Probiotics have shown potential in managing hypercholesterolemia and related metabolic conditions. This study evaluated the effects of Lactocaseibacillus (Lactobacillus) paracasei sup. paracasei TISTR 2593 on the gut microbiome and metabolic health in patients with hypercholesterolemia, and was registered in the Thai Clinical Trial Registry (TCTR 20220917002). In a randomized, double-blind, placebo-controlled trial, 22 hypercholesterolemic participants received either the probiotic or a placebo daily for 90 days. Fecal samples collected before and after the intervention revealed significant microbiome changes, including a decrease in Subdoligranulum, linked to rheumatoid arthritis, and an increase in Flavonifractor, known for its anti-inflammatory properties. Additionally, the probiotic group exhibited a significant reduction in low-density lipoprotein cholesterol (LDL-C) levels. These findings suggest that L. paracasei TISTR 2593 can modulate the gut microbiome and improve metabolic health, warranting further investigation into its mechanisms and long-term benefits.

Amphotericin B deoxycholate (AmpB) is used for the treatment of leishmaniasis caused by Leishmania (Mundinia) martiniquensis in Thailand, and relapse cases have been documented. To date, genomic analysis of drug-resistant L. martiniquensis strains is limited. In this study, comparative genome analyses were performed with an experimentally selected AmpB-resistant L. martiniquensis (AmpBRP2i) and two cryopreserved L. martiniquensis parasite strains isolated from a patient showing differences in response to AmpB treatment, LSCM1-WT (susceptible) and LSCM1-6 (resistant). Applying the GIP genome analyses package, we identified aneuploidy and gene copy number variations in all three samples, none of which correlated with AmpB resistance. In contrast, single nucleotide variant (SNV) analyses revealed an SNV in AmpB-resistant strains introduced a premature stop codon into a putative sterol C-24 reductase gene (C24R) (LSCM1_02556) involved in the ergosterol biosynthetic pathway in Leishmania. As Leishmania AmpB resistance has previously been linked to mutations in other genes of the ergosterol biosynthesis pathway in different species of Leishmania parasites, these results suggest that C24R may serve as an additional marker of AmpB resistance in Leishmania. We further identified two missense SNVs in AmpB-resistant strains in a putative 'ABC transporter-like/ABC transporter family' gene (LSCM1_01856) that could be involved in drug efflux. These initial findings pave the way for future research with a larger number of isolates to confirm the genomic signature we associate here with AmpB resistance.

Pustular skin diseases, with pustular psoriasis (PP) being the prototype, are immune-mediated diseases characterized by the presence of multiple pustules, resulting from neutrophil accumulation in the layer of epidermis. Sterile skin pustular eruption, like PP, is also observed in 20–30% of patients with adult-onset immunodeficiency syndrome (AOID) and anti-interferon γ autoantibodies (IFN-γ), leading to challenges in classification and diagnosis. While the mechanism underlying this similar phenotype remains unknown, genetic factors in relation to the immune system are suspected of playing an important role. Here, the association between human leukocyte antigen (HLA) genes, which play essential roles in antigen presentation, contributing to immune response, and the presence of skin pustules in AOID and PP was revealed. HLA genotyping of 41 patients from multiple centers in Thailand who presented with multiple sterile skin pustules (17 AOID patients and 24 PP patients) was conducted using a next-generation-sequencing-based approach. In comparison to healthy controls, HLA-B*13:01 (OR = 3.825, 95%CI: 2.08–7.035), C*03:04 (OR = 3.665, 95%CI: 2.102–6.39), and DQB1*05:02 (OR = 2.134, 95%CI: 1.326–3.434) were significantly associated with the group of aforementioned conditions having sterile cutaneous pustules, suggesting a common genetic-related mechanism. We found that DPB1*05:01 (OR = 3.851, p = 0.008) and DRB1*15:02 (OR = 3.195, p = 0.033) have a significant association with pustular reaction in AOID patients, with PP patients used as a control. A variant in the DRB1 gene, rs17885482 (OR = 9.073, p = 0.005), was observed to be a risk factor for PP when using AOID patients who had pustular reactions as a control group. DPB1*05:01 and DRB1*15:02 alleles, as well as the rs17885482 variant in the DRB1 gene, were proposed as novel biomarkers to differentiate PP and AOID patients who first present with multiple sterile skin pustules without known documented underlying conditions.

Background Early detection of hepatocellular carcinoma (HCC) remains a significant clinical challenge due to the limited sensitivity of current surveillance tools, alpha-fetoprotein (AFP) and ultrasound. Recently, cell-free DNA (cfDNA) fragmentation analysis has shown promise in cancer detection; however, current sequencing-based approaches remain costly and unsuitable for large-scale screening. Methods Here, we introduce a predictive model for early HCC detection called “CEliver” (CfDNA-based automated capillary Electrophoresis method for Liver cancer screening), a model leveraging high-dimensional fragmentation profiling from the intensity distribution of cfDNA fragment lengths using automated capillary electrophoresis. We developed CF-2D features, a computational framework that extracts over 300 quantitative features from electropherogram data, including cfDNA concentration, dominant fragment sizes, two-dimensional shape descriptors, and short-to-long fragment ratios. We integrated these features with AFP levels to build the CEliver model, developed in 111 individuals and validated in an independent cohort of 69 subjects. Results Here we show the CF-2D profiles differ significantly between HCC patients and high-risk individuals. The CEliver model achieves 98% sensitivity across all HCC cases, and 96% sensitivity with 99% specificity for early-stage HCC (stage 0/A), substantially outperforming AFP (60% overall sensitivity, 35% for early-stage). In external validation, CEliver shows 88% sensitivity and 100% specificity. Conclusions CEliver provides a practical and accurate strategy for early HCC detection. By enabling high-dimensional cfDNA fragmentomics analysis on a widely accessible electrophoresis platform, it bridges the gap between research-grade cfDNA technologies and real-world clinical implementation. This method represents a simple and scalable approach that could potentially be applied in HCC surveillance.

Tuanao, a traditional Northern Thai fermented soybean product, was profiled with an integrated multi-omics workflow to clarify how microbes and metabolites co-evolve during household fermentation. Soybeans were fermented spontaneously for three days; samples from four time points were analyzed by shotgun metagenomics alongside 1H-NMR and UHPLC-ESI-QTOF-MS/MS metabolomics. Bacillus spp. (phylum Bacilliota) quickly supplanted early Enterobacterales and dominated the mature microbiome. The rise of Bacillus coincided with genes for peptide and carbohydrate utilization and with the accumulation of acetate, free amino acids (glutamine, leucine, alanine, valine) and diverse oligopeptides, whereas citrate and glucose-1-phosphate were depleted. This Bacillus-linked metabolic shift indicates that Tuanao is a promising source of probiotics and bioactive compounds. Our study provides the first system-level view of Tuanao fermentation and offers molecular markers to guide starter-culture design and quality control.

At the DBCLS BioHackathon 2025, we converted metatranscriptomic analytical shell scripts into Common Workflow Language (CWL) containerized with Docker. Sub-workflows were created for metagenomic assembly, read mapping, and gene annotation, and validated with test datasets. The workflows, released on GitHub and WorkflowHub, improve reproducibility and address issues of reusability and software environment dependency. We also evaluated CWL best practices from the perspective of life scientists, classifying them by difficulty, importance, and applicability to promote FAIR principles and software quality.In parallel, we established a benchmarking framework for pangenome-based structural variant (SV) calling using data from the Dai population. Graph-based references from the Human and Chinese Pangenome Consortia were compared with linear references using minimap2 and vg giraffe. Results showed improved alignment accuracy and variant detection with pangenomes, demonstrating their value for reducing mapping bias and enhancing SV discovery.