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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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Genomic insights into arsenic and antibiotic resistance in Comamonas thiooxydans strains F1-6 and A7-5
(2026-04-01)
Sitlaothaworn, Kanchana
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Phongsopitanun, Wongsakorn
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Chitpirom, Kitja
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Kingkaew, Engkarat
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Lee, Jung Sook
Two arsenic-resistant, Gram-negative, aerobic rod-shaped bacterial strains, F1-6 and A7-5, which were isolated from agricultural soil in Thailand, were systematically studied. They grew at 30 °C, pH 5–11, and in 3% (w/v) NaCl. Ubiquinone with eight isoprene units (Q-8) and the cellular fatty acids C1<inf>6:0</inf>, C<inf>18:1</inf> ω7c, and C<inf>17:0</inf> CYCLO were the major components. Phylogenetic analysis via 16S rRNA gene sequences revealed that strains F1-6 and A7-5 were affiliated with the genus Comamonas and closely related to C. thiooxydans DF2T and C. testosteroni KCTC 2990T, with 99.79% and 99.86% similarity, respectively. The average nucleotide identity and digital DNA-DNA hybridization values between F1-6 and C. thiooxydans DF2T were 97.89% and 85.7%, respectively, whereas those between A7-5 and C. thiooxydans DF2T were 97.23% and 81.3%, respectively. Thus, both the F1-6 and A7-5 were identified as C. thiooxydans. The draft genome sizes of F1-6 and A7-5 were 5.2 and 5.3 Mb, comprising 87 and 84 contigs, with DNA G+C contents of 61.5% and 61.4%, respectively. The genomes of both strains contained ars cluster genes and many genes for growth and resistance to heavy metals and antibiotics, similar to those of C. testosteroni ATCC 11996T, C. thiooxydans CNB-1 substr. CNB-2 Chr, and C. terrae NBRC 106524T. Nevertheless, the acr3, qacG, and vanH genes in the vanO cluster were found only in C. terrae NBRC 106524T. This study provides more comprehensive insight into As-resistant bacteria and could be applied to the bioremediation of As and other heavy metals in the future.
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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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Genomic Assessment, Metabolic Profile Mapping, and Anti-Helicobacter pylori Activity of Lactococcus lactis SK2-659 from Thai Fermented Green Mustard (Pak-kad-dong)
(2026-01-01)
Kingkaew, Engkarat
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Woraprayote, Weerapong
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Sitdhipol, Jaruwan
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Vilaichone, Ratha Korn
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Visessanguan, Wonnop
Probiotics play crucial roles in promoting gut health, enhancing immunity, and combating pathogenic microorganisms, with increasing interest in their applications in the food and therapeutic industries. Lactococcus lactis, a well-known lactic acid bacterium, has emerged as a promising candidate owing to its probiotic traits and safety profile. In this study, we investigated the probiotic potential and genomic profile of Lactococcus lactis SK2-659, a strain isolated from Thai fermented green mustard (Pak-kad-dong). Genomic analysis revealed numerous genes associated with probiotic traits, including stress tolerance, adhesion, and antimicrobial activity, with a particular focus on bacteriocin SK2-659, which was effective against pathogenic bacteria such as Helicobacter pylori. The bacteriocin produced by L. lactis SK2-659, identified as nisin Z, disrupts bacterial membranes via pore formation, leading to cell lysis. Metabolomic profiling further highlighted its ability to increase carbohydrate and amino acid metabolism, supporting cell growth and survival in acidic environments. Also, amino acid metabolism (elevated tryptophan, tyrosine, histidine) supports acid tolerance and immune modulation. Tryptophan metabolism produces indole derivatives, which are known to benefit gut health and immunity. Additionally, strain SK2-659 demonstrated strong tolerance to gastrointestinal conditions, high adhesion capacity to intestinal cells, and immunomodulatory effects, contributing to gut health. Safety assessments confirmed the absence of virulence factors, pathogenic traits, and antibiotic resistance genes, along with a lack of biogenic amine production, underscoring its suitability for food and health applications. These findings establish L. lactis SK2-659 as a promising probiotic candidate with potential industrial applications in functional foods, food preservation, and therapeutic products. Given its probiotic properties, antimicrobial activity, and safety profile, this strain is particularly suited for the food industry as a functional food ingredient and natural bio-preservative, as well as the healthcare and pharmaceutical industries for use in therapeutic probiotics and gut health formulations.
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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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Genomic Characterization and Hydrolysis Enzyme of Piscibacillus salipiscarius RBU1-1ᵀ and Allobacillus salarius SKP4-8ᵀ Isolated from Fermented Fish Products
(2026-01-01)
Namwong, Sirilak
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Chaimongkol, Apichai
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Kingkaew, Engkarat
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Phongsopitanun, Wongsakorn
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Chamroensaksri, Nitcha
Two halophilic bacterial strains, Piscibacillus salipiscarius RBU1-1ᵀ and Allobacillus salarius SKP4-8ᵀ, were isolated from traditional Thai fermented foods, namely pla-ra from Ratchaburi, Thailand, and ka-pi from Samut Sakhon, Thailand, respectively. Comparative genomics confirmed their taxonomic distinctiveness, with RBU1-1ᵀ representing a novel species and SKP4-8ᵀ showing clear genomic separation from its closest relatives. The draft genomes were 2.99 Mb (36.7 mol% G+C) for RBU1-1ᵀ and 2.59 Mb (38.8 mol% G+C) for SKP4-8ᵀ. Both strains encoded hydrolytic enzymes and secondary metabolite pathways, with SKP4-8ᵀ displaying higher protease activity and RBU1-1ᵀ harboring ectoine biosynthetic and stress-response genes. RBU1-1ᵀ encoded the biosynthesis pathways for ectoine, tryptophan, and thiamine, while SKP4-8ᵀ encoded thiamine, riboflavin, coenzyme A, and menaquinone, indicating their potential contributions to postbiotic and nutritional value. Safety assessment revealed the absence of biogenic amine, antibiotic biosynthesis, and major virulence genes in both strains. Although antimicrobial resistance-associated genes were detected, no complete clusters were identified, suggesting low phenotypic risk. Computational pathogenicity prediction indicated a low probability for RBU1-1ᵀ (0.242) and a higher probability for SKP4-8ᵀ (0.945), though these require cautious interpretation. Overall, genomic evidence and enzymatic activity support RBU1-1ᵀ and SKP4-8ᵀ as safe, functional starter culture candidates, with RBU1-1ᵀ showing strong potential through postbiotic biosynthesis and SKP4-8ᵀ through proteolytic activity.
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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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