OBJECTIVES: To analyse characteristics of Clostridioides difficile PCR ribotype 176 clinical isolates from Poland, the Czech Republic and Slovakia with regard to the differences in its epidemiology. METHODS: Antimicrobial susceptibility testing and whole genome sequencing were performed on a selected group of 22 clonally related isolates as determined by multilocus variable-number tandem repeat analysis (n = 509). Heterologous expression and functional analysis of the newly identified methyltransferase were performed. RESULTS: Core genome multilocus sequence typing found 10-37 allele differences. All isolates were resistant to fluoroquinolones (gyrA_p. T82I), aminoglycosides with aac(6')-Ie-aph(2'')-Ia in six isolates. Erythromycin resistance was detected in 21/22 isolates and 15 were also resistant to clindamycin with ermB gene. Fourteen isolates were resistant to rifampicin with rpoB_p. R505K or p. R505K/H502N, and five to imipenem with pbp1_p. P491L and pbp3_p. N537K. PnimBG together with nimB_p. L155I were detected in all isolates but only five were resistant to metronidazole on chocolate agar. The cfrE, vanZ1 and cat-like genes were not associated with linezolid, teicoplanin and chloramphenicol resistance, respectively. The genome comparison identified six transposons carrying antimicrobial resistance genes. The ermB gene was carried by new Tn7808, Tn6189 and Tn6218-like. The aac(6')-Ie-aph(2'')-Ia were carried by Tn6218-like and new Tn7806 together with cfrE gene. New Tn7807 carried a cat-like gene. Tn6110 and new Tn7806 contained an RlmN-type 23S rRNA methyltransferase, designated MrmA, associated with high-level macrolide resistance in isolates without ermB gene. CONCLUSIONS: Multidrug-resistant C. difficile PCR ribotype 176 isolates carry already described and unique transposons. A novel mechanism for erythromycin resistance in C. difficile was identified.

• Keywords
• Clostridioides difficile infection, epidemiology, macrolide resistance methyltransferase, whole genome sequencing,
• MeSH
• Anti-Bacterial Agents * pharmacology   MeSH
• Drug Resistance, Bacterial * MeSH
• Bacterial Proteins genetics   MeSH
• Clostridioides difficile * genetics   drug effects   isolation & purification   classification   MeSH
• Genomic Islands * MeSH
• Clostridium Infections * microbiology   epidemiology   MeSH
• Humans MeSH
• Methyltransferases genetics   MeSH
• Microbial Sensitivity Tests MeSH
• Drug Resistance, Multiple, Bacterial * genetics   MeSH
• Multilocus Sequence Typing MeSH
• Ribotyping MeSH
• Whole Genome Sequencing MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Geographicals
• Czech Republic epidemiology   MeSH
• Poland epidemiology   MeSH
• Names of Substances
• Anti-Bacterial Agents * MeSH
• Bacterial Proteins MeSH
• Methyltransferases MeSH

To identify novel genes engaged in plant epidermal development, we characterized the phenotypic variability of rosette leaf epidermis of 310 sequenced Arabidopsis thaliana accessions, focusing on trichome shape and distribution, compositional characteristics of the trichome cell wall, and histologically detectable metal ion distribution. Some of these traits correlated with cLimate parameters of our accession's locations of origin, suggesting environmental selection. A novel metal deposition pattern in stomatal guard cells was observed in some accessions. Subsequent GWAS analysis identified 1546 loci with protein sequence-altering SNPs associated with one or more traits, including 5 genes with previously reported relevant mutant phenotypes and 80 additional genes with known or predicted roles in relevant developmental and cellular processes. Some candidates, including GFS9/TT9, exhibited environmentally correlated allele distribution. Several large gene famiLies, namely DUF674, DUF784, DUF1262, DUF1985, DUF3741, cytochrome P450, receptor-Like kinases, Cys/His-rich C1 domain proteins and formins were overrepresented among the candidates for various traits, suggesting epidermal development-related functions. A possible participation of formins in guard cell metal deposition was supported by observations in available loss of function mutants. Screening of candidate gene lists against the STRING interactome database uncovered several predominantly nuclear protein interaction networks with possible novel roles in epidermal development.

• Keywords
• Arabidopsis thaliana, BioClim, GWAS, guard cell, metal accumulation, phenotypic variability, trichome,
• MeSH
• Arabidopsis * genetics   growth & development   metabolism   MeSH
• Genome-Wide Association Study * MeSH
• Plant Epidermis * genetics   metabolism   growth & development   MeSH
• Phenotype MeSH
• Polymorphism, Single Nucleotide genetics   MeSH
• Metals metabolism   MeSH
• Plant Leaves genetics   metabolism   growth & development   MeSH
• Arabidopsis Proteins genetics   metabolism   MeSH
• Genes, Plant MeSH
• Trichomes * genetics   metabolism   growth & development   MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Metals MeSH
• Arabidopsis Proteins MeSH

The genus Oswaldocruzia represents a taxonomically diverse group of nematodes with global distribution. Although Oswaldocruzia species are widespread and exhibit a remarkably wide host range in some species, their genetic diversity and biogeographic patterns remain poorly understood. This study investigated the genetic variability and distribution of Oswaldocruzia spp. in nine anuran species from the genera Bufo, Bufotes, Pelophylax, and Rana across Central Europe and the Balkans. Two species were identified: Oswaldocruzia filiformis and O. ukrainae, each exhibiting a different range of host associations. Phylogenetic analyses based on mitochondrial COI sequences revealed significant haplotype diversity in the generalist O. filiformis, with low geographic and host-associated genetic structuring. In contrast, O. ukrainae, which is closely associated with Bufotes viridis, exhibited only one genetic variant across all samples, highlighting its restricted genetic diversity. The findings emphasize contrasting genetic diversities among nematode parasites exhibiting different levels of host-specificity and expand the known distribution of O. filiformis into new regions of the Balkans. In addition, they highlight the need for additional studies on the ecological and evolutionary factors that influence the genetic diversity of parasites in amphibians.

TITLE: Aperçu de la diversité génétique et de la répartition des espèces des nématodes Oswaldocruzia (Trichostrongylida : Molineidae) en Europe : absence apparente de structuration géographique et populationnelle chez les amphibiens. ABSTRACT: Le genre Oswaldocruzia représente un groupe de nématodes taxonomiquement diversifié, réparti à l’échelle mondiale. Bien que les espèces d’Oswaldocruzia soient répandues et présentent une gamme d’hôtes remarquablement large chez certaines espèces, leur diversité génétique et leurs profils biogéographiques restent mal compris. Cette étude a examiné la variabilité génétique et la répartition des espèces d’Oswaldocruzia chez neuf espèces d’anoures des genres Bufo, Bufotes, Pelophylax et Rana en Europe centrale et dans les Balkans. Deux espèces ont été identifiées : Oswaldocruzia filiformis et O. ukrainae, chacune présentant une gamme différente d’associations d’hôtes. Les analyses phylogénétiques basées sur les séquences COI mitochondriales ont révélé une diversité d’haplotypes significative chez l’espèce généraliste O. filiformis, avec une faible structuration génétique géographique et associée à l’hôte. En revanche, O. ukrainae, étroitement associé à Bufotes viridis, ne présentait qu’une seule variante génétique dans tous les échantillons, soulignant sa diversité génétique limitée. Ces résultats mettent en évidence les diversités génétiques contrastées parmi les nématodes parasites présentant différents niveaux de spécificité d’hôte et étendent la répartition connue d’O. filiformis à de nouvelles régions des Balkans. De plus, ils soulignent la nécessité de mener des études complémentaires sur les facteurs écologiques et évolutifs qui influencent la diversité génétique des parasites des amphibiens.

• Keywords
• Amphibian Nematodes, Genetic Diversity, Host-Parasite Dynamics, Oswaldocruzia filiformis, Phylogeography,
• MeSH
• DNA, Helminth genetics   isolation & purification   MeSH
• Phylogeny MeSH
• Phylogeography MeSH
• Genetic Variation * MeSH
• Haplotypes MeSH
• Host Specificity MeSH
• Electron Transport Complex IV genetics   MeSH
• Bufonidae parasitology   MeSH
• Trichostrongyloidea * genetics   classification   isolation & purification   MeSH
• Trichostrongyloidiasis * veterinary   parasitology   epidemiology   MeSH
• Anura * parasitology   MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Geographicals
• Europe epidemiology   MeSH
• Names of Substances
• DNA, Helminth MeSH
• Electron Transport Complex IV MeSH

Macrococci are usually found as commensals on the skin and mucosa of animals and have been isolated from mammal-derived fermented foods; however, they can also act as opportunistic pathogens. Here, we used whole-genome sequencing, comparative genomics, extensive biotyping, MALDI-TOF mass spectrometry, and chemotaxonomy to characterize Macrococcus sp. strains isolated from livestock and human-related specimens. Based on the results of polyphasic taxonomy, we propose the species Macrococcus psychrotolerans sp. nov. (type strain NRL/St 95/376T = CCM 8659T = DSM 111350T) belonging to the Macrococcus caseolyticus phylogenetic clade. It grows at 4°C, and the core genome of the isolates contains suspected genes contributing to low-temperature tolerance. Variable genetic elements include prophages, chromosomal islands, a composite staphylococcal cassette chromosome island, and many plasmids that affect the overall genome expansion and adaptation to specific ecological settings of the studied isolates. Large plasmids carrying the methicillin resistance gene mecB were identified in M. psychrotolerans sp. nov. strains and confirmed as self-transmissible to Staphylococcus aureus in vitro. In addition to plasmids with circular topology, a 150-kb-long linear plasmid with 14.1-kb-long inverted terminal repeats, harboring many IS elements and putative genes for a type IV secretion system was revealed. The described strains were isolated from human clinical material, food-producing animals, meat, and a wooden cheese board and have the potential to proliferate at refrigerator temperatures. Their presence in the food chain and human infections indicates that attention needs to be paid to this potential novel opportunistic pathogen.IMPORTANCEThe study offers insights into the phenotypic and genomic features of a novel species of the genus Macrococcus that occurs in livestock, food, and humans. The large number of diverse mobile genetic elements contributes to the adaptation of macrococci to various environments. The ability of the described microorganisms to grow at refrigerator temperatures, enabled by genes that are predicted to contribute to low-temperature tolerance, raises food safety concerns. Confirmed in vitro conjugative transfer of plasmid-borne mecB gene to S. aureus poses a significant risk of spread of broad β-lactam resistance. In addition, the intergeneric plasmid transfer to S. aureus is indicative of horizontal gene transfer events that may be more frequent than generally accepted. Determining a complete sequence and gene content of linear megaplasmid with exceptional topology for the Staphylococcaceae family suggests its possible role in shuttling adaptive traits through an exchange of genetic information.

• Keywords
• Gram-positive cocci, cephalosporin resistance, cold temperature tolerance, conjugation, food safety, linear plasmid, methicillin resistance,
• MeSH
• Anti-Bacterial Agents * pharmacology   MeSH
• Bacterial Proteins * genetics   metabolism   MeSH
• beta-Lactam Resistance * genetics   MeSH
• Livestock microbiology   MeSH
• Enterococcaceae * genetics   isolation & purification   drug effects   MeSH
• Phylogeny MeSH
• Genome, Bacterial MeSH
• Humans MeSH
• Plasmids MeSH
• Gene Transfer, Horizontal MeSH
• Whole Genome Sequencing MeSH
• Staphylococcal Infections microbiology   MeSH
• Staphylococcus aureus * genetics   drug effects   MeSH
• Animals MeSH
• Check Tag
• Humans MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Anti-Bacterial Agents * MeSH
• Bacterial Proteins * MeSH

UNLABELLED: Despite continuous investigation, reasons for both the abandonment of Roman Britain around 410 CE, and the separate collapse of the Western Roman Empire in 476 CE remain unclear. Here, we use tree ring-based climate reconstructions and written documentary sources to show that a sequence of severe summer droughts from 364 to 366 CE not only contributed to prolonged harvest failures and food shortages, but also played a role in the 'Barbarian Conspiracy', a catastrophic military defeat for Roman Britain in 367 CE. In line with contemporary reports from the historian Ammianus Marcellinus, this pivotal event in pre-modern history coincided with anomalous coin hoarding, and a gradual depopulation of Roman villas and towns. Expanding our climate-conflict analysis from Roman Britain as a case study to the entire Roman Empire and the period 350-476 CE reveals clear linkages between years in which battles occurred and preceding warm and dry summers. Based on these findings, we develop a mechanistic model to explain the vulnerability of agrarian societies to climate variability, whereby prolonged droughts cause harvest failures and food shortages (dependant on societal resilience) that lead to systematic pressure, societal instability, and eventually outright conflict. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10584-025-03925-4.

• Keywords
• Barbarian Conspiracy, Climate change, Conflict, Drought, Interdisciplinary, Resilience, Roman Empire,
• Publication type
• Journal Article MeSH

BACKGROUND: Understanding the temporal variability of the microbiome is critical for translating associations of the microbiome with health and disease into clinical practice. The aim of this study is to assess the extent of temporal variability of the human urinary microbiota. A pair of urine samples were collected from study participants at 3-40-month interval. DNA was extracted and the bacterial V4 hypervariable region of the 16S rRNA gene was sequenced on the Illumina MiSeq platform. The alpha diversity of paired samples was analyzed using Chao1 and Shannon indices and PERMANOVA was used to test the factors influencing beta diversity. RESULTS: A total of 63 participants (43 men and 20 women with a mean age of 63.0 and 57.1 years, respectively) were included in the final analysis. An average of 152 ± 128 bacterial operational taxonomic units (OTUs) were identified in each urine sample from the entire cohort. There was an average of 41 ± 32 overlapping OTUs in each sample pair, accounting for 66.3 ± 29.4% of the relative abundance. There was a clear correlation between the number of overlapping OTUs and the relative abundance covered. The difference in Chao1 index between paired samples was statistically significant; the difference in Shannon index was not. Beta diversity did not differ significantly within the paired samples. Neither age nor sex of the participants influenced the variation in community composition. With a longer interval between the collections, the relative abundance covered by the overlapping OTUs changed significantly but not the number of OTUs. CONCLUSION: Our findings demonstrated that, while the relative abundance of dominant bacteria varied, repeated collections generally shared more than 60% of the bacterial community. Furthermore, we observed little variation in the alpha and beta diversity of the microbial community in human urine. These results help to understand the dynamics of human urinary microbiota and enable interpretation of future studies.

• Keywords
• 16S rRNA gene, Bacterial community, Next-generation sequencing, Stability, Urinary microbiota, Variability,
• MeSH
• Bacteria * classification   genetics   isolation & purification   MeSH
• Biodiversity MeSH
• Time Factors MeSH
• DNA, Bacterial genetics   MeSH
• Middle Aged MeSH
• Humans MeSH
• Microbiota * genetics   MeSH
• Urine * microbiology   MeSH
• Prospective Studies MeSH
• RNA, Ribosomal, 16S genetics   MeSH
• Sequence Analysis, DNA MeSH
• Check Tag
• Middle Aged MeSH
• Humans MeSH
• Male MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Observational Study MeSH
• Names of Substances
• DNA, Bacterial MeSH
• RNA, Ribosomal, 16S MeSH

The globally distributed genus Zygogonium exhibits a narrow environmental range, with 19 morphologically described species. Its molecular characterization is poor, based on a single accession of the type species Z. ericetorum from Austria. We examined the genetic variability, morphology, and ultrastructure of field-collected Zygogonium material from different sampling sites in Austria, Norway, Ireland, Scotland, and the United States. Phylogenetic analysis based on partial sequences of the psbC gene distinguished three well-supported groups and one subgroup. AtpB gene sequences collected from a subset of samples also support this result, while rbcL gene data provided lower support. Group 1A contained the type species Z. ericetorum from Obergurgl/Austria and samples from Kühtai/Austria, Norway, and Scotland. The morphology was characterized by wide vegetative filaments (15-31 μm) and the occurrence of aplanospores with purple residue. Group 1B contained Z. cf. ericetorum from Ireland and Ellmau/Austria. Filaments were in a similar size range (12-30 μm) as in group 1A. This group had round unusual akinetes with green or purple content, had one or two chloroplasts, and was surrounded by a thick cell wall; no aplanospores were observed. Group 2 collected from Ireland had narrower filaments (8-12 μm), cells up to six times longer than wide, and contained elongated aplanospores. Therefore, we have described a new species Z. angustum sp. nov. Group 3 contained Z. cf. ericetorum from Norway and the United States, represented by vegetative filaments with an intermediate width (13-20 μm), but no other distinct morphological features. The morphological and genetic variability observed in Zygogonium is possibly related to habitat and ecology.

• Keywords
• Charophyta, Conjugatophyceae, atpB, conjugating green algae, phylogeny, plant terrestrialization, psbC, rbcL, streptophyte, ultrastructure,
• Publication type
• Journal Article MeSH

Monogenean parasites with a broad host range and direct life cycle provide insight into population genetic structure and dispersal processes. Dactylogyrus vistulae infects over 50 cyprinoid fish species across the western Palearctic, making it an ideal model for assessing host and geographic influences on parasite population structure. Herein, we utilized 20 microsatellite loci and mitochondrial COI sequences to analyze the genetic variability and structure of D. vistulae populations, with a deeper focus on Czech river systems. Low allelic variance was observed across most populations, except in the Aoos River, Greece, where high genetic diversity suggests either a large population size or an ancestral refugium. Moderate variance was detected in the Middle East, though some Anatolian populations exhibited reduced diversity, likely due to recent colonization. Czech populations showed weak genetic structuring despite occupying distinct river basins, likely due to fish translocations. Mitochondrial COI analysis revealed up to 18.5% haplotype divergence, with the highest diversity in the Padano-Venetian, Caspian Sea, and Dalmatian districts. Dalmatian haplotypes formed a distinct haplogroup, though genetic similarities between Padano-Venetian and Dalmatian populations suggest historical connections or fish host introductions. These results support a south-to-north D. vistulae dispersal through the Balkans, associated with cyprinoid fish migration. This study highlights the roles of host dispersal, environmental factors, and human influence in shaping fish parasite population structure, emphasizing the need for further genomic and ecological research.

• Keywords
• Biogeography, Fish parasites, Microsatellites, Mitochondrial markers, Monogenea, Population genetics,
• Publication type
• Journal Article MeSH

The house mouse, Mus musculus, is a widely used animal model in biomedical research, with classical laboratory strains (CLS) being the most frequently employed. However, the limited genetic variability in CLS hinders their applicability in evolutionary studies. Wild-derived strains (WDS), on the other hand, provide a suitable resource for such investigations. This study quantifies genetic and phenotypic data of 101 WDS representing 5 species, 3 subspecies, and 8 natural Y consomic strains and compares them with CLS. Genetic variability was estimated using whole mtDNA sequences, the Prdm9 gene, and copy number variation at two sex chromosome-linked genes. WDS exhibit a large natural variation with up to 2173 polymorphic sites in mitogenomes, whereas CLS display 92 sites. Moreover, while CLS have two Prdm9 alleles, WDS harbour 46 different alleles. Although CLS resemble M. m. domesticus and M. m. musculus WDS, they differ from them in 10 and 14 out of 16 phenotypic traits, respectively. The results suggest that WDS can be a useful tool in evolutionary and biomedical studies with great potential for medical applications.

• MeSH
• Alleles MeSH
• Animals, Wild genetics   MeSH
• Species Specificity MeSH
• Phenotype MeSH
• Genetic Variation * MeSH
• Histone-Lysine N-Methyltransferase genetics   MeSH
• DNA, Mitochondrial genetics   MeSH
• Mice * genetics   MeSH
• DNA Copy Number Variations MeSH
• Animals MeSH
• Check Tag
• Male MeSH
• Mice * genetics   MeSH
• Female MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Histone-Lysine N-Methyltransferase MeSH
• DNA, Mitochondrial MeSH
• prdm9 protein, mouse MeSH Browser

The nuclear ribosomal DNA Internal Transcribed Spacer (ITS) region is used as a universal fungal barcode marker, but often lacks a significant DNA barcoding gap between sister taxa. Here we tested the reliability of protein coding low-copy genes as alternative barcode markers. Mock communities of three unrelated agaric genera (Dermoloma, Hodophilus, and Russula) representing lineages of closely related species were sequenced by the Illumina platform targeting the ITS1, ITS2, the second largest subunit of RNA polymerase II gene (rpb2) and the transcription elongation factor 1-alpha gene (ef1-α) regions. Species representation and their relative abundances were similar across all tested barcode regions, despite a lower copy number in protein coding markers. ITS1 and ITS2 required more sophisticated sequence filtering because they produced a high number of chimeric sequences requiring reference-based chimera removal and had a higher number of sequence variants per species. Although clustering of filtered ITS sequences resulted in an average higher number of correctly clustered units at optimal similarity thresholds, these thresholds varied substantially among genera. Best-fitted thresholds of low-copy markers were more consistent across genera but frequently lacked species resolution due to low intraspecific variability. At some thresholds, we observed multiple species lumped together, and at the same time, species split into multiple partial clusters, which should be taken into consideration when assessing the best clustering thresholds and taxonomic identity of clusters. To achieve the best taxonomic resolution and improve species detection, we recommend combining different markers and applying additional reference-based sorting of clusters. The current availability of rpb2 and ef1-α reference sequences in public databases is far from being complete for all fungal groups, but a combined marker approach can be used for group-specific studies that can build reference data for their own purposes.

• Keywords
• amplicon abundance, chimera, sympatric species, threshold,
• Publication type
• Journal Article MeSH