Search Results (157)

Deep-sea sediment-derived fungal isolates remain underrepresented in organized living collections for phenotype-based screening. We applied 12 complementary isolation protocols—dilution plating, ethylenediaminetetraacetic acid (EDTA) pretreatment, and plate stamping—to four deep-sea sediment materials (2595–6000 m) representing three sampling units from the Mariana Trench slope region and the South China Sea. After morphotype-based purification, isolates were characterized by internal transcribed spacer (ITS) closest-match analysis and phylogenetic placement; selected representatives were further screened against five phytopathogenic strains using dual-culture, culture filtrate, and volatile organic compound (VOC) assays. In total, 159 isolates were placed within Ascomycota, Basidiomycota, and Mucoromycota, representing 35 closest-match genus-level groups and 22 low-similarity ITS phylotypes (<95% similarity) preserved as living cultures. Cladosporium, Penicillium, and Aspergillus were most frequent. Recovered diversity profiles varied among sediment materials and protocols, with plate stamping capturing a large, compositionally distinct subset of the collection. In dual culture, all 23 tested isolates inhibited at least one pathogen, with maximum mycelial growth inhibition reaching 98.74%. Culture filtrate and VOC assays produced partially discordant activity profiles, highlighting assay-format-dependent effects. This study establishes an ITS-organized living fungal collection and provides a phenotype-based framework for targeted taxonomic, chemical, and biocontrol-oriented follow-up. Full article

Potato (Solanum tuberosum L.) is an important staple and food security crop to many communities in the world. However, potato production and quality is greatly constrained by bacterial wilt, a disease caused by a soil-borne pathogen, Ralstonia solanacearum. Ralstonia solanacearum can be managed through clean seed systems and therefore laboratory testing is a pre-requisite for seed certification to confirm the absence of the pathogen in potato seeds before planting. Molecular diagnostics is the gold standard for detection of R. solanacearum in potato seeds. However, the extraction of genomic DNA from R. solanacearum for molecular diagnostics is complex, tedious, lengthy and/or costly procedure. A simple, rapid and reliable DNA extraction protocol is required for use in routine molecular diagnosis of R. solanacearum, a high-risk quarantine pathogen. In this study, we developed a simple and rapid protocol for extracting genomic DNA from symptomatic and asymptomatic potato tubers infected with R. solanacearum and verified its efficiency for the detection and molecular characterization of the pathogen. The protocol was developed from the evaluation of distilled water, Tris-EDTA (TE) and Tris buffer as a base solution for tissue maceration. The DNA quantity and integrity was determined using the NanoDrop 2000C spectrophotometer and agarose gel electrophoresis, respectively. Both hot and cold solutions produced intact high molecular weight genomic DNA of sufficient yield and purity for molecular-based applications. The detection and determination of phylotypes of R. solanacearum, based on conventional and multiplex polymerase chain reaction (PCR), amplified the expected 280 and 372 bp amplicons, respectively, confirming that the quantity and quality of the extracted pathogen genomic DNA was sufficient for molecular diagnostic applications. The sequencing of the amplified products of the endoglucanase gene produced good quality sequences, which confirmed the R. solanacearum isolates to be members of phylotype II sequevar 1. This protocol is a simple, fast and reliable tool for the extraction of sufficient genomic DNA with high quality, directly from R. solancearum-infected potato tubers for PCR and sequencing applications. Its simplicity and throughput make it valuable for use in routine diagnostics and can be adopted by certification programs to ensure distribution of clean potato seeds to farmers. Full article

Background/Objectives: Escherichia coli is the predominant pathogen in community-onset urinary tract infections (UTIs) requiring hospitalization. This study characterized antimicrobial resistance profiles, biofilm formation, extended-spectrum β-lactamase (ESBL) gene distribution, and phylogenetic background of E. coli isolates from hospitalized UTI patients in Western Mexico. Methods: Seventy isolates (September 2023–September 2024) underwent susceptibility testing (CLSI M100, 35th edition), multiplex PCR for blaTEM, blaCTX-M, and blaSHV genes, crystal violet biofilm quantification, and Clermont quadruplex PCR phylotyping. Associations were evaluated by Fisher’s exact test with Benjamini–Hochberg FDR (BH-FDR) correction. Results: ESBL phenotype and MDR were detected in 57.1% and 58.6% of isolates. After BH-FDR correction, ESBL production was significantly associated with amikacin (OR = 5.55; 95% CI: 1.80–18.74; q = 0.002) and TMP-SMX non-susceptibility (OR = 3.00; 95% CI: 1.02–9.23; q = 0.036); ciprofloxacin non-susceptibility was linked to MDR status (OR = 7.21; 95% CI: 1.28–75.66; q = 0.017) but not ESBL phenotype. Biofilm was detected in 77.1% of isolates. blaTEM predominated among ESBL producers (85.0%). Phylogroup B2 (51.4%) was inversely associated with recurrent UTI on both univariate (OR = 0.17; 95% CI: 0.03–0.73; p = 0.008) and adjusted analysis (adjusted OR = 0.19; 95% CI: 0.05–0.81; p = 0.025). Phylogroup C (22.9%) exhibited the highest MDR prevalence (81.3%) and the highest biofilm formation rate among phylogroups (87.5%). Conclusions: The high prevalence of ESBL-producing and MDR E. coli, combined with an unexpected predominance of blaTEM, reveals a distinctive local resistance landscape diverging from regional trends. The inverse association of phylogroup B2 with recurrence and TMP-SMX resistance reinforces the clinical value of phylogenetic surveillance in guiding UTI management strategies. Full article

Bacterial wilt (BW), caused by soil-borne bacteria of the Ralstonia solanacearum species complex (RSSC), is a serious disease affecting eggplant (Solanum melongena) in tropical and subtropical regions. Resistance to BW in eggplant has been identified in several accessions and wild relatives, but no source has shown broad and stable resistance across diverse strains and environmental conditions. In the first screening trial, six eggplant genotypes, including five previously identified as resistant to RSSC, were evaluated along with two tomato checks against eight BW strains representing two phylotypes (I and II) and three biovars (2, 3, and 4). In the second screening trial, 26 hybrids developed from seven parental eggplant genotypes (including the six evaluated genotypes in the first screening plus an additional one) were evaluated, together with the parents, against three BW strains (Pss97, Pss2016, and Pss4). The results showed that the parental line EG048 was highly susceptible, whereas EG44 was resistant to the three strains, with a disease index (DI) of ≤20%. Furthermore, fourteen hybrids were classified as resistant or moderately resistant to the three strains. Among them, hybrid EG27 was categorized as highly resistant to all three strains with a disease index of 5.6–7.3%. In addition, three hybrids (EG8, EG20, and EG29) were highly resistant or resistant to all three strains, with a disease index of 3.8–15.8%. A strong positive correlation was observed between wilting percentage and disease index in the eggplant hybrids across the tested strains. Our results provide valuable support for eggplant breeding programs aimed at developing hybrid rootstocks with broader and potentially broad-spectrum resistance to RSSC in tomato and eggplant. Full article

This study assessed the impact of a topical phytocomplex on the acne skin microbiota, encompassing bacterial, fungal, and phage communities. Skin samples obtained from participants exhibiting a positive response to the treatment were analyzed using high-throughput sequencing and bioinformatic approaches including taxonomic profiling, metagenome assembly, functional annotation, and phage identification. Results showed that after treatment, microbial diversity increased, reflecting a more balanced microbial composition. Cutibacterium acnes levels were reduced, particularly virulent IA1/IA2 phylotypes, whereas non-pathogenic or unclassified strains increased. Opportunistic pathogens such as Klebsiella pneumoniae were no longer detected, and beneficial genera including Psychrobacter and Dermabacter were enriched. Functional analysis showed reduced virulence- and biofilm-related pathways, alongside enhanced tryptophan metabolism, SCFA production, lipid synthesis, and riboflavin and folate biosynthesis. Fungal populations, dominated by Malassezia, became more evenly distributed, with notable post-treatment reductions in M. arunalokei, Exophiala spinifera, and Wickerhamomyces anomalus. Phage populations mirrored bacterial changes, with enrichment of Cutibacterium-associated phages post-treatment. These findings demonstrate that the phytocomplex promotes functional rebalancing of the skin microbiota by reducing pathogenic features while maintaining ecosystem stability. The inhibition of quorum sensing, potentially mediated by N-acyl-homoserine lactone acetylation, emerged from metabolic pathway annotation as a hypothetic key mechanism impairing bacterial communication and virulence associated with acne vulgaris. Full article

The genus Xylaria comprises numerous species, particularly prevalent in tropical ecosystems such as those of Ecuador. Despite its ecological importance, the taxonomy of the genus remains challenging, and much of its diversity in the Neotropics remains under-documented. This study provides a preliminary characterization of the Xylaria diversity at the Estación Científica San Francisco, an Andean biodiversity hotspot in Southern Ecuador. Through an integrated approach including detailed macro- and micro-morphological descriptions and nuclear ribosomal DNA (nrDNA ITS and LSU) phylogenetic analyses, 20 Xylaria specimens were examined. As a result, ten species were recognized: Xylaria adscendens, X. cf. anisopleura, X. apiculata, X. curta, X. enterogena, X. fissilis, X. globosa, X. aff. telfairii, X. tuberoides, and X. aenea, the latter representing a new record for Ecuador. The phylogenetic analysis presented here serves as a preliminary systematic positioning of these specimens within the genus rather than a comprehensive global reconstruction. While these ribosomal markers provided preliminary insights into species relationships, partial incongruence with morphospecies highlights the evolutionary complexity of certain lineages and underscores the need for future multilocus studies. Furthermore, four additional phylotypes found in their anamorphic state are documented, suggesting that local diversity exceeds current records. By providing detailed morphological documentation supported by preliminary barcode data from a poorly sampled region, this study contributes vital information to the global understanding of Xylaria and underscores the importance of Southern Ecuador as a reservoir of fungal diversity. Full article

This review discusses the microbiology of acne vulgaris, a chronic inflammatory condition of the pilosebaceous unit that affects most adolescents and can persist into adulthood. The current standard of care consists largely of antibacterial interventions, based on the traditional view of Cutibacterium acnes as a pathogen. Alternative treatments are suggested by the “comedo switch” hypothesis, which attributes acne to aberrant differentiation of LRIG1+ sebaceous progenitor cells. While there is strong evidence to support this idea, it does not explain the efficacy of antibacterial interventions. We propose a unified mechanism wherein C. acnes phylotype IA1 can act as a trigger for the comedo switch. Unlike commensal strains, phylotype IA1 has high lipase activity, hydrolyzing sebum triglycerides into free fatty acids, specifically palmitic acid. This metabolite stimulates LRIG1+ progenitors, inducing inflammation and initial comedo formation. The review discusses C. acnes phylotypes, emphasizing known virulence factors of IA1, such as enhanced biofilm formation. We evaluate the efficacy and limitations of both old and new antibacterials, noting how newer materials that selectively remove C. acnes IA1 can reduce non-inflammatory acne lesions, supporting a key role for this phylotype in the pathogenesis of acne. Full article

Background: Avian pathogenic Escherichia coli (APEC) are significant bacterial pathogens that cause economic losses in the poultry industry and can pose a potential foodborne zoonotic risk. Herein, we examined APEC distribution and antimicrobial resistance in E. coli isolated from slaughtered broiler chickens in northern Thailand. Methods: PCR was used to classify APEC as either virulent or avirulent on 108 stored E. coli strains, as well as to perform Clermont phylotyping. Antimicrobial susceptibility to ciprofloxacin, cefotaxime, ceftazidime, imipenem, and colistin was examined. Results: Of the 108 E. coli strains, 101 (93.5%) isolates were APEC, and the remaining isolates were non-APEC. Among the APEC isolates, 58.4% were classified as virulent APEC; these isolates showed a statistically significant association with phylogroups F and C and (n = 54, 56.8%) more frequently exhibited a ciprofloxacin-resistant phenotype than avirulent APEC (n = 35, 36.8%). Among the ten APEC virulence genes, hlyF, iroC, iroN, iutA, O78, and ompT were significantly associated with virulent APEC. Conclusions: This study reveals a high prevalence of virulent APEC with fluoroquinolone resistance in slaughtered broiler chickens. Almost all virulent APEC strains belong to phylogroups F and C. The prediction of virulent APEC using hlyF, iroC, iroN, iutA, O78, and ompT may be useful. Full article

Acne vulgaris is a prevalent chronic inflammatory skin disorder affecting over 85% of adolescents. Emerging evidence indicates that Cutibacterium acnes phylotype IA₁ contributes to acne initiation and progression, yet its precise mechanisms in epidermal keratinocytes remain unclear. This study investigated C. acnes IA1’s effects on keratinocyte behavior using an in vitro HaCaT cell model. Cells were co-cultured with live C. acnes IA₁ (CICC 10864) for 24 h. Transcriptomic profiling identified 769 differentially expressed genes (DEGs; adjusted p < 0.05, |log2FC| > 1), including 392 upregulated and 377 downregulated. The protein–protein interaction network analysis via Cytoscape revealed key hub genes (HNRNPA2B1, HNRNPM, RBM39). Enrichment analyses (GO, KEGG, Reactome, DO) highlighted significant involvement of the C-type lectin receptor (CLR) signaling pathway. Validation experiments showed cellular morphological changes, altered structure, and markedly elevated interleukin-6 (IL-6; p < 0.01), underscoring its role in inflammation. These findings suggest C. acnes IA₁ drives acne pathogenesis by regulating hub genes that influence sebaceous gland inflammation, immune activity, and keratinocyte proliferation, positioning them as potential biomarkers for microbiome-targeted therapies. Limitations include the in vitro model’s lack of in vivo skin microenvironment complexity and use of only one representative IA₁ strain. Full article

Despite being a commensal bacterium, Cutibacterium acnes has been widely considered a major opportunistic pathogen due to its capacity for biofilm production and inflammatory induction, causing device-related, post-implant infections, and skin inflammatory diseases. In this study, we isolated and characterised the novel bacteriophage Cutibacterium acnes phage KIT09 as a potential antimicrobial candidate for the treatment of Cutibacterium acnes-related infections such as acne vulgaris and postsurgical infections. Subsequently, phage-resistant bacterial mutants were generated through phage KIT09 exposure and characterised. Wastewater samples were collected for the isolation of C. acnes phages, followed by their characterisation using C. acnes National Institute of Technology and Evaluation (NITE) Biological Resources Center (NBRC) 107605 (phylotype IA1). Resistant mutants were isolated after prolonged exposure of the newly isolated phage to host bacteria and then characterised. A novel C. acnes phage, designated KIT09, was isolated, demonstrating prolonged bacteriolysis lasting up to 96 h at a multiplicity of infection of 10, and exhibiting high thermal and pH stability. Following sustained selective pressure by phage KIT09, three phage-resistant bacterial isolates were obtained, forming smaller colonies than the wild-type strain, but maintaining a high phage adsorption capacity (>90% after 20 min). Whole-genome sequencing revealed 12 nucleotide mutations across five genes, including six non-synonymous substitutions. Three genes encoding a two-component histidine kinase, DNA processing protein A (DprA), and a ThuA-containing domain protein were mutated in all resistant isolates. Characterisation of the novel phage KIT09 demonstrated its robust lytic activity and environmental stability against C. acnes phylotype IA1. Isolated resistant mutants retained high phage adsorption, accompanied by recurrent mutations in genes encoding a two-component histidine kinase, DprA, and a ThuA-domain protein, suggesting the presence of alternative, CRISPR-Cas–independent resistance mechanisms in C. acnes. Full article

Polyextremophilic microbial communities of Baikal Rift Zone hot springs have been studied fragmentarily, and these studies have typically focused on either phototrophic microbial mats or on the whole microbial community from one or a few sites. In our work, we conducted the first large-scale screening of microbial communities from seven hot spring groups in the Baikal Rift Zone, using metabarcoding of the V3-V4 regions of the 16S rRNA gene. Analysis of alpha and beta diversity, as well as co-occurrence network analysis, revealed that the microbial diversity of the studied springs is highly dependent on temperature values. This approach allowed classifying microbial communities into four distinct groups, characterized by significantly different taxa representing the key functional roles of primary producers, heterotrophic consumers, and terminal destructors of organic matter. Sulfate-reducing bacteria constituted a major metabolic group driving the final stage of organic matter mineralization. Moreover, the presence of alkalithermophilic dissimilatory iron reducers, whose existence was debatable, was proved in the studied samples by cultural methods. The phylotypes that gained an advantage on selective media with synthesized ferrihydrite and hydrogen or acetate added as an electron donor belonged to the genus Parvivirga of the order Anaerosomatales and several unknown representatives of the phylum Bacillota. Full article

The human skin microbiome, defined as a multifaceted ecosystem comprising bacteria, fungi, viruses, and mites, plays a pivotal role in maintaining skin homeostasis and regulating immune responses. In recent years, an increasing amount of evidence has illuminated the considerable influence exerted by microbiomes on the pathophysiology of dermatological ailments. This review provides a comprehensive synthesis of contemporary findings concerning the microbiome’s role in acne, aging, hyperpigmentation, and hair disorders, while also addressing the emerging concept of the gut–skin axis and how it could interfere in these skin disorders. Alterations in microbial composition, referred to as dysbiosis, have been associated with inflammatory processes and barrier dysfunction, thereby contributing to the severity and chronicity of diseases. Distinct microbial profiles have been identified as correlating with specific skin conditions. For instance, variations in Cutibacterium acnes phylotypes have been associated with the development of acne, whereas alterations in Corynebacterium and Staphylococcus species have been linked to the processes of aging and pigmentation patterns. Furthermore, the composition of the microbiome is examined in relation to its impact on cosmetic outcomes. It also engages with increasing interest in the modulation of microbiota through the topical application of bioactive compounds. The incorporation of prebiotics, probiotics, and postbiotics into cosmetic formulations constitutes a novel strategy aimed at enhancing skin health. In the domain of dermatological therapies, postbiotics have emerged as a significant class of substances, particularly due to their remarkable stability, safety, and immunomodulatory properties. These characteristics position them as promising candidates for incorporation into dermatological treatments. Recent studies have underscored the significance of microbiome-informed strategies within the domains of therapeutic and preventive dermatology, emphasizing the potential of such approaches to positively influence patient outcomes. As our understanding of this field continues to evolve, skin microbiomes are poised to emerge as a pivotal area of focus in the realm of personalized skin care and treatment. This development presents novel and innovative approaches for the management of skin conditions, characterized by enhanced specificity and efficacy. Full article

Cutibacterium acnes subspecies/phylotypes can cause infections requiring antibiotic therapy. Phylotyping of 73 (55 acneic and 18 non-acneic) C. acnes strains was performed, and antibiotic susceptibility was tested by E tests, breakpoint susceptibility test, or disk diffusion method. The dominant phylotype in both acneic and non-acneic strains was IA1 (56.2%). Phylotype II was >3-fold more frequent in non-acneic than acneic isolates. Resistance in acneic strains was >41% for clindamycin, 36.4% for tetracycline and 15.9% for levofloxacin, and that in non-acneic strains was >38% for clindamycin, 22.2% for tetracycline and 5.6% for levofloxacin. No strain was piperacillin/tazobactam or vancomycin resistant. Amoxicillin resistance was found in both acneic (5.4%) and non-acneic strains (11.1%), and was rare (1.8%) in phylotype I but higher (23.5%) in other strains. Double resistance was found in 32.6% of acneic and 22.2% of the non-acneic strains, and 9.3% of acneic strains displayed multidrug resistance. In conclusion, IA1 phylotype was dominant in both acneic and non-acneic strains, and type II was more frequent in non-acneic isolates. The detection (at >6%) of amoxicillin resistance represents a rare yet important finding. The presence of double/multidrug resistance strongly implies the need of susceptibility-guided therapy of the associated infections. Full article

Background/Objectives: Cutibacterium acnes is increasingly recognized as a relevant pathogen in orthopaedic implant-associated infections, yet treatment strategies remain largely empirical. With rising antimicrobial resistance and scarce data on drug interactions, optimizing targeted therapies is essential. This preclinical study investigated the efficacy and synergism of vancomycin (VA), gentamicin (GEN), and ceftriaxone (CTX) against two clinical phylotype IB strains from orthopaedic infections and the reference strain C. acnes ATCC 6919, using both in vitro and in vivo models. Methods: Minimum inhibitory concentrations (MICs) were determined using broth microdilution following BrCAST guidelines. Synergistic activity was assessed using the checkerboard assay and interpreted via fractional inhibitory concentration indices (FICIs). The in vivo efficacy of antibiotic combinations with bioactive glass S53P4 (BAG) was evaluated in the Galleria mellonella infection model. Results: All C. acnes strains exhibited uniformly low MICs. Synergistic activity was observed for CTX combined with GEN in strain 2 (FICI range 0.25–0.37), while partial synergy was detected for CTX with GEN in strain 1 (FICI ≈ 0.56–0.63), and for CTX combined with VA in the ATCC strain (FICI = 0.66). All other combinations demonstrated indifferent interactions. In the G. mellonella model, a high bacterial inoculum (OD₆₀₀ of 3.0) was needed to establish an infection. For all strains tested, the use of antibiotics in combination with BAG improved larval survival. For the clinical strains, the combination of CTX + GEN + BAG and BAG alone demonstrated greater efficacy in promoting larval survival. Conclusions: Acombination of a cephalosporin with an aminoglycoside, particularly when incorporated into a biomaterial matrix, enhances antimicrobial activity against both clinical and reference strains of C. acnes. Full article

The oral microbiome has garnered significant interest in recent years. Its profound implications for oral and systemic diseases have led to a considerable amount of research and analysis aimed at providing deeper insights into its composition. This study aimed to characterize oral bacterial communities comprehensively based on microorganisms indexed in the Human Oral Microbiome Database, which was systematically analyzed, and its taxonomic classification was used to describe the diversity of indexed bacteria in the oral cavity. A total of 522 bacteria were considered for the analysis. Among these, 49.04% were named, whereas 29.12% represent uncultivated phylotypes. The taxonomic characterization revealed that more than 80% of total taxa are distributed across five phyla: Bacillota, Bacteroidota, Actinomycetota, Pseudomonadota, and Fusobacteriota. Of these, Bacillota and Bacteroidota are the dominant ones with, respectively, 166 (31.80%) and 96 (18.39%) bacterial taxa. With the recent advances in genomics and bioinformatics, the HOMD is constantly updated, further enhancing our understanding of the bacterial community of the oral microbiome. However, the considerable diversity of the oral microbiome may present analytical challenges and the possible misperception of the implications of closely related species/subspecies in oral and systemic health. Full article