Displaying publications 81 - 100 of 142 in total

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  1. Nocardiopsis deserti sp. nov., isolated from a high altitude Atacama Desert soil
    Asem MD, Salam N, Idris H, Zhang XT, Bull AT, Li WJ, et al.
    Int J Syst Evol Microbiol, 2020 May;70(5):3210-3218.
    PMID: 32320378 DOI: 10.1099/ijsem.0.004158
    The taxonomic status of a Nocardiopsis strain, designated H13T, isolated from a high altitude Atacama Desert soil, was established by using a polyphasic approach. The strain was found to have chemotaxonomic, cultural and morphological characteristics consistent with its classification within the genus Nocardiopsis and formed a well-supported clade in the Nocardiopsis phylogenomic tree together with the type strains of Nocardiopsis alborubida, Nocardiopsis dassonvillei and Nocardiopsis synnematoformans. Strain H13T was distinguished from its closest relatives by low average nucleotide identity (93.2-94.9 %) and in silico DNA-DNA hybridization (52.5-62.4 %) values calculated from draft genome assemblies and by a range of phenotypic properties. On the basis of these results, it is proposed that the isolate be assigned to the genus Nocardiopsis as Nocardiopsis deserti sp. nov. with isolate H13T (=CGMCC 4.7585T=KCTC 49249T) as the type strain.
    Matched MeSH terms: Bacterial Typing Techniques
  2. Dickeya undicola sp. nov., a novel species for pectinolytic isolates from surface waters in Europe and Asia
    Oulghazi S, Pédron J, Cigna J, Lau YY, Moumni M, Van Gijsegem F, et al.
    Int J Syst Evol Microbiol, 2019 Aug;69(8):2440-2444.
    PMID: 31166160 DOI: 10.1099/ijsem.0.003497
    Strains 2B12T, FVG1-MFV-O17 and FVG10-MFV-A16 were isolated from fresh water samples collected in Asia and Europe. The nucleotide sequences of the gapA barcodes revealed that all three strains belonged to the same cluster within the genus Dickeya. Using 13 housekeeping genes (fusA, rpoD, rpoS, glyA, purA, groEL, gapA, rplB, leuS, recA, gyrB, infB and secY), multilocus sequence analysis confirmed the existence of a new clade. When the genome sequences of these three isolates and other Dickeya species were compared, the in silico DNA-DNA hybridization and average nucleotide identity values were found to be no more than 45.50 and 91.22 %, respectively. The closest relative species was Dickeya fangzhongdai. Genome comparisons also highlighted genetic traits differentiating the new strains from D. fangzhongdai strains DSM 101947T (=CFBP 8607T) and B16. Phenotypical tests were performed to distinguish the three strains from D. fangzhongdai and other Dickeya species. The name Dickeya undicola sp. nov. is proposed with strain 2B12T (=CFBP 8650T=LMG 30903T) as the type strain.
    Matched MeSH terms: Bacterial Typing Techniques
  3. Paracoccus rhizosphaerae sp. nov., isolated from the rhizosphere of the plant Crossostephium chinense (L.) Makino (Seremban)
    Kämpfer P, Lai WA, Arun AB, Young CC, Rekha PD, Martin K, et al.
    Int J Syst Evol Microbiol, 2012 Nov;62(Pt 11):2750-2756.
    PMID: 22286908 DOI: 10.1099/ijs.0.039057-0
    A Gram-negative, coccoid-shaped bacterium, strain CC-CCM15-8(T), was isolated from a rhizosphere soil sample of the plant Crossostephium chinense (L.) Makino (Seremban) from Budai Township, Chiayi County, Taiwan. 16S rRNA gene sequence analysis clearly allocated strain CC-CCM15-8(T) to the Paracoccus cluster, showing highest similarities to the type strains of 'Paracoccus beibuensis' (98.8%), Paracoccus homiensis (97.6%), Paracoccus aestuarii (97.7%) and Paracoccus zeaxanthinifaciens (97.7%). The fatty acid profile, comprising C(18:1)ω7c as the major component and C(10:0) 3-OH as the characteristic hydroxylated fatty acid, supported the placement of strain CC-CCM15-8(T) within the genus Paracoccus. The polyamine pattern consisted of putrescine and spermidine as major components. Ubiqinone Q-10 was the major quinone type (95%); ubiquinone Q-9 was also detected (5%). The complex polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, and unidentified phospholipids, lipids and glycolipids. Levels of DNA-DNA relatedness between strain CC-CCM15-8(T) and 'P. beibuensis' LMG 25871(T), P. aestuarii DSM 19484(T), P. zeaxanthinifaciens LMG 21993(T) and P. homiensis KACC 11518(T) were 24.9% (34.8%, reciprocal analysis), 15.7% (17.5%), 17.7% (23.4%) and 16.0% (25.4%), respectively. Physiological and biochemical test results allowed the phenotypic differentiation of strain CC-CCM15-8(T) from its closest relatives in the genus Paracoccus. Based on the data presented, it is concluded that strain CC-CCM15-8(T) represents a novel species of the genus Paracoccus, for which the name Paracoccus rhizosphaerae sp. nov. is proposed. The type strain is CC-CCM15-8(T) (=LMG 26205(T)=CCM 7904(T)).
    Matched MeSH terms: Bacterial Typing Techniques
  4. Amycolatopsis thermophila sp. nov. and Amycolatopsis viridis sp. nov., thermophilic actinomycetes isolated from arid soil
    Zucchi TD, Tan GYA, Goodfellow M
    Int J Syst Evol Microbiol, 2012 Jan;62(Pt 1):168-172.
    PMID: 21378137 DOI: 10.1099/ijs.0.029256-0
    The taxonomic positions of two thermophilic actinomycetes isolated from an arid Australian soil sample were established based on an investigation using a polyphasic taxonomic approach. The organisms had chemical and morphological properties typical of members of the genus Amycolatopsis and formed distinct phyletic lines in the Amycolatopsis methanolica 16S rRNA subclade. The two organisms were distinguished from one another and from the type strains of related species of the genus Amycolatopsis using a range of phenotypic properties. Based on the combined genotypic and phenotypic data, it is proposed that the two isolates be classified in the genus Amycolatopsis as Amycolatopsis thermophila sp. nov. (type strain GY088(T)=NCIMB 14699(T)=NRRL B-24836(T)) and Amycolatopsis viridis sp. nov. (type strain GY115(T)=NCIMB 14700(T)=NRRL B-24837(T)).
    Matched MeSH terms: Bacterial Typing Techniques
  5. Description of novel species of Aliinostoc, Desikacharya and Desmonostoc using a polyphasic approach
    Kabirnataj S, Nematzadeh GA, Talebi AF, Saraf A, Suradkar A, Tabatabaei M, et al.
    Int J Syst Evol Microbiol, 2020 May;70(5):3413-3426.
    PMID: 32375955 DOI: 10.1099/ijsem.0.004188
    Five cyanobacterial strains with Nostoc-like morphology from different localities of the Mazandaran province of Iran were characterized using a polyphasic approach. Three strains clustered within the Aliinostoc clade whereas one each of the remaining two strains clustered within the genera Desmonostoc and Desikacharya. The phylogenetic positioning of all the strains by the bayesian inference, neighbour joining and maximum parsimony methods inferred using 16S rRNA gene indicated them to represent novel species of the genera Aliinostoc, Desmonostoc and Desikacharya. The 16S-23S ITS secondary structure analysis revealed that all five strains under study represented novel species unknown to science. In accordance with the International Code of Nomenclature for algae, fungi and plants we describe three novel species of the genus Aliinostoc and one species each of the genera Desmonostoc and Desikacharya.
    Matched MeSH terms: Bacterial Typing Techniques
  6. Fulltext New emm (M protein gene) sequences of group A streptococci isolated from Malaysian patients
    Jamal F, Pit S, Facklam R, Beall B
    Emerg Infect Dis, 1999 Jan-Feb;5(1):182-3.
    PMID: 10081694
    Matched MeSH terms: Bacterial Typing Techniques
  7. Floricoccus tropicus gen. nov., sp. nov. and Floricoccus penangensis sp. nov. isolated from fresh flowers of durian tree and hibiscus
    Chuah LO, Yap KP, Shamila-Syuhada AK, Thong KL, Ahmad R, Liong MT, et al.
    Int J Syst Evol Microbiol, 2017 Dec;67(12):4979-4985.
    PMID: 29034853 DOI: 10.1099/ijsem.0.002386
    Three strains of Gram-staining-positive, coccus-shaped, lactic acid bacteria, designated as HibF3T, HibF2 and HibF5 were isolated from fresh flowers of hibiscus, and a fourth, DF1T, was isolated from fresh flowers of durian tree, in Penang, Malaysia. Taxonomic characterisation was performed by polyphasic analysis. Sequence similarities of the 16S rRNA gene and the housekeeping rpoA and pheS genes of these strains with their closely-related lactococcal and streptococcal relatives were 92-94, 78 and 81 %, respectively. The results of phylogenetic analysis indicated that strains DF1T, HibF2, HibF5 and HibF3T were clustered together but were clearly separated from species of the genera Streptococcus and Lactococcus, indicating that they represent members of a novel genus of the family Streptococcaceae. Calculation of average nucleotide identity (ANI) values between the genomes of DF1T and HibF3T yielded values of 92.50-92.93 %. ANI values below the cut-off value and distinctive chemotaxonomic characteristics supported the hypothesis that these strains represented two novel species. Major cellular fatty acids in DF1T, HibF2 and HibF5 were C18 : 1ω7c and C16 : 0, while C12 : 0 and C14 : 0 were also dominant, in addition to C18 : 1ω7c and C16 : 0, in HibF3T. A novel genus is proposed with the name Floricoccus gen. nov. which consists of two species, Floricoccus tropicus sp. nov as the type species, and Floricoccus penangensis sp. nov. The respective type strains are DF1T (=LMG 29833T=JCM 31733T) and HibF3T (=LMG 29831T=DSM 31735T).
    Matched MeSH terms: Bacterial Typing Techniques
  8. Devosia elaeis sp. nov., isolated from oil palm rhizospheric soil
    Mohd Nor MN, Sabaratnam V, Tan GYA
    Int J Syst Evol Microbiol, 2017 Apr;67(4):851-855.
    PMID: 27902276 DOI: 10.1099/ijsem.0.001683
    A bacterial isolate, designated strain S37T, was isolated from the rhizosphere of oil palm (Elaeis guineensis). Strain S37T was found to be Gram-stain-negative, aerobic, motile and rod shaped. Based on 16S rRNA gene sequence analysis, strain S37T was most closely related to Devosia albogilva IPL15T (97.3 %), Devosia chinhatensis IPL18T (96.8 %) and Devosia subaequoris HST3-14T (96.5 %). The G+C content of the genomic DNA was 63.0 mol%, and dominant cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), 11-methyl C18 : 1ω7c and C16 : 0. The predominant isoprenoid quinone was ubiquinone-10 (Q-10), and the major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, glycolipid and phospholipids. Based on the polyphasic taxonomic data, it is clear that strain S37T represents a novel species of the genus Devosia within the family Hyphomicrobiaceae, for which we propose the name Devosia elaeis sp. nov., with strain S37T (=TBRC 5145T=LMG 29420T) as the type strain.
    Matched MeSH terms: Bacterial Typing Techniques
  9. Microbulbifer aggregans sp. nov., isolated from estuarine sediment from a mangrove forest
    Moh TH, Furusawa G, Amirul AA
    Int J Syst Evol Microbiol, 2017 Oct;67(10):4089-4094.
    PMID: 28905698 DOI: 10.1099/ijsem.0.002258
    A novel, rod-shaped, Gram-stain-negative, halophilic and non-motile bacterium, designated CCB-MM1T, was isolated from a sample of estuarine sediment collected from Matang Mangrove Forest, Malaysia. The cells possessed a rod-coccus cell cycle in association with growth phase and formed aggregates. Strain CCB-MM1T was both catalase and oxidase positive, and able to degrade starch. Optimum growth occurred at 30 °C and pH 7.0 in the presence of 2-3 % (w/v) NaCl. The 16S rRNA gene sequence of strain CCB-MM1T showed 98.12, 97.46 and 97.33 % sequence similarity with Microbulbifer rhizosphaerae Cs16bT, Microbulbifer maritimus TF-17T and Microbulbifergwangyangensis GY2T respectively. Strain CCB-MM1T and M. rhizosphaerae Cs16bT formed a cluster in the phylogenetic tree. The major cellular fatty acids were iso-C17 : 1 ω9c and iso-C15 : 0, and the total polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphoaminolipid, two unidentified lipids, an unidentified glycolipid and an unidentified aminolipid. The major respiratory quinone was ubiquinone Q-8 and the genomic DNA G+C content of the strain was 58.9 mol%. On the basis of the phylogenetic, phenotypic and genotypic data presented here, strain CCB-MM1T represents a novel species of the genus Microbulbifer, for which the name Microbulbiferaggregans sp. nov. is proposed. The type strain is CCB-MM1T (=LMG 29920T=JCM 31875T).
    Matched MeSH terms: Bacterial Typing Techniques
  10. Fulltext Multilocus sequence types of clinical Burkholderia pseudomallei isolates from peninsular Malaysia and their associations with disease outcomes
    Zueter AR, Rahman ZA, Abumarzouq M, Harun A
    BMC Infect Dis, 2018 01 02;18(1):5.
    PMID: 29291714 DOI: 10.1186/s12879-017-2912-9
    BACKGROUND: Previous studies on the Burkholderia pseudomallei genetic diversity among clinical isolates from melioidosis-endemic areas have identified genetic factors contributing to differential virulence. Although it has been ruled out in Australian and Thai B. pseudomallei populations, it remains unclear whether B. pseudomallei sequence types (STs) correlate with disease in Malaysian patients with melioidosis.

    METHODS: In this study, multi-locus sequence typing (MLST) was performed on clinical B. pseudomallei isolates collected from Kelantan state of Malaysia, patients' clinical data were reviewed and then genotype-risk correlations were investigated.

    RESULTS: Genotyping of 83 B. pseudomallei isolates revealed 32 different STs, of which 13(40%) were novel. The frequencies of the STs among the 83 isolates ranged from 1 to 12 observations, and ST54, ST371 and ST289 were predominant. All non-novel STs reported in this study have also been identified in other Asian countries. Based on the MLST data analysis, the phylogenetic tree showed clustering of the STs with each other, as well as with the STs from Southeast Asia and China. No evidence for associations between any of B. pseudomallei STs and clinical melioidosis presentation was detected. In addition, the bacterial genotype clusters in relation with each clinical outcome were statistically insignificant, and no risk estimate was reported. This study has expanded the data for B. pseudomallei on MLST database map and provided insights into the molecular epidemiology of melioidosis in Peninsular Malaysia.

    CONCLUSION: This study concurs with previous reports concluding that infecting strain type plays no role in determining disease presentation.

    Matched MeSH terms: Bacterial Typing Techniques
  11. Vibrio coralliirubri sp. nov., a new species isolated from mucus of red coral (Corallium rubrum) collected at Procida island, Italy
    Poli A, Romano I, Mastascusa V, Buono L, Orlando P, Nicolaus B, et al.
    Antonie Van Leeuwenhoek, 2018 Jul;111(7):1105-1115.
    PMID: 29299771 DOI: 10.1007/s10482-017-1013-5
    Strain Corallo1T was isolated from mucus of red coral (Corallium rubrum) at Punta Pizzaco (Procida island, Naples, Italy). It was characterised as a Gram-stain negative, motile, rod-shaped bacterium. Strain Corallo1T was found to show positive responses for cytochrome-c oxidase, catalase, reduction of nitrate and nitrite, β-galactosidase activity and hydrolysis of starch, xylan, peptone, Tween 40, Tween 80 and casein. Strain Corallo1T was found to be mesophilic, neutrophilic to alkalophilic and slightly halophilic. According to analysis of the almost-complete 16S rRNA gene, strain Corallo1T is closely related to Vibrio celticus (100% sequence similarity), Vibrio gigantis (100%), Vibrio crassostreae (99.7%), Vibrio artabrorum (99.7%) and Vibrio pomeroyi (99.6%). MLSA of five housekeeping genes (atpA, pyrH, recA, rpoA and rpoD) was performed to refine the phylogenetic relationships of strain Corallo1T. A draft genome sequence of strain Corallo1T was obtained. The DNA G+C content of this strain was determined to be 44.5 mol %. The major cellular fatty acids of strain Corallo1T are C16:1, n-C16:0 and C18:1, and the major isoprenoid ubiquinone is Q8. ANI indexes, in silico estimations of DDH values and wet lab DDH values demonstrated that strain Corallo1T represents an independent genomospecies. Based on a polyphasic taxonomic characterisation, strain Corallo1T is concluded to represent a novel species of the genus Vibrio, for which the name Vibrio coralliirubri sp. nov. is proposed. The type strain is Corallo1T (= DSM 27495T = CIP 110630T).
    Matched MeSH terms: Bacterial Typing Techniques
  12. Nosocomial outbreak of Enterobacter gergoviae bacteraemia in a neonatal intensive care unit
    Ganeswire R, Thong KL, Puthucheary SD
    J Hosp Infect, 2003 Apr;53(4):292-6.
    PMID: 12660126
    A nosocomial outbreak of bacteraemia, caused by Enterobacter gergoviae infected 11 babies, nine of whom were premature, and was investigated in the neonatal intensive care unit (NICU) of a general hospital in Johor Bahru, Malaysia. The strain that was isolated from the babies was also isolated from the dextrose saline used for the dilution of parenteral antibiotics and from the hands of a healthcare worker on duty in the nursery. Pulsed-field gel electrophoresis (PFGE) of Xba I-digested chromosomal DNA confirmed a possible cross-contamination of parenteral dextrose saline and the healthcare worker. Prompt and effective control measures were initiated within NICU and the nosocomial infection of E. gergoviae was brought to an abrupt end. To the best of our knowledge, this is the first documented outbreak of E. gergoviae in the NICU in a hospital in the state of Johor, Malaysia.
    Matched MeSH terms: Bacterial Typing Techniques
  13. Molecular analysis of environmental and human isolates of Salmonella typhi
    Thong KL, Cordano AM, Yassin RM, Pang T
    Appl Environ Microbiol, 1996 Jan;62(1):271-4.
    PMID: 8572705
    Molecular characterization of a total of 54 isolates of Salmonella typhi from Santiago, Chile, was performed by pulsed-field gel electrophoresis (PFGE) after digestion of chromosomal DNA with three restriction endonucleases: XbaI (5'-TCTAGA-3'), AvrII (5'-CCTAGG-3'), and SpeI (5'-ACTAGT-3'). Thirteen of the 54 isolates were obtained from environmental sources (sewage and river water), and the rest were isolates from clinical cases of typhoid fever. Considerable genetic diversity was detected among the human isolates obtained in 1994, as evidenced by the presence of 14 to 19 different PFGE patterns among 20 human isolates, with F (coefficient of similarity) values ranging from 0.69 to 1.0 (XbaI), 0.61 to 1.0 (AvrII), and 0.70 to 1.0 (SpeI). A total of eight phage types were detected among these 20 isolates, with 50% possessing the E1 or 46 phage type. There was no correlation between PFGE pattern and phage types. Similar diversity was seen among 21 isolates obtained in 1983, with 17 to 19 PFGE patterns detected and F values of 0.56 to 1.0 (XbaI), 0.55 to 1.0 (AvrII), and 0.67 to 1.0 (SpeI). Comparison of these two groups of human isolates obtained 11 years apart indicated that certain molecular types of S. typhi are shared and are able to persist for considerable periods. A similar degree of genetic diversity was also detected among the environmental isolates of S. typhi, for which 10 to 12 different PFGE patterns were detected among the 13 isolates analyzed, with F values ranging from 0.56 to 1.0 (XbaI), 0.52 to 1.0 (AvrII), and 0.69 to 1.0 (SpeI). Certain molecular types present among the environmental isolates of S. typhi were also found among the human isolates from the same time period, providing evidence for the epidemiological link between environmental reservoirs and human infection.
    Matched MeSH terms: Bacterial Typing Techniques
  14. Phenotypic and genotypic characteristics and epidemiological significance of ctx+ strains of Vibrio cholerae isolated from seafood in Malaysia
    Chen CH, Shimada T, Elhadi N, Radu S, Nishibuchi M
    Appl Environ Microbiol, 2004 Apr;70(4):1964-72.
    PMID: 15066786
    Of 97 strains of Vibrio cholerae isolated from various seafoods in Malaysia in 1998 and 1999, 20 strains carried the ctx gene and produced cholera toxin. Fourteen, one, and five of these toxigenic strains belonged to the O139, O1 Ogawa, and rough serotypes, respectively. The rough strains had the rfb gene of the O1 serotype. The toxigenic strains varied in their biochemical characteristics, the amount of cholera toxin produced, their antibiograms, and the presence or absence of the pTLC plasmid sequence. DNA fingerprinting analysis by arbitrarily primed PCR, ribotyping, and a pulsed-field gel electrophoresis method classified the toxigenic strains into 3, 7, and 10 types, respectively. The relatedness of these toxigenic strains to clinical strains isolated in other countries and from international travelers was examined by using a dendrogram constructed from the pulsed-field gel electrophoresis profiles. The results of the examination of the antibiogram and the possession of the toxin-linked cryptic plasmid were consistent with the dendrogram-based relatedness: the O139 strains isolated from Malaysian seafoods could be separated into two groups that appear to have been introduced from the Bengal area independently. The rough strains of Malaysian seafood origin formed one group and belonged to a cluster unique to the Thailand-Malaysia-Laos region, and this group may have persisted in this area for a long period. The single O1 Ogawa strain detected in Malaysian seafood appears to have an origin and route of introduction different from those of the O139 and the rough strains.
    Matched MeSH terms: Bacterial Typing Techniques
  15. Fulltext Comparative characterisation of genotypically different clones of MRSA in the production of biofilms
    Atshan SS, Shamsudin MN, Lung LT, Sekawi Z, Ghaznavi-Rad E, Pei CP
    J Biomed Biotechnol, 2012;2012:417247.
    PMID: 22529705 DOI: 10.1155/2012/417247
    The ability to adhere and produce biofilms is characteristic of enhanced virulence among isolates of methicillin-resistant Staphylococcus aureus (MRSA). The aim of the study is to find out whether these characteristics are consistently similar among isolates variations of MRSA. The study used 30 various isolates of MRSA belong to 13 spa types and 5 MLST types and determined the aggregation, the adherence, and the production of biofilms and slime for each isolate. The methods used to evaluate these characteristics were a modified Congo red agar assay (MCRA), a microtiter plate assay (MPA), high-magnification light microscopy, scanning electron microscopy (SEM), and PCR. The study found that isolates belonging to similar Spa, SCCmec, and ST types have similar abilities to produce biofilms; however, their ability to produce slime on CRA was found to be different. Moreover, isolates that have different Spa types showed high variation in their ability to produce biofilms. The results of light microscope revealed the isolates that produced strong and weak biofilms and formed similar aggregation on the glass surfaces. SEM results showed that all 30 MRSA isolates that were tested were 100% positive for biofilm formation, although to varying degrees. Further testing using PCR confirmed that 100% of the 30 isolates tested were positive for the presence of the icaADBC, fnbA, eno, ebps, clfA, and clfB genes. The prevalence of fib, cna, fnbB, and bbp in MRSA clones was 90, 93.33, 53.33, and 10%, respectively. This study indicate that differences in biofilm production capacities are caused by the differences in surface protein A (Spa) type and are not due to differences in MLST and SCCmec types.
    Matched MeSH terms: Bacterial Typing Techniques
  16. Vitellibacter aquimaris sp. nov., a marine bacterium isolated from seawater
    Thevarajoo S, Selvaratnam C, Goh KM, Hong KW, Chan XY, Chan KG, et al.
    Int J Syst Evol Microbiol, 2016 Sep;66(9):3662-3668.
    PMID: 27334651 DOI: 10.1099/ijsem.0.001248
    A Gram-staining-negative, aerobic, yellow-orange-pigmented, rod-shaped bacterium designated D-24T was isolated from seawater from sandy shoreline in Johor, Malaysia. The 16S rRNA gene sequence analysis revealed that strain D-24T is affiliated with the genus Vitellibacter. It shared more than 96 % sequence similarity with the types of some of the validly published species of the genus: Vitellibactervladivostokensis KMM 3516T (99.5 %), Vitellibactersoesokkakensis RSSK-12T (97.3 %), VitellibacterechinoideorumCC-CZW007T (96.9 %), VitellibacternionensisVBW088T (96.7 %) and Vitellibacteraestuarii JCM 15496T (96.3 %). DNA-DNA hybridization and genome-based analysis of average nucleotide identity (ANI) of strain D-24T versus V.vladivostokensisKMM 3516T exhibited values of 35.9±0.14 % and 89.26 %, respectively. Strain D-24T showed an even lower ANI value of 80.88 % with V. soesokkakensis RSSK-12T. The major menaquinone of strain D-24T was MK-6, and the predominant fatty acids were iso-C15 : 0 and iso-C17 : 0 3-OH. Strain D-24T contained major amounts of phosphatidylethanolamine, two lipids and two aminolipids, and a phosphoglycolipid that was different to that of other species of the genus Vitellibacter. The genomic DNA G+C content was 40.6 mol%. On the basis of phenotypic properties, DNA-DNA relatedness, ANI value and chemotaxonomic analyses, strain D-24T represents a novel species of the genus Vitellibacter, for which the name Vitellibacter aquimaris sp. nov. is proposed. The type strain is D-24T (=KCTC 42708T=DSM 101732T).
    Matched MeSH terms: Bacterial Typing Techniques
  17. Sinomonas humi sp. nov., an amylolytic actinobacterium isolated from mangrove forest soil
    Lee LH, Azman AS, Zainal N, Yin WF, Mutalib NA, Chan KG
    Int J Syst Evol Microbiol, 2015 Mar;65(Pt 3):996-1002.
    PMID: 25563924 DOI: 10.1099/ijs.0.000053
    Strain MUSC 117(T) was isolated from mangrove soil of the Tanjung Lumpur forest in Pahang, Malaysia. This bacterium was yellowish-white pigmented, Gram-staining-positive, rod-coccus shaped and non-motile. On the basis of 16S rRNA gene sequence, strain MUSC 117(T) exhibited highest sequence similarity to Sinomonas atrocyanea DSM 20127(T) (98.0 %), Sinomonas albida LC13(T) (97.9 %) and Sinomonas soli CW 59(T) (97.8 %), and lower (<97.6 %) sequence similarity to other species of the genus Sinomonas. DNA-DNA hybridization experiments revealed a low level of DNA-DNA relatedness (less than 27 %) between strain MUSC 117(T) and closely related species. Chemotaxonomically, the peptidoglycan type was A3α, containing the amino acids lysine, serine, glycine, alanine, glutamic acid and muramic acid. The whole-cell sugars detected were rhamnose, ribose, glucose, galactose and a smaller amount of mannose. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and five unidentified glycolipids. The major fatty acids (>10.0 %) of the cell membrane were anteiso-C15 : 0 (39.4 %), C18 : 1ω7c (17.7 %), anteiso-C17 : 0 (17.2 %) and iso-C16 : 0 (11.4 %). The predominant respiratory quinones detected were MK-9(H2) and MK-9. The DNA G+C content was 67.3 mol%. A comparison of BOX-PCR fingerprints indicated that strain MUSC 117(T) represented a unique DNA profile. Results based on a polyphasic approach showed that strain MUSC 117(T) represents a novel species of the genus Sinomonas, for which the name Sinomonas humi sp. nov. is proposed. The type strain of Sinomonas humi sp. nov. is MUSC 117(T) ( = DSM 29362(T) = MCCC 1K00410(T) = NBRC 110653(T)).
    Matched MeSH terms: Bacterial Typing Techniques
  18. Chryseobacterium artocarpi sp. nov., isolated from the rhizosphere soil of Artocarpus integer
    Venil CK, Nordin N, Zakaria ZA, Ahmad WA
    Int J Syst Evol Microbiol, 2014 Sep;64(Pt 9):3153-9.
    PMID: 24958763 DOI: 10.1099/ijs.0.063594-0
    A bacterial strain, designated UTM-3(T), isolated from the rhizosphere soil of Artocarpus integer (cempedak) in Malaysia was studied to determine its taxonomic position. Cells were Gram-stain-negative, non-spore-forming rods, devoid of flagella and gliding motility, that formed yellow-pigmented colonies on nutrient agar and contained MK-6 as the predominant menaquinone. Comparative analysis of the 16S rRNA gene sequence of strain UTM-3(T) with those of the most closely related species showed that the strain constituted a distinct phyletic line within the genus Chryseobacterium with the highest sequence similarities to Chryseobacterium lactis NCTC 11390(T), Chryseobacterium viscerum 687B-08(T), Chryseobacterium tructae 1084-08(T), Chryseobacterium arthrosphaerae CC-VM-7(T), Chryseobacterium oncorhynchi 701B-08(T), Chryseobacterium vietnamense GIMN1.005(T), Chryseobacterium bernardetii NCTC 13530(T), Chryseobacterium nakagawai NCTC 13529(T), Chryseobacterium gallinarum LMG 27808(T), Chryseobacterium culicis R4-1A(T), Chryseobacterium flavum CW-E2(T), Chryseobacterium aquifrigidense CW9(T), Chryseobacterium ureilyticum CCUG 52546(T), Chryseobacterium indologenes NBRC 14944(T), Chryseobacterium gleum CCUG 14555(T), Chryseobacterium jejuense JS17-8(T), Chryseobacterium oranimense H8(T) and Chryseobacterium joostei LMG 18212(T). The major whole-cell fatty acids were iso-C15 : 0 and iso-C17 : 1ω9c, followed by summed feature 4 (iso-C15 : 0 2-OH and/or C16 : 1ω7t) and iso-C17 : 0 3-OH, and the polar lipid profile consisted of phosphatidylethanolamine and several unknown lipids. The DNA G+C content strain UTM-3(T) was 34.8 mol%. On the basis of the phenotypic and phylogenetic evidence, it is concluded that the isolate represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium artocarpi sp. nov. is proposed. The type strain is UTM-3(T) ( = CECT 8497(T) = KCTC 32509(T)).
    Matched MeSH terms: Bacterial Typing Techniques
  19. Pathogenicity and phenotypic analysis of sopB, sopD and pipD virulence factors in Salmonella enterica serovar typhimurium and Salmonella enterica serovar Agona
    Khoo CH, Sim JH, Salleh NA, Cheah YK
    Antonie Van Leeuwenhoek, 2015 Jan;107(1):23-37.
    PMID: 25312847 DOI: 10.1007/s10482-014-0300-7
    Salmonella is an important food-borne pathogen causing disease in humans and animals worldwide. Salmonellosis may be caused by any one of over 2,500 serovars of Salmonella. Nonetheless, Salmonella enterica serovar Typhimurium and Salmonella enterica serovar Agona are the second most prevalent serovars isolated from humans and livestock products respectively. Limited knowledge is available about the virulence mechanisms responsible for diarrheal disease caused by them. To investigate the contribution of sopB, sopD and pipD as virulence factors in intracellular infections and the uniqueness of these bacteria becoming far more prevalent than other serovars, the infection model of Caenorhabditis elegans and phenotypic microarray were used to characterize their mutants. The strains containing the mutation in sopB, sopD and pipD genes were constructed by using latest site-specific group II intron mutagenesis approach to reveal the pathogenicity of the virulence factors. Overall, we observed that the mutations in sopB, sopD and pipD genes of both serovars did not exhibit significant decrease in virulence towards the nematode. This may indicate that these virulence effectors may not be universal virulence factors involved in conserved innate immunity. There are significant phenotypic differences amongst strains carrying sopB, sopD and pipD gene mutations via the analysis of biochemical profiles of the bacteria. Interestingly, mutant strains displayed different susceptibility to chemical stressors from several distinct pharmacological and structural classes when compared to its isogenic parental strains. These metabolic and chemosensitivity assays also revealed multiple roles of Salmonella virulence factors in nutrient metabolism and antibiotic resistance.
    Matched MeSH terms: Bacterial Typing Techniques
  20. Microbacterium mangrovi sp. nov., an amylolytic actinobacterium isolated from mangrove forest soil
    Lee LH, Azman AS, Zainal N, Eng SK, Mutalib NA, Yin WF, et al.
    Int J Syst Evol Microbiol, 2014 Oct;64(Pt 10):3513-3519.
    PMID: 25056298 DOI: 10.1099/ijs.0.062414-0
    Strain MUSC 115(T) was isolated from mangrove soil of the Tanjung Lumpur river in the state of Pahang, Peninsular Malaysia. Cells of this strain stained Gram-positive and were non-spore-forming, short rods that formed yellowish-white colonies on different agar media. The taxonomy of strain MUSC 115(T) was studied by a polyphasic approach, and the organism showed a range of phylogenetic and chemotaxonomic properties consistent with those of the genus Microbacterium. The cell-wall peptidoglycan was of type B2β, containing the amino acids ornithine, alanine, glycine, glutamic acid and homoserine. The muramic acid was of the N-glycolyl form. The predominant menaquinones detected were MK-12, MK-13 and MK-11. The polar lipids consisted of phosphatidylglycerol, phosphoglycolipid, diphosphatidylglycerol, two unidentified lipids, three unidentified phospholipids and four unidentified glycolipids. The major fatty acids of the cell membrane were anteiso-C15:0 and anteiso-C17:0. The whole-cell sugars detected were ribose, glucose, mannose and galactose. Based on the 16S rRNA gene sequence, strain MUSC 115(T) showed the highest sequence similarity to Microbacterium immunditiarum SK 18(T) (98.1%), M. ulmi XIL02(T) (97.8%) and M. arborescens DSM 20754(T) (97.5%) and lower sequence similarity to strains of other species of the genus Microbacterium. DNA-DNA hybridization experiments revealed a low level of DNA-DNA relatedness (less than 24%) between strain MUSC 115(T) and the type strains of closely related species. Furthermore, BOX-PCR fingerprint comparison also indicated that strain MUSC 115(T) represented a unique DNA profile. The DNA G+C content determined was 70.9 ± 0.7 mol%, which is lower than that of M. immunditiarum SK 18(T). Based on the combination of genotypic and phenotypic data, it is proposed that strain MUSC 115(T) represents a novel species of the genus Microbacterium, for which the name Microbacterium mangrovi sp. nov. is proposed. The type strain is MUSC 115(T) ( = MCCC 1K00251(T) = DSM 28240(T) = NBRC 110089(T)).
    Matched MeSH terms: Bacterial Typing Techniques
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