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1.
Curr Microbiol ; 81(7): 187, 2024 May 22.
Artículo en Inglés | MEDLINE | ID: mdl-38777886

RESUMEN

Strain wdc7T, a rod-shaped bacterium, was isolated from soil in the Gotjawal Forest on Jeju Island, South Korea. Strain wdc7T was Gram stain-negative, facultatively anaerobic, catalase- and oxidase positive, yellow pigmented, and non-flagellated. It grew at 4-37 °C and pH 5.0-8.0 in 0-3% (w/v) NaCl. 16S rRNA gene sequencing analysis revealed that strain wdc7T belonged to the genus Chryseobacterium and was most closely related to Chryseobacterium salivictor NBC 122T, with a sequence similarity of 98.51%. Menaquinone 6 was the sole respiratory quinone, and C15:0 anteiso, C15:0 iso, and summed feature 9 were the major fatty acids. The genome length was 3.30 Mbp, with a 37% G + C content. Average amino acid identity, average nucleotide identity, and digital DNA-DNA relatedness between strain wdc7T and C. salivictor NBC 122T were 93.52%, 92.80%, and 49.7%, respectively. Digital genomic and polyphasic analyses showed that strain wdc7T likely represented a new species of the genus Chryseobacterium. We proposed the name Chryseobacterium gotjawalense sp. nov., with wdc7T (= KCTC 92440T = JCM 35602T) as the type strain.


Asunto(s)
Composición de Base , Chryseobacterium , ADN Bacteriano , Ácidos Grasos , Bosques , Filogenia , ARN Ribosómico 16S , Microbiología del Suelo , Chryseobacterium/genética , Chryseobacterium/clasificación , Chryseobacterium/aislamiento & purificación , ARN Ribosómico 16S/genética , ADN Bacteriano/genética , República de Corea , Ácidos Grasos/análisis , Islas , Técnicas de Tipificación Bacteriana , Análisis de Secuencia de ADN , Genoma Bacteriano , Vitamina K 2/análisis , Vitamina K 2/análogos & derivados
2.
Environ Microbiol Rep ; 16(1): e13226, 2024 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-38298071

RESUMEN

Flavobacterium plurextorum is a potential fish pathogen of interest, previously isolated from diseased rainbow trout (Oncorhynchus mykiss) and oomycete-infected chum salmon (Oncorhynchus keta) eggs. We report here the first complete genome sequence of F. plurextorum RSG-18 isolated from the gut of Schlegel's black rockfish (Sebastes schlegelii). The genome of RSG-18 consists of a circular chromosome of 5,610,911 bp with a 33.57% GC content, containing 4858 protein-coding genes, 18 rRNAs, 63 tRNAs and 1 tmRNA. A comparative analysis was conducted on 11 Flavobacterium species previously reported as pathogens or isolated from diseased fish to confirm the potential pathogenicity of RSG-18. In the SEED classification, RSG-18 was found to have 36 genes categorized in 'Virulence, Disease and Defense'. Across all Flavobacterium species, a total of 16 antibiotic resistance genes and 61 putative virulence factors were identified. All species had at least one phage region and type I, III and IX secretion systems. In pan-genomic analysis, core genes consist of genes linked to phages, integrases and matrix-tolerated elements associated with pathology. The complete genome sequence of F. plurextorum RSG-18 will serve as a foundation for future research, enhancing our understanding of Flavobacterium pathogenicity in fish and contributing to the development of effective prevention strategies.


Asunto(s)
Bacteriófagos , Enfermedades de los Peces , Oncorhynchus mykiss , Perciformes , Animales , Flavobacterium/genética , Virulencia/genética , Factores de Virulencia/genética , Peces/microbiología , Enfermedades de los Peces/microbiología , Oncorhynchus mykiss/microbiología
3.
Int J Syst Evol Microbiol ; 73(11)2023 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-37982814

RESUMEN

A milky-white-coloured, aerobic, Gram-stain-positive, rod-shaped and motile bacterial strain (GW78T) was isolated from forest soil. GW78T was catalase-positive and oxidase-negative. The strain was able to grow optimally at 37 °C and at pH 7.0 in Reasoner's 2A media. The phylogenetic and 16S rRNA gene sequence analysis of GW78T showed its affiliation with the genus Paenibacillus. The 16S rRNA gene sequence of GW78T revealed 98.3 % similarity to its nearest neighbour Paenibacillus mucilaginosus VKPM B-7519T. Its chemotaxonomic properties included MK-7 as the sole menaquinone, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmonomethylethanolamine and phosphatidylethanolamine as major polar lipids, and anteiso-C15 : 0, C16 : 1 ω11c and anteiso-C17 : 0 as predominant fatty acids. Digital DNA-DNA hybridization and average nucleotide identity results with its closest relatives were <74.0 % and <14.0 %, respectively. Overall, 16S rRNA gene sequence comparisons, phylogenetic and genomic evidence, and phenotypic and chemotaxonomic data allow the differentiation of GW78T from other members of the genus Paenibacillus. Thus, we propose that strain GW78T represents a novel species of the genus Paenibacillus, with the name Paenibacillus caseinilyticus sp. nov. The type strain is GW78T (=KCTC 43430T=NBRC 116023T).


Asunto(s)
Ácidos Grasos , Paenibacillus , Ácidos Grasos/química , Fosfolípidos/química , Filogenia , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , Composición de Base , ADN Bacteriano/genética , Técnicas de Tipificación Bacteriana , Microbiología del Suelo , Bosques
4.
JMIR Mhealth Uhealth ; 11: e46911, 2023 10 05.
Artículo en Inglés | MEDLINE | ID: mdl-37800887

RESUMEN

Background: Hearing loss is a growing health concern worldwide. Hearing aids (HAs) are the treatment of choice for hearing rehabilitation in most cases of mild-to-moderate hearing loss. However, many patients with hearing loss do not use HAs due to their high cost, stigma, and inaccessibility. Since smartphones are widely used, many apps that mimic the amplification function of HAs have been introduced. Smartphone-based HA apps (SHAAs) are affordable and easy to access. However, the audiological benefit of SHAAs has not been determined. Objective: We compared the audiological performance between an SHAA and a conventional HA in a prospective, multicenter randomized controlled trial. Methods: Patients with mild-to-moderate hearing loss were prospectively enrolled from 2 tertiary hospitals and randomly assigned to either an SHAA (Petralex; IT4YOU Corp LLC) or a conventional HA (Siya 1 miniRITE; Oticon A/S). For the cross-over study design, participants used the alternate device and repeated the same 2-month trial. Audiological measurements were obtained using hearing tests, real-ear measurements, and the hearing-in-noise test (HINT). Subjective satisfaction was evaluated using the Abbreviated Profile of Hearing Aid Benefit (APHAB) and International Outcome Inventory for Hearing Aids (IOI-HA). Results: Overall, 63 participants were screened and 38 completed the study. In sound-field audiometry testing, the SHAA showed a 20- to 60-dB gain in the low-to-high frequencies of the hearing threshold level. The HA provided adequate gain in the middle-to-high frequencies (55, 65, and 75 dB in real-ear measurements), which is the sound level for most speaking volumes. However, the SHAA could not improve word recognition at 50 dB. The HA showed better audiological performance than the SHAA in both quiet and noisy conditions in the HINT. The IOI-HA scores were significantly improved by both the HA and SHAA versus unaided conditions. Among the SHAA users, 37% (14/38), 42% (16/38), 24% (9/38), and 32% (12/38) showed improvement in APHAB scores for ease of communication, reverberation, background noise, and aversiveness of sounds, respectively. There were no differences in adverse events between the 2 study groups. Conclusions: The HA showed better performance than the SHAA in word recognition and the HINT. However, the SHAA was significantly better than unaided hearing in terms of amplification. The SHAA may be a useful hearing assistance device for patients with mild-to-moderate hearing loss when listening to soft sounds in quiet conditions. The SHAA demonstrated poorer performance than the HA in the mid- to high-frequency sounds that are important for word recognition, sound quality, and hearing in noisy conditions. Further development of the signal technology of SHAAs is needed to improve the sound quality of mid- to high-frequency sounds and overcome noisy environments.


Asunto(s)
Audífonos , Pérdida Auditiva Sensorineural , Pérdida Auditiva , Aplicaciones Móviles , Humanos , Teléfono Inteligente , Estudios Cruzados , Estudios Prospectivos , Estudios de Factibilidad
5.
Antonie Van Leeuwenhoek ; 116(10): 975-986, 2023 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-37542623

RESUMEN

In the late 1970s, Flavobacterium bizetiae was first isolated from diseased fish in Canada. After four decades of preservation, it was reported as a novel species in 2020. Here, we report the first complete genome sequence of HJ-32-4, a novel strain of F. bizetiae. Interestingly, HJ-32-4 was isolated from soil in Gangwon-do, Republic of Korea, unlike the other two previously reported F. bizetiae strains which were isolated from fish. We generated a single circular chromosome of HJ-32-4, comprising 5,745,280 bp with a GC content of 34.2%. The average nucleotide identity (ANI) value of 96.2% indicated that HJ-32-4 belongs to F. bizetiae CIP 105534T. The virulence factor was not detected in the genome. Comparative genomic analysis of F. bizetiae and major flavobacterial pathogens revealed that F. bizetiae had a larger genome size and the ratio of peptidases (PEP) and glycoside hydrolase (GH) genes of F. bizetiae were lower than those of the rest strains, implying that F. bizetiae exhibits similar characteristics with non-pathogenic strains from a genomic point of view. However, further experimental verification is required to ensure these in silico predictions. This study will provide insight into the overall characteristics of HJ-32-4 compared to other strains.


Asunto(s)
Flavobacterium , Suelo , Animales , Flavobacterium/genética , Análisis de Secuencia de ADN , Genómica , Factores de Virulencia/genética , Peces , Filogenia , ADN Bacteriano/genética , ARN Ribosómico 16S/genética , Ácidos Grasos
6.
Microbiol Spectr ; : e0100323, 2023 Aug 18.
Artículo en Inglés | MEDLINE | ID: mdl-37594286

RESUMEN

Members of the genus Flavobacterium are widely distributed and produce various polysaccharide-degrading enzymes. Many species in the genus have been isolated and characterized. However, few studies have focused on marine isolates or fish pathogens, and in-depth genomic analyses, particularly comparative analyses of isolates from different habitat types, are lacking. Here, we isolated 20 strains of the genus from various environments in South Korea and sequenced their full-length genomes. Combined with published sequence data, we examined genomic traits, evolution, environmental adaptation, and putative metabolic functions in total 187 genomes of isolated species in Flavobacterium categorized as marine, host-associated, and terrestrial including freshwater. A pangenome analysis revealed a correlation between genome size and coding or noncoding density. Flavobacterium spp. had high levels of diversity, allowing for novel gene repertories via recombination events. Defense-related genes only accounted for approximately 3% of predicted genes in all Flavobacterium genomes. While genes involved in metabolic pathways did not differ with respect to isolation source, there was substantial variation in genomic traits; in particular, the abundances of tRNAs and rRNAs were higher in the host-associdated group than in other groups. One genome in the host-associated group contained a Microviridae prophage closely related to an enterobacteria phage. The proteorhodopsin gene was only identified in four terrestrial strains isolated for this study. Furthermore, recombination events clearly influenced genomic diversity and may contribute to the response to environmental stress. These findings shed light on the high genetic variation in Flavobacterium and functional roles in diverse ecosystems as a result of their metabolic versatility. IMPORTANCE The genus Flavobacterium is a diverse group of bacteria that are found in a variety of environments. While most species of this genus are harmless and utilize organic substrates such as proteins and polysaccharides, some members may play a significant role in the cycling for organic substances within their environments. Nevertheless, little is known about the genomic dynamics and/or metabolic capacity of Flavobacterium. Here, we found that Flavobacterium species may have an open pangenome, containing a variety of diverse and novel gene repertoires. Intriguingly, we discovered that one genome (classified into host-associated group) contained a Microviridae prophage closely related to that of enterobacteria. Proteorhodopsin may be expressed under conditions of light or oxygen pressure in some strains isolated for this study. Our findings significantly contribute to the understanding of the members of the genus Flavobacterium diversity exploration and will provide a framework for the way for future ecological characterizations.

7.
Antonie Van Leeuwenhoek ; 116(8): 791-799, 2023 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-37227603

RESUMEN

The taxonomic position of strain EF45031T, isolated from the Neungam Carbonate hot spring, was examined using the polyphasic taxonomic approach. Strain EF45031T shared the highest percentage of 16S rRNA gene sequence with Brachybacterium nesterenkovii CIP 104813 T (97.7%). The average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) values between strain EF45031T and the type strains B. nesterenkovii CIP 104813 T and B. phenoliresistens Phenol-AT were 77.0%, 69.15%, 21.9% and 75.73%, 68.81%, 20.5%, respectively. Phylogenomic analysis using an up-to-date bacterial core gene (UBCG) set revealed that strain EF45031T belonged to the genus Brachybacterium. Growth occurred between 25 and 50 ℃ at pH 6.0-9.0 and could tolerate salinity up to 5% (w/v). Strain had anteiso-C15:0 and anteiso-C17:0 as major fatty acids. Menaquinone-7 (MK-7) was the predominant respiratory menaquinone. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, three aminolipids, and two unidentified glycolipids. The cell-wall peptidoglycan contained meso-diaminopimelic acid as a diagnostic diamino acid. The genome comprised 2,663,796 bp, with a G + C content of 70.9%. Stress-responsive periplasmic chaperone/protease coding genes were identified in the genome of EF45031T and were not detected in other Brachybacterium species. The polyphasic taxonomic properties indicate that the strain represents a novel species within the genus Brachybacterium, for which the name Brachybacterium sillae sp. nov. is proposed. The type strain is EF45031T (= KCTC 49702 T = NBRC 115869 T).


Asunto(s)
Actinomycetales , Manantiales de Aguas Termales , Fosfolípidos/química , ARN Ribosómico 16S/genética , Ácidos Grasos/química , Filogenia , Vitamina K 2/química , ADN , ADN Bacteriano/genética , Análisis de Secuencia de ADN , Técnicas de Tipificación Bacteriana
8.
Curr Microbiol ; 80(2): 83, 2023 Jan 21.
Artículo en Inglés | MEDLINE | ID: mdl-36680647

RESUMEN

The wetland is an important ecosystem for purifying pollutants and circulating nutrients. Numerous microorganisms contribute to maintaining this function. We obtained Flavobacterium enshiense R6S-5-6 which was isolated from Ungok (Ramsar) Wetland and conducted whole-genome sequencing to investigate what contribution R6S-5-6 could make to the wetland community. The complete genome sequence of R6S-5-6 has a size of 3,251,289 bp with 37.68% of GC content. Gene annotation revealed that R6S-5-6 has several pathways to break down pollutants, including denitrification, assimilatory sulfate reduction (ASR), and polyphosphate-accumulating process. Furthermore, R6S-5-6 has genes that can have a positive effect on plants living in wetlands, such as storing essential nutrients, promoting plant growth, and protecting plants against pathogens.


Asunto(s)
Ecosistema , Contaminantes Ambientales , Humedales , Desarrollo de la Planta
9.
Arch Microbiol ; 205(1): 22, 2022 Dec 10.
Artículo en Inglés | MEDLINE | ID: mdl-36495352

RESUMEN

Tidal flat microbes play an important ecological role by removing organic pollutants and providing an energy source. However, bacteria isolated from tidal flats and their genomes have been scarcely reported, making it difficult to elucidate which genes and pathways are potentially involved in the above roles. In this study, strain BSSL-CR3, the third reported species among the tidal flat Flavobacterium was analyzed using whole-genome sequencing to investigate its adaptability and functionality in tidal flats. BSSL-CR3 is comprised of a circular chromosome of 5,972,859 bp with a GC content of 33.84%. Genome annotation and API ZYM results showed that BSSL-CR3 has a variety of secondary metabolic gene clusters and enzyme activities including α-galactosidase. BSSL-CR3 had more proteins with a low isoelectric point (pI) than terrestrial Flavobacterium strains, and several genes related to osmotic regulation were found in the genomic island (GI). Comparative genomic analysis with other tidal flat bacteria also revealed that BSSL-CR3 had the largest number of genes encoding Carbohydrate Active EnZymes (CAZymes) which are related to algae degradation. This study will provide insight into the adaptability of BSSL-CR3 to the tidal flats and contribute to facilitating future comparative analysis of bacteria in tidal flats.


Asunto(s)
Flavobacterium , Genómica , Flavobacterium/genética , Islas Genómicas , Plantas
10.
Arch Microbiol ; 204(12): 691, 2022 Nov 05.
Artículo en Inglés | MEDLINE | ID: mdl-36334148

RESUMEN

Strain JK7-1T isolated from marine sediment collected from Jeju Island of South Korea was strictly aerobic, Gram-stain-negative, catalase-positive, oxidase-positive, motile, and rod-shaped bacterium that is circular and convex with white pigment. Strain JK7-1T could grow at 10-30 °C and pH 6-9 with 1-6% (w/v) NaCl. Phylogenetic analysis based on its 16S rRNA gene sequence indicated that strain JK7-1T belonged to genus Sulfitobacter, sharing high sequence similarities with Sulfitobacter undariae W-BA2T (97.90%), Sulfitobacter donghicola KCTC 12864T (97.61%), and Sulfitobacter mediterraneus KCTC 32188T (97.47%). Strain JK7-1T possessed only ubiquinone-10 (Q-10) as a sole respiratory quinone and summed feature 8 as the major fatty acid (81.02%). A dominant polar lipid phosphatidylglycerol was identified in strain JK7-1T. Strain JK7-1T had a complete genome of 3,441,674 bp in length with a mean G + C content of 63.96%. Polyphasic and genomic analyses revealed that strain JK7-1T represented a novel species in the genus Sulfitobacter, for which a name of Sulfitobacter albidus sp. nov. was proposed. Its type strain is JK7-1T (= KCTC 72819T = NBRC 114632T = KMM 6821T).


Asunto(s)
Sedimentos Geológicos , Agua de Mar , ARN Ribosómico 16S/genética , Filogenia , Agua de Mar/microbiología , ADN Bacteriano/genética , Técnicas de Tipificación Bacteriana , Hibridación de Ácido Nucleico , Análisis de Secuencia de ADN , Ácidos Grasos/química , Fosfolípidos/química
11.
Microbiol Resour Announc ; 11(9): e0005422, 2022 Sep 15.
Artículo en Inglés | MEDLINE | ID: mdl-35993777

RESUMEN

Here, we report the complete genome sequence of Flavobacterium sediminilitoris YSM-43T, isolated from a tidal flat in Yeosu, Republic of Korea. The whole genome consists of one circular chromosome of 3,913,692 bp. A total of 3,599 genes were predicted, comprising 3,537 coding DNA sequences (CDSs), 50 tRNAs, 9 rRNAs, and 3 noncoding RNAs (ncRNAs).

12.
Mar Genomics ; 63: 100950, 2022 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-35568405

RESUMEN

Erythrobacter sp. JK5, a marine heterotrophic bacterium, was isolated from marine sediment in Jeju island, the Republic of Korea. Here, we report information on the complete genome of strain JK5, including a putative capability for photosynthesis. The genome of JK5 consisted of 3.34 Mbp with 64.2% G + C content, and contained 3210 protein-coding sequences and three rRNA genes. Genomic analysis revealed that strain JK5 might be grown under oxic, microoxic, or anoxic conditions using two types of terminal oxidase (high and low oxygen affinity) or nitrate reductase. The types IV and VI secretion systems presented in strain JK5 genome might reveal a survival advantage against their ecological competitors in the marine environment.


Asunto(s)
Sphingomonadaceae , Composición de Base , ADN Bacteriano/genética , Filogenia , ARN Ribosómico 16S/genética , Agua de Mar/microbiología , Análisis de Secuencia de ADN , Sphingomonadaceae/genética
13.
Curr Microbiol ; 78(8): 3321-3327, 2021 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-34170378

RESUMEN

A Gram-stain-negative, rod-shaped, and strictly aerobic bacterium designated strain G2-bT was isolated from the marine sediment around Jeju Island, South Korea. Strain G2-bT was found to be catalase- and oxidase-positive, white-pigmented, motile with polar flagellum, and to grow optimally at 25 °C, pH 7.0 in the presence of 4% (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain G2-bT belongs to the genus Salinimonas and was closely related Salinimonas sediminis N102T (96.7% sequence similarity), Salinimonas iocasae KX18D6T (95.4%), Salinimonas lutimaris DPSR-4T (94.7%), and Salinimonas chungwhensis BH030046T (94.6%). Strain G2-bT possessed ubiquinone 8 as the sole respiratory quinone, summed feature 3 and summed feature 8 as the major fatty acids, and phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. The genome size and G + C content of the strain G2-bT were determined to be 3,765,169 bp, and 49.7%, respectively, as a complete circular genome. Based on the genomic analyses (e.g., average nucleotide identity and digital DNA-DNA hybridization), the strain G2-BT likely represents a new species in the genus Salinimonas, for which we propose to name this novel bacterium Salinimonas marina sp. nov., and the type strain is designated G2-BT (= KCTC 72817T = VTCC 910110T).


Asunto(s)
Sedimentos Geológicos , Fosfolípidos , Alteromonadaceae , Técnicas de Tipificación Bacteriana , ADN Bacteriano/genética , Ácidos Grasos/análisis , Filogenia , ARN Ribosómico 16S/genética , República de Corea , Análisis de Secuencia de ADN
14.
Arch Microbiol ; 203(6): 3633-3639, 2021 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-33993324

RESUMEN

A Gram-stain-negative, rod-shaped, aerobic and non-motile bacterium, designated P2-65T, was isolated from Moonsan stream water in the Republic of Korea. The temperature, NaCl concentration and pH ranges for growth of strain P2-65T were 10-37 °C, 0.0-3.0% (w/v) and 6.5-8.5 with optimum growth at 25-30 °C, 0.0-1.0% and 7.0-7.5, respectively. Comparison of 16S rRNA gene sequence showed that strain P2-65T was closely related to Flavobacterium cauense (95.4%) and Flavobacterium cheniae (95.3%). The major fatty acids were iso-C15:0, iso C17:0 3-OH, summed feature 3 (C16:1ω7c and/or C16:1ω6c), summed feature 9 (iso-C17:1 ω9c and/or 10-methyl C16:0) and iso-C15:0 3-OH. The predominant respiratory quinone was menaquinone-6 (MK-6). The major polar lipids detected in the strain were phosphatidylethanolamine, one aminophospholipid, one unidentified aminolipid and one unidentified polar lipid. The G + C content of the genomic DNA was 39.7%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values for strain P2-65T with closely related Flavobacterium species were below 74.8% and 20%, respectively. Based on polyphasic features, strain P2-65T is considered to represent a novel species of the genus Flavobacterium, for which the name Flavobacterium inviolabile sp. nov. is proposed. The type strain is P2-65T (= KCTC 62055T = NBRC 112953T).


Asunto(s)
Flavobacterium/clasificación , Microbiología del Agua , Ácidos Grasos/análisis , Flavobacterium/química , Flavobacterium/genética , Fosfatidiletanolaminas/análisis
15.
Arch Microbiol ; 203(7): 3803-3809, 2021 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-33993373

RESUMEN

A Gram-stain-negative, catalase- and oxidase-positive, rod-shaped bacterium, designated as JK6T was isolated from a coastal marine sediment in Jeju Island. Strain JK6T was characterized by polyphasic investigation including genome features. It grew at pH 5.0-9.0 (optimum 7.5), 18-30 °C (optimum 25 °C) and 1.0-7.0% (w/v) NaCl (optimum 2.0%). Strain JK6T utilized D-mannose, D-glucose, L-fucose, propionate and acetate as carbon and energy sources. The sole quinone was ubiquinone-10, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, and sphingolipid. Strain JK6T was closely related to Parasphingorhabdus flavimaris SW-151T (98.2%), Parasphingorhabdus marina DSM 22363T (97.6%) and Parasphingorhabdus litoris FR1093T (97.6%) based on 16S rRNA gene sequence similarity. Genome length and GC content were 3.29 Mbp and 53.0%, respectively. Digital DNA-DNA relatedness, average nucleotide identity, and average amino acid identity between strain JK6T and P. flavimaris SW-151T were 16.6%, 73.9%, and 77.6%, respectively. These results showed that the strain can be recognized as a novel bacterium named Parasphingorhabdus halotolerans. The type strain of Parasphingorhabdus halotolerans sp. nov. is JK6T (= KCTC 72818T = VTCC 910111T).


Asunto(s)
Sedimentos Geológicos , Sphingomonadaceae , Adenoma de Células de los Islotes Pancreáticos , Ácidos Grasos/análisis , Sedimentos Geológicos/microbiología , Fosfolípidos , Filogenia , ARN Ribosómico 16S/genética , República de Corea , Especificidad de la Especie , Sphingomonadaceae/clasificación , Sphingomonadaceae/genética
16.
Arch Microbiol ; 203(6): 3435-3442, 2021 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-33895889

RESUMEN

A Gram-negative, aerobic, flagellated, rod-shaped, and pink-pigmented bacterium, strain 17Sr1-43 T, was isolated from a soil sample collected in Nowongu, Seoul, Korea. The isolate could grow at 18-37 °C (optimum, 28-30 °C), pH 6.0-8.0 (optimum, pH 7.0) and in the presence of 0-1.0% (w/v) NaCl (optimum, 0%) with aeration. The major cellular fatty acids were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c) and summed feature 2 (iso-C16:1 I and/or C14:0 3-OH). The predominant respiratory quinone was Q-10 and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phospholipid, and diphosphatidylglycerol. The G + C content of genomic DNA was 69.1 mol%. Strain 17Sr1-43 T was closely related to Methylobacterium gregans KACC 14808 T (98.4% 16S rRNA gene sequence similarity), Methylobacterium hispanicum KACC 11432 T (97.9%), and Methylobacterium phyllosphaerae CBMB27T (96.1%). The complete genome of strain 17Sr1-43 T contains essential genes related to DNA repair processes including bacterial RecBCD dependent pathway and UmuCD system. Based on the phenotypic, genotypic, and chemotaxonomic characteristics, strain 17Sr1-43 T represents a novel species in the genus Methylobacterium, for which the name Methylobacterium radiodurans sp. nov. is proposed. The type strain is strain 17Sr1-43 T (= KCTC 52906 T = NBRC 112875 T).


Asunto(s)
Methylobacterium , Microbiología del Suelo , Reparación del ADN/genética , Methylobacterium/clasificación , Methylobacterium/genética , Methylobacterium/efectos de la radiación , Hibridación de Ácido Nucleico , Fosfolípidos/análisis , Filogenia , ARN Ribosómico 16S/genética , Tolerancia a Radiación , Especificidad de la Especie
17.
Curr Microbiol ; 78(6): 2440-2446, 2021 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-33904976

RESUMEN

A Gram-stain-negative, long-rod shaped, and facultatively anaerobic bacterium, designated as strain M1T, was isolated from the marine sediment of Jeju Island, South Korea. Strain M1T was found to be catalase- and oxidase-positive, light yellow-pigmented, non-motile, and non-flagellated, growing optimally at 30 °C, pH 7.0, and in the presence of 3% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain M1T belongs to the genus Draconibacterium and is closely related to Draconibacterium orientale FH5T (97.2%), Draconibacterium sediminis JN14CK-3 T (96.5%), "Draconibacterium filum" F2T (96.5%) and Draconibacterium mangrovi GM2-18 T (96.3% sequence similarity). The values for digital DNA-DNA hybridization ranged from 37.6 to 38.3% against D. orientale FH5T, D. sediminis KN14CK-3 T, and D. mangrovi GM2-18 T, clearly indicating that strain M1T represents a distinct species of the genus Draconibacterium. Strain M1T has a 40.0% G + C content estimated by genome sequence, menaquinone 7 as the sole respiratory quinone, C15:0 anteiso and C15:0 iso as the major fatty acids, and phosphatidylethanolamine, an unidentified phospholipid, and unidentified lipids as the polar lipids. Based on the polyphasic characteristics, it is suggested that strain M1T be assigned to the genus Draconibacterium as the type strain of a novel species, for which the name Draconibacterium halophilum sp. nov. is proposed. The type strain is M1T (= KCTC 72809 T = VTCC 910107 T).


Asunto(s)
Ácidos Grasos , Sedimentos Geológicos , Técnicas de Tipificación Bacteriana , Bacteroidetes , Composición de Base , ADN Bacteriano/genética , Ácidos Grasos/análisis , Filogenia , ARN Ribosómico 16S/genética , República de Corea , Análisis de Secuencia de ADN , Vitamina K 2
18.
Arch Microbiol ; 203(2): 755-762, 2021 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-33044623

RESUMEN

Two bacterial strains designated as MA3T and BT182 were isolated from a soil sample in South Korea. Cells of the two strains were Gram-stain-negative, non-motile, rod-shaped and formed red colonies on R2A agar at 25 °C. The 16S rRNA genes of the two strains shared a sequence similarity of 99.8%. Both strains shared the highest 16S rRNA gene similarity of 96.8% with Hymenobacter edaphi NLT, followed by Hymenobacter paludis KBP-30T (96.3%), Hymenobacter coalescens WW84T (96.3%) and Hymenobacter gummosus ANT-18T (96.3%). Growth was observed at 15-37 °C (optimum 30 °C), pH 6-8 (optimum pH 7) and in the presence up to 1% NaCl. The genome size of strains MA3T and BT182 is 4.9 Mb and 4.8 Mb, respectively. The genomic G + C content of both strains is 62.0 mol%. The main polar lipid of the strains was phosphatidylethanolamine, the only respiratory quinone detected was menaquinone-7 and the major fatty acids were anteiso-C15:0, iso-C15:0, summed feature 4 (iso-C17:1 I/anteiso-C17:1 B) and summed feature 3 (C16:1 ω6c/C16:1 ω7c), supporting the affiliation of these strains with the genus Hymenobacter. Based on the phylogenetic, genotypic, phenotypic and chemotaxonomic data, strains MA3T and BT182 represent a novel species of the genus Hymenobacter, for which the name Hymenobacter busanensis is proposed. The type strain is MA3T (= KCTC 72631T = NBRC 114193T).


Asunto(s)
Cytophagaceae/clasificación , Filogenia , Microbiología del Suelo , Bacteroidetes/clasificación , Bacteroidetes/genética , Composición de Base , Cytophagaceae/genética , Cytophagaceae/efectos de la radiación , Ácidos Grasos/análisis , Genoma Bacteriano/genética , ARN Ribosómico 16S/genética , República de Corea , Especificidad de la Especie
19.
Artículo en Inglés | MEDLINE | ID: mdl-33270003

RESUMEN

Strain M2T, isolated from marine sediment collected at Jeju Island, was an aerobic, Gram-stain-negative, oxidase- and catalase-positive, motile, rod-shaped bacterium that formed circular, raised, yellow colonies. Strain M2T grew at 15-42 °C, pH 5.5-9.0 and with 1-9 % (w/v) NaCl. Phylogenetic analysis based on its 16S rRNA gene sequences indicated that strain M2T was closely related to Kineobactrum sediminis F02T (98.0 % sequence similarity). Ubiquinone-8 was determined to be the sole respiratory quinone. Summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c) and summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c) were identified as the predominant fatty acids. The DNA G+C content and digital DNA-DNA relatedness between strain M2T and K. sediminis F02T were 60.7 mol% and 19.5 %, respectively. Phosphatidylglycerol and phosphatidylethanolamine were identified as the major polar lipids. Thus, polyphasic characterization revealed that strain M2T represents a novel species in the genus Kineobactrum, for which the name Kineobactrum salinum sp. nov. is proposed. The type strain is M2T (=KCTC 72815T=VTCC 910108T).


Asunto(s)
Gammaproteobacteria/clasificación , Sedimentos Geológicos/microbiología , Filogenia , Agua de Mar/microbiología , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , Ácidos Grasos/química , Gammaproteobacteria/aislamiento & purificación , Hibridación de Ácido Nucleico , Fosfolípidos/química , ARN Ribosómico 16S/genética , República de Corea , Análisis de Secuencia de ADN , Ubiquinona/química
20.
Curr Microbiol ; 78(2): 796-802, 2021 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-33249533

RESUMEN

A novel light-yellow-coloured, Gram-stain-positive, nearly-coccoid, aerobic bacterium, designated strain ID2601ST was isolated from a car evaporator core collected from South Korea. Strain ID2601ST was catalase positive and oxidase negative, able to grow at pH 6.0-8.0, temperature 20-45 °C, and 0-6.0% (w/v) NaCl concentration. The 16S rRNA gene sequence analysis showed that strain ID2601ST belonged to the genus Flexivirga, with the nearest phylogenetic neighbour being Flexivirga endophytica YIM 7505T (97.9% sequence similarity). The strain comprised diphosphatidylglycerol as the main polar lipid; MK-8(H4) as a predominant respiratory quinone; serine, alanine, glycine, glutamic acid, and lysine as main components of peptidoglycan and iso-C16:0, summed feature 9 (iso-C17:1ω9c and/or C16:0 10-methyl), anteiso-C17:0, and C17:0 10-methyl as the major fatty acids. The average nucleotide identity (ANI) values between strain ID2601ST and the closest species (Flexivirga endophytica YIM 7505T and Flexivirga caeni BO-16T) were < 78%. The in silico DNA-DNA hybridization (dDDH) values of strain ID2601ST with the closest species were < 22%. These observations were below the threshold values of 95% (for ANI) and 70% (for dDDH) used for species delineation. The DNA G+C content was 69.8 mol%. Based on the polyphasic taxonomic data, the novel species Flexivirga aerilata sp. nov. is proposed with the type strain ID2601ST (=KCTC 49353T =NBRC 114622T).


Asunto(s)
Aire Acondicionado , Automóviles , Actinobacteria , Técnicas de Tipificación Bacteriana , ADN Bacteriano/genética , Ácidos Grasos , Hibridación de Ácido Nucleico , Fosfolípidos , Filogenia , ARN Ribosómico 16S/genética , República de Corea , Análisis de Secuencia de ADN
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