Streptomyces krungchingensis sp. nov., isolated from soil

A novel actinomycete, designated strain KC-035T, was isolated from soil collected from Krung Ching Waterfall National Park, Nakhon Si Thammarat Province, Thailand. Its taxonomic position was determined using a polyphasic approach. The strain had morphological and chemotaxonomic properties typical of members of the genus Streptomyces: flexuous spore chain; ll-diaminopimelic acid in the cell-wall peptidoglycan; MK-9(H8), MK-9(H6) and MK-9(H4) as menaquinones; diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside as phospholipids; anteiso-C15 : 0, C16 : 0, iso-C16 : 0, iso-C15 : 0 and iso-C14 : 0 as major cellular fatty acids; and DNA G+C content of 72 mol%. 16S rRNA gene sequence analysis revealed that strain KC-035T showed high similarity to Streptomyces albiflavescens n20T (99.16 %) and Streptomyces siamensis KC-038T (98.43 %) as well as formed a monophyletic clade with them in the phylogenetic tree. On the basis of comparison of phenotypic properties and the low level of DNA-DNA relatedness, strain KC-035T could be distinguished from its closely related Streptomyces species and is considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces krungchingensis sp. nov. is proposed. The type strain is KC-035T (=NBRC 110087T=KCTC 29503T=TISTR 2402T).

Preliminary Studies of Lactic Acid Bacteria Isolated from Feces of Thai Newborns

BACKGROUND

The microbiota of human plays an important role in the health improvement, and found abundant in the gastrointestinal tract. In recent years, probiotics have been increasingly used in prevention of certain intestinal diseases. The most important population to study the microbiome is probably in the healthy newborns.

OBJECTIVE

The preliminary study aimed to isolate and identify the gut microbiota of newborns for the assessment of prevalent Lactic Acid Bacteria (LAB) distribution.

MATERIAL AND METHOD

Thirty eight Thai newborns, 0-5 days old of both sexes were subjected for fecal samples collection. Isolated bacteria were cultivated on the MRS selective media and further phenotypically characterized by conventional methods including Gram stain, catalase, and lactic acid production. Genotypic identification was completed by 16S rRNA gene sequencing and phylogenetic analysis.

RESULTS

Forty five isolates of LAB and non-LAB bacteria were obtained from feces of newborns. The most prevalence LAB found in this population were 45% Enterococcus faecalis, 14% E. faecium, 11% E. hirae, 11% Lactobacillus paracasei, and 2% L. gasseri. Unusually, Gram-negative bacteria including Klebsiella pneumoniae, Enterobacter hormaechei, Escherichia fergusonii, Leclercia adecarboxylata, and Shigella flexneri were isolated among LAB strains on the selective MRS media.

CONCLUSION

The gut microbiota was a great resource of beneficial LAB which was remarkably distributed among this population of Thai newborns. Further study on individual LAB isolates for the effective probiotics development would be essentially investigated for future alternative treatment of gastrointestinal diseases.

Streptomyces phyllanthi sp. nov., isolated from the stem of Phyllanthus amarus

The novel endophytic actinomycete strain PA1-07T was isolated from the stem of Phyllanthus amarus. The strain displayed the consistent characteristics of members of the genus Streptomyces. The strain produced short spiral spore chains on aerial mycelia. It grew at pH 5-9, at 40 °C and with a maximum of 5 % (w/v) NaCl. It contained ll-diaminopimelic acid, glucose and ribose in the whole-cell hydrolysate. The major cellular menaquinones were MK-9(H4), MK-9(H6) and MK-9(H8), while the major cellular fatty acids were C16 : 0, iso-C14 : 0, iso-C16 : 0 and anteiso-C15 : 0. The polar lipids were composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannoside and four unknown lipids. The DNA G+C content of the strain was 71 mol%. The strain showed the highest 16S rRNA gene sequence similarity with Streptomyces curacoi JCM 4219T (98.77 %). The DNA-DNA relatedness values between strain PA1-07T and S. curacoi JCM 4219T were lower than 70 %, the cut-off level for assigning strains to the same species. On the basis of these phenotypic and genotypic characteristics, the strain could be distinguished from closely related species of the genus Streptomyces and thus represents a novel species of the genus Streptomyces, for which the name Streptomyces phyllanthi sp. nov. is proposed. The type strain is PA1-07T (=JCM 30865T=KCTC 39785T=TISTR 2346T).

Streptomyces verrucosisporus sp. nov., isolated from marine sediments

Five actinomycete isolates, CPB1-1T, CPB2-10, BM1-4, CPB3-1 and CPB1-18, belonging to the genus Streptomyces were isolated from marine sediments collected from Chumphon Province, Thailand. They produced open loops of warty spore chains on aerial mycelia. ll-Diaminopimelic acid, glucose and ribose were found in their whole-cell hydrolysates. Polar lipids found were diphosphatidylglycerol, phosphatidylethanolamine, lysophosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. Menaquinones were MK-9(H6), MK-9(H8), MK-10(H6) and MK-10(H8). Major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The taxonomic position of the strains was described using a polyphasic approach. blastn analysis of the 16S rRNA gene sequence revealed that these five strains exhibited the highest similarities with 'Streptomyces mangrovicola' GY1 (99.0 %), Streptomyces fenghuangensisGIMN4.003T (98.6 %), Streptomyces barkulensisRC 1831T (98.5 %) and Streptomyces radiopugnans R97T (98.3 %). However, their phenotypic characteristics and 16S rRNA gene sequences as well as DNA-DNA relatedness differentiated these five strains from the other species of the genus Streptomyces. Here, we propose the novel actinomycetes all being representatives of the same novel species, Streptomyces verrucosisporus, with type strain CPB1-1T (=JCM 18519T=PCU 343T=TISTR 2344T).

Micromonospora sediminis sp. nov., isolated from mangrove sediment

The novel actinomycete, strain CH3-3T, was isolated from mangrove sediment collected from Chonburi Province, Thailand. On the basis of its spore morphology and chemotaxonomic characteristics, the strain belonged to the genus Micromonospora. It contained meso-diaminopimelic acid, glucose, mannose, xylose, ribose and rhamnose in the whole-cell hydrolysate, MK-10(H4), MK-10(H6) and MK-10(H8) as major menaquinones, and iso-C15 : 0, iso-C16 : 0 and iso-C17 : 0 as major cellular fatty acids. blast analysis of 16S rRNA gene sequences revealed that the strain showed highest similarity with Micromonospora palomenae NEAU-CX1T (98.97 %) and Micromonospora coxensis 2-30-b(28)T (98.97 %). Based on phylogenetic tree analysis of the 16S rRNA gene sequence, the strain formed a cluster with M. palomenae NEAU-CX1T, Micromonospora halophytica DSM 43171T, M. coxensis 2-30-b(28)T and Micromonospora purpureochromogenes DSM 43821T. On the basis of phenotypic differences and DNA-DNA relatedness evidence, strain CH3-3T could be clearly distinguished from the closely related species of the genus Micromonospora and represents a novel species of the genus Micromonospora for which the name Micromonospora sediminis sp. nov. is proposed. The type strain is CH3-3T (=JCM 18523T=PCU 350T=TISTR 2396T).

Ideonella sakaiensis sp. nov., isolated from a microbial consortium that degrades poly(ethylene terephthalate)

A Gram-stain-negative, aerobic, non-spore-forming, rod-shaped bacterium, designed strain 201-F6T, was isolated from a microbial consortium that degrades poly(ethylene terephthalate) (PET) collected in Sakai city, Japan, and was characterized on the basis of a polyphasic taxonomic study. The cells were motile with a polar flagellum. The strain contained cytochrome oxidase and catalase. It grew within the pH range 5.5-9.0 (optimally at pH 7-7.5) and at 15-42 ºC (optimally at 30-37 ºC). The major isoprenoid quinone was ubiquinone with eight isoprene units (Q-8). C16 : 0, C17 : 0 cyclo, C18 :1ω7c and C12 : 0 2-OH were the predominant cellular fatty acids. The major polar lipids were phosphatidylethanolamine, lyso-phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The G+C content of genomic DNA was 70.4 mol%. Phylogenetic analysis using the 16S rRNA gene sequences showed that strain 201-F6T was affiliated to the genus Ideonella, and was closely related to Ideonella dechloratans LMG 28178T (97.7 %) and Ideonella azotifigens JCM 15503T (96.6 %). Strain 201-F6T could be clearly distinguished from the related species of the genus Ideonella by its physiological and biochemical characteristics as well as by its phylogenetic position and DNA-DNA relatedness. Therefore, the strain represents a novel species of the genus Ideonella, for which the name Ideonella sakaiensis sp. nov. (type strain 201-F6T=NBRC 110686T=TISTR 2288T) is proposed.

Streptomyces andamanensis sp. nov., isolated from soil

A novel actinomycete, strain KC-112T, was isolated from soil collected from Similan Islands, Phang-Nga Province, Thailand. The strain exhibited morphological and chemotaxonomic characteristics consistent with those of members of the genus Streptomyces. The formation of smooth spiral spore chains was observed on aerial mycelia. ll-Diaminopimelic acid was detected in whole-cell hydrolysates, but no diagnostic sugars were detected and the strain lacked mycolic acids. The N-acyl type of muramic acid was acetyl. The major menaquinones were MK-9(H8), MK-9(H6) and MK-9(H2). The predominant cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and C16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, an unknown phospholipid, an unknown aminolipid, unknown lipids and an unknown glycolipid. The DNA G+C content was 73 mol%. On the basis of 16S rRNA gene sequence analysis, strain KC-112T was closely related to Streptomyces fumanus NBRC 13042T (98.8 % 16S rRNA gene sequence similarity), Streptomyces anandii NBRC 13438T (98.8 %) and Streptomyces capillispiralis NBRC 14222T (98.8 %). DNA-DNA relatedness values among strain KC-112T and type strains of closely related species were lower than 70 %. On the basis of evidence from this taxonomic study using a polyphasic approach, strain KC-112T represents a novel species of the genus Streptomyces, namely Streptomyces andamanensis sp. nov. The type strain is KC-112T ( = KCTC 29502T = NBRC 110085T = PCU 347T = TISTR 2401T).

Paenibacillus cathormii sp. nov., isolated from tree bark

A Gram-stain-positive, facultatively anaerobic, rod-shaped and endospore-forming bacterium, strain BK114-2^T isolated from tree bark in Thailand was characterized taxonomically using a polyphasic approach. Analysis based on comparison of 16S rRNA gene sequences indicated that strain BK114-2^T was affiliated to the genus Paenibacillus, and was closely related to Paenibacillus timonensis 2301032^T (96.7 % 16S rRNA gene sequence similarity), Paenibacillus phoenicis 3PO2SA^T (96.6 %) and Paenibacillus barengoltzii SAFN-016^T (96.4 %). Strain BK114-2^T contained meso-diaminopimelic acid in its cell-wall peptidoglycan. The polar lipids were composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unknown phospholipids, five unknown aminophospholipids and six unknown lipids. The only menaquinone detected was MK-7 and the dominant cellular fatty acids were C_16 : 0 (22.9 %), anteiso-C_15 : 0 (22.6 %), iso-C_16 : 0 (19.4 %) and anteiso-C_17 : 0 (14.7 %). The DNA G+C content was 52.0 mol%. Based on these results, strain BK114-2^T repreesents a novel species of the genus Paenibacillus, for which the name Paenibacillus cathormii sp. nov. is proposed. The type strain is BK114-2^T ( = KCTC 33251^T = TISTR 2282^T).

Trichosporon heliocopridis sp. nov., a urease-negative basidiomycetous yeast associated with dung beetles (Heliocopris bucephalus Fabricius)

Ninety-six yeast isolates associated with dung beetles (Heliocopris bucephalus Fabricius) were examined based on a culture-dependent method. A comparison of the colony morphology and PCR-fingerprints obtained by (GTG)₅ microsatellite-primed PCR indicated that 84 of these isolates belonged to one group. Five strains (DD1-1^T, DD2-33, DD4-11, DD5-15 and DD6-1) were selected as the representatives of this main group, where each of the five selected strains had been derived from a different dung beetle collected in northern Thailand. A comparison of the D1/D2 domain sequence of the large subunit rRNA gene (LSU D1/D2) and the internal transcribed spacer (ITS) sequences revealed that these five strains were the same and were related to the genus Trichosporon. Phylogenetic analysis based on the LSU D1/D2 plus ITS sequences placed this group within the Trichosporon brassicae clade, but it was clearly separated from any known species. In addition, physiological tests showed that this group had the unusual property of the inability to hydrolyse urea, which was distinctly different from the related taxon. Therefore a novel yeast species named Trichosporon heliocopridis sp. nov. (ex-type strain DD1-1^T = TISTR 5946^T = JCM 30786^T = CBS 14168^T) is proposed. The MycoBank number is MB812098.

Actinoplanes lichenis sp. nov., isolated from lichen

A novel species of the genus Actinoplanes, strain LDG1-22T, for which we propose the name Actinoplanes lichenis sp. nov., was isolated from a lichen sample collected from tree bark in Thailand. The taxonomic position of the species has been described based on a polyphasic approach. Strain LDG1-22T produced irregular sporangia on agar media. It contained meso-diaminopimelic acid in the cell-wall peptidoglycan. The major menaquinone was MK-9(H4); the polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and phosphatidylglycerol. Whole-cell hydrolysates contained ribose, glucose, mannose and small amounts of arabinose and xylose. The major cellular fatty acids were anteiso-C15 : 0 (31.2 %) and iso-C16 : 0 (14.2 %). Mycolic acids were absent. The G+C content was 73.6 %. 16S rRNA gene sequence analysis of strain LDG1-22T showed highest similarity (98.8 %) to Actinoplanes friuliensis DSM 45797T and it clustered with Actinoplanes nipponensis JCM 3264T and Actinoplanes missouriensis JCM 3121T in phylogenetic tree analysis. On the basis of the phenotypic characteristics and DNA-DNA relatedness, strain LDG1-22T could be distinguished from related species of the genus Actinoplanes and so represents a novel species of this genus. The type strain of Actinoplanes lichenis sp. nov. is LDG1-22T ( = JCM 30485T = TISTR 2343T = PCU 344T).

Amycolatopsis stemonae sp. nov., isolated from a Thai medicinal plant

A novel actinomycete, strain ST1-08T, was isolated from the stem of Stemona sp. in Thailand. The taxonomic position of this isolate was determined by using a polyphasic approach. Strain ST1-08T contained meso-diaminopimelic acid in the cell-wall peptidoglycan, and arabinose and galactose as diagnostic sugars of the whole-cell hydrolysate, which are typical properties of members of the genus Amycolatopsis. Strain ST1-08T grew at 15-40 °C, pH 6-9 and on 5 % (w/v) NaCl. Gelatin liquefaction, starch hydrolysis and skimmed milk peptonization were positive. The strain utilized l-arabinose, d-glucose, glycerol, myo-inositol, d-mannitol and l-rhamnose. The predominant menaquinone was MK-9(H4) and the major cellular fatty acids were iso-C16 : 0 and iso-C15 : 0.The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, hydroxyl-phosphatidylethanolamine, phosphatidylinositol and phosphatidylglycerol. The 16S rRNA gene sequence analysis revealed that the strain was closely related to Amycolatopsis pretoriensis JCM 12673T (98.99 %) and Amycolatopsis lexingtonensis JCM 12672T (98.87 %). The DNA G+C content of strain ST1-08T was 71.2 mol%. The DNA-DNA relatedness values among strain ST1-08T, A. pretoriensis JCM 12673T and A. lexingtonensis JCM 12672T were lower than 70 %, the cut-off level for assigning strains to the same species. On the basis of phenotypic and genotypic characteristics, strain ST1-08T represents a novel species of the genus Amycolatopsis, for which the name Amycolatopsis stemonae is proposed. The type strain is ST1-08T( = JCM 30050T = PCU 339T = TISTR 2278T).

Antimicrobial Properties of a Potential Probiotic Lactobacillus from Thai Newborn Feces

BACKGROUND

Probiotics are increasingly used to treat infectious diarrhea and antibiotic-associated diarrhea. Many probiotic bacteria are classified in general such as Lactobacillus and are able to colonize the gastrointestinal tracts of infants.

OBJECTIVE

This study was performed to detect antimicrobial substances and activity in 200 Lactobacillus isolates obtained from healthy Thai newborn feces.

MATERIAL AND METHOD

Reuterin production was detected by the spot overlay technique and colorimetric assay. Antimicrobial activity was tested by using a well diffusion, agar method.

RESULTS

Lactobacillus strain MSMC64-1 produced reuterin and demonstrated potent antimicrobial activity against seven pathogenic indicator strains with very strong inhibitory activities against Salmonella typhi DMST 5784 and methicillin resistant Staphylococcus aureus (MRSA) DMST 20651. There was strong inhibitory activity against methicillin resistant Staphylococcus aureus (MRSA) DMST20654, Vibrio parahaemolyticus DMST 5665 and Shigella dysenteriae DMST 15111. There was moderate to weak inhibitory activities against Vibrio cholerae DMST 2873 and Helicobacter pylori (H40). The Lactobacillus strain MSMC 64-1 showed resistance to acidic pH (pH 2, 3, 4) and tolerance to 1%, 2%, 3%, and 4% bile concentrations. Sequencing of the 16S ribosomal DNA identified the candidate's strain as Lactobacillus reuteri with 98% sequence homology.

CONCLUSION

The active isolate could potentially be used as a probiotic to prevent and treat enteric infections.

Micromonospora fluostatini sp. nov., isolated from marine sediment

The novel actinomycete strain PWB-003T, which produced fluostatins B and C antibiotics, was isolated from nearshore sediment collected from Panwa Cape, Phuket Province, Thailand. Data from the present polyphasic study indicated that strain PWB-003T represented a member of the genus Micromonospora. It produced single spores on substrate mycelia and contained meso-diaminopimelic acid in the cell-wall peptidoglycan. Whole-cell hydrolysate contained ribose, xylose, arabinose, mannose and glucose. The predominant menaquinone was MK-10 (H4). Cellular fatty acids comprised C18 : 1ω9c, iso-C16 : 0, anteiso-C17 : 0, iso-C15 : 0 and iso-C17 : 0. On the basis of 16S rRNA gene sequence similarity analysis, the novel strain was closely related to Micromonospora eburnea LK2-10T (99.38 %), Micromonospora chaiyaphumensis MC5-1T (99.16 %), Micromonospora yangpuensis FXJ6.011T (98.97 %), Micromonospora echinaurantiaca DSM 43904T (98.97 %), Micromonospora pallida DSM 43817T (98.97 %), Micromonospora sagamiensis DSM 43912T and Micromonospora auratinigra JCM 12357T (both 98.97 %). The G+C content of the DNA was 74.5 mol%. DNA-DNA relatedness values among strain PWB-003T and related type strains ranged from 11.3 ± 1.3 to 38.8 ± 1.1 %. On the basis of these observations, strain PWB-003T could be distinguished from its closely related type strains and is considered to represent a novel species of the genus Micromonospora, for which the name Micromonospora fluostatini sp. nov. (type strain PWB-003T = JCM 30529T = PCU 341T = TISTR 2345T) is proposed.

Lactobacillus plajomi sp. nov. and Lactobacillus modestisalitolerans sp. nov., isolated from traditional fermented foods

Three Lactobacillus-like strains, NB53T, NB446T and NB702, were isolated from traditional fermented food in Thailand. Comparative 16S rRNA gene sequence analysis indicated that these strains belong to the Lactobacillus plantarum group. Phylogenetic analysis based on the dnaK, rpoA, pheS and recA gene sequences indicated that these three strains were distantly related to known species present in the L. plantarum group. DNA–DNA hybridization with closely related strains demonstrated that these strains represented two novel species; the novel strains could be differentiated based on chemotaxonomic and phenotypic characteristics. Therefore, two novel species of the genus Lactobacillus, Lactobacillus plajomi sp. nov. (NB53T) and Lactobacillus modestisalitolerans sp. nov. (NB446T and NB702), are proposed with the type strains NB53T ( = NBRC 107333T = BCC 38054T) and NB446T ( = NBRC 107235T = BCC 38191T), respectively.