Association between the gut mycobiome and atopic dermatitis was investigated in 9–12-month-old infants using metagenomics. Two groups of atopic dermatitis infants were classified according to their symptom development as outgrown (recovered) and persisted (still undergoing). The evenness and diversity of the mycobiome in the persisted group were higher than in the healthy and outgrown groups. Dysbiosis of the microbiome in the persisted group was observed by a reduction in the Ascomycota/Basidiomycota ratio. Five fungi were selected as markers from each sample group. In the persisted group, Rhodotorula sp. abundance increased significantly, while Wickerhamomyces sp. and Kodamaea sp. abundance increased in the healthy group, and Acremonium sp. and Rhizopus sp. abundance increased considerably in the outgrown group. Metaproteomic analysis revealed that the persisted group had a high abundance of fungal proteins, particularly those from Rhodotorula sp. Unique proteins such as RAN-binding protein 1 and glycerol kinase from Rhodotorula sp. were hypothesized to be related to atopic dermatitis manifestation in infants.

Background/Objectives: Limosilactobacillus fermentum KUB-D18, a heterofermentative lactic acid bacterium with promising probiotic properties, is known for promoting gut health and nutrient absorption. Originally isolated from chicken intestines, this strain demonstrates versatile metabolic capabilities in diverse gastrointestinal environments. However, the metabolic functions and sugar transport-related genes remain largely unexplored. This study thus aimed to dissect metabolic functions and sugar transports of L. fermentum KUB-D18. Methods: Next-generation and third-generation sequencing techniques using integrative genomic platform towards transportome analysis were performed. Results: The complete genome, sized at 2.12 Mbps with a GC content of 51.36%, revealed 2079 protein-encoding genes, of which 1876 protein functions were annotated and identified in top categories involved in amino acids, nucleotide, energy, and carbohydrate transports and metabolisms. Comparative genes analysis identified 50 core and 12 strain-specific genes linked to probiotic properties, e.g., acid resistances and bile tolerances, antioxidant functions, or anti-inflammatory properties. Further, sugar transportome analysis uncovered 57 transporter genes, demonstrating diverse carbon utilization and phosphotransferase (PTS) systems, corroborated by API 50 CHL test results for carbohydrate metabolism profile. Conclusions: These findings enhance the comprehensive metabolic understanding of L. fermentum KUB-D18, supporting its industrial potential and applications in engineered probiotics.

Kombucha is a well-known fermented drink that gained interest due to its gut health benefits. However, it has a harsh taste of acetic acid and is hard to consume. Thai Cannabis leaves (Cannabis sativa sp. Hang Kra Rog Phu phan ST1) contain high protein and phytochemicals which can improve the growth of lactic acid bacteria (LAB) and enhance the organoleptic quality of the Kombucha. This study revealed the effect of infusing assam green tea leaves with cannabis leaves on the fermentation rate, microbial communities, volatile compounds, and overall quality and taste of the kombucha. The high protein content (23.10%) of Cannabis leaves was found. Phytonutrients and phytochemicals found in the leaves promotes LAB growth, which resulted in the higher number of LAB in the treatment with cannabis leaves. At the end of fermentation (day 7), the highest LAB count (5.53 log CFU mL⁻¹) was presented in kombucha infused with 30% cannabis leaves. Kombucha with better quality, higher pH, and less acidity was obtained in a dose manner. The change in microbial communities was detected using metagenomic analysis. The prominence of Dekkera and Komagataeibacter, with low abundance of Zygosaccharomyces and Weissella were identified. These microorganisms improved flavor by lessening strong fermented odor and harsh acidic taste. From volatile compounds, HS-SPME-GCMS revealed that kombucha infused with 30% cannabis leaves possessed less acetic acid, ethanol, and carbon dioxide and gave a better odor and taste. Hence, cannabis leaves was the novel substrate for kombucha fermentation by enhancing LAB growth and improving the overall qualities.

This study applied a guided culturomics workflow to isolate and characterize gut-associated yeasts as probiotic candidates. Culture conditions were optimized using Dixon agar and Modified Schädler Agar with a moderate antibiotic cocktail (colistin, chloramphenicol, vancomycin) to suppress bacteria without impairing yeast growth, combined with incubation at 37 °C under anaerobic conditions to mimic the intestinal environment. From three healthy donors, 305 isolates were recovered (MSA: 193; Dixon: 112). After excluding pseudohyphal morphotypes and PCR positive Candida isolates, 127 non-Candida strains remained. Safety screening (hemolysis, DNase, coagulase) reduced the pool to 26 safe isolates. Simulated gastrointestinal stress tests showed that 20 out of 26 exhibited at least 50 percent survival under pH 2.0 or 0.5% bile salts. Functional assays revealed strain-specific antimicrobial activity against Staphylococcus aureus, Escherichia coli including O157:H7 and Salmonella species, with several isolates (Y6, Y22, Y42, Y48, Y55, Y56, Y73, Y105, Y127) showing broad and strong inhibition. Two isolates Y44 and Y55 further demonstrated robust bile and acid tolerance (>50% survivability) in both conditions. All isolates displayed intracellular but not extracellular bile salt hydrolase activity, indicating a viability dependent cholesterol lowering potential. Overall, the workflow minimized bacterial interference while enriching for safe and functional yeasts.