1. Association of asthma and anti-asthmatic therapy with oral health and microbiota alterations in children - a cross-sectional studyVojko Berce, Boris Egić, Anja Pintarič Lonzarić, Maja Rupnik, Aleksander Mahnič, 2026, original scientific article Abstract: Background: Asthma and its treatments are recognized as risk factors for oral health in children. The composition of oral microbiota is linked to asthma, as well as to the development of caries and other oral conditions. This study aimed to assess the impact of asthma and anti-asthmatic therapy on children`s oral health and explore the role of salivary microbiota in this relationship.
Methods: A cross-sectional study was conducted, including 100 children with asthma, aged 6 to 18 years, and 50 matched healthy controls. Oral health was assessed using the decayed, missing and filled teeth (DMFT/dft) index, the simplified oral hygiene index (OHI-S) to evaluate dental plaque and calculus, and the gingival index. Saliva flow rate and pH were measured, and the salivary microbiota composition was analyzed using 16 S amplicon sequencing. Results: Children with asthma had a median DMFT/dft index of 4, versus 0 in controls (p < 0.01), a median OHI-S of 0.9 versus 0 (p < 0.01) and a median gingival index of 1 versus 0 (p < 0.01). Daily use of inhaled corticosteroids (ICS) was associated with a higher median OHI-S (1 vs. 0.8, p < 0.01) but had no effect on the DMFT/dft or gingival index. The median unstimulated saliva flow rate and pH were 1.3 mL and 6.25 in children with asthma compared to 2.5 mL and 7.00 in controls (p < 0.01 for both). Children with asthma daily using ICS had a lower saliva flow (1.0 mL) and pH (6.25) compared to non-ICS users (1.5 ml and 6.75, p < 0.01 for both). The salivary microbiota composition in children with asthma differed significantly from controls (p < 0.01), showing increased abundances of Streptococcus, Gemella, and Streptobacillus. Alpha diversity was lower in children with asthma, with reduced richness (p < 0.01) and evenness (p = 0.012). However, no significant associations were identified between salivary microbiota and specific oral health indicators.
Conclusions: Asthma negatively affects children`s oral health, including reduced salivary flow, and is associated with alterations in the oral microbiota. However, the development of caries in children with asthma cannot be attributed solely to medications or microbiota alterations. Therefore, meticulous oral hygiene and other preventive measures are especially important in children with asthma.
Keywords: asthma, anti-asthmatic agents, child, microbiota, oral health, saliva
Published in DiRROS: 29.06.2026; Views: 213; Downloads: 126
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2. Gut microbiomes of wild and domesticated mammals and birds in Slovenia, Europe : 16S rRNA sequencing dataTanja Žlender, Maja Rupnik, 2026, other scientific articles Abstract: From a One Health perspective, the gut microbiota of animals acts as a major driver of microbial exchange between animals and the environment. Animals continuously release gut microbes into their surroundings, shaping environmental and human microbial communities and potentially dispersing pathogens. Characterizing gut microbiota across diverse animal hosts is therefore critical for understanding the patterns of microbial spread through ecosystems and their impact on animal, human and environmental health. Here, we introduce a large, taxonomically diverse dataset of fecal microbiomes from 715 individual animals representing over 50 mammalian and avian species. We collected samples from both wild and domestic animals with an emphasis on capturing microbial diversity across a wide range of taxa and ecological contexts. The samples were subjected to 16S rRNA gene sequencing, targeting the V3–V4 hypervariable region. Bioinformatic analysis was performed using Usearch to generate zero-radius operational taxonomic units (ZOTUs). This dataset was generated primarily for the development of microbial source tracking (MST) assays used for identifying the sources of fecal pollution in contaminated water. However, it provides a valuable resource for broader microbiome research. It enables comparative studies across host species, trophic guilds, and environmental contexts such as domestication.
Keywords: gut microbiota, 16S rRNA gene, metagenome, animal feces
Published in DiRROS: 18.05.2026; Views: 232; Downloads: 230
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3. Microbiome-derived short-chain fatty acids and tryptophan metabolites in children with autism spectrum disorder : a stool–urine multi-omics analysisJoško Osredkar, Teja Fabjan, Uroš Godnov, Maja Jekovec-Vrhovšek, Damjan Osredkar, Petra Finderle, Kristina Kumer, Maša Zorec, Lijana Fanedl, Gorazd Avguštin, 2026, original scientific article Abstract: Autism spectrum disorder (ASD) has been associated with alterations in the gut microbiota and its metabolites, particularly short-chain fatty acids (SCFAs) and microbiota-derived tryptophan catabolites, which may influence neurodevelopment through immune and epigenetic mechanisms. We investigated whether stool SCFAs and tryptophan-pathway metabolites differ between children with ASD and typically developing controls, and whether these metabolites associate with ASD severity and systemic biochemical signatures. In this cross-sectional study, we analyzed stool samples from 229 children (160 with ASD, 69 controls) with complete SCFA and tryptophan-metabolite data, while urine metabolomics data were available for a subset and were used for exploratory stool–urine integration analyses. Children with ASD and controls were similar in age, but the ASD group had a higher proportion of males. Absolute concentrations of individual SCFAs, total SCFAs, and derived indices were broadly comparable between groups; nominal differences in propionate/acetate ratio and caproate did not remain significant after false discovery rate correction. Similarly, stool tryptophan-pathway metabolites reported as ng/a.u. based on the NanoDrop-derived proxy (tryptophan, kynurenine, indole-3-acetic, indole-3-lactic, indole-3-propionic, indole-3-aldehyde, N-acetyl-tryptophan, serotonin, melatonin, tryptamine) and functional ratios (kynurenine/tryptophan, indole-derived/tryptophan, serotonin/tryptophan) showed no robust ASD–control differences; N-acetyl-tryptophan was nominally higher in ASD but did not survive multiple-testing correction. In the ASD subgroup with available Childhood Autism Rating Scale (CARS) data (n = 34), SCFA and tryptophan indices showed only weak, non-significant correlations with global ASD severity. In contrast, correlation analyses revealed two coherent metabolic modules, i.e., an SCFA block with very strong internal correlations among individual SCFAs and total SCFAs and a tryptophan block with strong correlations between metabolites and their normalized ratios, while cross-module correlations were modest. These results indicate that stool SCFA and microbiota-derived tryptophan profiles do not robustly distinguish ASD from controls in this cohort, but they form stable metabolic modules compatible with microbiome–epigenome frameworks.
Keywords: autism spectrum disorder, gut microbiota, short-chain fatty acids, tryptophan metabolism, indole metabolites, kynurenine pathway, epigenetics, microbiome–epigenome interaction, metabolomics, pediatrics
Published in DiRROS: 05.05.2026; Views: 312; Downloads: 234
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4. The genetic blueprint of obesity : from pathogenesis to novel therapiesGašper Tonin, Stjepan Eržen, Zala Mlinarič, Dubravka Jurišić-Eržen, Simon Horvat, Tanja Kunej, Jasna Klen, 2025, review article Keywords: CRISPR/Cas9, dual therapy, energy homeostasis, gene therapy, gut–brain axis, microbiota, personalized medicine
Published in DiRROS: 22.04.2026; Views: 275; Downloads: 274
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5. Urinary uremic toxin signatures and the metabolic index of gut dysfunction (MIGD) in autism spectrum disorder : a stool-phenotype-stratified analysisJoško Osredkar, Teja Fabjan, Kristina Kumer, Maja Jekovec-Vrhovšek, Joanna Giebułtowicz, Barbara Bobrowska-Korczak, Gorazd Avguštin, Uroš Godnov, 2025, original scientific article Abstract: Gut-derived uremic toxins may play a key role in neurodevelopmental conditions such as autism spectrum disorder (ASD) via host-microbe metabolic interactions. We evaluated five uremic toxins—p-cresyl sulfate (PCS), indoxyl sulfate (IS), trimethylamine N-oxide (TMAO), asymmetric dimethylarginine (ADMA), and symmetric dimethylarginine (SDMA)—in urine samples of 97 children with ASD and 71 neurotypical controls, stratified by Bristol Stool Chart (BSC) consistency types. Four of these toxins (PCS, IS, TMAO, ADMA) were integrated into a novel composite biomarker called the Metabolic Index of Gut Dysfunction (MIGD), while SDMA was measured as a complementary renal function marker. While individual metabolite levels showed no statistically significant differences, group-wise analysis by stool phenotype revealed distinct trends. ASD children with hard stools (BSC 1–2) showed elevated PCS levels and the MIGD score (median 555.3), reflecting phenolic fermentation dominance with reduced indolic detoxification. In contrast, children with loose stools (BSC 6–7) had the lowest MIGD values (median 109.8), driven by higher IS and lower ADMA concentrations, suggestive of enhanced indole metabolism. These findings indicate that MIGD may serve as a novel biomarker to stratify metabolic phenotypes in ASD, linking urinary metabolite patterns to gut function. Further validation in larger and longitudinal cohorts is warranted to confirm its potential utility in precision microbiota-targeted interventions.
Keywords: autism spectrum disorder, uremic toxins, microbiota–host interactions, p-cresyl sulfate, indoxyl sulfate, gut metabolic dysfunction, urinary biomarkers, Bristol stool chart
Published in DiRROS: 14.04.2026; Views: 303; Downloads: 225
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6. Systemic uremic toxin burden in autism spectrum disorder : a stratified urinary metabolite analysisJoško Osredkar, Teja Fabjan, Uroš Godnov, Maja Jekovec-Vrhovšek, Joanna Giebułtowicz, Barbara Bobrowska-Korczak, Gorazd Avguštin, Kristina Kumer, 2025, original scientific article Abstract: Autism spectrum disorder (ASD) is increasingly associated with microbial and metabolic disturbances, including the altered production of gut-derived uremic toxins. We investigated urinary concentrations of five representative uremic toxins—indoxyl sulfate (IS), p-cresyl sulfate (PCS), trimethylamine N-oxide (TMAO), asymmetric dimethylarginine (ADMA), and symmetric dimethylarginine (SDMA)—in 161 children with ASD and 71 healthy controls. Toxins were measured using LC-MS/MS and were normalized to creatinine. Subgroup analyses were performed by sex, age group (2–5.9 vs. 6–17 years), and autism severity based on the Childhood Autism Rating Scale (CARS). In addition to individual concentrations, we calculated the total toxin burden, proportional contributions, and functional ratios (IS/PCS, PCS/TMAO, and IS/ADMA). While individual toxin levels did not differ significantly between groups, stratified analyses revealed that PCS was higher in girls and in severe cases of ASD, whereas IS and TMAO were reduced in younger and more severely affected children. The functional ratios shifted consistently with severity—IS/PCS declined from 1.69 in controls to 0.99 in severe cases of ASD, while PCS/TMAO increased from 12.2 to 20.5. These patterns suggest a phenolic-dominant microbial signature and an altered host–microbial metabolic balance in ASD. Functional toxin profiling may offer a more sensitive approach to characterizing metabolic disturbances in ASD than concentration analysis alone.
Keywords: autism spectrum disorder, uremic toxins, p-cresyl sulfate, indoxyl sulfate, metabolomics, urinary biomarkers, gut microbiota, TMAO, ADMA
Published in DiRROS: 14.04.2026; Views: 308; Downloads: 243
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7. Negative-control-anchored urinary microbiome profiling with absolute 16S quantification : a pilot study in newly diagnosed, treatment-naive bladder cancer and healthy individualsTomaž Accetto, Katja Strašek Smrdel, Milena Taskovska, Marjanca Starčič Erjavec, Tomaž Smrkolj, Katja Seme, Mateja Erdani-Kreft, 2026, original scientific article Keywords: bladder cancer, midstream urine, microbiota, urinary tract infection, next-generation sequencing, nonmetric multidimensional scaling, absolute quantification, negative controls, low biomass
Published in DiRROS: 07.04.2026; Views: 326; Downloads: 128
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8. Alterations in gut microbiota after upper gastrointestinal resections : should we implement screening to prevent complications?Urška Novljan, Žan Bohinc, Niko Kaliterna, Uroš Godnov, Tadeja Pintar, 2025, original scientific article Abstract: Background: Surgical procedures and alterations of the gastrointestinal (GI) tract increase the risk of small intestinal bacterial overgrowth (SIBO), which is associated with GI symptoms and complications that compromise postoperative recovery. However, the prevalence and clinical impact of SIBO after various upper GI surgical procedures remain poorly understood. Objective: This study aimed to evaluate the prevalence of SIBO after different types of upper GI surgery and to investigate the associated clinical factors. Methods: We conducted an observational study involving 157 patients with a history of upper GI surgery: Roux-en-Y gastric bypass (RYGB), laparoscopic single-anastomosis gastric bypass (OAGB), subtotal (STG) or total gastrectomy (TG), subtotal (SP)or total pancreatectomy (TP), cephalic duodenopancreatectomy (WR), and small bowel resection for Crohn’s disease. A glucose–hydrogen breath test was performed, and demographic, clinical, and treatment-related data were collected. Statistical analyses included t-tests, non-parametric tests, ANOVA, and correlation analyses using R software. Results: At a median follow-up of 25.7 ± 18.1 months, 31% (48/157) of patients tested positive for SIBO. The highest prevalence was observed after RYGB and OAGB (43%), followed by TG (30%), STG (29%), TP/WR (28%), and Crohn’s disease bowel resection (19%). No cases of SIBO were observed after SP. SIBO positivity was significantly associated with bloating and flatulence (p = 0.002), lactose intolerance (p = 0.047), systemic sclerosis (p = 0.042), T2D (p = 0.002), and exposure to adjuvant chemotherapy (p = 0.001) and radiotherapy (p = 0.027). In addition, the risk of SIBO increased proportionally with the duration of GI resection or exclusion (p = 0.013). Conclusions: In our study, the prevalence of SIBO after upper GI surgery was 31%, with the highest incidence (43%) observed in metabolic surgery patients. Importantly, adjuvant radio/chemotherapy was associated with an increased risk of SIBO, and extensive small bowel resection or exclusion was strongly associated with an increased risk of SIBO. Furthermore, the limitations of current diagnostic methods, which lack sufficient sensitivity and specificity, highlight the importance of early screening and standardization of diagnostic techniques to improve patient management and outcomes.
Keywords: small intestinal bacterial overgrowth, gut dysbiosis, intestinal microbiota, upper GI surgery, glucose–hydrogen breath test, exocrine pancreatic insufficiency, pancreatic cancer, gastric cancer, Crohn’s disease, metabolic bariatric surgery, postoperative complications
Published in DiRROS: 24.02.2026; Views: 634; Downloads: 269
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9. Therapeutic potential of butyrate supplementation in sepsis : a review of preclinical evidence and translational perspectivesNicola Benvenuto, Filippo Mearelli, Gianni Biolo, Filippo Giorgio Di Girolamo, Erik Roman-Pognuz, Abbas Yadegar, Annalisa Serio, Nina Grasselli Kmet, 2026, review article Abstract: Sepsis remains a major global health problem and is responsible for millions of deaths annually despite significant progress in antimicrobial therapy and organ support. Increasing evidence highlights the role of the gut–immune axis in shaping host responses during sepsis, with particular interest in microbiota-derived metabolites such as short-chain fatty acids (SCFAs). Among these, butyrate has emerged as a promising candidate due to its anti-inflammatory, immunomodulatory, and intestinal barrier–preserving properties. This narrative review summarizes current evidence regarding the biological activities of butyrate and its potential therapeutic relevance in sepsis and septic shock. A comprehensive literature search of PubMed and additional sources up to April 2025 identified experimental and clinical studies evaluating butyrate supplementation in sepsis. Preclinical studies show that butyrate improves function across organ systems (neurologic, hepatic, intestinal, cardiac, pulmonary, and renal) mainly by reducing inflammation, oxidative stress, and epithelial barrier disruption. In models like cecal ligation and puncture (CLP) or endotoxemia, survival improved by 20–40 % with butyrate administration. Human data are limited: an observational study found higher circulating β-hydroxybutyrate levels in sepsis survivors, while a randomized trial reported fewer gastrointestinal complications and ventilator-associated pneumonia in patients with synbiotic-induced butyrate increases. Overall, current evidence suggests that butyrate may modulate key pathophysiological pathways in sepsis and holds potential as an adjunctive therapy. Nonetheless, dedicated early-phase clinical trials are required to clarify safety, optimal dosing, pharmacodynamics, and clinical effectiveness.
Keywords: butyrate, gut microbiota, sepsis, septic shock, short-chain fatty acids
Published in DiRROS: 29.01.2026; Views: 572; Downloads: 494
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10. Cultivable bacterial microbiota from choanae of free-living birds captured in SloveniaJure Škraban, Tjaša Matjašič, Franc Janžekovič, Gottfried Wilharm, Janja Trček, 2017, original scientific article Abstract: 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.
Keywords: birds, microbiota, choanae, pathogenic bacteria, diet
Published in DiRROS: 28.01.2026; Views: 623; Downloads: 454
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