1. Customized 16S-23S rDNA ITS amplicon metagenomics for acetic acid bacteria species identification in vinegarsand kombuchasAlja Ribič, Janja Trček, 2024, izvirni znanstveni članek Opis: Acetic acid bacteria (AAB) are involved in food and beverage production bioprocesses, like
those in vinegar and kombucha. They oxidize sugars and alcohols into various metabolites, resulting
in the final products’ pleasant taste and aroma. The 16S rDNA amplicon metagenomics using
Illumina technology is usually used to follow the microbiological development of these processes.
However, the 16S rRNA gene sequences among different species of AAB are very similar, thus not
enabling a reliable identification down to the species level but only to the genus. In this study, we
have constructed primers for amplifying half of the 16S-23S rRNA gene internal transcribed spacer
(ITS) for library construction and further sequencing using Illumina technology. This approach was
successfully used to estimate the relative abundance of AAB species in defined consortia. Further
application of this method for the analysis of different vinegar and kombucha samples proves
it suitable for assessing the relative abundance of AAB species when these bacteria represent a
predominant part of a microbial community.
Ključne besede: ITS metagenomics, microbiota, consortia, Acetobacter, Komagataeibacter, Novacetimonas
Objavljeno v DKUM: 04.02.2025; Ogledov: 0; Prenosov: 8
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2. Microbiota in vitro modulated with polyphenols shows decreased colonization resistance against Clostridioides difficile but can neutralize cytotoxicityAleksander Mahnič, Jennifer Auchtung, Nataša Poklar Ulrih, Robert A. Britton, Maja Rupnik, 2020, izvirni znanstveni članek Opis: While the knowledge on gut microbiota - C. difficile interactions has improved over the years, the understanding of the underlying mechanisms providing colonization resistance as well as preventative measures against the infection remain incomplete. In this study the antibiotic clindamycin and polyphenol extracts from pomegranate and blueberries were used individually and in combination to modulate fecal microbial communities in minibioreactor arrays (MBRA). Modulated communities were inoculated with C. difficile (ribotype 027). Subsequent 7-day periodical monitoring included evaluation of C. difficile growth and activity of toxins TcdA and TcdB as well as analysis of MBRA bacterial community structure (V3V4 16%S metagenomics). Polyphenols affected multiple commensal bacterial groups and showed different synergistic and antagonistic effects in combination with clindamycin. Exposure to either clindamycin or polyphenols led to the loss of colonization resistance against C. difficile. The successful growth of C. difficile was most significantly correlated with the decrease in Collinsella and Lachnospiraceae. Additionally, we demonstrated that Clostridium sporogenes decreased the activity of both C. difficile toxins TcdA and TcdB. The feature was shown to be common among distinct C. sporogenes strains and could potentially be applicable as a non-antibiotic agent for the alleviation of C. difficile infection.
Ključne besede: microbiota in vitro, Clostridioides difficile, resistance, cytotoxicity
Objavljeno v DKUM: 29.01.2025; Ogledov: 0; Prenosov: 5
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3. Corrigendum: Evaluation of human milk microbiota by 16S rRNA gene next-generation sequencing (NGS) and cultivation/MALDI-TOF mass spectrometry identificationPrimož Treven, Aleksander Mahnič, Maja Rupnik, Majda Golob, Tina Pirš, Bojana Bogovič Matijašić, Petra Mohar Lorbeg, 2020, drugi sestavni deli Ključne besede: milk microbiota, microbiota assembly, breastfeeding, breast pump, probiotic drops
Objavljeno v DKUM: 06.01.2025; Ogledov: 0; Prenosov: 3
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4. Evaluation of human milk microbiota by 16S rRNA gene next-generation sequencing (NGS) and cultivation/MALDI-TOF mass spectrometry identificationPrimož Treven, Aleksander Mahnič, Maja Rupnik, Majda Golob, Tina Pirš, Bojana Bogovič Matijašić, Petra Mohar Lorbeg, 2019, izvirni znanstveni članek Opis: The aim of the present study was to characterize human milk microbiota (HMM) with 16S rRNA gene amplicon next-generation sequencing and cultivation/matrix-assisted laser desorption/ionization (MALDI)-time of flight (TOF) mass spectrometry (MS) identification approaches. We analyzed 31 human milk samples from healthy Slovenian mothers. To check the accuracy of MALDI-TOF MS identification, several colonies representing most abundant genera and those, which could not be reliably identified by MALDI-TOF, were subjected to Sanger sequencing of their 16S rRNA gene. We showed that cultivation/MALDI-TOF MS was a suitable tool for culture-dependent determination of HMM. With both approaches, Staphylococcus and Streptococcus were found as predominant genera in HMM and the abundance of Staphylococcus was associated with decreased microbial diversity. In addition, we characterized factors that might influence HMM. The use of a breast pump was significantly associated with composition of HMM, higher microbial load, and lower abundance of cultivable staphylococci. Moreover, our study suggests that administration of probiotics to the suckling infant might influence HMM by increased abundance of lactobacilli and the presence of viable probiotic bacteria in human milk. However, since our study was observational with relatively small sample size, more targeted studies are needed to study possible transfer of probiotics to the mammary gland via an external route and the physiological relevance of these events.
Ključne besede: milk microbiota, microbiota assembly, breastfeeding, breast pump, probiotic drops
Objavljeno v DKUM: 27.12.2024; Ogledov: 0; Prenosov: 3
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5. Overview of the efficacy of using probiotics for neurosurgical and potential neurosurgical patientsSabina Fijan, Tomaž Šmigoc, 2024, pregledni znanstveni članek Opis: This review delves into the emerging field of the gut microbiota-brain axis, emphasizing its bidirectional communication and implications for neurological health, particularly in trauma and neurosurgery. While disruptions in this axis can lead to dysbiosis and hinder neurological recovery, recent studies have highlighted the therapeutic potential of interventions like probiotics in targeting this axis. This review aims to focus on the efficacy of probiotic supplementation to support the gut microbiota-brain axis in trauma, neurosurgery, or pain based on the current clinical trials to assess the complex interplays among probiotics, the gut microbiota, and the central nervous system (CNS). This comprehensive literature review identified 10 relevant publications on probiotic interventions for various neurosurgical conditions across multiple countries. These studies demonstrated diverse outcomes, with significant improvements observed in gastrointestinal mobility, inflammatory responses, and infection rates, particularly in post-traumatic brain injury and spinal surgery. Probiotics also showed promise in mitigating antibiotic-associated diarrhea and modulating inflammatory cytokines. Despite the promising findings, the complex interplays among probiotics, the gut microbiota, and the central nervous system (CNS) call for cautious interpretation. Conflicting outcomes emphasize the need for better-designed trials to understand strain-specific and disease-specific effects accurately. In conclusion, probiotics offer a promising adjuvant therapy for neurosurgical patients, traumatic brain injuries, and post-spinal surgery. However, further well-designed randomized controlled trials are essential to elucidate the intricate relationship between microbiome-modulating interventions and the CNS via the gut microbiota-brain axis.
Ključne besede: neurologic injury, neurosurgery, probiotics, synbiotics, microbiota, brain injury
Objavljeno v DKUM: 21.11.2024; Ogledov: 0; Prenosov: 6
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6. 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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7. Genetic diversity of exopolysaccharides from acetic acid bacteria isolates originating from apple cider vinegarsTadeja Vajdič, 2022, izvirni znanstveni članek Opis: Acetic acid bacteria (AAB) produce acetic acid but are also gaining importance as safe microorganisms for producing extracellular polysaccharides (EPSs). The best-known homopolysaccharides among them are cellulose and levan. In addition, acetic acid bacteria also produce heteropolysaccharides, water-soluble acetans. Isolates from the broth of organic and conventional apple cider vinegar production were screened for biofilm production. Phenotypic and genomic diversity of EPS-producing isolates was assessed. The diversity of phenotypically different EPSs of apple cider vinegar isolates was investigated at the gene level for the following novel strains:
Komagataeibacter (K.) melomenusus SI3083, K. oboediens SI3053, K. pomaceti SI3133, and Gluconacetobacter (Ga.) entanii SI2084. Strain K. melomenusus SI3083 possesses cellulose operons bcs1, bcs2, and bcs4 together with the type I acetan cluster in the absence of the levan operon, strain K. oboediens SI3053 has the operons bcs1, bcs2, bcs3, and bcs4, the levan operon, and the acetan cluster (type I), and the strains K. pomaceti SI3133 and Ga. entanii SI2084 both contain recently described novel ace-type II cluster in addition to the incomplete operon bcs1. A comparison of the genetic diversity of these EPSs to those of the reference strains suggests that the studied EPSs are not species-descriptive. The results of this study deepen our understanding of the genetic variability of the EPS genes in AAB, thereby enabling us to better characterize and exploit the various insoluble and soluble exopolysaccharides produced by AAB for biotechnological applications in the future.
Ključne besede: acetic acid bacteria genomes, apple cider vinegar microbiota, biofilm production, bacterial cellulose, acetan, Acetobacter, Komagataeibacter
Objavljeno v DKUM: 26.09.2024; Ogledov: 0; Prenosov: 16
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8. 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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9. The efficacy of probiotics as antiviral agents for the treatment of rotavirus gastrointestinal infections in children : an updated overview of literatureAndrej Steyer, Dušanka Mičetić-Turk, Sabina Fijan, 2022, pregledni znanstveni članek Opis: Enteric viruses, including the rotavirus, norovirus, and adenoviruses, are the most common cause of acute gastroenteritis. The rotavirus disease is especially prevalent among children, and studies over the past decade have revealed complex interactions between rotaviruses and the gut microbiota. One way to treat and prevent dysbiosis is the use of probiotics as an antiviral agent. This review focuses on the latest scientific evidence on the antiviral properties of probiotics against rotavirus gastroenteric infections in children. A total of 19 studies exhibited a statistically significant antiviral effect of probiotics. The main probiotics that were effective were Saccharomyces cerevisiae var. boulardii, Lacticaseibacillus rhamnosus GG, and various multi-strain probiotics. The underlying mechanism of the probiotics against rotavirus gastroenteric infections in children included immune enhancement and modulation of intestinal microbiota leading to shortening of diarrhoea. However, several clinical studies also found no significant difference in the probiotic group compared to the placebo group even though well-known strains were used, thus showing the importance of correct dosage, duration of treatment, quality of probiotics and the possible influence of other factors, such as the production process of probiotics and the influence of immunisation on the effect of probiotics. Therefore, more robust, well-designed clinical studies addressing all factors are warranted.
Ključne besede: probiotics, microbiota, rotaviruses
Objavljeno v DKUM: 05.07.2024; Ogledov: 95; Prenosov: 11
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