QUAST: quality assessment tool for genome assemblies

Epidemiology of Tularemia among Humans and Animals, Baden-Wuerttemberg, Germany, 2012-2022

Tularemia, a zoonosis caused by Francisella tularensis, is endemic in Baden-Wuerttemberg, Germany. To determine tularemia epidemiology in this region, we characterized the genetic diversity of F. tularensis in human and animal isolates during 2012-2022 by using whole-genome sequencing, combined with human and veterinary surveillance data analysis. Human case numbers varied; most cases occurred in 2021 (n = 34). Arthropod bites were reported most in cases with information on animal exposure (45%, n = 43). Poisson regression confirmed a significant increase in human cases during the study period (p<0.001). No seasonal pattern was identified, but case numbers were lowest in winter. Human surveillance data often lacked exposure details. Positivity rates in animals were 5%-34%, increasing since 2017. Human isolates often clustered with hare-derived strains, although transmission routes often remain unclear. These findings emphasize the importance of combining genome sequencing with detailed epidemiologic tracing to identify infection sources and improve surveillance data.

Phylogenomic insights into the taxonomy, ecology, and mating systems of the lorchel family Discinaceae (Pezizales, Ascomycota)

Lorchels, also known as false morels (Gyromitra sensu lato), are iconic due to their brain-shaped mushrooms and production of gyromitrin, a deadly mycotoxin. Molecular phylogenetic studies have hitherto failed to resolve deep-branching relationships in the lorchel family, Discinaceae, hampering our ability to settle longstanding taxonomic debates and to reconstruct the evolution of toxin production. We generated 75 draft genomes from cultures and ascomata (some collected as early as 1960), conducted phylogenomic analyses using 1542 single-copy orthologs to infer the early evolutionary history of lorchels, and identified genomic signatures of trophic mode and mating-type loci to better understand lorchel ecology and reproductive biology. Our phylogenomic tree was supported by high gene tree concordance, facilitating taxonomic revisions in Discinaceae. We recognized 10 genera across two tribes: tribe Discineae (Discina, Maublancomyces, Neogyromitra, Piscidiscina, and Pseudodiscina) and tribe Gyromitreae (Gyromitra, Hydnotrya, Paragyromitra, Pseudorhizina, and Pseudoverpa); Piscidiscina was newly erected and 26 new combinations were formalized. Paradiscina melaleuca and Marcelleina donadinii formed their own family-level clade sister to Morchellaceae, which merits further taxonomic study. Genome size and CAZyme content were consistent with a mycorrhizal lifestyle for the truffle species (Hydnotrya spp.), whereas the other Discinaceae genera possessed genomic properties of a saprotrophic habit. Lorchels were found to be predominantly heterothallic-either MAT1-1 or MAT1-2-but a single occurrence of colocalized mating-type idiomorphs indicative of homothallism was observed in Gyromitra esculenta strain CBS101906 and requires additional confirmation and follow-up study. Lastly, we confirmed that gyromitrin has a phylogenetically discontinuous distribution, having been detected exclusively in two distantly related genera (Gyromitra and Piscidiscina) belonging to separate tribes. Our genomic dataset will facilitate further investigations into the gyromitrin biosynthesis genes and their evolutionary history. With additional sampling of Geomoriaceae and Helvellaceae-two closely related families with no publicly available genomes-these data will enable comprehensive studies on the independent evolution of truffles and ecological diversification in an economically important group of pezizalean fungi.

Transcriptome sequencing on different ages of Saraca asoca bark: Insights from tannin biosynthetic pathways and EST-SSR marker design

The bark of Saraca asoca is extensively used for treating gynecological issues, primarily due to its tannin content. This study focused on transcriptome sequencing of young (BY; 0-6 years), middle-aged (BM; 6-12 years), and old (BO; >12 years) Ashoka barks. The de novo assembly produced 1,37,451 unigenes of 1,31,647,800 bp from BY, 1,16,825 unigenes of 1,15,283,571 bp from BM, and 81,825 unigenes of 68,553,092 bp from BO samples. These transcripts closely matched with Glycine max and Cajanus cajan. Transcriptome analysis identified key genes and enzymes in the tannin biosynthetic pathway, with higher levels of phenylpropanoid and flavonoid pathways observed in middle-aged samples, followed by young and old samples. Pathway enrichment analysis indicated that the Differentially Expressed Genes (DEGs) were predominantly in the biosynthetic pathways of flavonoids, isoflavonoids, anthocyanins, terpenoids, and isoquinoline alkaloids. The study also examined the up-regulated and down-regulated DEGs involved in tannin production across the different sample comparisons, revealing the flavonoid pathway to be the most regulated. Additionally, 9612, 8053, and 4659 simple sequence repeats (SSRs) were identified from BY, BM, and BO transcripts, respectively. Fourteen EST-SSR markers specific to tannins were designed and validated, with one found to be polymorphic. This research represents the first report on transcriptome sequencing and EST-SSR markers from various ages of Saraca asoca bark, providing a foundation for future genetic mapping and conservation efforts of this vulnerable species.

Reclassification of Pasteurella skyensis as Phocoenobacter skyensis comb. nov. and description of Phocoenobacter atlanticus sp. nov. isolated from diseased Atlantic salmon (Salmo salar) and lumpfish (Cyclopterus lumpus), with subdivision into Phocoenobacter atlanticus subspecies atlanticus subsp. nov. and Phocoenobacter atlanticus subspecies cyclopteri subsp. nov

Gram-negative bacteria, similar in 16S rRNA gene sequence to Pasteurella skyensis, have been irregularly cultured from diseased Atlantic salmon (Salmo salar) sea-farmed in Norway since the 1980s and more commonly in later years from diseased lumpfish (Cyclopterus lumpus) farmed in the northeast Atlantic area. Phenotypic and genetic analyses confirmed that the majority of Norwegian isolates in the present study, cultured from both salmon and lumpfish, are closely related to, yet distinct from, P. skyensis and represent a hitherto undescribed species. We further argue, based on genetic similarity levels, that the original placement of P. skyensis within Pasteurella was erroneous and that this species belongs within Phocoenobacter, as Phocoenobacter skyensis comb. nov. Accordingly, we propose the name Phocoenobacter atlanticus sp. nov. for the new species characterized here. Furthermore, this species separates into two genetically and phenotypically distinct lineages, respectively, associated with Atlantic salmon and lumpfish, and for which we propose the names Ph. atlanticus subsp. atlanticus subsp. nov. and Ph. atlanticus subsp. cyclopteri subsp. nov., respectively. The type strain for Ph. atlanticus subsp. atlanticus subsp. nov. is strain NVIB3624T (NCIMB 15512T, CCUG 77520T), and the type strain for Ph. atlanticus subsp. cyclopteri subsp. nov. is strain NVIO9100T (NCIMB 15511T, CCUG 77521T).

Comparative pangenomics of Streptococcus pneumoniae from Malawi: uncovering genetic variability and pathogenicity

Streptococcus pneumoniae is a significant cause of bacterial infections, including pneumonia, meningitis and septicemia, primarily affecting children, the elderly and immunocompromised individuals. This study aimed to elucidate the serotype and lineage distribution and molecular mechanisms underlying pneumococcal invasiveness through a comprehensive pangenomic analysis of 1416 isolates from Malawi. Our analysis comprised 810 isolates from asymptomatic carriers and 606 isolates from patients with bacteraemia or meningitis. We identified 58 serotypes, with serotypes 1, 5 and 12F exhibiting significantly higher prevalence among patients. These serotypes likely exhibit reduced nasopharyngeal colonization and demonstrate rapid dissemination to sterile sites. Notably, these serotypes form a distinct lineage with distinct genomic characteristics, including the absence of V-type ATP synthase. The pangenome analysis revealed two highly conserved surface protein complexes, F-type ATP synthase and SecA1-SecY, which deserve further investigation as potential targets for novel therapeutic interventions.

Novel genomic features in entomopathogenic fungus Beauveria bassiana ILB308: accessory genomic regions and putative virulence genes involved in the infection process of soybean pest Piezodorus guildinii

BACKGROUND

Biological control methods involving entomopathogenic fungi like Beauveria bassiana have been shown to be a valuable approach in integrated pest management as an environmentally friendly alternative to control pests and pathogens. Identifying genetic determinants of pathogenicity in B. bassiana is instrumental for enhancing its virulence against insects like the resistant soybean pest Piezodorus guildinii. This study focused on comparative genomics of different B. bassiana strains and gene expression analyses to identify virulence genes in the hypervirulent strain ILB308, especially in response to infection of P. guildinii and growth on hydrocarbon HC15, a known virulence enhancer.

RESULTS

Strain ILB308 showed the highest number of virulence-related features, such as candidate virulence proteins, effectors, small secreted proteins and biosynthetic gene clusters. ILB308 also had a high percentage of unique DNA sequences, including six accessory scaffolds. Gene expression analysis at 4 days post inoculation revealed upregulation of known virulence factors, including Tudor domain proteins, LysM motif-containing proteins, subtilisin-like proteases and novel genes encoding secreted effectors and heat-labile enterotoxins. Growth on HC15 led to the upregulation of genes associated with oxidoreductase activity related to cuticular alkane degradation and fermentation metabolism/antioxidant responses in the hemolymph. The low number of known B. bassiana virulence genes points to novel or unknown mechanisms acting on the interaction between P. guildinii and strain ILB308.

CONCLUSION

The presence of accessory genomic regions and unique virulence genes in ILB308 may contribute to its higher virulence. These genes could be considered as potential targets for enhancing fungal virulence through genetic manipulation. © 2025 Society of Chemical Industry.

Bacteriocin production facilitates nosocomial emergence of vancomycin-resistant Enterococcus faecium

Gastrointestinal colonization by the nosocomial pathogen vancomycin-resistant Enterococcus faecium (VREfm) can lead to bloodstream infections with high mortality rates. Shifts in VREfm lineages found within healthcare settings occur, but reasons underlying these changes are not understood. Here we sequenced 710 VREfm clinical isolates collected between 2017 and 2022 from a large tertiary care centre. Genomic analyses revealed a polyclonal VREfm population, although 46% of isolates formed genetically related clusters, suggesting a high transmission rate. Comparing these data to a global collection of 15,631 publicly available VREfm genomes collected between 2002 and 2022 identified replacement of the sequence type (ST) 17 VREfm lineage by emergent ST80 and ST117 lineages at the local and global level. Comparative genomic and functional analyses revealed that emergent lineages encoded bacteriocin T8, which conferred a competitive advantage over bacteriocin T8-negative strains in vitro and upon colonization of the mouse gut. Bacteriocin T8 carriage was also strongly associated with strain emergence in the global genome collection. These data suggest that bacteriocin T8-mediated competition may have contributed to VREfm lineage replacement.

Functional and Genomic Potential of Burkholderia contaminans PB_AQ24 Isolate for Boosting the Growth of Bamboo Seedlings in Heavy Metal Contaminated Soils

The present study investigated the genomic and functional potential of Burkholderia contaminans PB_AQ24, a bacterial strain isolated from the municipal solid waste dumpsite, for boosting the growth of Dendrocalamus strictus (Male bamboo) seedlings. The isolated strain exhibited high potency for metal solubilization and ACC (1-Aminocyclopropane-1-carboxylate) deaminase activity. Its genome harbored diverse genes responsible for nitrogen and phosphorus utilization (trpABCDES, iaaH, acdS, pstABCS, phoAUD, pqqABCDE, kdpABC, gln, and nirBD) and also an abundance of heavy metal tolerant genes (ftsH, hptX, iscX-fdx-hscAB-iscAUR, mgtA, corA, and copC). Seeds priming experiments carried out in heavy metal contaminated soils (such as waste dumpsite soil (WDS), fly ash dumpsite soil (FAS) and natural garden soil (NGS control)) augmented with Burkholderia contaminans sp. PB_AQ24 showed 85% sustenance of seedlings in WDS and 80% in FAS. The study thus highlighted the potential features in isolated bacterial strain Burkholderia sp. PB_AQ24 (NCBI accession no. JAQOUG000000000), which could boost the growth of bamboo seedlings in heavy metal contaminated soils and may be applied for restoration and rejuvenation of contaminated sites.

Clostridioides difficile in raw mechanically separated poultry meat and pasteurized product made from contaminated meat

OBJECTIVES

Clostridioides difficile (C. difficile) is an important foodborne pathogen found in a wide range of products. This study investigated the occurrence of C. difficile in mechanically separated chicken and turkey meat (MSM) and in pasteurized products made from contaminated MSM.

METHODS

The presence of C. difficile was analysed in 56 MSM samples (32 from turkey and 24 from chicken) and in six pasteurized meat products made from raw meats previously identified as C. difficile-positive. After enrichment, detection was performed by real-time PCR, and culture on selective media for C. difficile. The isolated strains were then characterized by PCR-ribotyping, toxinotyping, and whole-genome sequencing (WGS).

RESULTS

C. difficile was detected in 16.1 % of MSM samples via real-time PCR, with a 10.7 % isolation rate. One pasteurized product also tested positive. The six isolates obtained displayed diverse PCR-ribotypes, five of which were toxigenic. Notably, the PCR-ribotypes and sequence types in the pasteurized product differed from those identified in the raw meat used for its production.

CONCLUSIONS

The presence of C. difficile in raw and subsequently pasteurized meat product indicates that the pathogen can survive the pasteurization process and may be present in such products.

Synteny Enabled Upgrade of the Galapagos Giant Tortoise Genome Improves Inferences of Runs of Homozygosity

The utility and importance of whole-genome sequences are recognized across various fields, including evolution and conservation. However, for some taxa, like extinct species, using methods to generate contiguous genomes that rely on high-quality DNA is impossible. In such cases, an alternative may be to employ synteny-based methods using a genome from a closely related taxon to generate more complete genomes. Here we update the reference genome for the Pinta Island Galapagos giant tortoise (Chelonoidis abingdonii) without conducting additional sequencing through rescaffolding against the most closely related chromosome-level genome assembly, the Aldabra giant tortoise (Aldabrachelys gigantea). This effort resulted in a much more contiguous genome, CheloAbing_2.0, with an N50 that is two orders of magnitude longer and large reductions in L50 and the number of gaps. We then examined the impact of the CheloAbing_2.0 genome on estimates of runs of homozygosity (ROH) using genome resequencing data from 37 individual Galapagos giant tortoises from the 13 extant lineages to test the mechanisms by which a fragmented assembly may over- or underestimate the number and extent of ROH. The use of CheloAbing_2.0 resulted in individual estimates of inbreeding, including ROH proportion (FROH), number (NROH), and cumulative length (SROH), that were statistically different from those derived from the earlier genome assembly. This improved genome will serve as a resource for future efforts focusing on the ecology, evolution, and conservation of this species group. More broadly, our results highlight that synteny-based scaffolding is promising for generating contiguous genomes without needing additional data types.

Genomic Insights into Post-Domestication Expansion and Selection of Body Size in Ponies

Horse domestication revolutionizes human civilization by transforming transportation, agriculture, and warfare patterns. Despite extensive studies on modern domestic horse origins, the intricate demographic history and genetic signatures underlying pony size remain unexplored. Here, a high-quality genome assembly of the Chinese Debao pony is presented, and 452 qualified individuals from 64 horse breeds worldwide are extensively analyzed. The authors' results reveal the conservation of ancient components in East Asian horses and close relationships between Asian horses and Western pony lineages. Genetic analyses suggest an Asian paternal origin for European pony breeds. These pony-sized horses share close genetic affinities, potentially attributed to their early expansion and adaptation to local environments. In addition, promising cis-regulatory elements influencing horse withers height by regulating genes such as RFLNA and FOXO1 are identified. Overall, this study provides insightful perspectives on the dispersal history and genetic determinants underlying body size in ponies, offering broader implications for horse population management and improvement.

Comparison of nanopore with illumina whole genome assemblies of the Epstein-Barr virus in Burkitt lymphoma

Endemic Burkitt lymphoma (eBL) is one of the most prevalent cancer in children in sub-Saharan Africa, and while prior studies have found that Epstein-Barr virus (EBV) type and variation may alter the tumor driver genes necessary for tumor survival, the precise relationship between EBV variation and EBV-associated tumorigenesis remains unclear due to lack of scalable, cost-effective, viral whole-genome sequencing from tumor samples. This study introduces a rapid and cost-effective method of enriching, sequencing, and assembling accurate EBV genomes in BL tumor cell lines through a combination of selective whole genome amplification (sWGA) and subsequent 2-tube multiplex polymerase chain reaction along with long-read sequencing with a portable sequencer. The method was optimized across a range of parameters to yield a high percentage of EBV reads and sufficient coverage across the EBV genome except for large repeat regions. After optimization, we applied our method to sequence 18 cell lines and 3 patient tumors from fine needle biopsies and assembled them with median coverages of 99.62 and 99.68%, respectively. The assemblies showed high concordance (99.61% similarity) to available Illumina-based assemblies. The improved method and assembly pipeline will allow for better understanding of EBV variation in relation to BL and is applicable more broadly for translational research studies, especially useful for laboratories in Africa where eBL is most widespread.

A wheat tandem kinase activates an NLR to trigger immunity

The role of nucleotide-binding leucine-rich repeat (NLR) receptors in plant immunity is well studied, but the function of a class of tandem kinases (TKs) that confer disease resistance in wheat and barley remains unclear. In this study, we show that the SR62 locus is a digenic module encoding the Sr62TK TK and an NLR (Sr62NLR), and we identify the corresponding AvrSr62 effector. AvrSr62 binds to the N-terminal kinase 1 of Sr62TK, triggering displacement of kinase 2, which activates Sr62NLR. Modeling and mutation analysis indicated that this is mediated by overlapping binding sites (i) on kinase 1 for binding AvrSr62 and kinase 2 and (ii) on kinase 2 for binding kinase 1 and Sr62NLR. Understanding this two-component resistance complex may help engineering and breeding plants for durable resistance.

Exploring the occurrence of Pseudomonas aeruginosa and comprehensive whole genome analysis of the bcsir_p4_s20 strain from municipal wastewater in Chattogram

Various studies reported the existence of multidrug-resistant (MDR) Pseudomonas aeruginosa in environmental samples, including hospital wastewater, municipal wastewater, and surface water. In this study, we investigated the impact of untreated municipal wastewater transmitting antibiotic-resistant P. aeruginosa strains in wastewater networks of Chattogram City, Bangladesh, through antibiotic susceptibility profiles and whole-genome sequencing (WGS) of the MDR P. aeruginosa bcsir_p4_s20. Forty-two P. aeruginosa isolates were identified from eight locations using polymerase chain reaction (PCR), targeting the oprI and oprL genes, and antibiotic susceptibility was determined against 11 antibiotics by the disc diffusion method. Resistant isolates were identified at all locations, with the highest resistance frequency displayed towards meropenem, cefepime, and colistin. The WGS of bcsir_p4_s20 was performed using the NextSeq 2000 platform. Several bioinformatics tools, like FastQC, Trimmomatic, SPAdes, and Prokka, were used for quality evaluation, low-quality read and adapter filtration, de novo assembly, and functional annotation. Comprehensive Antibiotic Resistance Database (CARD), AMRFinderPlus, and virulence factor database (VFDB) were employed to determine resistance genes and virulence factors. The strain belongs to the O7 serogroup and sequence type ST357. The analysis identified antibiotic resistance genes (blaPDC-11, sul1, and others) that cause resistance through efflux pump and inactivation mechanisms, and virulent genes responsible for adherence (flagella, type IV pili), enzyme (phospholipase C), iron uptake (pyoverdine), secretion system (exoT, exoU), and toxin (toxA) secretion. Therefore, municipal wastewater is a potential reservoir for MDR P. aeruginosa, and establishing wastewater treatment plants (WWTPs) at the primary source points before discharging it to the wastewater network is suggested to mitigate the risk of outbreaks.

Menominin A and B: Cytotoxic Cyclodepsipeptides from the Freshwater Sponge-Associated Cyanobacterium Nostoc sp. UIC 10607

Menominin A (1) and B (2), two cyclodepsipeptides containing a 3,8-dihydroxy-2-methyltetradecanoic acid residue, were isolated from the freshwater sponge-associated cyanobacterium, Nostoc sp. UIC 10607, using bioactivity-guided and spectroscopic approaches. The planar structures of 1 and 2 were established using HRESIMS and one- and two-dimensional NMR experiments. Comparative genomic analysis revealed unique differences in the putative menominin biosynthetic gene cluster compared to that of the closely related cyanobacterial cyclic lipodepsipeptide, hapalosin, assisting in structure elucidation and highlighting the structural diversity of this class of compounds. Configuration assignments were determined using a combination of J-based configuration analysis, chiral HPLC, modified Mosher's ester analysis, and DFT calculations. Menominin A and B demonstrate antiproliferative bioactivity against the high-grade serous ovarian cancer cell line OVCAR3 (IC50 = 3.1 (1) and 2.4 μM (2)). Menominin A and B are the first reported secondary metabolites from a freshwater sponge-associated cyanobacterium, underscoring the potential of freshwater sponges as a microbial culture source in natural product discovery.

Sludge amended soil induced multidrug and heavy metal resistance in endophytic Exiguobacterium sp. E21L: genomics evidences

The emergence of multidrug-resistant bacteria in agro-environments poses serious risks to public health and ecological balance. In this study, Exiguobacterium sp. E21L, an endophytic strain, was isolated from carrot leaves cultivated in soil amended with sewage treatment plant-derived sludge. The strain exhibited resistance to clinically relevant antibiotics, including beta-lactams, fluoroquinolones, aminoglycosides, and macrolides, with a high Multi-Antibiotic Resistance Index of 0.88. Whole-genome sequencing revealed a genome of 3.06 Mb, encoding 3894 protein-coding genes, including antimicrobial resistance genes (ARGs) such as blaNDM, ermF, tetW, and sul1, along with heavy metal resistance genes (HMRGs) like czcD, copB, and nikA. Genomic islands carrying ARGs and stress-related genes suggested potential horizontal gene transfer. The strain demonstrated robust biofilm formation, high cell hydrophobicity (> 80%), and significant auto-aggregation (90% at 48 h), correlating with genes associated with motility, quorum sensing, and stress adaptation. Notably, phenotypic assays confirmed survival under simulated gastrointestinal conditions, emphasizing its resilience in host-associated environments. Comparative genomics positioned Exiguobacterium sp. E21L near Exiguobacterium chiriqhucha RW-2, with a core genome of 2716 conserved genes. Functional annotations revealed genes involved in xenobiotic degradation, multidrug efflux pumps, and ABC-type transporters, indicating versatile resistance mechanisms and metabolic capabilities. The presence of ARGs, HMRGs, and MGEs (mobile genetic elements) highlights the potential role of Exiguobacterium sp. E21L as a reservoir for resistance determinants in agricultural ecosystems. These findings emphasized the need for stringent regulations on sludge-based fertilizers and advanced sludge treatment strategies to mitigate AMR risks in agro-environments.

Comparative genome analysis of 15 Streptococcus thermophilus strains isolated from Turkish traditional yogurt

Streptococcus thermophilus plays a pivotal role in yogurt fermentation, yet strains from traditional fermented products remain largely unexplored compared to their industrial counterparts. This study aimed to characterize the genomic diversity and functional potential of 15 S. thermophilus strains isolated from Turkish traditional yogurts, and to compare them with industrial strains. Through whole-genome sequencing and advanced bioinformatics analyses, we revealed distinct phylogenetic patterns and genetic features that differentiate these traditional strains from industrial isolates. The genomes (1.68-1.86 Mb) exhibited high genetic homogeneity (ANI > 98.69%) while maintaining significant functional diversity. Pan-genome analysis identified 1160 core genes and 5694 accessory genes, highlighting substantial genomic plasticity that enables niche adaptation. Our analysis uncovered several distinctive features: (1) unique phylogenetic clustering patterns based on both housekeeping genes and whole-genome SNPs, suggesting geographical isolation effects; (2) an extensive repertoire of carbohydrate-active enzymes (CAZymes), comprising 111 Glycoside Hydrolases, 227 Glycosyl Transferases, and 44 Carbohydrate Esterases and 13 Carbohydrate-Binding Modules, demonstrating sophisticated carbohydrate metabolism adaptation significantly enriched compared to industrial strains; (3) widespread GABA biosynthesis pathways in 8 strains, including complete gadB gene, indicating potential health-promoting properties; (4) multiple genomic islands containing genes for galactose utilization and stress response, suggesting specific adaptation to traditional fermentation environments; (5) diverse exopolysaccharide biosynthesis and bacteriocin gene clusters; and (6) widespread CRISPR-Cas systems with variable spacer content. Notably, we identified vanY glycopeptide resistance genes across all strains, with two strains additionally harboring vanT. These results reveal the genetic mechanisms behind S. thermophilus adaptation to traditional yogurt environments, offering valuable insights for developing starter cultures and preserving the unique qualities and potential health benefits of traditional dairy products.

Phenotypic and Genomic Insights into Schleiferilactobacillus harbinensis WU01, a Candidate Probiotic with Broad-Spectrum Antimicrobial Activity Against ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter) Pathogens

The increasing prevalence of multidrug-resistant (MDR) pathogens, particularly ESKAPE bacteria, necessitates alternative antimicrobial strategies. Probiotics, particularly lactic acid bacteria, protect against pathogenic infections. This study aimed to characterize Schleiferilactobacillus harbinensis WU01, isolated from fermented palm sap, and evaluate its probiotic potential and antimicrobial activity. Its probiotic characteristics were assessed based on low-pH and bile tolerance, auto-aggregation, hydrophobicity, and adhesion to Caco-2 cells. Antimicrobial activity against ESKAPE pathogens was evaluated using the agar well diffusion assay. Whole-genome sequencing (WGS) and in silico analysis were performed to identify bacteriocin-related genes, virulence factors, and antibiotic-resistance genes. WU01 exhibited a strong tolerance to gastrointestinal conditions, with high survival rates under acidic and bile-salt environments. S. harbinensis WU01 demonstrated significant auto-aggregation, high hydrophobicity, and strong adhesion to Caco-2 cells. Antimicrobial assays revealed inhibitory activity against MDR ESKAPE pathogens, which correlated with the presence of bacteriocin-related genes, including those homologous to Carnocin_CP52. Molecular dynamics (MDs) simulations confirmed the interaction of Carnocin_CP52 with bacterial membranes, suggesting a mechanism for pathogen disruption. WGS confirmed the absence of virulence and antimicrobial-resistance genes, confirming its safety for probiotic applications. These findings suggest that S. harbinensis WU01 possesses probiotic properties and antimicrobial activity against ESKAPE pathogens. The combined results highlight its potential application in functional foods and therapeutic interventions.

Inoculum of Endophytic Bacillus spp. Stimulates Growth of Ex Vitro Acclimatised Apple Plantlets

In vitro shoot culture and cryopreservation (CP) are techniques essential for the ex situ preservation of genetic resources and the production of plant propagation material of clonally propagated horticultural crops. Changes in plant-associated microbiota diversity and composition induced by in vitro cultivation and CP treatment could have a negative effect on the growth and ex vitro adaptation of the in vitro propagated shoots. Therefore, the aim of the present study was to assess changes in endophytic bacteria diversity in domestic apple tissues induced by in vitro cultivation and CP treatment and to investigate the potential of the bacterial inoculum to improve the rooting and ex vitro acclimatisation of the propagated shoots. Metataxonomic analysis revealed a variation in the endophytic bacteria diversity and taxonomic composition between the field-grown tree dormant bud and the in vitro propagated or CP-treated shoot samples of apple cv. Gala. Whereas Sphingobacteriaceae, Sphingomonadaceae, Pseudomonadaceae, and Beijerinckiaceae families were the most prevalent families in the bud samples, Enterobacteriaceae, Bacillaceae, and Lactobacillaceae were dominant in the in vitro shoots. The bacterial inoculum effect on rooting and ex vitro acclimatisation was assessed using four isolates selected by screening the endophytic isolate collection. Bacillus sp. L3.4, B. toyonensis Nt18, or a combined inoculum resulted in a 21%, 36%, and 59% increase in cumulative root length and a 41%, 46%, and 35% increase in the biomass accumulation of ex vitro acclimatised plantlets, respectively. Root zone microbiota functional diversity analysis implied that growth stimulation was not related to improved nutrient uptake but could involve a pathogen-suppressing effect. The results demonstrate that the application of plant growth-promoting bacteria can potentially improve the performance of the in vitro propagated germplasm.

De novo transcriptome assembly of the plant Helianthemum marifolium for the study of adaptive mechanisms

The genus Helianthemum, commonly known as rockroses, encompasses 140 species primarily distributed in the Palearctic region, with notable diversification driven by climatic and geological changes. These plants are valuable for studying speciation processes and ecological divergence. The chemical properties of the leaves have also been investigated for containing valuable bioactive compounds with several therapeutic properties. However, the availability of genomic resources for species in this genus are almost entirely lacking. Here, we assembled and annotated the first reference transcriptome of Helianthemum marifolium, a species with wide morphological variability and infraspecific diversity. Illumina paired-end RNA sequences were generated using leaves from 16 individuals, representing the four recognized subspecies, all cultivated in a greenhouse. RNA reads were assembled with Trinity and Oases, and EvidentialGene produced a transcriptome with 122,002 transcripts. The transcriptome showed 59524 hits on the UniProtBK database through BLASTx. This transcriptome will be an invaluable resource for transcriptome-level population studies, conservation genetics of the many endangered species within the genus, and for deepen into the metabolic pathways of leaf-derived compounds.

Isolation, characterization, and genomic analysis of three novel Herelleviridae family lytic bacteriophages against uropathogenic isolates of Staphylococcus saprophyticus

BACKGROUND

Staphylococcus saprophyticus (S. saprophyticus) is the second most prevalent etiological agent of urinary tract infections (UTIs) in young women. However, there is a paucity of data regarding its bacteriophage (phage). Therefore, this study was conducted to isolate and identify new lytic phages from municipal wastewater with the objective of increasing knowledge about phages and their genomes.

METHODS

A total of 11 clinical isolates of S. saprophyticus and 30 wastewater samples were used to isolate three lytic phages (vB_SsapH-Golestan-100, vB_SsapH-Golestan101-M, and vB_SsapH-Golestan-105-M). The morphology, behavioral characteristics, and complete DNA genomes of these phages were analyzed.

RESULTS

The microscopic images of the phages revealed that the sizes of their heads and tail lengths fell within the ranges of 90-111 nm and 234-266 nm, respectively. All phages exhibited high adsorption rates (99.5% in 15 min) and burst sizes (150-210 PFU per infected cell), with a potential for a narrow host range. Genomic analysis of Staphylococcus phages indicated a size of 136,433 base pairs (bp) with a guanine-cytosine (GC) content of 33.7% and 192 open reading frames (ORFs) for vB_SsapH-Golestan-100, 144,081 bp with a GC content of 29.6% and 205 ORFs for vB_SsapH-Golestan101-M, and 142,199 bp with a GC content of 30.6% and 203 ORFs for vB_SsapH-Golestan-105-M. A bioinformatics analysis indicated that all three phages belong to the Twortvirinae subfamily of Herelleviridae. Among the three phages, vB_SsapH-Golestan-100 exhibited the least similarity to previously known phages, with less than 21% similarity with its closest counterparts in genomic databases.

CONCLUSIONS

This study identified new phages that have the ability to destroy a broad range of S. saprophyticus isolates and may potentially be classified as a new genus and species within the Herelleviridae family in future studies.

High-quality genome assembly of the azooxanthellate coral Tubastraea coccinea (Lesson, 1829)

Coral reefs are among the most biodiverse and economically significant ecosystems globally, yet they are increasingly degrading due to global climate change and local human activities. The sun coral Tubastraea coccinea (T. coccinea) an obligate heterotroph lacking symbiotic zooxanthellae, exhibits remarkable tolerance to conditions that cause bleaching and mortality in zooxanthellate species. With its extensive low-latitude distribution across multiple oceans, T. coccinea has become a highly invasive species, adversely impacting native species, degrading local ecosystems, and causing significant socio-economic challenges that demand effective management. Despite substantial research efforts, the molecular biology of T. coccinea remains insufficiently characterized. To address this gap, we generated a draft genome assembly for T. coccinea using PacBio Hi-Fi long-read sequencing. The assembly spans 875.9 Mb with a scaffold N50 of 694.3 kb and demonstrates high completeness, with a BUSCO score of 97.4%. A total of 37,307 protein-coding sequences were identified, 95.2% of which were functionally annotated through comparisons with established protein databases. This reference genome provides a valuable resource for understanding the genetic structure of T. coccinea, advancing research into its adaptive mechanism to environmental changes, and informing conservation and management strategies to mitigate its invasive impact.

Chromosome-scale genome assembly of Trigonella corniculata (L.)L. (Nagauri pan /Kasuri methi), an important spice

Trigonella corniculata (L) L. or Nagauri pan /Kasuri methi, is an important spice crop with high nutraceutical potential. We report the de novo chromosome-scale assembly of T. corniculata genome using high coverage PacBio, Illumina and Hi-C reads. The assembly spans 798 Mb (Megabases) in 282 scaffolds with a scaffold N50 of 99.6 Mb. More than 98% of the sequence length is captured in eight different pseudomolecules with an average length of 98 Mb. A BUSCO score of over 97% is suggestive of the high degree of completeness and contiguity of the genome. A total of 64,801 protein-coding genes are predicted. Genome-wide Simple Sequence Repeats (99,149) have been identified and wet lab validated at forty-eight loci. The chromosome-scale genome assembly of T. corniculata and the SSR markers identified in this study will provide a strong foundation for future structural and functional genomics studies in T. corniculata and other fenugreek species.

Comprehensive genome analysis of Streptomyces caeruleatus S14 isolated from rice rhizosphere

Rice blast, caused by Magnaporthe oryzae, is one of the most devastating diseases affecting rice crops. We investigated effectiveness of Streptomyces spp. against M. oryzae. The results revealed that among the Streptomyces spp., Streptomyces caeruleatus strain S14 demonstrated superior effectiveness in inhibiting the mycelial growth of M. oryzae (74.7%). The strain was identified by sequencing 16S rRNA region. Further, the complete genome sequence of this highly effective strain was acquired using the Illumina NovaSeq 6000 (PE 150), revealing a total genome length of 9,750,804 base pairs (9.7 Mb). The genome comprises 9,191 protein-coding sequences (CDS), 68 transfer RNA (tRNA) genes, 6 ribosomal RNA (rRNA) genes, with an average G+C content of 71.03%. The Streptomyces caeruleatus S14 genome, annotated with RASTtk and genetic code 11, falls under the superkingdom Bacteria. According to annotation statistics from PATRIC, it is a high-quality genome with 97.9% coarse consistency, 93.7% fine consistency, and completeness of 99.9%. The genome included genes related to metabolism, protein processing, defense, virulence, energy, stress response, membrane transport, regulation, cell signaling, cell envelope, DNA processing, cellular activities, RNA processing, and miscellaneous. The complete genome sequence of S. caeruleatus suggests that it offers valuable insights into its antimicrobial activity and provide key genetic traits responsible for pathogen suppression. Incidentally this is the first whole genome sequencing report of S. caeruleatus isolated from rice rhizosphere soil in India.

Do Organic Amendments Foster Only Beneficial Bacteria in Agroecosystems?: The Case of Bacillus paranthracis TSO55

Bacterial strain TSO55 was isolated from a commercial field of wheat (Triticum turgidum L. subsp. durum), under organic amendments, located in the Yaqui Valley, Mexico. Morphological and microscopical characterization showed off-white irregular colonies and Gram-positive bacillus, respectively. The draft genome sequence of this strain revealed a genomic size of 5,489,151 bp, with a G + C content of 35.21%, N50 value of 245,934 bp, L50 value of 8, and 85 contigs. Taxonomic affiliation showed that strain TSO55 belongs to Bacillus paranthracis, reported as an emergent human pathogen. Genome annotation identified 5743 and 5587 coding DNA sequences (CDSs), respectively, highlighting genes associated with indole production, phosphate and potassium solubilization, and iron acquisition. Further in silico analysis indicated the presence of three CDSs related to pathogenicity islands and a high pathogenic potential (77%), as well as the presence of multiple gene clusters related to antibiotic resistance. The in vitro evaluation of plant growth promotion traits was negative for indole production and phosphate and potassium solubilization, and it was positive but low (18%) for siderophore production. The biosynthetic gene cluster for bacillibactin (siderophore) biosynthesis was confirmed. Antifungal bioactivity of strain TSO55 evaluated against wheat pathogenic fungi (Alternaria alternata TF17, Bipolaris sorokiniana TPQ3, and Fusarium incarnatum TF14) showed minimal fungal inhibition. An antibiotic susceptibility assay indicated resistance to three of the six antibiotics evaluated, up to a concentration of 20 µg/mL. The beta hemolysis result on blood agar reinforced TSO55's pathogenic potential. Inoculation of B. paranthracis TSO55 on wheat seedlings resulted in a significant decrease in root length (-8.4%), total plant height (-4.2%), root dry weight (-18.6%), stem dry weight (-11.1%), and total plant dry weight (-15.2%) compared to the control (uninoculated) treatment. This work highlights the importance of analyzing the microbiological safety of organic amendments before application. Comprehensive genome-based taxonomic affiliation and bioprospecting of microbial species introduced to the soil by organic agricultural practices and any microbial inoculant will prevent the introduction of dangerous species with non-beneficial traits for crops, which affect sustainability and generate potential health risks for plants and humans.

Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius

Crucian carp (Carassius carassius), a member of the carp family (Cyprinidae), is known for its remarkable anoxia tolerance. The physiological responses and adaptations to anoxia are well documented, but there is a need for better understanding of the molecular regulation and evolutionary mechanisms behind these adaptations. Here we present a high-quality, functionally annotated, chromosome-level genome assembly that can facilitate such further studies. Genomic DNA was obtained from a wild-caught crucian carp specimen and used for PacBio long-read, Illumina short-read and Hi-C sequencing. Short-read mRNA data were used for structural annotation using the BRAKER3 pipeline, while PacBio long-read RNA sequencing data were used for annotation of untranslated regions and refinement of gene-isoform relationships, using the PASA pipeline. The full assembly had a contig-level N50 of 15Mbp in 290 scaffolds and 98.6% of the total length (1.65Gbp) placed in 50 chromosomes. Structural annotation resulted in 82,557 protein-coding transcripts (in 45,667 genes), with a BUSCO completeness of 99.6% and of which 77,370 matched a protein in the UniProtKB/Swiss-Prot database.

Tryptic oncopeptide secreted from the gut bacterium Cronobacter malonaticus PO3 promotes colorectal cancer

The involvement of Cronobacter, which is frequently associated with meningitis and necrotizing enterocolitis, in human colorectal cancer remains unexplored. In this study, we isolate and characterize a novel strain of C. malonaticus designated PO3 from a fecal sample of a colon cancer patient and demonstrate its proliferative effects on colorectal cancer both in vitro and in vivo. The secretome of PO3 significantly promoted cell proliferation, as evidenced by increased cell viability, fluorescence intensity, and Ki-67 expression, without inducing cell death. Furthermore, using high-resolution mass spectrometry (HRMS), we identified a novel tryptic oncopeptide designated P506, in the PO3 secretome that promotes colorectal cancer. Synthetic P506 further stimulated human colorectal adenocarcinoma cell line HT-29 cell proliferation in a dose-dependent manner. Experiments with the BALB/c mouse model in vivo revealed that both the PO3 secretome and P506 contributed to the development of colorectal polyps and associated histological changes, including dysplasia and altered colonic architecture. These findings suggest that P506, a potent peptide from the PO3 secretome, may have oncogenic potential, promoting colorectal cancer progression.

Chinese chestnut did not induce negative plant soil feedback during centuries of growth

Certain tree species can reach ages of centuries, whereas lifespan of species like apple are markedly shorter. The latter is caused by negative plant-soil feedback that results in microbiome changes. We hypothesized that tree species with a long lifespan will be able to avoid such negative feedback and their root-associated microbiomes will be similar in trees of different ages. To test this, we used Chinese chestnut (Castanea mollissima) trees, ranging from 8 to 830 years old from a Ming orchard at the Great Wall. Their root-associated microbiomes were analysed by using meta-amplicon sequencing analysis. Their root-associated bacterial microbiomes were rather similar although based on linear regression models we cannot exclude that age has a weak correlation with microbiome compositions. When chestnut seedlings were grown for 3 months in soil associated with young or old trees, the plants were healthy and their growth was similar. This strongly supported that negative feedback had not occurred. Pseudomonas OTU1, a member of the core microbiome and representing >50 % of the rhizosphere community, strongly inhibited growth of chestnut pathogens and stimulated plant growth. Such properties of the microbiome, in combination with a high number of resistance genes can contribute to longevity of chestnut.

A multi-omics reciprocal analysis for characterization of bacterial metabolism

Introduction

Exploiting microbial natural products is a key pursuit of the bioactive compound discovery field. Recent advances in modern analytical techniques have increased the volume of microbial genomes and their encoded biosynthetic products measured by mass spectrometry-based metabolomics. However, connecting multi-omics data to uncover metabolic processes of interest is still challenging. This results in a large portion of genes and metabolites remaining unannotated. Further exacerbating the annotation challenge, databases and tools for annotation and omics integration are scattered, requiring complex computations to annotate and integrate omics datasets.

Methods

Here we performed a two-way integrative analysis combining genomics and metabolomics data to describe a new approach to characterize the marine bacterial isolate BRA006 and to explore its biosynthetic gene cluster (BGC) content as well as the bioactive compounds detected by metabolomics.

Results and Discussion

We described BRA006 genomic content and structure by comparing Illumina and Oxford Nanopore MinION sequencing approaches. Digital DNA:DNA hybridization (dDDH) taxonomically assigned BRA006 as a potential new species of the Micromonospora genus. Starting from LC-ESI(+)-HRMS/MS data, and mapping the annotated enzymes and metabolites belonging to the same pathways, our integrative analysis allowed us to correlate the compound Brevianamide F to a new BGC, previously assigned to other function.

Subclinical Mastitis Related to Streptococcus canis Infection in Dairy Cattle

In the present study, we isolated S. canis from milk samples in a dairy farm with suspicions of subclinical mastitis. Milk samples testing positive on California Mastitis Test (CMT) were collected from different cows for bacteriological and genomic analyses to identify the causative pathogen, and somatic cell counts (SCC) were determined. A multiplex qPCR assay was conducted to detect 15 potential pathogens, and all samples showed negative results. Conventional bacteriology procedures were performed; DNA of the bacterial strains was extracted, sequenced, and submitted to bioinformatic analysis. Three CMT positive milk samples showed SCC > 200 × 103 cell/mL. However, these same three samples were positive for bacteria phenotypically identified as Streptococci, and the strains were confirmed as S. canis using MS MALDI-TOF methodology. In susceptibility testing, resistance against tetracycline was detected, revealing a potential chronic infection in one cow, while the presence of the same bacteria was observed in two other cows. Genomic DNA from four S. canis isolates, obtained in the first and second sampling, was sequenced. Genetic relationships revealed a unique sequence type (ST24). The gene (tetM) related with resistance to TE was highlighted. Although the association between S. canis and mastitis is not routinely detected, early diagnosis of bacterial infections and the study of the antimicrobial profile are crucial for effective therapy. Pets could act as a potential reservoir, so improving hygienic conditions is needed to prevent new infections.

Staphylococcus aureus ST764-SCCmecII high-risk clone in bloodstream infections revealed through national genomic surveillance integrating clinical data

Antimicrobial resistance is a global health concern, and methicillin-resistant Staphylococcus aureus (MRSA) is one of the highest-priority organisms exhibiting this phenotype. Here, we performed a national surveillance integrating patient clinical data of S. aureus isolated from bloodstream infections. We performed genome sequencing, standardized antimicrobial susceptibility testing, and collected clinical metadata of 580 S. aureus isolates collected during 2019-2020. We focused on three predominant clonal complexes (CC1, CC5, and CC8) and assesses their microbiological and clinical significance, as well as their distribution across eastern and western Japan. Furthermore, we conducted a genomic comparison of the isolates of 2019-2000 with those of 1994-2000 and investigated the evolutionary trajectory of emerging clones from the three dominant clonal complexes. We revealed that the emerging MRSA ST764-SCCmecII showed the highest mortality rate within 30 days of hospitalization. This high-risk clone diverged from the New York/Japan clone (ST5-SCCmecII), which was inferred to have undergone repeated infections with phages carrying superantigen toxin genes and acquired antimicrobial resistance genes via mobile genetic elements, leading to its emergence around 1994. Overall, we provide a blueprint for a national genomic surveillance study that integrates clinical data and enables the identification and evolutionary characterization of a high-risk clone.

AI-2 Signaling: A Potential Driver of Bacteremia in Non-Typhoidal Salmonella Infections

Introduction

Non-typhoidal Salmonella (NTS) infections typically present as localized inflammation near the intestinal mucosal epithelium. However, some NTS strains can breach the intestinal barrier and enter the bloodstream, leading to bacteremia and severe systemic infections. The mechanisms by which NTS invades the bloodstream remain unclear.

Methods

In this study, we isolated 36 NTS strains from patients with diarrhea and bacteremia at First Affiliated Hospital of Huzhou University. Strains represented two distinct clinical manifestations, and were subjected to whole-genome sequencing, comparative genomics, and genetic differentiation analysis to identify genes potentially involved in bloodstream invasion. Additionally, we conducted inhibition assays using quercetin, a chemical inhibitor of the identified gene pathways, to validate our findings.

Results

Our analysis revealed that genes distinguishing the bloodstream Salmonella isolates from the fecal Salmonella isolates were primarily involved in the AI-2 quorum sensing pathway and biofilm-associated protein transport. Subsequent biofilm formation assays demonstrated that the bloodstream isolates exhibited significantly higher biofilm formation capacity compared to the fecal isolates. Upon the addition of quercetin, biofilm formation was equally inhibited in both groups. Collectively, these findings suggest that genes involved in the AI-2 pathway and biofilm-associated protein transport may be key factors contributing to the development of bacteremia in NTS infections.

Bumble bee gut microbial community structure differs between species and commercial suppliers, but metabolic potential remains largely consistent

Bumble bees are key pollinators for natural and agricultural plant communities. Their health and performance are supported by a core gut microbiota composed of a few bacterial taxa. However, the taxonomic composition and community structure of bumble bee gut microbiotas can vary with bee species, environment, and origin (i.e., whether colonies come from the wild or a commercial rearing facility), and it is unclear whether metabolic capabilities therefore vary as well. Here we used metagenomic sequencing to examine gut microbiota community composition, structure, and metabolic potential across bumble bees from two different commercial Bombus impatiens suppliers, wild B. impatiens, and three other wild bumble bee species sampled from sites within the native range of all four species. We found that the community structure of gut microbiotas varied between bumble bee species, between populations from different origins within species, and between commercial suppliers. Notably, we found that Apibacter is consistently present in some wild bumble bee species-suggesting it may be a previously unrecognized core phylotype of bumble bees-and that commercial B. impatiens colonies can lack core phylotypes consistently found in wild populations. However, despite variation in community structure, the high-level metabolic potential of gut microbiotas was largely consistent across all hosts, including for metabolic capabilities related to host performance, though metabolic activity remains to be investigated.IMPORTANCEOur study is the first to compare genome-level taxonomic structure and metabolic potential of whole bumble bee gut microbiotas between commercial suppliers and between commercial and wild populations. In addition, we profiled the full gut microbiotas of three wild bumble bee species for the first time. Overall, our results provide new insight into bumble bee gut microbiota community structure and function and will help researchers evaluate how well studies conducted in one bumble bee population will translate to other populations and species. Research on taxonomic and metabolic variation in bumble bee gut microbiotas across species and origins is of increasing relevance as we continue to discover new ways that social bee gut microbiotas influence host health, and as some bumble bee species decline in range and abundance.

The research on the identification, taxonomy, and comparative genomics analysis of nine Bacillus velezensis strains significantly contributes to microbiology, genetics, bioinformatics, and biotechnology

Introduction

Next-generation sequencing (NGS) has played a pivotal role in the advancement of taxonomics, allowing for the accurate identification, differentiation, and reclassification of several bacteria species. Bacillus velezensis is a Gram-positive, facultatively aerobic, spore-forming bacterium known for its antimicrobial and antifungal properties. Strains of this species are highly relevant in agriculture, biotechnology, the food industry, and biomedicine.

Methods

In this study, we characterized the genomes of nine Bacillus strains isolated from soil in the state of Bahia (Brazil) using NGS with Illumina platform. Identification was performed by Average Nucleotide Identity (ANI) and digital DNA-DNA hybridization (dDDH) analyses, which revealed a match between the genomic information of the isolates and B. velezensis NRRL B-41580, with a variation of 89.3% to 91.8% by dDDH in TYGS and 95% to 98.04% by ANI in GTDBtk.

Results and discussion

Two strains, BAC144 and BAC1273, exhibited high similarity to B. amyloliquefaciens subsp. plantarum FZB42. However, the latter strain was subsequently reclassified as B. velezensis. The division pattern observed during identification was confirmed in the phylogenomic analysis, where BAC144 and BAC1273 clustered with Bacillus amyloliquefaciens subsp. plantarum, while the other strains clustered with B. velezensis NRRL B-41580, forming a clade with high genetic similarity, with a bootstrap value of 100%. Furthermore, a synteny analysis demonstrated greater conservation among the strains from this study compared to the reference strain, with the formation of distinct collinear groups. The pangenome analysis revealed an open pangenome, highlighting the genetic diversity within the species. Based on this analysis, a functional annotation was performed to compare exclusive gene repertoires across groups, uncovering distinct adaptations and functional profiles. The identification of bacterial strains belonging to this species is of great importance due to their high applicability. The strains identified in this study underscore the need for more robust taxonomic technologies to accurately classify prokaryotes, which are subject to constant evolutionary changes, requiring the reclassification of several species within the genus Bacillus, many of which are heterotypic synonyms of B. velezensis like Bacillus oryzicola, B. amyloliquefaciens subsp. plantarum and Bacillus methylotrophicus.

A chromosome-level genome assembly of the European green toad (Bufotes viridis)

The European green toad (Bufotes viridis) is geographically widely distributed. While the species global conservation status is labeled as of least concern by the IUCN, it is declining in many parts of its range where populations are fragmented and isolated. A high-quality reference genome is an important resource for conservation genomic researchers who are trying to understand and interpret the genomic signals of population decline, inbreeding, and the accumulation of deleterious mutations. Here, we assembled and annotated a chromosome-level reference genome for B. viridis as part of the European Reference Genome Atlas pilot project. The genome assembly, with a size of ∼3.89 Gb consists of 11 chromosomes and an additional 2,096 unplaced scaffolds. The final assembly had a scaffold N50 value of 478.39 Mb and covered 90.4% single copy tetrapod orthologs, and 46.7% repetitive elements. Finally, a total of 23,830 protein-coding genes matching a known gene, together with 56,974 mRNAs were predicted. This high-quality reference genome will benefit amphibian evolutionary genomics research and enable conservation genetic studies to inform practical conservation work on this species.

Diets shape thermal responses in Chinese giant salamanders by altering liver metabolism

Diet can influence the thermal performance of ectotherms, providing potential strategies for biological conservation in the context of global warming. The endangered Andrias davidianus is susceptible to heat stress due to energy deficiency in the liver when fed a worm-based diet rich in carbohydrates. A fish-based diet, rich in protein and lipids, improves their thermal performance, but the underlying physiological mechanisms remain unclear. In this study, we used metabolomics and metagenomics to examine the combined effects of temperature (15, 20, and 25°C) and diet (fish-based and worm-based) on liver metabolism and gut microbiota. Our results show that both temperature and diet shape liver metabolism, with several vital metabolic pathways (e.g., TCA cycle and sulfate metabolism) regulated by their combined effects. Notably, diet-dependent thermal responses in energy metabolism were observed, with fish-fed salamanders exhibiting a marked upregulation of the TCA cycle intermediates under heat stress, a response absent in worm-fed individuals. Given the role of TCA cycle in heat susceptibility of A. davidianus, these findings suggest that the TCA cycle likely mediates the interactive effects of temperature and diet on thermal performance. We then examined whether the gut microbiota is also a target of interactive effects or a mediator of the diet's influence on liver metabolism. While both temperature and diet shape microbiota composition, functional shifts occur only in response to temperature, indicating that the microbiota is not a major link between diet and liver metabolism. However, several bacterial groups (e.g., Thiosulfatimonas and Alcanivorax), jointly regulated by temperature and diet, correlate with liver metabolites, suggesting alternative, function-independent pathways through which dietary-related microbial changes may influence liver metabolism and even thermal tolerance. Overall, this study provides molecular insights into the dietary modulation of thermal performance in A. davidianus and highlight the potential of dietary microbial management strategies for amphibian conservation.

Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly

The guppy Y Chromosome has been a paradigmatic model for studying the genetics of sex-linked traits and Y Chromosome-driven evolution for more than a century. Despite strong efforts, knowledge on genomic organization and molecular differentiation of the sex chromosome pair remains unsatisfactory and partly contradictory with respect to regions of reduced recombination. Especially the border between pseudoautosomal and male-specific regions of the Y has not been defined so far. To circumvent the problems in assigning the repeat-rich differentiated hemizygous or heterozygous sequences of the sex chromosome pair, we sequenced a YY male generated by a cross of a sex-reversed Maculatus strain XY female to a normal XY male from the inbred Guanapo population. High-molecular-weight genomic DNA from the YY male was sequenced on the Pacific Biosciences platform, and both Y haplotypes were reconstructed by Trio binning. By mapping of male specific SNPs and RADseq sequences, we identify a single male specific-region of ∼5 Mb length at the distal end of the Y (MSY). Sequence divergence between X and Y in the segment is on average five times higher than in the proximal part in agreement with reduced recombination. The MSY is enriched for repeats and transposons but does not differ in the content of coding genes from the X, indicating that genic degeneration has not progressed to a measurable degree.

Reference genome of Calochortus tolmiei Hook. & Arn. (Liliaceae), a cat's ear mariposa lily

Calochortus tolmiei Hook. & Arn., a bulbous monocot with cat's ear flowers in the angiosperm family Liliaceae, is a perennial herb native to northern California, Oregon, and Washington. Calochortus exhibits substantial morphological and karyotype diversity with multiple floral forms and a haploid chromosome number varying from 6 to 10. Here, we present the first high-quality reference assembly in Liliaceae for C. tolmiei, with a scaffolded assembly of 2.9 Gb with an N50 of 296 Mb. Notably, 92% of the assembled genome is scaffolded into 10 pseudomolecules, matching the documented chromosome count of C. tolmiei. The genome contains 31,049 protein-coding genes, with 86.2% being functionally annotated. The closest reference-quality genome assembly to C. tolmiei is from Chionographis japonica (Willd.) Maxim. (Melianthiaceae), which diverged ∼83 Mya, providing a valuable genomic resource in the Liliales, an order which lacks genomic resources.

A rapid detection of Avian Pathogenic Escherichia coli (APEC) strains based on minimal number of virulence markers identified by whole genome sequencing

BACKGROUND

Colibacillosis is an important epidemiological and economic issue in poultry farming and breeding. A common problem with avian pathogenic Escherichia coli strains (APEC) that cause this disease is a lack of an uniform identification system, resulting from a variety of serotypes, phylogenetic groups, sequence types and combinations of virulence factors. There are no clearly defined features that can be associated with pathogenicity. Therefore, without precise identification of pathogenic strains and differentiation from commensal strains, there is no possibility of appropriate selection of targeted therapy. The widespread use of whole genome sequencing (WGS) in recent years creates new possibilities in diagnostics. Therefore, the purpose of this study was to select features defining the APEC pathotype, based on next generation sequencing (NGS), and design a diagnostic test based on selected factors.

RESULTS

A PCR diagnostic test is proposed. Three predictors of virulence were chosen according to in silico analysis: two virulence genes: iroC and hlyF, as well as one molecular marker of O78 serotype (wzx-O-antigen flippase of the O78 serotype). A choice of markers was supported by a chicken embryo model.

CONCLUSIONS

Whole genome sequencing of E. coli genomes allowed for the development of a rapid diagnostic method identifying pathogenic strains for poultry: APEC. The developed test can support field observations connected with the strain isolation source and clinical symptoms of the disease.

Towards unraveling antimicrobial resistance dynamics: a longitudinal exploration of rectal swab metagenomes

The increasing prevalence of antimicrobial resistance (AMR) poses significant challenges in clinical settings. In particular, early screening and detection of colonization by multidrug-resistant organisms (MDROs) in patients at admission is crucial. In this context, the clinical use of metagenomics (mNGS) holds promise for fast and untargeted diagnostic methods. Here, we aimed to evaluate the long-term stability of the rectal microbiome and the diagnostic accuracy of mNGS in comparison to culture and whole-genome sequencing (WGS) of MDROs. We analyzed rectal swabs from 26 patients with two consecutive admissions over a four-year period. The detected antimicrobial resistance genes and assembled metagenomes were compared to those obtained via classical culture-based antimicrobial susceptibility testing and WGS of isolated MDROs. Our results showed that the rectal microbiome is variable during the two timepoints, highlighting the variability in the niche. Nevertheless, we also observed strong co-occurrence of taxa, suggesting that the rectal swab microbiome is also a regulated environment with cooperative biotic interactions. In total, we isolated and sequenced 6 MDROs from 6 patients at individual timepoints. Almost all AMR genes from the genomes of the isolates (median: 100%, range: 84.6-100%) could be detected by mNGS of the rectal swabs at the time of isolation of the MDRO but not at the time of culture negativity. In addition, we detected AMR genes and potentially pathogenic species in patients with negative cultures. In conclusion, our study showed that, in principle, mNGS of rectal swabs can detect clinically relevant AMR profiles. However, the cooccurrence of AMR genes and potentially-pathogenic species does not always correlate with culture-based diagnostic results but rather indicates a potential risk of horizontal AMR gene transfer. However, it is unclear whether the observed discrepancies are due to transient or locally confined colonization of MDROs, limits of detection, or variability of the sampling method and specimens.

Dissecting Metabolic Functions and Sugar Transporters Using Genome and Transportome of Probiotic Limosilactobacillus fermentum KUB-D18

Background/Objectives:Limosilactobacillus fermentum KUB-D18, a heterofermentative lactic acid bacterium with promising probiotic properties, is known for promoting gut health and nutrient absorption. Originally isolated from chicken intestines, this strain demonstrates versatile metabolic capabilities in diverse gastrointestinal environments. However, the metabolic functions and sugar transport-related genes remain largely unexplored. This study thus aimed to dissect metabolic functions and sugar transports of L. fermentum KUB-D18. Methods: Next-generation and third-generation sequencing techniques using integrative genomic platform towards transportome analysis were performed. Results: The complete genome, sized at 2.12 Mbps with a GC content of 51.36%, revealed 2079 protein-encoding genes, of which 1876 protein functions were annotated and identified in top categories involved in amino acids, nucleotide, energy, and carbohydrate transports and metabolisms. Comparative genes analysis identified 50 core and 12 strain-specific genes linked to probiotic properties, e.g., acid resistances and bile tolerances, antioxidant functions, or anti-inflammatory properties. Further, sugar transportome analysis uncovered 57 transporter genes, demonstrating diverse carbon utilization and phosphotransferase (PTS) systems, corroborated by API 50 CHL test results for carbohydrate metabolism profile. Conclusions: These findings enhance the comprehensive metabolic understanding of L. fermentum KUB-D18, supporting its industrial potential and applications in engineered probiotics.

Chloroplast Genome of Arisaema takesimense: Comparative Genomics and Phylogenetic Insights into the Arisaema

Arisaema takesimense (Araceae) is a unique species found exclusively in Ulleung Island of Korea. This study presents the complete chloroplast (cp.) genome of A. takesimense, which comprises 174, 361 base pairs and exhibits a typical tetrad structure. The genome encodes 112 unique genes, including 78 protein-coding genes (CDS), 30 tRNA genes, and 4 rRNA genes. In this study, a total of 49 long repeats and 139 simple sequence repeats (SSRs) were identified, predominantly located in intergenic spacer regions (IGS). Additionally, several hotspot regions, including trnS-G, accD-psaI, ndhF and rps15-ycf1, were identified, which are commonly shared among Araceae species. The analysis of these repeats revealed species-specific SSR types and hotspot regions that can be utilized for population genetic studies and species identification. A comparative genomic analysis of eleven Arisaema taxa revealed that the large single copy region (LSC) exhibits the most variability, with non-coding genes displaying more variation than coding genes. The borders between the LSC-IR-SSC regions in Arisaema taxa were generally well-preserved, and there were notable exceptions in the positions of LSC/IRa, LSC/IRb and SSC/IRb junctions for A. takesimense, A. ringens, and A. nepenthoides. A phylogenetic analysis based on the cp. genome revealed a close relationship between A. takesimense and A. bockii. The outcomes of this study substantially increase the genomic resources available for Araceae, serving as a valuable resource for species identification and evaluating intraspecific diversity within the Arisaema genus.

Co-occurrence of qacEΔ1 disinfectant resistance gene and ARGs among Salmonella Indiana and its correlation with resistance to sodium hypochlorite

Sodium hypochlorite (SHC) is the most commonly utilized carcass and equipment disinfectant in the poultry industry. However, prolonged exposure to SHC can result in the development of bacterial tolerance and exert co-selection on antimicrobial resistance. This study investigated the co-resistance to SHC and multiple antimicrobial agents among Salmonella enterica serovar Indiana (S. Indiana), with a specific focus on the co-occurrence of disinfectant resistance gene qacEΔ1 and the antimicrobial resistance genes (ARGs) revealed by whole genome sequencing (WGS). Additionally, the study examined the transcriptional response of qacEΔ1 and its closely associated ARGs under SHC pressure. Moreover, the study determined the optimal SHC concentration for the decontamination of multidrug-resistant (MDR) S. Indiana on chicken. The results indicated that S. Indiana exhibited a resistance rate of 73.31 % to SHC, and varying levels of resistance to 13 antimicrobial agents. Furthermore, the analysis revealed a significant correlation between the qacEΔ1 gene and ARGs, including catB3, sul1, arr-3 and blaOXA-1. The genetic contexts surrounding the qacEΔ1 gene demonstrated a high degree of homology, allowing for the categorization into 11 distinct genetic context types, among which the gene cluster aacA4-blaOXA-1-catB3-arr-3-qacEΔ1-sul1 was the most prevalent. Further analysis of the MDR IndS97 strain using PacBio SMRT sequencing revealed that the qacEΔ1 gene was located on plasmid pLKQY01, with IS26 and ISRle7 positioned at the flanks of the composite transposon aacA4-blaOXA-1-catB3-arr-3-qacEΔ1-sul1. The transcription levels of qacEΔ1, arr-3 and sul1 genes in response to SHC stress initially increased, followed by a decline as SHC concentrations rose. At an SHC concentration of 0.5 MIC, the transcription levels of these genes were notably low, and the results indicated a decontamination efficacy of 86.51 % against Salmonella contamination while relatively preserving the freshness of the chicken. This study enhanced the understanding of disinfectant effects on the antimicrobial resistance of S. Indiana and provided evidence to support the regulated use of disinfectants.

Antibiotic resistance and viral co-infection in children diagnosed with pneumonia caused by Mycoplasma pneumoniae admitted to Russian hospitals during October 2023-February 2024

BACKGROUND

Mycoplasma pneumoniae (MP) is a common bacterial respiratory infection that can cause pneumonia, particularly in children. Previously published data have highlighted the high incidence of viral co-infections and the problem of increasing macrolide resistance in MP worldwide.

AIMS

(1) to estimate the impact of viral infections circulating in a local population on the spectrum of co-infection in hospitalized children with Mycoplasma pneumoniae pneumonia (MPP), (2) to determine if there are differences in resistance mutation rate for samples from hospitals of Russia located in the European and Far East, (3) to describe genomic characteristics of MP from Russian patients during the MPP outbreaks in the fall-winter of 2023-2024.

METHODS

The carriage of viral pathogens was analyzed by real-time PCR in children with MPP from the European Part and Far East of Russian Federation and compared with the infections from two control groups. The V region of the 23S gene and the quinolone resistance-determining regions (QRDRs) of the parC and gyrA genes were sequenced to detect resistance-associated mutations in MP. Whole-genome sequencing method was used to determine the genetic relationship of a Russian MP isolate with known MP isolates.

RESULTS

The 62% of patients with MPP had a viral co-infection, with HPIV and SARS-CoV-2 predominating at 47% and 12.4%, respectively. The 15% of patients were infected with two or more viruses. In the control groups, 21% of healthy children and 43% of healthy adults were infected with Coronaviruses and Human Parainfluenza Viruses (HPIV-3 and -4), respectively. The 2063 A/G mutation of the 23S gene was found in 40.8% of patients from European Russia and in 35.7% of patients from the Far East. The result of core genes demonstrates that the sequence obtained from Russia clusters with sequences from clade 1.

CONCLUSIONS

Both HPIV and SARS-CoV-2 circulated in the population among healthy children and adults in December 2023 and they also were predominated in children with MPP. The rate of macrolide resistance was ⁓40%, which is higher than in European countries and significantly lower than in patients from Asian countries. Phylogenetic analysis showed the MP genome form Russia related to P1 type 1 (clade 1).

Metagenomic deciphers the mobility and bacterial hosts of antibiotic resistance genes under antibiotics and heavy metals co-selection pressures in constructed wetlands

Both antibiotics and heavy metals exert significant selection pressures on antibiotic-resistance genes (ARGs). This study aimed to investigate the co-selection effects of doxycycline (DC) and cadmium (Cd) on ARGs in constructed wetlands (CWs). The results demonstrated that under antibiotic and heavy metal co-selection pressures, single high concentration DC/Cd or double high, relative abundances of metagenomics assembled genomes all reached 55.1%; meanwhile, the average ratio of ARG-containing contigs located on chromosomes was 61.8% (ranging from 50.4% to 70.6%) suggesting a more stable inheritance of ARGs. Antibiotic and heavy metal co-selection in single high concentration DC/Cd or double high groups stimulate the enrichment of ARG host bacteria, which exhibited complex multiple-resistant patterns accompanied by a host-specific pattern. Additionally, the potential transfer abilities of ARGs mediated by plasmids and integrative and conjugative elements (ICEs) were enhanced under single high-concentration DC/Cd or double high stresses. Together, antibiotic and heavy metal co-selection pressures increased occurrence frequencies of ARGs, MGEs, and their combinations and altered structural communities of ARG host bacteria, increasing the risk of the spread of ARGs. This study was helpful in understanding the dissemination of ARGs and simultaneously preventing the spread of heavy metal-resistant bacteria and ARGs under antibiotic and heavy metal co-selection in small- and micro-wetlands.

A glimpse of microbial potential in metal metabolism in the Clarion-Clipperton Fracture Zone in the eastern Pacific Ocean based on metagenomic analysis

The polymetallic nodules distributed in the abyssal ocean floor are full of economic value, rich in manganese, iron, copper and rare-earth elements. Little is currently known about the diversity and the metabolic potential of microorganisms inhabiting the Clarion-Clipperton Fracture Zone (CCFZ) in eastern Pacific Ocean. In this study, the surface sediments (0-8 cm), which were divided into eight parts at 1 cm intervals were collected from the CCFZ. The microbial diversity and the metabolic potential of metal were examined by metagenomic sequencing and binning. The metal redox genes and metal transporter genes also showed a certain trend at different depths, the highest in the surface layer, about the same at 0-6 cm, and greater changes after >6 cm. 58 high- and medium metagenome-assembled genomes (MAGs) were recovered and assigned to 14 bacterial phyla and 1 archaeal phylum after dereplication. Alphaproteobacteria mainly carried out the oxidation of Fe/Mn and the reduction of Hg, Gammaproteobacteria mainly for the oxidation of Mn/Cu and the reduction of Cr/Hg and Methylomirabilota mainly for the oxidation of Mn and the reduction of As/Cr/Hg. Among the five Thermoproteota MAGs identified, only one had genes annotated for Mn oxidation, suggesting a limited but potentially significant role in this process at the bottom layer. By identifying the microbial diversity and the metabolic potential of metal in different depth, our study strengthens the understanding of metal metabolism in CCFZ and provides the foundation for further analyses of metal metabolism in such ecosystems.

A Possible More Precise Management Unit Delineation Based on Epigenomic Differentiation of a Long-Distance-Migratory Marine Fish Scomberomorus niphonius

Understanding population structure and adaptive history is critical for designing appropriate management regulations for fisheries and conserving adaptive potential for the future. However, this is not easy for marine fish, especially those with long-distance migration abilities. In this study, we constructed a high-quality reference genome for Japanese Spanish mackerel (Scomberomorus niphonius) and explored its population structure using whole genomic and epigenomic data. Despite the high depth of the sequence data, we failed to identify geographical genetic differentiation of Japanese Spanish mackerel across Chinese coastal waters. However, whole-genome bisulphite sequencing can classify this species into the Bohai-Yellow Sea group and the East China Sea-South China Sea group. Genes involved in embryonic skeletal system development, limb morphogenesis functions, and adult locomotory behaviour were differentially methylated in the southern (Zhanjiang, ZJ) and northern (Western Dalian, WDL) populations and may play important roles as drivers of population structure in Japanese Spanish mackerel. Our study not only provides the first reference genome of the Japanese Spanish mackerel and sheds light on population differentiation at the epigenomic level, but also provides a methylome-based framework for population structure analyses of marine fish with long-distance migration ability. These findings are expected to facilitate the development of scientific programmes for the successful conservation of marine fishery resources.

In Vitro and In Silico Assessment of the Probiotic and Technological Potential of Lacticaseibacillus rhamnosus MW019593 Isolated from Algerian Cow's Milk

This study evaluated the in vitro and in silico probiotic potential and technological characteristics of Lacticaseibacillus rhamnosus MW019593 isolated from Algerian cow's milk. Safety was verified by the absence of hemolytic activity, biogenic amine production, and antibiotic sensitivity. Functional probiotic properties of L. rhamnosus MW019593 included moderate inhibition of gastrointestinal pathogens such as Salmonella, Listeria, Clostridioides, and Escherichia coli, tolerance to pH 2-3 and up to 1% bile salts, 46.4% hydrophobicity, 42.4% autoaggregation, and 12.9% adhesion to Caco-2/TC7 cells without cytotoxicity. The ability to form biofilms with a thickness of 23.7 µm, comparable to L. rhamnosus ATCC 53103, was observed using confocal microscopy. Technologically, L. rhamnosus MW019593 and ATCC 53103 showed similar growth profiles and biomass yields, reaching approximately 5 × 109 CFU/mL with a 63% yield after lyophilization. No significant difference in strain viability was noted at 4 °C and - 20 °C, which are suitable temperatures to maintain their viability for 3 months. Whole genome sequencing (WGS) was conducted on L. rhamnosus MW019593, followed by comprehensive in silico genomic analysis. Taxonomic validation using average nucleotide identity (ANI) and genome-to-genome distance hybridization (GGDH) confirmed the strain's affiliation to this species. Gene screening revealed the absence of virulence and antibiotic resistance genes, while beneficial genes, including those for bacteriocin production, were identified. These findings, supported by the demonstrated safety, functional, and technological properties of the strain, highlight its promising potential for food and therapeutic applications, pending in vivo validation.

Illuminating ecology and distribution of the rare fungus Phellinidium pouzarii in the Bavarian Forest National Park

Due to their cryptic lifestyle, hidden diversity and a lack of ecological knowledge, conservation of wood-inhabiting fungi continues to be a niche interest. Molecular methods are able to provide deeper insights into the ecology of rare fungal species. We investigated the occurrence of the rare wood-inhabiting fungus Phellinidium pouzarii across the Bavarian Forest National Park in Germany using a fruit body survey, amplicon sequencing and qPCR. Additionally, we sequenced the genome of P. pouzarii and characterized the chemical substances responsible for its distinctive scent. Our approach gave matching results between amplicon sequencing and qPCRs, however, we found no evidence that P. pouzarii is more abundant in the National Park than we can assume based on fruit body inventories, underlining the species' critically endangered status. Genomics revealed P. pouzarii's repertoire of ligninolytic enzymes, pointing towards a white rot lifestyle. Two main components of P. pouzarii's distinct odour we identified (2-phenylethanol, methyl p-anisate) are known to act as insect attractants and/or to possess antimicrobial properties.

Molecular and biological characteristics of two rare bloodstream Candida isolates: Candida nonsorbophila and Candida sonorensis

BACKGROUND

The incidence of new infections caused by rare Candida species has been steadily increasing, particularly in immunocompromised patients. This study investigates two rare Candida species responsible for Candida bloodstream infections and explores their molecular characteristics.

METHODS

Clinical Candida strains were continuously isolated from the lower respiratory tract and blood specimens of a patient. Identification was performed using conventional culture techniques, ITS sequencing, and whole-genome sequencing. Additionally, antifungal susceptibility testing, phylogenetic analysis, macrophage survival assays, and in vivo survival experiments were conducted to evaluate the antifungal resistance, infection source, and pathogenicity of the isolates.

RESULTS

Molecular identification confirmed that the RP (pinkish-purple colonies from respiratory specimens), RW (pinkish-white colonies from respiratory specimens), and BP (pinkish-purple colonies from peripheral blood) strains were Candida nonsorbophila, while the BW (pinkish-white colonies from peripheral blood) strain was identified as Candida sonorensis. Phylogenetic analysis revealed that the RP strain from the lower respiratory tract and the BP strain from the bloodstream belonged to the same clonal lineage, suggesting that the pulmonary isolate entered the bloodstream, resulting in candidemia. Antifungal susceptibility testing showed that C. nonsorbophila RW strain exhibited significant resistance to fluconazole, likely due to the E70D mutation in the ERG11 gene. Both C. sonorensis and C. nonsorbophila exhibited relatively weak virulence, with no significant differences in pathogenicity between single-strain infections and mixed infections of both species (P > 0.05).

CONCLUSION

This study successfully isolated C. nonsorbophila and C. sonorensis from clinical specimens, providing detailed microbiological and molecular characterization. Rare fungal infections in immunocompromised patients require careful consideration.