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Povzetek: Groundwater is the most important source of drinking water supply, irrigation, and industrial use, as well as a habitat for a diverse range of (micro)organisms. Some of the first studies of underground environments were carried out in the Dinaric Karst region of Slovenia, which harbors one of the highest subterranean biodiversities in the world. Despite their ecological importance, groundwater microbial communities remain underexplored. In this study, we conducted a comprehensive microbiome analysis of karst groundwater, investigating the abundance and diversity of viruses, archaea, bacteria, fungi, and protozoa. We detected a high diversity of both prokaryote- and eukaryote-infecting viruses, indicating the connection of subterranean environments with surface waters. In the archaeal community, seven different phyla were identified, dominated by members of "Candidatus Woesearchaeota" and Nitrososphaerota (syn. Thermoproteota). In the bacterial community of majority of the samples, the Pseudomonadota was the most abundant phylum, followed by Bacteroidota, Actinomycetota, and Verrucomicrobiota. Fungal abundance and diversity differed greatly between cave water samples, with the Ascomycota families Cladosporiaceae, Didymellaceae, Aspergillaceae and saprotrophic Basidiomycota detected in all samples. Besides fungi, microscopic eukaryotic diversity consisted of ciliates, copepods and golden-brown algae present in all samples. Differences in microbial communities between the sampling sites highlight the need for tailored site-specific groundwater conservation and monitoring strategies. Moreover, the identification of microbes associated with anthropogenic activities underscores their potential as source-specific indicators of groundwater pollution. As the first holistic overview of microbial diversity of subterranean water, the study establishes a valuable baseline for future research and conservation of these unique karst ecosystems.
Ključne besede: Karst cave water, high-throughput sequencing, viruses, archaea, bacteria, fungi, protozoa
Objavljeno v DiRROS: 02.03.2026; Ogledov: 150; Prenosov: 80
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Povzetek: We have analysed the structure of cultivable choanal microbiota from free-living birds in relation to bird diet, its richness and the relative number of opportunistic bacteria acquired from the environment. For this purpose, we have taken choanal swabs from 25 free-living birds representing 13 different bird species captured in Slovenia. From the grown cultures, 98 bacterial colonies were isolated and their 16S rRNA genes sequenced. Most of the bacteria belonged to the phylum Actinobacteria (52 %), Proteobacteria (31 %), Firmicutes (15 %) and Bacteroidetes (4 %). Thirty-two percent of sampled birds were colonized by known human opportunists and 44 % of birds by at least one known plant pathogen. Hierarchical clustering of the analyzed microbiota grouped the birds according to their predominant diet. The richness of choanal microbiota from birds feeding mainly on insects was poorer compared to the birds feeding on diverse animal and plant material. The study has shown that the free-living birds carry an important reservoir of opportunistic human and plant pathogenic bacteria in their upper respiratory tract. To get a deeper insight into its composition, a bigger pool of birds will have to be analyzed in the future.
Ključne besede: birds, microbiota, choanae, pathogenic bacteria, diet
Objavljeno v DiRROS: 28.01.2026; Ogledov: 254; Prenosov: 129
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Povzetek: Rapid identification of pathogens is critical in severe pneumonia patients for timely therapy in mechanically ventilated intensive care unit patients. Conventional diagnostics are time-consuming. The Allplex Respiratory Panels 1-4 detect 16 viruses and seven bacteria and provide faster results; however, because this molecular assay does not yield viable organisms, antimicrobial susceptibility testing cannot be performed. We compared conventional diagnostics with commercial panels to evaluate diagnostic performance and clinical utility. In this prospective study, a total of 30 bronchoalveolar lavage fluids and 80 tracheal aspirates were obtained from 110 unique ICU patients with severe pneumonia (January 2014 and April 2016). Conventional diagnostics were performed during illness, whereas testing of these specimens by commercial panels was performed retrospectively. Pathogen detection rates and co-detections were analyzed by pneumonia type (community-acquired, hospital-acquired, and ventilator-associated). Conventional diagnostics detected pathogens in 87 of 110 patients (79.1%) versus 70 of 110 (63.6%) detected by the commercial approach (P = 0.016). Detection of viruses was most frequent, predominantly influenza A and human rhinoviruses; common bacterial detections included Haemophilus influenzae, Legionella pneumophila, and Streptococcus pneumoniae. Co-detections occurred in 12.7% patients by the commercial approach and in 21.8% by the conventional approach, including virus-bacterium co-detections in 10.9% and 14.5% of cases, respectively. The commercial approach missed eight bacterial and four fungal detections identified by conventional methods. Conventional diagnostics showed higher yield in hospital-acquired pneumonia (82.5% vs 50.0%; P = 0.004), whereas both approaches were comparable in community-acquired cases (75% vs 73.4%). Conventional diagnostics (including culture-based methods) provide broader detection and offer the ability for phenotypic antimicrobial susceptibility testing to be performed, whereas commercial panels offer speed; together, they may optimize pathogen detection and therapy in critically ill patients.IMPORTANCESevere pneumonia in critically ill patients remains a major clinical challenge due to its diverse etiology, rapid progression, and the need for timely, targeted therapy. This study demonstrates that conventional diagnostic approaches-combining culture and molecular tests-identify the etiology more effectively than a commercial multiplex PCR-based syndromic panel in ICU patients. While the molecular approach offers faster results, it lacks the breadth of bacterial and fungal targets and does not provide the opportunity for antimicrobial susceptibility testing. Importantly, viral pathogens-particularly influenza A and rhinoviruses-were frequently detected, underscoring their role in severe pneumonia and the relevance of viral-bacterial co-infections. This work highlights that syndromic molecular diagnostics may be valuable for rapid screening or in community-acquired pneumonia but are insufficient for hospital- or ventilator-associated pneumonia. Our findings support a complementary diagnostic strategy to optimize pneumonia management in ICU settings, improve antimicrobial stewardship, and ultimately impact clinical outcomes for patients with life-threatening respiratory infections.
Ključne besede: bacteria, fungi, intensive care unit, molecular methods, severe pneumonia, viruses
Objavljeno v DiRROS: 08.01.2026; Ogledov: 239; Prenosov: 133
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Povzetek: Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom - forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish - enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to ‘jellyfish - associated’ and ‘free - living’ bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into possible changes in bacterial population dynamics and nutrient pathways following jellyfish blooms which have important implications for ecology of coastal waters.
Ključne besede: sea, medusae, research programmes, DGGE, Pelagia noctiluca, gel electrophoresis, oligotrophic waters, Adriatic Sea, jellyfish, gelatinous zooplankton, bacteria, flavobacteria
Objavljeno v DiRROS: 26.03.2025; Ogledov: 917; Prenosov: 704
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Povzetek: Background Phages are critical components of the gut microbiome, influencing bacterial composition and function as predators, parasites, and modulators of bacterial phenotypes. Prophages, integrated forms of these phages, are prevalent in many bacterial genomes and play a role in bacterial adaptation and evolution. However, the diversity and stability of prophages within gut commensals, particularly in the genera Bacteroides and Phocaeicola, remain underexplored. This study aims to screen and characterize prophages in these genera, providing insights into their diversity, host range, and temporal dynamics in the human gut. Results Using a combination of three bioinformatic tools—Cenote-Taker 3, Vibrant, and PHASTER—we conducted a comprehensive analysis of prophages in Bacteroides and Phocaeicola. Cenote-Taker 3 identified the most diverse set of prophages, with significant overlaps observed between the tools. After clustering high-quality prophages, we identified 22 unique viral operational taxonomic units (vOTUs). Notably, comparisons between prophages identified in isolated bacterial genomes, metaviromes, and large public gut virome databases revealed a broader host range than initially observed in single isolates. Certain prophages were consistent across time points and individuals, suggesting temporal stability. All identified prophages belonged to the Caudoviricetes class and contained genes related to antibiotic resistance, toxin production, and metabolic processes. Conclusions The combined use of multiple prophage detection tools allowed for a more comprehensive assessment of prophage diversity in Bacteroides and Phocaeicola. The identified prophages were not only prevalent but also exhibited broad host ranges and temporal stability. The presence of antibiotic resistance and toxin genes suggests that these prophages may significantly influence bacterial community structure and function in the gut, with potential implications for human health. These findings highlight the importance of using diverse detection tools to accurately assess prophage diversity and dynamics.
Ključne besede: prophage detection, Bacteroides, Phocaeicola, gut microbiome, prophage diversity, Caudoviricetes, antibiotic resistance, phage-bacteria interactions, temporal stability
Objavljeno v DiRROS: 06.03.2025; Ogledov: 998; Prenosov: 766
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