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Characterization, comparative genomics, and metabolome analysis of Streptomyces tuberiscabiei sp. nov., a novel actinomycete causing potato scab disease in Long Khot, Chiang Mai Province, Thailand
(2026-07-01)
Inthong, Tanchanok
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Wannawong, Thippawan
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Mhuantong, Wuttichai
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Hongprasit, Aphinan
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Tanasupawat, Somboon
Three actinomycete strains, WSLK1–3T, WSLK1–4, and WSLK1–5, associated with scabby potato tuber, were characterized using polyphasic and genome-based taxonomy. All strains were found to be Gram-stain-positive, filamentous bacteria, including LL-diaminopimelic acid in cell-wall peptidoglycan. Whole-cell sugars were glucose, mannose, rhamnose, and ribose. MK-9(H<inf>6</inf>) and MK-9(H<inf>10</inf>) were major menaquinones; C<inf>16:0</inf>, isoC<inf>16:0</inf>, ante iso-C<inf>15:0</inf>, and anteiso -C<inf>17:0</inf> were major cellular fatty acids; diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylinositol mannoside were major phospholipids; and DNA G + C contents were 71.5 mol%. Phylogenetic analysis based on 16S rRNA gene and genome sequences indicated that strains WSLK1–3T, WSLK1–4, and WSLK1–5 are closely related to Streptomyces canus DSM 40017T (=JCM 4212T), and S. pseudovenezuelae DSM 40212T (=JCM 11516T), respectively. The 16S rRNA gene sequences, average nucleotide identity based on BLAST (ANIb) and MUMmer (ANIm), and digital DNA-DNA hybridization (dDDH) values among the three strains were 100%, 99.12%, 99.33%, and 94.3%, respectively, indicating that these strains belong to the same species. Strains WSLK1–3T, WSLK1–4, and WSLK1–5 showed 88.54–90.62% ANIb, 90.99–92.27% ANIm, and 40.4–45.1% to their closely related type strains: S. canus JCM 4212T, and S. pseudovenezuelae JCM 11516T. All novel strains were pathogenic, causing necrosis on potato tuber slices, inhibiting plant seedlings, and inducing superficial to raised scab lesions on potato tubers. Based on the phenotypic, chemotaxonomic, pathogenic, and genomic data, strains WSLK1–3T, WSLK1–4, and WSLK1–5 could be assigned to the novel species within the genus Streptomyces for which the name Streptomyces tuberiscabiei sp. nov. is proposed. The type strain is WSLK1–3T (=TBRC 19150T = LMG 33893T).
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Integrative genome analysis of bacteriocin-producing Lactiplantibacillus pentosus LNP1-39 and its synbiotic role in suppressing food-borne pathogens
(2026-06-01)
Jirakanjanasit, Thanadol
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Choovet, Natladda
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Booncharoen, Auttaporn
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Kingkaew, Engkarat
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Poothong, Saranporn
Lactic acid bacteria were isolated from traditional Thai-fermented foods. Among these, the strain LNP1-39, closely related to Lactiplantibacillus pentosus, was selected for further study because of its non-pathogenic profile. The bacteriocins produced by L. pentosus LNP1-39 were proteinaceous substances that exhibited strong antimicrobial activity across a wide pH range (pH 2–11; 6400–2400 AU/mL) and thermal stability at 100 °C for 40 min (400 AU/mL). These bacteriocins showed a narrow antimicrobial spectrum, effectively targeting Gram-positive pathogens, such as Kocuria rhizophila MIII, Enterococcus faecalis JCM 5803 T, and Listeria monocytogenes ATCC 19115. Comprehensive safety assessments, including whole-genome analysis and in vitro tests, confirmed a low risk of antibiotic resistance and the absence of virulence factors. Strain LNP1-39 was confirmed to be closely related to L. pentosus DSM 20314 T via digital DNA‒DNA hybridization (dDDH; 75.4%), with average nucleotide identity (ANI) at 96.56% ANIb and 97.22% ANIm values. Additionally, LNP1-39 produces pediocin with notable similarity (76.29% identity to pediocin) and presents low risks for antibiotic-resistance genes or transfer genes while providing antioxidant properties. Strain LNP1-39 survived harsh gastrointestinal tract conditions and exhibited a favorable prebiotic index and positive prebiotic activity score when paired with polydextrose or isomalto-oligosaccharide. These findings support L. pentosus LNP1-39 as potential bacteriocin-producing lactic acid bacteria for further application in food preservation and pathogen control or as a synbiotic.
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Functional and genomic characterization of Pediococcus pentosaceus NR4-4 reveals a safe bacteriocinogenic probiotic with strong anti-listerial activity and prebiotic metabolism
(2026-05-01)
Ratthanachot, Natnarin
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Woraprayote, Weerapong
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Janyaphisan, Thitiphorn
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Tanasupawat, Somboon
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Ochaikul, Duangjai
The growing interest in bacteriocin-producing lactic acid bacteria from traditional fermented foods has highlighted the value of strains that combine antimicrobial activity, probiotic functionality, and genome-supported safety. This study presents an integrated functional and probiogenomic characterization of Pediococcus pentosaceus NR4-4 isolated from Thai fermented mustard greens. The strain was found to produce a heat-stable class IIa bacteriocin with pronounced inhibitory activity against Listeria monocytogenes . In addition, NR4-4 exhibited strong tolerance to simulated gastrointestinal conditions and demonstrated effective adhesion to Caco-2 intestinal epithelial cells. In vitro safety evaluations confirmed that the strain was non-hemolytic and did not exhibit cytotoxic effects toward AGS or Caco-2 cell lines. Whole-genome sequencing verified species identity and revealed the presence of pediocin-related gene clusters, carbohydrate-active enzymes associated with fructooligosaccharide utilization, and a favorable genome-based safety profile. Notably, no virulence factors, biogenic amine biosynthesis pathways, plasmids, or transferable antimicrobial resistance determinants were detected. The preferential metabolism of fructooligosaccharides further suggests compatibility with synbiotic formulations. Overall, these findings indicate that P. pentosaceus NR4-4 is a genomically supported, safe, and multifunctional probiotic candidate with potential applications in food biopreservation and functional food development.
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Optimization of astaxanthin production by Rhodotorula toruloides CB6-10/1 using response surface methodology and its genome analysis
(2026-02-01)
Butsararattanagomen, Pornthipa
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Tanasupawat, Somboon
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Kingkaew, Engkarat
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Kotatha, Ditpon
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Soontorngun, Nitnipa
Astaxanthin is a valuable carotenoid with potent antioxidant properties and has broad applications in the pharmaceutical, nutraceutical, and cosmetic industries. In this study, Rhodotorula toruloides CB6-10/1, isolated from Canna indica L. flowers, was evaluated for astaxanthin production. The orange-red pigment was confirmed as astaxanthin via thin-layer chromatography and high-performance liquid chromatography, with quantification performed by spectrophotometry. Comprehensive genome analysis and production optimization of R. toruloides CB6-10/1 confirmed the presence of key astaxanthin biosynthesis genes, such as CrtYB, CrtI, CrtW, CrtZ, and CrtR, which facilitate the conversion of β-carotene to astaxanthin through hydroxylation and ketolation. The key parameters, including carbon and nitrogen sources, their concentrations, trace elements, agitation speed, and pH, were systematically evaluated to optimize production. Although copper appeared beneficial in the Plackett–Burman screening, its effect and those of other metals were not significant. Optimization using Response Surface Methodology for cost-effective nitrogen sources determined that a combination of 1.10 g/L yeast extract, 10.0 g/L peptone, and 0.50 g/L ammonium sulfate yielded the maximum astaxanthin production of 4.728 mg/L, under cultivation conditions of pH 4.5, 200 rpm, and 30 g/L glucose, representing a fourfold increase compared with the basal medium. This optimization not only enhances pigment production efficiency but also reduces dependency on costly trace elements, improving process scalability and economic feasibility. Overall, these results demonstrate R. toruloides CB6-10/1 as a promising microbial source for sustainable astaxanthin production with potential further applications.
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Characterization of red pigmented yeasts and genes associated with astaxanthin synthesis in Rhodotorula mucilaginosa HL26-1 and Rhodotorula paludigena LL69-1
(2026-01-01)
Hoondee, Patcharaporn
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Tedsree, Nisachon
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Phuengjayaem, Sukanya
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Kingkaew, Engkarat
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Sritularak, Boonchoo
Background: Astaxanthin, a red xanthophyll carotenoid, is a powerful antioxidant, anticancer, and glucose and lipid homeostasis regulator. Some pigmented yeasts belonging to the genus Rhodotorula, the well-known yeast for beta-carotene production, have been reported as natural astaxanthin producers. However, the lack of genomic data on astaxanthin-producing strains within these species hinders the identification of biosynthetic routes, molecular characterization of these pathways, and gene editing applications. Methods: This study explored the diversity and astaxanthin production capability of cultivable pigmented yeast in flower samples. The astaxanthin production ability was inspected by three consecutive methods, including thin-layer chromatography (TLC) for the preliminary step, followed by quantitative spectrophotometry and high-performance liquid chromatography (HPLC) for qualitative validation. The draft genome sequence and astaxanthin-producing genes of astaxanthin-producing yeasts were examined. Results: Twelve of 23 yeasts from floral samples exhibited natural pigmentation, with colors ranging from pinkish-orange to red, and exhibited the potential for astaxanthin synthesis. These yeasts were Rhodotorula paludigena (three strains) and Rhodotorula mucilaginosa (nine strains). Among R. mucilaginosa strains, HL26-1 had the greatest astaxanthin content (104.98 ± 0.13 μg/g DCW) and yield (0.9280 ± 0.0012 mg/L). Strain LL69-1 has the greatest astaxanthin content (251.78 ± 0.27 μg/g DCW) and yield (1.8632 ± 0.0023 mg/L) among R. paludigena strains. The 18.78 Mbp R. mucilaginosa HL26-1 genome includes 5,711 protein-coding genes. Conversely, the R. paludigena LL69-1 genome was 20.99 Mbp, encompassing 6,782 predicted genes. A comprehensive investigation of draft genome sequences of these two strains identified CrtE, CrtYB, CrtI, CrtS, and CrtR as potential astaxanthin transcription genes. Conclusion: Here, our results highlight the outstanding potential of two naturally pigmented yeasts, R. mucilaginosa HL26-1 and R. paludigena LL69-1, for astaxanthin production. Furthermore, our findings provide information on the whole genome and protein-encoded genes associated with astaxanthin production, which serve as valuable biological resources for various biotechnological applications.
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Enhancement of astaxanthin production in novel red yeast Rhodosporidiobolus sp. SP3-3/4 and genomic characterization
(2025-10-01)
Phuengjayaem, Sukanya
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Kingkaew, Engkarat
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Hoondee, Patcharaporn
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Tanasupawat, Somboon
Astaxanthin is a red carotenoid and potent antioxidant with anti-inflammatory, anti-cancer, neuroprotective, and immuno-enhancing benefits. This study focused on enhancing astaxanthin production using a novel red yeast, strain SP3-3/4, through genomic analysis. Strain SP3-3/4 shared 99.66% sequence identity in the D1/D2 domain of the large subunit rRNA gene with Rhodosporidiobolus ruineniae CBS 5001T. Whole-genome analysis indicated 82.54% similarity to R. ruineniae JCM 8097T, with average nucleotide identity (ANI) values below 80% for other strains. The ANI result, lower than the 95% cutoff, confirms SP3-3/4 as a novel species, Rhodosporidiobolus sp. SP3-3/4. Key astaxanthin synthesis genes, including CrtE, CrtYB, CrtI, CrtS, CrtR, CrtW, CrtO, and CrtZ, were annotated. Astaxanthin production was verified using HPLC and LC-MS. Optimization of medium composition and physical parameters identified optimal conditions as 20 g/L sucrose, 3 g/L yeast extract, and 5 g/L peptone, with an initial medium pH of 6.5. Maximum cell growth and astaxanthin content, reaching 9.615 g/L and 0.46 mg/g DCW, respectively, were achieved after 5 days of cultivation, corresponding to an astaxanthin yield of 6.93 mg/L and a productivity rate of 1.39 mg/L/day. Notably, a maximum productivity of 1.45 mg/L/day occurred in 3 days. These findings elucidated comprehensive optimization of astaxanthin production, incorporating functional genomic assessment and analysis of protein-encoded genes of astaxanthin-producing yeast Rhodosporidiobolus sp. SP3-3/4. Such insights represent valuable biological resources with significant implications for diverse biotechnological and bioinformatics applications.
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Antioxidant Activity, γ-Aminobutyric Acid, and Genome Analysis of Lactiplantibacillus plantarum FL13-2 from Fermented Rice Flour
(2025-09-01)
Songsumanus, Apakorn
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Pinyosnit, Natawadee
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Kingkaew, Engkarat
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Panngeun, Thanapol
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Charunanthasunthon, Worasan
Ten rod-shaped isolates of lactic acid bacteria (LAB) from the traditional fermented rice flour, khao-khab were identified as belonging to the genus Lactobacillus based on phenotypic characteristics. Group I isolates (FL12-1, FL18-1, FL19-1S, FL23-1, FL24-1, FL25-1, and FL26-1) were closely related to Limosilactobacillus fermentum, exhibiting 16S rRNA gene sequence similarity of 99.4%–100%. Group II included FL13-2 and FL22-2 (Group IIA) and FL17B (Group IIB), closely related to Lactiplantibacillus plantarum (99.9%–100%) and Lactiplantibacillus pentosus (100%), respectively. All isolates demonstrated strong antioxidant potential, with 2,2-Diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity—measured by the standard DPPH assay—ranging from 78.49±1.01% to 91.18±3.95%, surpassing that of ascorbic acid. Strain FL13-2, identified as L. plantarum through genomic analysis (Average Nucleotide Identity (ANI) 98.5%, digital DNA-DNA hybridization (dDDH) 92.5%), produced 2.43 g/L of γ-aminobutyric acid (GABA). It harbored key biosynthesis and transport genes (gadB, gadC, gatABCD, pdxK). Phylogenetic analysis confirmed high sequence similarity of these genes with other LAB strains, supporting their functional roles. The gad system was implicated in acid resistance and GABA production under low pH conditions. Genome annotation revealed bacteriocin genes (Enterocin X β, Plantaricin E, and F) and indicated low pathogenicity and absence of virulence factors. Antimicrobial resistance genes (vanH, vanT, vanY) were detected; however, these are intrinsic to LAB and associated with essential cell wall biosynthesis rather than acquired resistance. Additionally, the presence of the qacJ efflux pump and hlyIII gene—both commonly found in probiotic strains—further supports the safety profile of FL13-2. These findingshighlight L. plantarum FL13-2 as a promising multifunctional probiotic candidate with potent antioxidative, GABA-producing, and antimicrobial properties.
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Evaluating the safety and efficacy of Lacticaseibacillus paracasei TISTR 2593 as a therapeutic probiotic for obesity prevention
(2025-01-01)
Sitdhipol, Jaruwan
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Niwasabutra, Kanidta
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Chaiyawan, Neungnut
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Nuankham, Kamonsri
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Thanagornyothin, Thanaphol
Several recent studies have reported the potential of probiotics in reducing body weight and fat mass and improving glucose and lipid metabolism. Therefore, probiotic administration is considered an alternative approach for treating obesity. The objective of this study was to evaluate the probiotic properties and antiadipogenic potential of the strain TISTR 2593. Through whole-genome sequence analysis, the strain TISTR 2593 was identified as Lacticaseibacillus paracasei. L. paracasei TISTR 2593 exhibited γ-hemolytic activity (nonhemolysis) and demonstrated susceptibility to antibiotics, indicating that it is generally safe for consumption. Additionally, this strain displayed desirable probiotic properties, including tolerance to artificial gastric juice and bile salts, adhesion to Caco-2 cells, and the ability to inhibit pathogens. Furthermore, L. paracasei TISTR 2593 exhibited cholesterol-reducing capability and demonstrated antiadipogenic activity. In 3T3-L1 adipocytes, treatment with 10% (w/v) heated L. paracasei TISTR 2593 cells resulted in an approximately 50% reduction in lipid accumulation, similar to the positive control (quercetin). Moreover, L. paracasei TISTR 2593 heat-killed cells dose-dependently decreased the expression levels of CCAAT/enhancer-binding protein-α and peroxisome proliferator-activated receptor-γ, two vital transcription factors involved in the early stage of adipocyte differentiation. These findings suggest that L. paracasei TISTR 2593 possesses probiotic and functional properties, including antiadipogenic activity, supporting its potential as a therapeutic probiotic supplement for preventing obesity. Overall, the results of this study indicate that L. paracasei TISTR 2593 exhibits promising probiotic characteristics and beneficial effects on adipogenesis modulation, reinforcing its potential as a therapeutic option in obesity prevention.
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Genomic comparison of gamma-aminobutyric acid-producing Levilactobacillus brevis and Companilactobacillus zhachilii strains from Thai fermented foods
(2025-01-01)
Pakdeeto, Amnat
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Phuengjayaem, Sukanya
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Kingkaew, Engkarat
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Tungkajiwangkoon, Santhita
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Phitchayaphon, Chantharat
Importance of the work: The GABA-producing Companilactobacillus zhachilii isolated from fermented pork (‘nham’) demonstrates both efficacy and safety in GABA production. Objectives: To identify the GABA-producing strains ASK-1 and ANB-1 to compare their genomes with those of Levilactobacillus brevis and Companilactobacillus zhachilii strains. Materials and Methods: Two fermented food samples were collected and used for the isolation of lactic acid bacteria. The strains obtained were evaluated for GABA production. The selected strains were identified based on their phenotypic and genotypic characteristics. Genomic comparisons of the GABA-producing strains were performed using genome sequencing, assembly, annotation and comparative analysis. This analysis included the examination of CRISPR regions, antimicrobial genes, functional attributes and genome visualization. Results: The GABA-producing lactic acid bacteria (ASK-1 and ANB-1) were isolated from traditional Thai fermented foods (‘sai-krog-prieo’ and ‘nham’). The strains ASK-1 and ANB-1 produced 9.12 ± 0.51 g/L GABA and 12.73 ± 0.57 g/L GABA, respectively. On the basis of phenotypic characteristics and 16S rRNA gene sequencing, strain ASK-1 presented 100% sequence similarity to Levilactobacillus brevis ATCC 14687T, whereas ANB-1 presented 99.93% similarity to Companilactobacillus zhachilii HBUAS52074T. Genome analysis identified ASK-1 as L. brevis ATCC 367, with an average nucleotide identity based on a BLAST (ANIb) value of 98.86% and ANB-1 with an ANIb value of 96.92%, to C. zhachilii HBUAS52074T. Additionally, genomic studies revealed GABA-producing genes (gadA and gadB) via the KofamKOALA-KEGG Orthology database. Main finding: Levilactobacillus brevisASK-1 and Companilactobacillus zhachiliiANB-1 efficiently and safely produced GABA and exhibited probiotic properties, making them promising starter cultures for functional food production in both local food and industrial fermentation processes.
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ENHANCING SUGAR RECOVERY FROM SUGARCANE BAGASSE: OPTIMIZING MICROWAVE-ASSISTED ALKALINE PRETREATMENT METHODS FOR BIOBASED ENERGY
(2025-01-01)
Kingkaew, Engkarat
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Tanasupawat, Somboon
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Phuengjayaem, Sukanya
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Poothong, Saranporn
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Ochaikul, Duangjai
This study optimized microwave-assisted alkaline pretreatment for enhancing sugar recovery from sugarcane bagasse. Bagasse was dried, ground, and sieved to a uniform particle size before undergoing pretreatment with sodium hydroxide (NaOH). The effects of microwave power, duration, and NaOH concentration were investigated. Optimal conditions were identified as 800 W microwave power, 8% (w/v) NaOH, and a 2-minute duration (18.69 ± 0.05 g/L). An NaOH concentration of 8% (w/v) achieved high sugar recovery while minimizing chemical use, highlighting the balance between efficiency and sustainability. These findings provide a foundation for improving lignocellulosic biomass pretreatment for biofuel and biochemical production.

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