1. Comparison of microbial populations in saliva and feces from healthy and celiac adolescents with conventional and molecular approaches after cultivation on gluten-containing media : an exploratory studyTilen Seničar, Andraž Kukovičič, Valerija Tkalec, Aleksander Mahnič, Jernej Dolinšek, Maja Rupnik, 2021, izvirni znanstveni članek Opis: Microbes capable of metabolizing gluten are common in various parts of the intestinal tract. In this study, saliva and fecal samples were obtained from 10 adolescents (13-18 years of age), five of which had celiac disease (CD) and five of which were healthy volunteers (HV). Culture-enriched saliva and fecal samples were compared with molecular profiling, and microorganisms displaying lysis zones on gluten-containing media (i.e., gluten-degrading microorganisms; GDMs) were isolated. In total, 45 gluten-degrading strains were isolated, belonging to 13 genera and 15 species, including Candida albicans and Veillonella. GDMs were more common in HVs compared to CD patients and more diverse in saliva compared to feces. In saliva, GDMs showed partial overlap between HVs and CD patients. Bacterial communities in fecal samples determined with amplicon sequencing significantly differed between CD patients and HVs. Overall, 7-46 of all operational taxonomic units (OTUs) per sample were below the detection limit in the fecal samples but were present in the cultivated samples, and mainly included representatives from Lactobacillus and Enterococcus. Furthermore, differences in fecal short-chain fatty-acid concentrations between CD patients and HVs, as well as their correlations with bacterial taxa, were demonstrated.
Ključne besede: gluten-degrading microorganisms, veillonella, candida, short-chain fatty acids, celiac disease, microbiota, sequencing
Objavljeno v DKUM: 14.10.2024; Ogledov: 0; Prenosov: 18
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2. Analysis of seed-associated bacteria and fungi on staple crops using the cultivation and metagenomic approachesValerija Tkalec, Aleksander Mahnič, Peter Gselman, Maja Rupnik, 2022, izvirni znanstveni članek Opis: One of the key factors afecting seed quality is microbial communities residing on and in the seeds. In this study, microbial populations of seeds of conventionally and organically produced wheat, barley, and maize were analyzed using two diferent approaches: the cultivation method and metagenomics. For cultivation, three basic media were used: DG18 (for fungi), and nutrient agar or tryptic soy agar supplemented with cycloheximide or nystatin (for bacteria). Metagenomic sequencing was performed using the Illumina MiSeq platform. A total of 452 bacterial isolates comprising 36 genera and 5 phyla and 90 fungal isolates comprising 10 genera and 3 phyla were obtained from the seed surfaces. Among bacteria, representatives from the genera Bacillus, Pantoea, Paenibacillus, and Curtobacterium predominated, and among fungi, Aspergillus predominated. A total of 142 fungal OTUs and 201 bacterial OTUs were obtained from all the samples. Proteobacteria, Firmicutes, Bacteroides, and Actinobacteria comprised most of the bacterial OTUs, and Ascomycota comprised most of the fungal OTUs. Only 3 fungal OTUs (representatives of Curvibasidium, Venturia, and Dermateaceae) were exclusively present only within seeds and not on the seed surfaces. Barley seeds had the highest microbial load and richness, whereas corn had the lowest. Wheat and barley shared a higher number of OTUs than either of them did with corn with higher overlap between conventionally grown cereals than between organically grown cereals. Some OTUs were farming specifc. This study demonstrates that the microbiome of cereal seeds is greatly dependent on the species of the host and is less afected by agricultural practices.
Ključne besede: Microbiota, Wheat, Barley, Corn, NGS, Culture
Objavljeno v DKUM: 05.07.2024; Ogledov: 119; Prenosov: 15
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3. International Clostridium difficile animal strain collection and large diversity of animal associated strainsSandra Janežič, Valerija Tkalec, Bart Pardon, Alexander Indra, Branko Kokotovic, Jose Luis Blanco, Christian Seyboldt, Rodriguez Diaz, Ian Poxton, Vincent Perreten, Ilenia Drigo, Alena Jiraskova, Matjaž Ocepek, Scott Weese, Glenn Songer, Mark Wilcox, Maja Rupnik, 2014, izvirni znanstveni članek Opis: Background: Clostridium difficile is an important cause of intestinal infections in some animal species and animals might be a reservoir for community associated human infections. Here we describe a collection of animal associated C. difficile strains from 12 countries based on inclusion criteria of one strain (PCR ribotype) per animal species per laboratory.
Results: Altogether 112 isolates were collected and distributed into 38 PCR ribotypes with agarose based approach and 50 PCR ribotypes with sequencer based approach. Four PCR ribotypes were most prevalent in terms of number of isolates as well as in terms of number of different host species: 078 (14.3% of isolates; 4 hosts), 014/020 (11.6%; 8 hosts); 002 (5.4%; 4 hosts) and 012 (5.4%; 5 hosts). Two animal hosts were best represented; cattle with 31 isolates (20 PCR ribotypes; 7 countries) and pigs with 31 isolates (16 PCR ribotypes; 10 countries).
Conclusions: This results show that although PCR ribotype 078 is often reported as the major animal C. difficile type, especially in pigs, the variability of strains in pigs and other animal hosts is substantial. Most common human PCR ribotypes (014/020 and 002) are also among most prevalent animal associated C. difficile strains worldwide. The widespread dissemination of toxigenic C. difficile and the considerable overlap in strain distribution between species furthers concerns about interspecies, including zoonotic, transmission of this critically important pathogen.
Ključne besede: Clostridium difficile, animals, ribotyping, geographic distribution, strain collection
Objavljeno v DKUM: 29.06.2017; Ogledov: 1320; Prenosov: 400
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4. Clostridium difficile genotypes other than ribotype 078 that are prevalent among human, animals and environmental isolatesSandra Janežič, Matjaž Ocepek, Valerija Tkalec, Maja Rupnik, 2012, izvirni znanstveni članek Opis: Background: Characterising the overlap of C. difficile genotypes in different reservoirs can improve our understanding of possible transmission routes of this pathogen. Most of the studies have focused on a comparison of the PCR ribotype 078 isolated from humans and animals. Here we describe for the first time a comparison of C. difficile genotypes isolated during longer time intervals from different sources including humans, animals and the non-hospital environment.
Results: Altogether 786 isolates from time interval 2008-2010 were grouped into 90 PCR ribotypes and eleven of them were shared among all host types and the environment. Ribotypes that were most common in humans were also present in water and different animals (014/020, 002, 029). Interestingly, non-toxigenic isolates were very common in the environment (30.8%) in comparison to humans (6.5%) and animals (7.7%). A high degree of similarity was observed for human and animal isolates with PFGE. In human isolates resistance to erithromycin, clindamycin and moxifloxacin was detected, while all animal isolates were susceptible to all antibiotics tested.
Conclusion: Our results show that many other types in addition to PCR Ribotype 078 are shared between humans and animals and that the most prevalent genotypes in humans have the ability to survive also in the environment and several animal hosts. The genetic relatedness observed with PFGE suggests that transmission of given genotype from one reservoir to the other is likely to occur.
Ključne besede: Clostridium difficile, genotypes, PCR ribotype 078, isolates
Objavljeno v DKUM: 29.06.2017; Ogledov: 1206; Prenosov: 207
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5. Highly divergent Clostridium difficile strains isolated from the environmentSandra Janežič, Mojca Potočnik, Valerija Tkalec, Maja Rupnik, 2016, izvirni znanstveni članek Opis: Clostridium difficile is one of the most important human and animal pathogens. However, the bacterium is ubiquitous and can be isolated from various sources. Here we report the prevalence and characterization of C. difficile in less studied environmental samples, puddle water (n = 104) and soil (n = 79). C. difficile was detected in 14.4% of puddle water and in 36.7% of soil samples. Environmental strains displayed antimicrobial resistance patterns comparable to already published data of human and animal isolates. A total of 480 isolates were grouped into 34 different PCR ribotypes. More than half of these (52.9%; 18 of 34) were already described in humans or animals. However, 14 PCR ribotypes were new in our PCR ribotype library and all but one were non-toxigenic. The multilocus sequence analysis of these new PCR ribotypes revealed that non-toxigenic environmental isolates are phylogenetically distinct and belong to three highly divergent clades, two of which have not been described before. Our data suggest that environment is a potential reservoir of genetically diverse population of C. difficile.
Ključne besede: clostridium difficile, environment, isolation
Objavljeno v DKUM: 19.06.2017; Ogledov: 1565; Prenosov: 405
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