Yo-Chia Chen

Volcanic fumaroles are extreme habitats with high temperatures, sulfur‑rich gases, and low pH, creating challenging niches for life. Soil microbiota in these environments remain underexplored, particularly at near‑vent sites with pH below 2. We characterized bacterial communities in hyperacid soils of Taiwan's Tatun Volcanic Group to examine how season and soil properties shape these communities. We sampled 39 soils and 8 hot spring waters from four fumaroles during dry and wet seasons. Soil pH, nutrients (nitrate, ammonium), organic matter, and altitude were recorded, and bacterial diversity was profiled via 16S rRNA gene sequencing. Pseudomonadota overwhelmingly dominated the communities, followed by Bacillota and Actinomycetota. Wet-season soils displayed more homogeneous assemblages, whereas dry-season soils exhibited greater heterogeneity. Soil taxonomy and texture also modulated patterns, with Andisols supporting more consistent communities than Inceptisols. Environmental variables such as nitrate, ammonium, organic matter, and altitude correlated with community composition. Heatmap and network analyses highlighted Delftia and Pseudomonas as key taxa. Extreme acidity and seasonal hydrology thus select for specialized bacterial assemblages in these fumarolic soils. These findings advance understanding of microbial adaptation to geochemical extremes and reveal how seasonal and edaphic factors structure communities, offering implications for biogeochemical cycling and astrobiology.

The intensification of animal farming is associated with increased infectious and zoonotic disease risks. The black soldier fly larvae (BSFL) have antimicrobial activity that could potentially be used to suppress diseases and improve animal health. This study used carbohydrate-rich sweet potato and lauric acid-rich desiccated coconut to differentiate the primary source of lauric acid. The study also investigated the effect of pre-fermenting the substrates with Bacillus sp. and Klebsiella sp. on the BSFL growth performance and fatty acid composition, particularly on lauric acid. Correlation analyses were conducted between the larvae fed with fresh substrate and fermented substrate. Overall, the sweet potato enhanced the lauric acid biosynthesis, and the fermented sweet potato-based substrate resulted in a remarkable lauric acid production of 82%, i.e., 365 mg g ⁻¹ in the BSFL biomass. Pre-fermentation aided production of precursors like oleic acid, linoleic acid, and glycolysis of readily available carbohydrates, which spiked the lauric acid biosynthesis.

Background: Urban pigeons frequently carry zoonotic, antibiotic-resistant Staphylococcus spp. and are increasingly recognized as reservoirs of multidrug-resistant (MDR) gut pathogens with One Health implications. Probiotic Bacillus strains and their lipopeptide products, such as surfactin, are promising antibiotic-sparing alternatives, but their in vivo effects on host gut microbiota and pathogen carriage in apparently healthy birds remain poorly characterized. Results: To explore alternative antimicrobial strategies, Bacillus subtilis 1–4 was isolated from soil and shown to produce surfactin, a potent antimicrobial peptide. In vitro, surfactin exhibited bactericidal activity against S. aureus and S. intermedius by compromising membrane integrity. To evaluate its in vivo effects, pigeons ( Columba livia ) were treated with surfactin for seven days, and changes in their gut microbiota were characterized using full-length 16 S rRNA gene sequencing. While microbial α- and β-diversity remained largely unchanged, the surfactin-treated microbiota displayed enhanced compositional stability relative to controls. Conclusions: These findings support surfactin’s potential as a targeted antimicrobial agent with minimal disruption to the host gut microbiota.

Nuoc mam chay, a plant-based fermented fish sauce alternative, is gaining popularity for its flavor and vegan appeal, but concerns remain regarding histamine accumulation during fermentation. This study evaluated the potential of Bacillus subtilis BCRC 14714 and three isolates (N1, N2, N3) to control histamine formation during nuoc mam chay fermentation of at salt concentrations of 15–20% (w/v) and 30 °C over one month. Phylogenetic analysis based on 16S rRNA gene sequencing identified N2 as B. subtilis, while N1 and N3 were closely related to Paenibacillus lautus. Molecular assays showed that N2 lacked the histidine decarboxylase (hdc) gene and produced no detectable histamine, whereas N1, N3, and BCRC 14714 13.50–24.04 mg/L histamine. N2 also exhibited elevated expression amine oxidase gen, suggesting a potential capacity for histamine degradation. Next-generation sequencing revealed that Bacillus dominated the inoculated fermentations, while naturally fermented controls were enriched with histamine-producing and potentially pathogenic genera. N2 inoculation notably suppressed Staphylococcus, Pseudomonas, and Clostridium. These results suggest that B. subtilis N2 is a promising starter culture for improving the microbial safety and quality of fermented plant-based condiments through histamine control.

Fish sauce, a seasoning commonly utilized in East Asian cuisine, is produced from fish combined with a substantial quantity of salt. However, biogenic amines (BAs) accumulation poses safety concerns in fermented fish sauce during fermentation. This study characterized Tetragenococcus halophilus A003, isolated from fish sauce, which exhibited the weakest decarboxylase gene activation and lowest BA production among the tested strains. Starter inoculation with A003 yielded minimal chemical alteration compared to natural fermentation. Cadaverine levels were substantially lower (19.1 ± 1.49 mg/l) than those in sauce fermented without a starter or with T. halophilus BCRC12250. Histamine and tyramine were undetectable in isolate A003-inoculated samples. Metagenomic analysis revealed an enrichment of low BA-producing taxa, notably Tetragenococcus and Staphylococcus, comprising 97.91% of the community. These findings suggest T. halophilus A003 confers a selective advantage for low BA microbiota during fish sauce fermentation.

Xylooligosaccharides (XOS) are functional oligosaccharides with recognized prebiotic properties and growing industrial relevance, typically obtained through enzymatic depolymerization of xylan-rich lignocellulosic substrates. In this study, a recombinant endo-β-1,4-xylanase (XynA) from Clostridium acetobutylicum was employed for XOS production. The xynA gene was cloned into the expression vector pET-21a(+) and heterologously expressed in Escherichia coli BL21(DE3) under induction with isopropyl β-D-1-thiogalactopyranoside (IPTG). The recombinant protein, with an estimated molecular mass of 37.5 kDa, was verified by SDS-PAGE and Western blot analysis. Functional characterization via thin-layer chromatography revealed that XynA efficiently hydrolyzed beechwood xylan and rye arabinoxylan, predominantly yielding xylobiose. Additionally, the enzyme catalyzed the conversion of xylotriose into xylobiose and trace amounts of xylose. Notably, XynA demonstrated hydrolytic activity against autohydrolysed and alkali-pretreated coconut husk biomass, facilitating the release of XOS. These results underscore the potential of C. acetobutylicum XynA as a biocatalyst for the valorization of lignocellulosic residues into high-value oligosaccharides.

(1) Background: Non-alcoholic fatty liver disease (NAFLD) is a major global health concern. The increasing prevalence of NAFLD has been related to type 2 diabetes mellitus (T2D). However, the relationship between short-chain fatty acids (SCFAs) and NAFLD severity is ambiguous in T2D subjects. This study aimed to explore the association of SCFAs with the severity of NAFLD in T2D patients. (2) Methods: We employed echography to examine the severity of hepatic steatosis. The serum levels of nine SCFAs, namely, formate, acetate, propionate, butyrate, isobutyrate, methylbutyrate, valerate, isovalerate, and methylvalerate, were measured using gas chromatography mass spectrometry. (3) Results: A total of 259 T2D patients was enrolled in this cross-sectional study. Of these participants, 117 with moderate to severe NAFLD had lower levels of formate, isobutyrate, and methylbutyrate than the 142 without NAFLD or with mild NAFLD. Lower circulating levels of isobutyrate and methylbutyrate were associated with an increased severity of NAFLD. A relationship between NAFLD severity and circulating isobutyrate and methylbutyrate levels was found independently of a glycated hemoglobin (HbA1C) level of 7.0%. (4) Conclusion: Circulating levels of isobutyrate and methylbutyrate were significantly and negatively correlated with NAFLD severity in the enrolled T2D patients. SCFAs may be related to NAFLD severity in T2D patients.

The regulatory role of microRNAs (miRNAs) in HBV-associated HCC pathogenesis has been reported previously. This study aimed to investigate the association between serum miR-125b and liver fibrosis progression in chronic hepatitis B (CHB) patients after nucleos(t)ide analog (NA) treatment. Baseline serum miR-125b levels and other relevant laboratory data were measured for 124 patients who underwent 12-month NA therapy. Post-12-month NA therapy, serum miR-125, platelet, AST, and ALT levels were measured again for post-treatment FIB-4 index calculation. Univariate and multivariate logistic regression analyses were performed to identify independent risk factors for a higher post-treatment FIB-4 index. Results showed that baseline miR-125b levels were inversely correlated with the post-treatment FIB-4 index (ρ = −0.2130, p = 0.0082). In logistic regression analyses, age (OR = 1.17, p < 0.0001), baseline platelet level (OR = 0.98, p = 0.0032), and ALT level (OR = 1.00, p = 0.0241) were independent predictors of FIB-index > 2.9 post-12-month treatment. The baseline miR-125b level was not significantly associated with a higher post-treatment FIB-4 index (p = 0.8992). In 59 patients receiving entecavir (ETV) monotherapy, the alternation of serum miR-125b in 12 months and age were substantially associated with a higher post-treatment FIB-4 index (>2.9), suggesting that miR-125b is a reliable biomarker for detecting early liver fibrosis under specific anti-HBV NA treatments (e.g., ETV).