and grain-based diets in a randomized block design, evaluating microbial dynamics, methane emissions, and feed efficiency. Quantitative PCR (qPCR) quantified bacterial, archaeal, fungal, and protozoal populations. Grain-based diets reduced bacterial and fungal counts compared to forage diets (1.1 × 10¹¹ vs. 2.8 × 10¹¹ copies of 16S rRNA genes and 1.5 × 10³ vs. 3.5 × 10⁴ copies of 18S rRNA genes/mL, respectively), while protozoan and methanogen populations remained stable. Microbial abundance correlated with feed intake metrics, including dry matter and neutral detergent fiber intakes. Methane emissions were lower in grain-fed bulls (14.8 vs. 18.0 L CH₄/kg DMI), though feed efficiency metrics showed no direct association with microbial abundance. Comparative analysis revealed adaptive microbial shifts in response to dietary changes, with functional redundancy maintaining rumen stability and supporting host performance. These findings provide insights into how feed composition shapes rumen microbial dynamics and host phenotypes, highlighting the functional adaptability of the rumen microbiome during dietary transitions. Full article

(This article belongs to the Special Issue Gut Microbiota of Food Animal)

19 pages, 692 KiB

Open AccessArticle

Dicentrine Purified from the Leaves of Ocotea puberula Controls the Intracellular Spread of L. (L.) amazonensis and L. (V.) braziliensis Amastigotes and Has Therapeutic Activity as a Topical Treatment in Experimental Cutaneous Leishmaniasis

by Jéssica Adriana Jesus, Gabriela Venicia Araujo Flores, Dalete Christine da Silva Souza, Daniela Costa Tristão, Dolores Remedios Serrano, Aikaterina Lalatsa, Márcia Dalastra Laurenti, João Henrique Ghilardi Lago, Humberto Gomes Ferraz, Rosana Pereira da Silva and Luiz Felipe Domingues Passero

Microorganisms 2025, 13(2), 309; https://doi.org/10.3390/microorganisms13020309 - 30 Jan 2025

Viewed by 351

Abstract

Leishmaniasis, a complex disease caused by protozoal parasites of the genus Leishmania, presents various clinical forms, particularly a cutaneous clinical form. Treatment is typically performed with pentavalent antimonial and amphotericin B, both of which have severe side effects that hinder patient compliance. [...] Read more.

Leishmaniasis, a complex disease caused by protozoal parasites of the genus Leishmania, presents various clinical forms, particularly a cutaneous clinical form. Treatment is typically performed with pentavalent antimonial and amphotericin B, both of which have severe side effects that hinder patient compliance. This emphasizes the need for the development of new, effective, and safe treatments. In this study, the leishmanicidal activity of the methanolic extract, an alkaloid-enriched fraction and dicentrine, the main alkaloid of the leaves of Ocotea puberula (Lauraceae), a native Brazilian plant traditionally used by the indigenous population to treat skin affections, was investigated in vitro. Additionally, an in vivo study evaluated the efficacy of a topical cream containing 0.5% dicentrine. The in vitro studies demonstrated high activity and selectivity of methanolic extract, alkaloid-enriched fraction, and dicentrine against the promastigote and amastigote forms of Leishmania (Leishmnia) amazonensis and Leishmania (Viannia) braziliensis. The leishmanicidal effect of dicentrine was related to the modulation of macrophage microbicidal activity. A cream containing 0.5% dicentrine showed high stability and, in permeation studies, dicentrine was retained in a skin-mimicking artificial membrane. This cream effectively inhibited the progression of the skin lesion in BALB/c mice infected with L. (L.) amazonensis, together with a reduced parasite number. Thus, dicentrine offers a promising alternative to the treatment of skin leishmaniasis. Full article

(This article belongs to the Special Issue Research on Leishmania and Leishmaniasis)

14 pages, 1414 KiB

Open AccessArticle

High Spatial but Low Temporal Variability in Ectomycorrhizal Community Composition in Abies alba Forest Stands

by Tina Unuk Nahberger, Hojka Kraigher and Tine Grebenc

Microorganisms 2025, 13(2), 308; https://doi.org/10.3390/microorganisms13020308 - 30 Jan 2025

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Abstract

The ectomycorrhizal symbionts of silver fir have rarely been analyzed and identified, so little is known about their diversity and distribution. The aim of this study was (1) to analyze the diversity of ectomycorrhizal fungal species in three geographically distinct forest stands of [...] Read more.

The ectomycorrhizal symbionts of silver fir have rarely been analyzed and identified, so little is known about their diversity and distribution. The aim of this study was (1) to analyze the diversity of ectomycorrhizal fungal species in three geographically distinct forest stands of Abies alba and (2) to demonstrate the high temporal variability of the ectomycorrhizal community over two consecutive growing seasons using repeated monthly sampling. Root samples were taken every month during two growing seasons in three silver fir-dominated forest stands. The ectomycorrhizal root tips were first assigned to a morphotype based on morphological characteristics and then identified by sequencing the internal transcribed spacer region. Alpha and beta diversity differed significantly between all three study sites, with the most diverse and even ectomycorrhizal community described in plot Jelovški boršt. The diversity indices over the growing season were different at two of the three study sites, supporting the idea of a fluctuation of ectomycorrhizal taxa during the growing seasons of the two consecutive years. While significant temporal variability was only confirmed for certain ectomycorrhizal taxa, there were no significant changes in the ectomycorrhizal community in general. Thus, we confirmed the high spatial but low temporal variability of the ectomycorrhizal community associated with silver fir. Full article

(This article belongs to the Special Issue Fungal Biology and Interactions, 2nd Edition)

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20 pages, 1914 KiB

Open AccessArticle

Production, Purification, and Biochemical Characterization of a Novel ATP-Dependent Caseinolytic Protease from the Marine Bacterium Cobetia amphilecti KMM 296

by Yulia Noskova, Olga Nedashkovskaya and Larissa Balabanova

Microorganisms 2025, 13(2), 307; https://doi.org/10.3390/microorganisms13020307 - 30 Jan 2025

Viewed by 305

Abstract

A novel caseinolytic protease (ClpP) of the S14 family from Cobetia amphilecti KMM 296 (CamClpP), comprising 206 amino acids, with a calculated molecular weight of 22.66 kDa and a pI of 4.88, was expressed in Escherichia coli cells to verify the functional annotation [...] Read more.

A novel caseinolytic protease (ClpP) of the S14 family from Cobetia amphilecti KMM 296 (CamClpP), comprising 206 amino acids, with a calculated molecular weight of 22.66 kDa and a pI of 4.88, was expressed in Escherichia coli cells to verify the functional annotation of the encoding gene that has low identity with known structures. The proteolytic activity of the purified recombinant enzyme was found to be 2824 U/mg, using 1% casein as a substrate. Enzyme activity was maximal at pH 5.6 and 7.4 in phosphate buffer and was maintained over a wide pH range of 4-10. The optimum temperature for protease activity was 45 °C. The enzyme in its optimal state required the presence of either NaCl or KCl at concentrations of 0.3 and 0.2 M, respectively. The addition of the metal ions Mg²⁺, Ca²⁺, Ni²⁺, Mn²⁺, Li⁺, and Zn²⁺ at 2 mM resulted in a significant inhibition of the protease activity. However, the presence of Co²⁺ led to a marked activation of the enzyme in the absence of ATP. The enzyme activity was inhibited by ethanol, isopropanol, glycerol, SDS, EGTA, and EDTA. The presence of Triton X-100, acetone, DTT, and PMSF resulted in a significant increase in the CamClpP protease activity. The protease CamClpP effectively and preferentially degrades high-polymer wheat and rye flour proteins. This new proteolytic enzyme with unique properties is of great ecological and biotechnological importance. Full article

(This article belongs to the Special Issue Cold-Adapted Bacteria and Marine Bacteria)

13 pages, 520 KiB

Open AccessArticle

The Efficacy of Calcium Hypochlorite and Peroxyacetic Acid Treatments in Inactivating Enterohemorrhagic Escherichia coli on Alfalfa Seeds and Sprouts

by Myung-Ji Kim, Wim Dejonghe, Murli Manohar and Jinru Chen

Microorganisms 2025, 13(2), 306; https://doi.org/10.3390/microorganisms13020306 - 30 Jan 2025

Viewed by 428

Abstract

For several decades, recurring outbreaks of human gastrointestinal infections associated with contaminated sprouts have posed an enduring challenge, highlighting the necessity of controlling the etiological agents on contaminated sprout seeds. This study investigated the efficacy of calcium hypochlorite and peroxyacetic acid treatments in [...] Read more.

For several decades, recurring outbreaks of human gastrointestinal infections associated with contaminated sprouts have posed an enduring challenge, highlighting the necessity of controlling the etiological agents on contaminated sprout seeds. This study investigated the efficacy of calcium hypochlorite and peroxyacetic acid treatments in inactivating the cells of four enterohemorrhagic Escherichia coli (EHEC) isolates—viz. E. coli O157:H7 K4492, F4546, and H1730, as well as E. coli O104:H4 BAA-2326—on alfalfa seeds and sprouts. The 2–3 log CFU/g of EHEC cells inoculated to sprout seeds became undetectable (≤1.40 log CFU/g) after treatment with the two sanitizers, even with the enrichment steps. Sprouts grown from calcium hypochlorite- and peroxyacetic acid-treated seeds had mean EHEC populations that were 4.54–4.60 log CFU/g and 1.25–1.52 log CFU/g lower, respectively, compared to those on sprouts grown from the untreated control seeds. Significantly (p ≤ 0.05) different from one another, the mean populations of the four EHEC isolates on harvested sprout samples were in the descending order of E. coli O157:H7 K4492, F4546, H1730, and E. coli O104:H4 BAA-2326. The results suggest that both sanitizing treatments effectively suppressed EHEC growth on alfalfa seeds and sprouts, but their effectiveness was bacterial-isolate-dependent. Full article

(This article belongs to the Section Plant Microbe Interactions)

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13 pages, 1366 KiB

Open AccessArticle

Diet Supplementation with Pomegranate Fruit Alters Distal Gut Microbiota of Healthy Female College Students

by Brant Bandow, Entsar S. Shaaban, Sumudu Rajakaruna, Zeinab Saleh, Sahar A. Abdelaziz, Laila Hussein and Oleg Paliy

Microorganisms 2025, 13(2), 305; https://doi.org/10.3390/microorganisms13020305 - 30 Jan 2025

Viewed by 491

Abstract

Pomegranate is a fruit that grows abundantly in the Middle East and Africa. It is rich in polyphenols, sugars, fiber, and vitamins, and has long been associated in traditional and alternative medicine with numerous health benefits, including the treatment of diarrhea and gut [...] Read more.

Pomegranate is a fruit that grows abundantly in the Middle East and Africa. It is rich in polyphenols, sugars, fiber, and vitamins, and has long been associated in traditional and alternative medicine with numerous health benefits, including the treatment of diarrhea and gut inflammation. We assessed how regular daily intake of fresh pomegranate can affect the distal gut microbiota of young healthy female students in Egypt, a region with abundant pomegranate production and frequent occurrence of gut dysbiosis. Interrogation of microbiota structure based on the sequencing of the 16S ribosomal RNA gene amplicons indicated that subject-to-subject variability was the main driver of microbiota community differences. Nevertheless, pomegranate consumption led to changes in the abundances of several genera including increased levels of Saccharofermentans, Enterococcus, and Prevotella. The relative counts of Dysosmobacter, Coprococcus, and Collinsella decreased after pomegranate intake. The magnitude of community structure shift after diet intervention correlated with the increase in the total polyphenol concentration measured in subjects’ urine. The overall ratio of presumed beneficial-to-detrimental microbes was also improved with pomegranate addition to the diet, supporting the advantageous effects of pomegranate eating. Full article

(This article belongs to the Special Issue Probiotics, Prebiotics, and Gut Microbes—Second Edition)

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15 pages, 3829 KiB

Open AccessCommunication

PK/PD Analysis of High-Dose Daptomycin Use in the Treatment of Bone and Joint Infections: Data from a Real-World Setting

by Jacopo Angelini, Simone Giuliano, Francesco Russiani, Francesco Lo Re, Sarah Flammini, Barbara Cadeo, Luca Martini, Carlo Tascini and Massimo Baraldo

Microorganisms 2025, 13(2), 304; https://doi.org/10.3390/microorganisms13020304 - 30 Jan 2025

Viewed by 448

Abstract

Background: Daptomycin is widely used in bone and joint infections (BJIs) caused by Gram-positive cocci. The pharmacokinetics of daptomycin are characterized by relevant variability in terms of drug exposure. Due to these pharmacological properties, the dosing suggested by the Summary of medical Product [...] Read more.

Background: Daptomycin is widely used in bone and joint infections (BJIs) caused by Gram-positive cocci. The pharmacokinetics of daptomycin are characterized by relevant variability in terms of drug exposure. Due to these pharmacological properties, the dosing suggested by the Summary of medical Product Characteristics could result in sub-therapeutic or toxic concentrations, especially considering the high doses recommended for BJIs. Therapeutic Drug Monitoring (TDM) of daptomycin helps clinicians in verifying the patient’s exposure, due to the lack of pharmacokinetic/pharmacodynamic (PK/PD) data in this clinical setting. Methods: We retrospectively analyzed 170 daptomycin plasma concentrations of 77 patients with BJIs from July 2022 to December 2023. We focused on the pharmacokinetics of daptomycin to investigate when drug plasma concentrations achieved adequate PK/PD targets. Results: In the first TDM, 7.8% of patients were underexposed according to the estimated area under the curve (eAUC_0–24h < 666 mg·h/L), whereas 35.1% were on target according to both the eAUC and trough plasma concentration (eAUC_0–24h 666 − 939 mg·h/L; C_min < 24.3 mg/L). The patients who were overexposed had trough plasma concentrations > 24.3 mg/L (27.3%) or eAUC_0–24h > 1174 mg·h/L (33.8%). Differences in drug exposure were observed according to weight and sex. Conclusions: Due to the difficult management of this drug’s dosing, analyzing daptomycin plasma concentrations through TDM represents a powerful tool in BJIs. Full article

(This article belongs to the Section Medical Microbiology)

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18 pages, 1691 KiB

Open AccessArticle

Enhanced Recovery of Food-Grade Euglena gracilis Biomass Through Synergistic pH-Modified Chitosan Flocculation and Green Light Stimulation

by Jiangyu Zhu, Lan Yang, Li Ding, Zhengfei Yang, Yongqi Yin, Minato Wakisaka, Shahram Ashouri, Mohammadhadi Jazini and Weiming Fang

Microorganisms 2025, 13(2), 303; https://doi.org/10.3390/microorganisms13020303 - 30 Jan 2025

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Abstract

The efficient and cost-effective harvesting of food-grade Euglena gracilis remains a critical challenge in microalgal food production. This study presents an innovative, food-safe approach integrating pH preconditioning, chitosan biopolymer flocculation, and green light irradiation to leverage E. gracilis’ natural phototactic behavior. Response surface [...] Read more.

The efficient and cost-effective harvesting of food-grade Euglena gracilis remains a critical challenge in microalgal food production. This study presents an innovative, food-safe approach integrating pH preconditioning, chitosan biopolymer flocculation, and green light irradiation to leverage E. gracilis’ natural phototactic behavior. Response surface methodology optimized the parameters (pH 6.49, 46.10 mg·L⁻¹ chitosan, and 60 min green light), achieving 93.07% biomass recovery, closely matching the predicted 92.21%. The synergistic effects of pH-modified chitosan flocculation and phototaxis significantly enhanced the harvesting efficiency compared to conventional methods. Notably, harvested cells maintained substantial photosynthetic capability, as evidenced by chlorophyll fluorescence analysis, ensuring the preservation of nutritional quality. Economic analysis revealed exceptional harvesting cost-effectiveness at 2.35 USD per kg of dry weight biomass harvested. The method’s use of food-grade chitosan and non-invasive light stimulation ensures product safety while minimizing the environmental impact. This sustainable and economical approach offers a promising solution for industrial-scale production of food-grade E. gracilis while demonstrating potential applicability to other phototactic microalgae species. Full article

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

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