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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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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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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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Lentilactobacillus terminaliae sp. nov., isolated from tree bark (Terminalia ivorensis Chev.) and its antioxidant activity
(2025-01-01)
Phuengjayaem, Sukanya
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Kingkaew, Engkarat
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Chamroensaksri, Nitcha
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Phongsopitanun, Wongsakorn
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Tanasupawat, Somboon
A Gram-stain-positive, facultatively anaerobic, rod-shaped strain, designated SPB1-3T, was isolated from tree bark. This strain exhibited heterofermentative production of dl-lactic acid from glucose. Optimal growth was observed at 25–40 °C, pH 4.0–7.0, and in the presence of 3% (w/v) NaCl. The cell wall peptidoglycan contained lysine and aspartic acid. The predominant fatty acids identified were C<inf>16:0</inf> and the Summed feature 7 (C<inf>19:1</inf> ω7c/C<inf>19:1</inf> ω6c and/or C<inf>19:1</inf> ω6c/ω7c/19cy). The polar lipid profile included phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol, along with two unidentified phospholipids, two unidentified amino lipids and two unidentified lipids. Phylogenetic analysis based on 16S rRNA gene sequences positioned strain SPB1-3T within the genus Lentilactobacillus, showing a close relation to Lentilactobacillus kosonis NBRC 111893T (99.86%) and Lentilactobacillus curieae CCTCC M 2011381T (98.65%). The whole genome of strain SPB1-3T comprised 1 932 998 base pairs with 1955 coding genes and a DNA G+C content of 37.8%. Digital DNA–DNA hybridization between strain SPB1-3T and closely related type strains ranged from 19.50 to 27.20%. The average nucleotide identity ranged from 84.21 to 85.56%, and the average amino acid identity ranged from 57.25 to 85.99%, both falling below the established thresholds for species delineation. Strain SPB1-3T was clearly distinguishable from related Lentilactobacillus species based on its phenotypic and chemotaxonomic char-acteristics, 16S rRNA gene sequence similarity and whole genome analysis. Additionally, the strain exhibited radical scavenging activity at 66.92% and demonstrated 82.32% inhibition in the tyrosinase inhibitory assay. These findings support the classification of strain SPB1-3T as a novel species within the genus Lentilactobacillus, for which the name Lentilactobacillus terminaliae sp. nov. is proposed. The type strain is SPB1-3T (=JCM 35081T=TISTR 10005T).
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Paracraurococcus lichenis sp. nov., isolated from lichen in Thailand
(2024-10-01)
Kingkaew, Engkarat
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Kato, Shingo
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Iino, Takao
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Itoh, Takashi
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Ohkuma, Moriya
A novel bacterium, designated as strain LOR1-02T and isolated from a lichen sample collected from Kham Riang Subdistrict, Kantharawichai District, Maha Sarakham Province, Thailand, underwent thorough investigation utilizing a polyphasic taxonomic approach. Strain LOR1-02T demonstrated growth within a temperature range of 20–42 °C (optimal at 30 °C), pH range of 5.0–7.5 (optimal at pH 7.0), and tolerance to 4.0% (w/v) NaCl. Phylogenetic analysis revealed its close relation to Paracraurococcus ruber JCM 9931T, with a 16S rRNA gene sequence similarity of 97.16%, placing it within the genus Paracraurococcus. The approximate genome size of strain LOR1-02T was determined to be 8.6 Mb, with a G + C content of 70.9 mol%. Additionally, ANIb, ANIm, and AAI values between the whole genomes of strain LOR1-02T and type strains were calculated as 82.6–83.4%, 86.1–86.8%, and 81.4–82.2%, respectively, while the dDDH value was determined to be 26.3–28.5% (C.I. 24.0–31.0%). The predominant fatty acids detected were C<inf>18:1</inf>ω7c and/or C<inf>18:1</inf>ω6c, C<inf>16:0</inf>, and C<inf>18:1</inf>2OH. The major ubiquinone identified was Q-10, and the polar lipids included phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol, along with unidentified phosphoaminolipid, lipids, and an amino lipid. Based on comprehensive phenotypic, chemotaxonomic, and genotypic characterization, it is concluded that strain LOR1-02T represents a novel species within the genus Paracraurococcus, for which the name Paracraurococcus lichenis sp. nov. is proposed. The type strain designation is LOR1-02T (= JCM 33121T = NBRC 112776T = TISTR 2503T).
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Actinomycetospora termitidis sp. nov., an insect-derived actinomycete isolated from termite (Odontotermes formosanus)
(2024-05-01)
Supong, Khomsan
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Niemhom, Nantawan
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Suriyachadkun, Chanwit
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Phongsopitanun, Wongsakorn
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Tanasupawat, Somboon
Strain Odt1-22T, an insect-derived actinomycete was isolated from a termite (Odontotermes formosanus) that was collected from Chanthaburi province, Thailand. Strain Odt1-22T was aerobic, Gram-stain-positive, and produced bud-like spore chain on the substrate hypha. According to chemotaxonomic analysis, strain Odt1-22T contained meso-diaminopimelic acid in peptidoglycan and the whole-cell hydrolysates contained arabinose, galactose, glucose, and ribose. The major menaquinone was MK-8(H<inf>4</inf>). The diagnostic phospholipids were diphosphatidylglycerol, hydroxyphosphatidylethanolamine, phosphatidylethanolamine and phosphatidylglycerol. Phylogenetic analysis based on 16 S rRNA gene sequence revealed that strain Odt1-22T was identified to the genus Actinomycetospora and showed high similarity values with A. chiangmaiensis DSM 45062 T (99.24%), A. soli SF1T (99.24%) and A. corticicola 014-5 T (98.17%). The genomic size of strain Odt1-22T was 6.6 Mbp with 73.8% G + C content and 6355 coding sequences (CDSs). The genomic analysis, strain Odt1-22T and closely related species A. chiangmaiensis DSM 45062 T, A. soli SF1T and A. corticicola DSM 45772 T displayed the values of average nucleotide identity-blast (ANIb) at 83.7–84.1% and MUMmer (ANIm) at 86.6–87.0%. Moreover, the results of digital DNA-DNA hybridization values between strain Odt1-22T and related Actinomycetospora species were 45.8−50.5% that lower than the threshold value of commonly used to delineate separated species level. On the basis of phenotypic, chemotaxonomic, and genotypic data, strain Odt1-22T represented a novel species within the genus Actinomycetospora, for which the name Actinomycetospora termitidis sp. nov. is proposed. The type strain of the species is Odt1-22T (= TBRC 16192 T = NBRC 115965 T).
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Lactiplantibacillus argentoratensis and Candida tropicalis Isolated from the Gastrointestinal Tract of Fish Exhibited Inhibitory Effects against Pathogenic Bacteria of Nile Tilapia
(2023-02-01)
Siangpro, Noppadon
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Chuakrut, Songkran
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Sirimanapong, Wanna
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Tanasupawat, Somboon
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Phongsopitanun, Wongsakorn
Nile tilapia is one of the most consumed farmed fish in the world. The outbreak of pathogenic bacterial diseases causes high mortality rates and economic losses in Nile tilapia farming. Antibiotic administrations are commonly utilized to inhibit and prevent bacterial infections. However, antibiotics are expensive and cause serious concerns for antibiotic resistance in fish that can be potentially transferred to humans. As an alternative solution, probiotics can be used to prevent infection of pathogenic bacteria in fish. In this work, both bacteria and yeast were isolated from fish gastrointestinal tracts and their inhibitory activity against Nile tilapia pathogenic bacteria was evaluated, as well as other probiotic properties. In this study, 66 bacteria and 176 acid tolerant yeasts were isolated from fish gastrointestinal tracts. Of all isolated microorganisms, 39 bacterial and 15 yeast isolates with inhibitory effect against pathogens were then examined for their probiotic properties (acidic and bile salt resistance, adhesion potential, and biofilm formation), formation of antibacterial factor survival rate under simulated gastrointestinal fluid, and safety evaluation. AT8/5 bacterial isolate demonstrated probiotic properties and the highest inhibition against all 54 tested pathogens while YON3/2 yeast isolate outperformed the inhibitory effect among all yeast isolates. These two probiotic isolates were further identified by 16S rDNA and the D1/D2 domain of 26S rDNA sequence analysis for bacterial and yeast identification, respectively. AT8/5 and YON3/2 showed the highest similarity to Lactiplantibacillus argentoratensis and Candida tropicalis, respectively. This is the first report on isolated L. argentoratensis and C. tropicalis with antipathogenic bacteria of Nile tilapia properties. Collectively, AT8/5 and YON3/2 could be potentially used as promising alternatives to existing antibiotic methods to prevent pathogenic bacteria infection in Nile tilapia farming.
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Streptomyces chumphonensis sp. nov., isolated from marine sediments
(2014-01-01)
Phongsopitanun, Wongsakorn
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Thawai, Chitti
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Suwanborirux, Khanit
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Kudo, Takuji
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Ohkuma, Moriya
Two actinomycete strains, KK1-2T and CPB4-7, were isolated from marine sediments collected in Chumphon province, Thailand. Chumphon province, Thailand. Their taxonomic positions were determined using a polyphasic approach. The morphological, cultural and chemotaxonomic characteristics of these isolates were consistent with the classification of the strains as representing a member of the genus Streptomyces. They contained LL-diaminopimelic acid in their cell wall peptidoglycan; the whole-cell sugars were ribose and glucose. The predominant menaquinones were MK9-(H<inf>6</inf>) and MK9-(H<inf>8</inf>). The major polar lipids were phosphatidylethanolamine, phosphatidylinositol, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol mannosides. The predominant cellular fatty acids were anteiso-C<inf>15: 0</inf>, iso-C<inf>16: 0</inf> and iso-C<inf>15: 0</inf>. On the basis of 16S rRNA gene sequence similarity studies, these isolates were determined to be closely related to Streptomyces xinghaiensis JCM 16958T (98.2 %), Streptomyces rimosus subsp. paromomycinus JCM 4541T (98.1 %), Streptomyces sclerotialus JCM 4828T (98.1 %) and Streptomyces flocculus JCM 4476T (98.0 %). The G+C contents of the genomic DNA of strains KK1-2T and CPB4-7 were 73.3 and 74.2 mol%, respectively. They could be clearly distinguished from the related type strains by a low DNA-DNA relatedness and phenotypic differences. On the basis of these results, these strains represent a novel species of the genus Streptomyces, for which the name Streptomyces chumphonensis sp. nov. (type strain KK1-2T = JCM 18522T = TISTR 2106T = PCU 330T) is proposed. © 2014 IUMS.
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Identification of lactic acid bacteria and yeasts from fermented rice product (Khao-khab)
(2013-01-01)
Tanasupawat, Somboon
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Phongsopitanun, Wongsakorn
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Lorliam, Wanlapa
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Luangsakul, Naphatrapi
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Chatanon, Lawan
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