Functional genome analysis and anti-Helicobacter pylori activity of a novel bacteriocinogenic Lactococcus sp. NH2-7C from Thai fermented pork (Nham).

Helicobacter pylori, linked to gastric diseases, is targeted for probiotic treatment through bacteriocin production. Bacteriocins have gained recognition for their non-toxic effects on host cells and their ability to combat a wide range of pathogens. This study aimed to taxonomically characterize and evaluate the safety and probiotic properties of the novel species of Lactococcus sp. NH2-7C isolated from fermented pork, as well as its bacteriocin NH2-7C, both in vitro and in silico. Comparative genotypic analysis revealed an average nucleotide identity of 94.96%, an average amino acid identity of 94.29%, and a digital DNA-DNA hybridization value of 63.80% when compared to Lactococcus lactis subsp. lactis JCM 5805T. These findings suggest that strain NH2-7C represents a novel species within the genus Lactococcus. In silico assessments confirmed the non-pathogenic nature of strain NH2-7C and the absence of genes associated with virulence and biogenic amine formation. Whole-genome analysis revealed the presence of the nisA gene responsible for nisin A production, indicating its potential as a beneficial compound with anti-Helicobacter pylori activity and non-toxic characteristics. Probiotic assessments indicated bile salt hydrolase and cholesterol assimilation activities, along with the modulation of interleukin-6 and tumour necrosis factor-α secretion. Strain NH2-7C demonstrated gastrointestinal tolerance and the ability to adhere to Caco-2 cells, affirming its safety and probiotic potential. Additionally, its ability to produce bacteriocins supports its suitability as a functional probiotic strain with therapeutic potential. However, further in vitro and in vivo investigations are crucial to ensure its safety and explore potential applications for Lactococcus sp. NH2-7C as a probiotic agent.

Weizmannia acidilactici sp. nov., a lactic acid producing bacterium isolated from soils.

The strains designed PP-18T, JC-4 and JC-7 isolated from soils, were Gram-stain-positive rods, facultative anaerobe, endospore-forming bacteria. The strains produced l-lactic acid from glucose. They showed positive for catalase but negative for oxidase, nitrate reduction and arginine hydrolysis. Strains P-18T, JC-4 and JC-7 were closely related to Weizmannia coagulans LMG 6326T (97.27-97.64%) and W. acidiproducens KCTC 13078T (96.46-96.74%) based on 16S rRNA gene sequence similarity, respectively. They contained meso-diaminopimelic acid in cell wall peptidoglycan and had seven isoprene units (MK-7) as the predominant menaquinone. The major cellular fatty acids of strain PP-18T were iso-C15:0, anteiso-C17:0, iso-C16:0 and anteiso-C15:0. The ANIb and ANIm values among the genomes of strains PP-18T, JC-4 and JC-7 are above 99.4% while their ANIb and ANIm values among them and W. coagulans LMG 6326T and W. acidiproducens KCTC 13078T were ranged from 76.61 to 79.59%. These 3 strains showed the digital DNA-DNA hybridization (dDDH) values of 20.7-23.6% when compared with W. coagulans LMG 6326T and W. acidiproducens DSM 23148T. The DNA G + C contents of strains PP-18T, JC-4 and JC-7 were 45.82%, 45.86% and 45.86%, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphoglycolipids. The results of phenotypic and chemotaxonomic characteristics and whole-genome analysis indicated that the strains PP-18T, JC-4 and JC-7 should be represented as a novel species within the genus Weizmannia for which the name Weizmannia acidilactici sp. nov. is proposed. The type strain is PP-18T (=KCTC 33974T = NBRC 113028T = TISTR 2515T).

The functional starter and its genomic insight for histamine degradation in fish sauce.

Histamine is a biogenic amine significantly formed in fish sauce leading to a major concern in consumers. This study aimed to identify a halophilic bacterium for histamine degradation in fish sauce, and understand its genomic insight to enhance histamine degradation activity. We discovered the novel halophilic bacterium, Bacillus piscicola FBU1786, degrading histamine and other biogenic amines. Its histamine breakdown was growth-associated in a wide range of NaCl concentrations, pH, and temperature from 4% to 18%, 6.0 to 9.0, and 30 to 45 °C, respectively. Genome sequencing revealed the presence of Cu2+-binding oxidase-encoding genes and their heterologous expression with Cu2+ supplementation triggered histamine degradation in E. coli. The degree of histamine breakdown in B. piscicola FBU1786 could be enhanced by Cu2+ addition. Histamine degradation of the culture was evaluated in raw fish sauce mixtures to partially mimic the condition during fish sauce fermentation. Histamine degradation was suppressed to the extent of raw fish sauce, but could be restored by Cu2+ supplementation. Together, this study disclosed B. piscicola FBU1786 with the potent histamine degradation activity, identified Cu2+-binding oxidases responsible for histamine breakdown, and enhanced histamine degradation of the culture using Cu2+ supplementation.

Comparative genomics and proposal of Streptomyces radicis sp. nov., an endophytic actinomycete from roots of plants in Thailand.

Strains DS1-2T and AZ1-7, which were isolated from roots of plants, were taxonomically characterized based on polyphasic taxonomic and taxogenomic approaches. Both strains were Gram-stain-positive and filamentous bacteria which contained LL-diaminopimelic acid in cell-wall peptidoglycan and glucose and ribose in whole-cell hydrolysates. MK-9(H6), MK-10(H6), MK-9(H8), MK-10(H8) and MK-10(H4) were major menaquinones; iso-C16:0 and iso-C16:1G were predominant cellular fatty acids; diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol mannoside presented as major phospholipids; and the DNA G+C contents of 73.2 mol%. Strains DS1-2T and AZ1-7 showed 97.6-98.0 % 16S rRNA gene sequence similarity, 81.0-82.0 % ANIb, 84.8-85.3 % ANIm and 22.0-23.1 % digital DDH to their related type strains: S. specialis GW41-1564T and S. hoynatensis S1412T. Comparative genomics results of these strains and their related type strains also revealed the differences and distributions of key genes associated with stress responses, environmental variables, plant interactions and bioactive metabolites. Based on the phenotypic, chemotaxonomic and genomic data, strains DS1-2T and AZ1-7 could be assigned to the novel species within the genus Streptomyces for which the name Streptomyces radicis sp. nov. is proposed. The type strain is DS1-2T (=JCM 32152T =KCTC 39738T =TISTR 2403T).

Halobacillus fulvus sp. nov., a moderately halophilic bacterium isolated from shrimp paste (Ka-pi) in Thailand.

An aerobic, Gram-stain-positive, endospore-forming, rod-shaped and moderately halophilic strain SKP4-6T, was isolated from shrimp paste (Ka-pi) collected from Samut Sakhon Province, Thailand. Phylogenetic analysis revealed that strain SKP4-6T belonged to the genus Halobacillus and was most closely related to Halobacillus salinus JCM 11546T (98.6 %), Halobacillus locisalis KCTC 3788T (98.6 %) and Halobacillus yeomjeoni KCTC 3957T (98.6 %) based on 16S rRNA gene sequence similarity. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain SKP4-6T and its related species were 18.2-19.3 % and 69.84-84.51 %, respectively, which were lower than the threshold recommended for species delineation. The strain grew optimally at 30-40 °C, at pH 7.0 and with 10-15 % (w/v) NaCl. It contained l-Orn-d-Asp in the cell wall peptidoglycan. The DNA G+C content was 44.8 mol%. The major fatty acids were iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The predominant isoprenoid quinone was MK-7. Phosphatidylglycerol and diphosphatidylglycerol were present as major polar lipids. Based on this polyphasic approach, digital DNA-DNA relatedness and ANI values, strain SKP4-6T represents a novel species of the genus Halobacillus, for which the name Halobacillus fulvus sp. nov. is proposed. The type strain is SKP4-6T (=JCM 32624T=TISTR 2595T).

Genome analysis and optimization of γ-aminobutyric acid (GABA) production by lactic acid bacteria from plant materials.

Gamma-aminobutyric acid (GABA) plays a key role as an inhibitory neurotransmitter in the mammalian sympathetic nervous system and has other health benefits. Molecular characterization, genome analysis, and optimization were investigated to improve GABA production of a selected strain of lactic acid bacteria. Eleven isolates from plant materials were screened for GABA productivity and were identified based on phenotypic and genotypic characteristics. The most potent strain was chosen for genome analysis and GABA production optimization using the response surface methodology (RSM). Each of the two strains was closely related to Lactobacillus plantarum, Lactobacillus brevis, Weissella cibaria, Leuconostoc pseudomesenteroides while each strain was similar to Lactobacillus pentosus, Enterococcus lactis, and Leuconostoc mesenteroides. They produced GABA ranging from 0.036 ± 0.000 to 17.315 ± 0.171 g/L at 72 h-cultivation. Among them, the most potent strain, SL9-6, showed the highest GABA production (17.315 g/L) when cultivated with 10% (v/v) inoculum for 48 h. The draft genome sequence of strain SL9-6 exhibited 96.90% average nucleotide identity value and 74.50% digital DNA-DNA hybridization to Lactobacillus brevis NCTC 13768T. This strain contained a glutamate decarboxylase gene system (gadA, gadB, and gadC). Optimal culture conditions were determined as 40.00 g/L glucose, 49.90 g/L monosodium glutamate, pH 5.94, and 31.10°C by RSM, giving maximum GABA production of 32.48 g/L. Results from RSM also indicated that monosodium glutamate concentration, pH, and temperature were significant variables. GABA production significantly improved here could promise further application of strain SL9-6.

Characterization and comparative genomic analysis of gamma-aminobutyric acid (GABA)-producing lactic acid bacteria from Thai fermented foods.

OBJECTIVES: This study aimed to screen, characterize, and annotate the genome along with the comparison of GABA synthesis genes presented in lactic acid bacteria (LAB). RESULTS: Thirty-five LAB isolates from fermented foods were screened for GABA production using thin-layer chromatography (TLC). Fifteen isolates produced GABA ranging from 0.07 to 22.94 g/L. Based on their GTG5 profiles, phenotypic, and genotypic characteristics, isolates LSI1-1, LSI1-5, LSI2-1, LSI2-2, LSI2-3, LSI2-5, and LSM3-1-4 were identified as Lactobacillus plantarum subsp. plantarum; isolate LSM1-4 was Lactobacillus argentoratensis; isolates CAB1-2, CAB1-5, CAB1-7, and LSI1-4 were Lactobacillus pentosus; and CAB1-1, LSM3-1-1 and LSM3-2-3 were Lactobacillus fermentum. Strains LSI2-1 and CAB1-7 from pickled vegetables were selected for genome analysis. The gadA gene (1410 bp, 470aa) was encountered in GABA production of both strains and no other glutamate decarboxylase (GAD) genes were found in the genomes when compared with other LAB strains. The presence of gadA is evidence for GABA production. Strains LSI2-1 and CAB1-7 produced 22.94 g/L and 11.59 g/L of GABA in GYP broth supplemented with 3% (w/v) MSG at 30 °C for 72 h, respectively. CONCLUSIONS: Our report highlights the characterization of LAB and GABA production of L. plantarum LSI2-1 strain with its GABA synthesis gene. GABA production of strains LSI2-1 and CAB1-7 in GYP broth with 3% (w/v) MSG and comparative GAD genes.

Micromonospora musae sp. nov., an endophytic actinomycete isolated from roots of Musa species.

Two novel actinobacterial strains, MS1-9T and NGC1-4, were isolated from roots of Musa (ABB) cv. 'Kluai Namwa', collected from Chachoengsao province, and Musa (ABB) cv. 'Kluai Chang', from Suphan Buri province, Thailand, respectively. Comparative analysis of 16S rRNA gene (98.0 to 98.9% similarity), gyrase subunit B (gyrB) gene and whole-genome sequences emphasised that the strains MS1-9T and NGC1-4 showed closely related with Micromonospora peucetia DSM 43363T, M. krabiensis JCM 12869T and M. avicenniae DSM 45758T, respectively. Strains MS1-9T and NGC1-4 contained meso-diaminopimelic acid in cell-wall peptidoglycan. Whole-cell sugars were glucose, xylose, mannose, and ribose. The acyl type of peptidoglycan was glycolyl. MK-10(H6), MK-9(H6), and MK-10(H8) were presented as the major menaquinones. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylinositol were detected as predominant phospholipid profiles. The major cellular fatty acids consisted of iso-C15:0, anteiso-C15:0, anteiso-C17:0, iso-C17:0 and C17:0. The DNA G+C content of strains MS1-9T and NGC1-4 were 72.2 and 72.3mol%, respectively. Draft genome sequences indicated by ANI values and digital DNA-DNA hybridisation analysis asserted that the strains MS1-9T and NGC1-4 should be represented as a novel species within the genus Micromonospora for which the name Micromonospora musae sp. nov. is proposed. The type strain is MS1-9T (=JCM 32149T=TISTR 2659T).

Lentibacillus lipolyticus sp. nov., a moderately halophilic bacterium isolated from shrimp paste (Ka-pi).

A Gram-stain-positive, aerobic, spore-forming, moderately halophilic bacterium, SSKP1-9T, was isolated from traditional salted shrimp paste (Ka-pi) produced in Samut Sakhon Province, Thailand. This strain grew optimally at 37-40 °C, pH 7.0 and in the presence of 8-16 % (w/v) NaCl. The 16S rRNA gene sequence similarity values between strain SSKP1-9T and Lentibacillus juripiscarius TISTR 1535T and Lentibacillus halophilus TISTR 1549T were 98.7 and 97.2 %, respectively. Based on 16S rRNA gene sequence similarity, strain SSKP1-9T represents a distinct novel species, as shown by phenotypic traits, DNA-DNA hybridization and average nucleotide identity values. In addition, the whole-cell protein profile confirmed the novelty of the taxon. The genomic DNA G+C content was 44.6 mol%. The major isoprenoid quinone was MK-7. The cell-wall peptidoglycan contained meso-diaminopimelic acid. Polar lipid analysis revealed the presence of phosphatidylglycerol, diphosphatidylglycerol, four unidentified lipids, an unidentified phospholipid and an unidentified glycolipid. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The results of phenotypic and chemotaxonomic characteristics and whole-genome analysis support that strain SSKP1-9T represents a novel species of Lentibacillus, for which the name Lentibacilluslipolyticus sp. nov. is proposed. The type strain is SSKP1-9T (=JCM 32625T=TISTR 2597T).

Enterococcus florum sp. nov., isolated from a cotton flower (Gossypium hirsutum L.).

A Gram-stain-positive and catalase negative coccus, designated strain Gos25-1T, isolated from a cotton flower (Gossypium hirsutum L.) collected from Khao Wong district, Kalasin province, Thailand. The taxonomic position of this strain was systematically studied based upon polyphasic taxonomic methods. The strain was facultatively anaerobic and produced l-lactic acid from glucose. The predominant cellular fatty acids were the straight-chain fatty acids C18 : 1ω9c and C16 : 0. According to 16S rRNA and phenylalanyl-tRNA synthase alpha subunit (pheS) gene sequence similarity, this strain was closely related to Enterococcus pallens NBRC 100697T, E. hermanniensis CIP 108559T, E. avium NBRC 100477T and E. raffinosus NBRC 100492T with 98.9-99.1 % and 77.0-82.0 % sequence similarities, respectively. Phylogenetic analysis indicated that strain Gos25-1T was clearly distinguished from closely related species of the genus Enterococcus. Draft genome of Gos25-1T had a size of 3.99 Mb which was contained 3788 coding sequences with in silico G+C content of 42.4 mol%. The ANIb and a digital DNA-DNA hybridisation (dDDH) values between strain Gos25-1T and the closest related species, E. pallens NBRC 100697T were 73.65 and 21.10 %, respectively. According to polyphasic characterisation, this strain represents a novel species of the genus Enterococcus, for which the name Enterococcus florum sp. nov. is proposed. The type strain is Gos25-1T (=CIP 110956T=LMG 29007T=NBRC 111461T=TISTR 2382T).