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1.
Changes in the relative abundance of two Saccharomyces species from oak forests to wine fermentations
Jure Piškur, Justin C. Fay, Lorena Butinar, Sofia Dashko, Helena Volk, Ping Liu, 2016, izvirni znanstveni članek

Opis: 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.
Najdeno v: ključnih besedah
Povzetek najdenega: ...and associated substrates. Analysis of the uncultured microbiome shows that both S. cerevisiae and S....
Ključne besede: Wine, microbiome, yeast, Ecology, Fermentation
Objavljeno: 12.02.2016; Ogledov: 3148; Prenosov: 145
.pdf Polno besedilo (3,21 MB)

2.
Outlier based literature exploration for cross-domain linking of Alzheimer's disease and gut microbiota
Tanja Urbančič, Nada Lavrač, Bojan Cestnik, Elsa Fabbretti, Donatella Gubiani, 2017, izvirni znanstveni članek

Opis: 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.
Najdeno v: ključnih besedah
Ključne besede: Literature-based discovery, Outlier detection, Alzheimer's disease, Gut microbiome
Objavljeno: 26.05.2017; Ogledov: 2939; Prenosov: 0
.pdf Polno besedilo (3,13 MB)

3.
Pig Farmers’ Homes Harbor More Diverse Airborne Bacterial Communities Than Pig Stables or Suburban Homes
Ditte 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, izvirni znanstveni članek

Najdeno v: ključnih besedah
Povzetek najdenega: ...bacteria, pig stables, built environment, microbiome, airborne bacteria, 16S rRNA gene...
Ključne besede: bacteria, pig stables, built environment, microbiome, airborne bacteria, 16S rRNA gene
Objavljeno: 04.01.2021; Ogledov: 350; Prenosov: 15
.pdf Polno besedilo (1,79 MB)

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