1. The response of microbes to anthropogenically induced perturbations in the Gulf of Trieste (northern Adriatic Sea) : dissertationNeža Orel, Tinkara Tinta, 2025, doctoral dissertation Abstract: Marine ecosystems are constantly influenced by anthropogenic pressures, including inputs of nutrients, pollutants, and allochthonous microorganisms. These inputs can disrupt the dynamics of marine microbiomes, which encompass the majority of biomass and highest diversity of all life forms, controlling most biogeochemical cycles in the ocean realm. Despite their importance for public safety and potential influence on marine ecosystems functioning, knowledge of the impact of these perturbations on coastal microbiome dynamics remains in its infancy. The research objectives of this dissertation were to: (1) characterize the composition of the coastal microbiome in anthropogenically impacted coastal ecosystem; (2) investigate the genetic potential of selected microorganisms for pathogenicity and ecological adaptations; and (3) explore the effects of wastewater on the dynamics and functioning of the coastal microbiome, as well as its implications for the biogeochemical state of the ecosystem.
To address the first aim, we conducted a year-round in situ survey of the pelagic microbiome within anthropogenically impacted coastal ecosystem, focusing on the seasonal and spatial dynamics of traditional and alternative faecal bacterial indicators. We used a culture-independent approach combined with 16S rRNA amplicon sequencing, which overcome limitations of culture-based methods. This analysis revealed that the microbiome was primarily structured by seasonal changes, regardless of proximity to pollution sources. The statistical tool and oceanographic model we applied indicated that riverine water serves as a key vector for introducing allochthonous microbes. This study underscores the importance of molecular approaches combined with statistical and oceanographic modelling for advancing environmental health assessments and detecting microbial indicators.
To address the second aim, we applied whole-genome sequencing to assess the pathogenic potential and genomic features of selected Vibrio isolates. During the analysis, we identified cross-contamination in one isolate, which presented an opportunity to evaluate the effectiveness of bioinformatics workflows for contaminant removal and genome recovery. We reconstructed high-quality genomes of one Vibrio isolate from both axenic and contaminated cultures. Genomic analyses revealed that this isolate belongs to a sub-lineage of Vibrio campbellii associated with diseases in marine organisms. Moreover, this genome harboured a novel Vibrio plasmid linked to bacterial defense mechanisms and horizontal gene transfer, potentially offering a competitive advantage to this putative pathogen. This study highlights the utility of WGS and advanced bioinformatics in overcoming challenges posed by non-axenic cultures and provides new insights into the genomic characteristics of V. campbellii.
To address the third aim, we conducted a short-term microcosm experiment simulating wastewater discharge into coastal seawater, testing two types of wastewaters: (a) unfiltered, containing nutrients, pollutants, and allochthonous microbes, and (b) pre-filtered, retaining only nutrients and pollutants. Our results showed that wastewater, significantly increased nutrient levels (dissolved organic carbon, ammonium, orthophosphate). Using a multi-omics approach with measurements of microbial metabolic activity, we found that nutrient enrichment significantly influenced bacterial metabolism. This was evidenced by enriched protein profiles and increased leucine aminopeptidase and olease activity, indicating bacterial degradation of complex proteins and lipids. At the same time, the phosphate input resulted in a decreased alkaline phosphatase activity, with important implications for phosphorus cycling. Overall, wastewater primarily induced functional shifts in coastal microbiomes, highlighting the resilience and functional redundancy of coastal microbial communities and hence the biogeochemical processes they operate.
Keywords: coastal microbiome, anthropogenic impact, wastewater pollution, bacterial community dynamics, allochthonous microorganisms, potential pathogens, Vibrio campbellii, multi-omics, whole-genome assembly, dissertations
Published in RUNG: 16.04.2025; Views: 69; Downloads: 0
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2. Composition and diversity analysis of the lung microbiome in patients with suspected ventilator-associated pneumoniaDominic Fenn, Mahmoud Abdel-Aziz, Pouline van Oort, Paul Brinkman, Waqar Ahmed, Timothy Felton, Antonio Artigas, Pedro Póvoa, Ignacio Martin-Loeches, Marcus Schultz, Paul Dark, Stephen Fowler, Iain R. White, 2022, original scientific article Abstract: Background: Ventilator-associated pneumonia (VAP) is associated with high morbidity and health care costs, yet diagnosis remains a challenge. Analysis of airway microbiota by amplicon sequencing provides a possible solution, as pneumonia is characterised by a disruption of the microbiome. However, studies evaluating the diagnostic capabilities of microbiome analysis are limited, with a lack of alignment on possible biomarkers. Using bronchoalveolar lavage fluid (BALF) from ventilated adult patients suspected of VAP, we aimed to explore how key characteristics of the microbiome differ between patients with positive and negative BALF cultures and whether any differences could have a clinically relevant role. Methods: BALF from patients suspected of VAP was analysed using 16s rRNA sequencing in order to: (1) differentiate between patients with and without a positive culture; (2) determine if there was any association between microbiome diversity and local inflammatory response; and (3) correctly identify pathogens detected by conventional culture. Results: Thirty-seven of 90 ICU patients with suspected VAP had positive cultures. Patients with a positive culture had significant microbiome dysbiosis with reduced alpha diversity. However, gross compositional variance was not strongly associated with culture positivity (AUROCC range 0.66–0.71). Patients with a positive culture had a significantly higher relative abundance of pathogenic bacteria compared to those without [0.45 (IQR 0.10–0.84), 0.02 (IQR 0.004–0.09), respectively], and an increased interleukin (IL)-1β was associated with reduced species evenness (rs = − 0.33, p < 0.01) and increased pathogenic bacteria presence (rs = 0.28, p = 0.013). Untargeted 16s rRNA pathogen detection was limited by false positives, while the use of pathogen-specific relative abundance thresholds showed better diagnostic accuracy (AUROCC range 0.89–0.998). Conclusion: Patients with positive BALF culture had increased dysbiosis and genus dominance. An increased caspase-1-dependent IL-1b expression was associated with a reduced species evenness and increased pathogenic bacterial presence, providing a possible causal link between microbiome dysbiosis and lung injury development in VAP. However, measures of diversity were an unreliable predictor of culture positivity and 16s sequencing used agnostically could not usefully identify pathogens; this could be overcome if pathogen-specific relative abundance thresholds are used.
Keywords: Microbiome, Next-generation sequencing, Ventilator-associated pneumonia
Published in RUNG: 26.10.2022; Views: 2449; Downloads: 0
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3. Pig Farmers’ Homes Harbor More Diverse Airborne Bacterial Communities Than Pig Stables or Suburban HomesDitte V. Vestergaard, Gitte J. Holst, Ioannis Basinas, Grethe Elholm, Vivi Schlünssen, Allan Linneberg, Tina Šantl Temkiv, Kai Finster, Torben Sigsgaard, Ian P. G. Marshall, 2018, original scientific article Keywords: bacteria, pig stables, built environment, microbiome, airborne bacteria, 16S rRNA gene
Published in RUNG: 04.01.2021; Views: 3972; Downloads: 66
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4. Outlier based literature exploration for cross-domain linking of Alzheimer's disease and gut microbiotaDonatella Gubiani, Elsa Fabbretti, Bojan Cestnik, Nada Lavrač, Tanja Urbančič, 2017, original scientific article Abstract: In knowledge discovery, experts frequently need to combine knowledge from different domains to get new insights and derive new conclusions. Intelligent systems should support the experts in the search for relationships between concepts from different domains, where huge amounts of possible combinations require the systems to be efficient but also sufficiently general, open and interactive to enable the experts to creatively guide the discovery process. The paper proposes a cross-domain literature mining methodology that achieves this functionality by combining the functionality of two complementary text mining tools: clustering and topic ontology creation tool OntoGen and cross-domain bridging terms exploration tool CrossBee. Focusing on outlier documents identified by OntoGen contributes to the efficiency, while CrossBee allows for flexible and user-friendly bridging concepts exploration and identification. The proposed approach, which is domain independent and can support cross-domain knowledge discovery in any field of science, is illustrated on a biomedical case study dealing with Alzheimer’s dis- ease, one of the most threatening age-related diseases, deteriorating lives of numerous individuals and challenging the ageing society as a whole. By applying the proposed methodology to Alzheimer’s disease and gut microbiota PubMed articles, we have identified Nitric oxide synthase (NOS) as a potentially valuable link between these two domains. The results support the hypothesis of neuroinflammatory nature of Alzheimer’s disease, and is indicative for the quest for identifying strategies to control nitric oxide- associated pathways in the periphery and in the brain. By addressing common mediators of inflammation using literature-based discovery, we have succeeded to uncover previously unidentified molecular links between Alzheimer’s disease and gut microbiota with a multi-target therapeutic potential.
Keywords: Literature-based discovery, Outlier detection, Alzheimer's disease, Gut microbiome
Published in RUNG: 26.05.2017; Views: 6375; Downloads: 0
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5. Changes in the relative abundance of two Saccharomyces species from oak forests to wine fermentationsSofia Dashko, Ping Liu, Helena Volk, Lorena Butinar, Jure Piškur, Justin C. Fay, 2016, original scientific article Abstract: Saccharomyces cerevisiae and its sibling species S. paradoxus are known to inhabit temperate arboreal habitats across the globe. Despite their sympatric distribution in the wild, S. cerevisiae is predominantly associated with human fermentations. The apparent ecological differentiation of these species is particularly striking in Europe where S. paradoxus is abundant in forests and S. cerevisiae is abundant in vineyards. However, ecological differences may be confounded with geographic differences in species abundance. To compare the distribution and abundance of these two species we isolated Saccharomyces strains from over 1,200 samples taken from vineyard and forest habitats in Slovenia. We isolated numerous strains of S. cerevisiae and S. paradoxus as well as small number of S. kudriavzevii strains from both vineyard and forest environments. We find S. cerevisiae less abundant than S. paradoxus on oak trees both within and outside the vineyard, but more abundant on grapevines and associated substrates. Analysis of the uncultured microbiome shows that both S. cerevisiae and S. paradoxus are rare species in soil and bark samples, but can be much more common in grape must. In contrast to S. paradoxus, European strains of S. cerevisiae have acquired multiple traits thought to be important for life in the vineyard and dominance of wine fermentations. We conclude that S. cerevisiae and S. paradoxus currently share both vineyard and non-vineyard habitats in Slovenia and we discuss factors relevant to their global distribution and relative abundance.
Keywords: Wine, microbiome, yeast, Ecology, Fermentation
Published in RUNG: 12.02.2016; Views: 7211; Downloads: 203
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