scholarly journals Bartonella japonica sp. nov. and Bartonella silvatica sp. nov., isolated from Apodemus mice

2010 ◽  
Vol 60 (4) ◽  
pp. 759-763 ◽  
Author(s):  
Kai Inoue ◽  
Hidenori Kabeya ◽  
Hatsumi Shiratori ◽  
Kenji Ueda ◽  
Michael Y. Kosoy ◽  
...  
Keyword(s):  
16S Rrna ◽  
Novel Species ◽  
Biochemical Properties ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Phenotypic Characterization ◽  
Sequencing Analysis ◽  
Field Mouse ◽  
Bacterial Strains ◽  
Apodemus Speciosus

Two bacterial strains, Fuji 18-1T and Fuji 23-1T, were isolated from the blood of the small Japanese field mouse (Apodemus argenteus) and the large Japanese field mouse (Apodemus speciosus), respectively, specimens of which were captured in the forest of Mount Fuji, Japan. Phenotypic characterization (growth conditions, incubation periods, biochemical properties and cell morphologies), DNA G+C contents (40.1 mol% for strain Fuji 18-1T and 40.4 mol% for strain Fuji 23-1T) and sequence analyses of the 16S rRNA genes indicated that both strains were members of the genus Bartonella. Using rpoB and gltA sequencing analysis, the highest sequence similarities between strains Fuji 18-1T, Fuji 23-1T and other recognized species of the genus Bartonella showed values considerably lower than 91.4 % and 89.9 % in the rpoB gene and 89.1 % and 90.4 % in the gltA gene, respectively. It is known that similarities of 95.4 % for the rpoB gene and 96.0 % for the gltA gene can be applied as cut-off values for the designation of novel species of the genus Bartonella. In a phylogenetic tree based on the merged set of concatenated sequences of seven loci [16S rRNA, ftsZ, gltA, groEL, ribC and rpoB genes and the intergenic spacer region (ITS)], strains Fuji 18-1T and Fuji 23-1T formed a distinct clade from other recognized species of the genus Bartonella. These data support the classification of strains Fuji 18-1T and Fuji 23-1T as novel species of the genus Bartonella. The names Bartonella japonica sp. nov. and Bartonella silvatica sp. nov. are proposed for these novel species. The type strains of Bartonella japonica sp. nov. and Bartonella silvatica sp. nov. are Fuji 18-1T (=JCM 15567T=CIP 109861T) and Fuji 23-1T (=JCM 15566T=CIP 109862T), respectively.

scholarly journals Streptococcus orisuis sp. nov., isolated from the pig oral cavity

2007 ◽  
Vol 57 (6) ◽  
pp. 1272-1275 ◽  
Author(s):  
Kazuko Takada ◽  
Masatomo Hirasawa
Keyword(s):  
16S Rrna ◽  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Mutans Streptococci ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Oral Streptococci ◽  
The Novel ◽  
Bacterial Strains

Five bacterial strains, designated as NUM 1001T, NUM 1002, NUM 1003, NUM 1004 and NUM 1005, were isolated from the oral cavities of pigs. Colonies grown on mitis salivarius agar were similar in morphology to those of mutans streptococci. The novel isolates were analysed biochemically using the Rapid ID 32 Strep microsystem, subjected to DNA–DNA hybridization with oral streptococci and had their 16S rRNA genes sequenced. On the basis of the phylogenetic and phenotypic evidence obtained, the strains represent a novel species of the genus Streptococcus, for which the name Streptococcus orisuis sp. nov. is proposed. The type strain is NUM 1001T (=JCM 14035T=DSM 18307T).

Bartonella jaculi sp. nov., Bartonella callosciuri sp. nov., Bartonella pachyuromydis sp. nov. and Bartonella acomydis sp. nov., isolated from wild Rodentia

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1734-1740 ◽  
Author(s):  
Shingo Sato ◽  
Hidenori Kabeya ◽  
Yuta Fujinaga ◽  
Kai Inoue ◽  
Yumi Une ◽  
...  
Keyword(s):  
16S Rrna ◽  
Phylogenetic Trees ◽  
Novel Species ◽  
Amino Acid Sequences ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Phenotypic Characterization ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type

Four novel strains of members of the genus Bartonella , OY2-1T, BR11-1T, FN15-2T and KS2-1T, were isolated from the blood of wild-captured greater Egyptian jerboa (Jaculus orientalis), plantain squirrel (Callosciurus notatus), fat-tailed gerbil (Pachyuromys duprasi) and golden spiny mouse (Acomys russatus). All the animals were imported to Japan as pets from Egypt, Thailand and the Netherlands. The phenotypic characterization (growth conditions, incubation periods, biochemical properties and cell morphologies), DNA G+C contents (37.4 mol% for strain OY2-1T, 35.5 mol% for strain BR11-1T, 35.7 mol% for strain FN15-2T and 37.2 mol% for strain KS2-1T), and sequence analyses of the 16S rRNA genes indicated that those strains belong to the genus Bartonella . Sequence comparisons of gltA and rpoB genes suggested that all of the strains should be classified as novel species of the genus Bartonella . In phylogenetic trees based on the concatenated sequences of five loci, including the 16S rRNA, ftsZ, gltA and rpoB genes and the ITS region, and on the concatenated deduced amino acid sequences of three housekeeping genes (ftsZ, gltA and rpoB), all strains formed distinct clades and had unique mammalian hosts that could be discriminated from other known species of the genus Bartonella . These data strongly support the hypothesis that strains OY2-1T, BR11-1T, FN15-2T and KS2-1T should be classified as representing novel species of the genus Bartonella . The names Bartonella jaculi sp. nov., Bartonella callosciuri sp. nov., Bartonella pachyuromydis sp. nov. and Bartonella acomydis sp. nov. are proposed for these novel species. Type strains of Bartonella jaculi sp. nov., Bartonella callosciuri sp. nov., Bartonella pachyuromydis sp. nov. and Bartonella acomydis sp. nov. are OY2-1T ( = JCM 17712T = KCTC 23655T), BR11-1T ( = JCM 17709T = KCTC 23909T), FN15-2T ( = JCM 17714T = KCTC 23657T) and KS2-1T ( = JCM 17706T = KCTC 23907T), respectively.

scholarly journals Effects of Supplement of Marichromatium gracile YL28 on Water Quality and Microbial Structures in Shrimp Mariculture Ecosystems

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 40
Author(s):  
Liang Cui ◽  
Bitong Zhu ◽  
Xiaobo Zhang ◽  
Zhuhua Chan ◽  
Chungui Zhao ◽  
...  
Keyword(s):  
Water Quality ◽  
16S Rrna ◽  
Relative Abundance ◽  
Animal Health ◽  
Denitrifying Bacteria ◽  
Nitrite Reduction ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sequencing Analysis ◽  
Shrimp Culture

The elevated NH3-N and NO2-N pollution problems in mariculture have raised concerns because they pose threats to animal health and coastal and offshore environments. Supplement of Marichromatium gracile YL28 (YL28) into polluted shrimp rearing water and sediment significantly decreased ammonia and nitrite concentrations, showing that YL28 functioned as a novel safe marine probiotic in the shrimp culture industry. The diversity of aquatic bacteria in the shrimp mariculture ecosystems was studied by sequencing the V4 region of 16S rRNA genes, with respect to additions of YL28 at the low and high concentrations. It was revealed by 16S rRNA sequencing analysis that Proteobacteria, Planctomycete and Bacteroidetes dominated the community (>80% of operational taxonomic units (OTUs)). Up to 41.6% of the predominant bacterial members were placed in the classes Gammaproteobacteria (14%), Deltaproteobacteria (14%), Planctomycetacia (8%) and Alphaproteobacteria (5.6%) while 40% of OTUs belonged to unclassified ones or others, indicating that the considerable bacterial populations were novel in our shrimp mariculture. Bacterial communities were similar between YL28 supplements and control groups (without addition of YL28) revealed by the β-diversity using PCoA, demonstrating that the additions of YL28 did not disturb the microbiota in shrimp mariculture ecosystems. Instead, the addition of YL28 increased the relative abundance of ammonia-oxidizing and denitrifying bacteria. The quantitative PCR analysis further showed that key genes including nifH and amoA involved in nitrification and nitrate or nitrite reduction significantly increased with YL28 supplementation (p < 0.05). The supplement of YL28 decreased the relative abundance of potential pathogen Vibrio. Together, our studies showed that supplement of YL28 improved the water quality by increasing the relative abundance of ammonia-oxidizing and denitrifying bacteria while the microbial community structure persisted in shrimp mariculture ecosystems.

scholarly journals Ureibacillus composti sp. nov. and Ureibacillus thermophilus sp. nov., isolated from livestock-manure composts

2007 ◽  
Vol 57 (12) ◽  
pp. 2908-2911 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Seon-Young Lee ◽  
Byung-Yong Kim ◽  
Hyung-Jun Noh ◽  
Peter Schumann ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Strains ◽  
Phylogenetic Affiliation ◽  
Dna Reassociation ◽  
Compost Facility

Two Gram-negative, rod-shaped, thermophilic bacterial strains, HC145T and HC148T, were isolated from a compost sample from a compost facility in Ichon, Korea. Sequencing of the 16S rRNA genes of HC145T and HC148T and comparative analyses of the resulting sequences clearly showed that these strains had a phylogenetic affiliation to the genus Ureibacillus. The level of 16S rRNA similarity between the two novel strains was 98.4 % and the levels of sequence similarity between them and existing Ureibacillus species were 97.8–98.1 (HC145T) and 97.4–98.7 % (HC148T). The DNA–DNA reassociation values between the two strains and the type strains of Ureibacillus species ranged from 38 to 51 %. The polar lipid profiles for both isolates consisted of phosphatidylglycerol, diphosphatidylglycerol, phospholipids and glycolipids of unknown composition. The major quinones were MK-8, MK-9 and MK-7, the peptidoglycan type was l-Lys←d-Asp and the main cellular fatty acid was iso-C16 : 0. The DNA G+C contents of strains HC145T and HC148T were 42.4 and 38.5 mol%, respectively. On the basis of the data from this polyphasic study, strains HC145T and HC148T represent members of the genus Ureibacillus, for which the names Ureibacillus composti sp. nov. and Ureibacillus thermophilus sp. nov., respectively, are proposed. The type strain of U. composti is HC145T (=KACC 11361T =DSM 17951T) and the type strain of U. thermophilus is HC148T (=KACC 11362T =DSM 17952T).

scholarly journals Mycoplasma anserisalpingitidis sp. nov., isolated from European domestic geese (Anser anser domesticus) with reproductive pathology

2020 ◽  
Vol 70 (4) ◽  
pp. 2369-2381 ◽  
Author(s):  
Dmitriy V. Volokhov ◽  
Dénes Grózner ◽  
Miklós Gyuranecz ◽  
Naola Ferguson-Noel ◽  
Yamei Gao ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

In 1983, Mycoplasma sp. strain 1220 was isolated in Hungary from the phallus lymph of a gander with phallus inflammation. Between 1983 and 2017, Mycoplasma sp. 1220 was also identified and isolated from the respiratory tract, liver, ovary, testis, peritoneum and cloaca of diseased geese in several countries. Seventeen studied strains produced acid from glucose and fructose but did not hydrolyse arginine or urea, and all grew under aerobic, microaerophilic and anaerobic conditions at 35 to 37 ˚C in either SP4 or pleuropneumonia-like organism medium supplemented with glucose and serum. Colonies on agar showed a typical fried-egg appearance and transmission electron microscopy revealed a typical mycoplasma cellular morphology. Molecular characterization included analysis of the following genetic loci: 16S rRNA, 23S rRNA, 16S–23S rRNA ITS, rpoB, rpoC, rpoD, uvrA, parC, topA, dnaE, fusA and pyk. The genome was sequenced for type strain 1220T. The 16S rRNA gene sequences of studied strains of Mycoplasma sp. 1220 shared 99.02–99.19 % nucleotide similarity with M. anatis strains but demonstrated ≤95.00–96.70 % nucleotide similarity to the 16S rRNA genes of other species of the genus Mycoplasma . Phylogenetic, average nucleotide and amino acid identity analyses revealed that the novel species was most closely related to Mycoplasma anatis . Based on the genetic data, we propose a novel species of the genus Mycoplasma , for which the name Mycoplasma anserisalpingitidis sp. nov. is proposed with the type strain 1220T (=ATCC BAA-2147T=NCTC 13513T=DSM 23982T). The G+C content is 26.70 mol%, genome size is 959110 bp.

scholarly journals Comparative Study of PCR-Based Approaches for the Genetic Characterization of Three Strains of Acidithiobacillus caldus Isolated from Different Sites in China

2013 ◽  
Vol 62 (4) ◽  
pp. 351-358
Author(s):  
Xueling Wu ◽  
Hong Duan ◽  
Hongwei Fan ◽  
Zhenzhen Zhang ◽  
Lili Liu
Keyword(s):  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Intergenic Spacers ◽  
Acidithiobacillus Caldus ◽  
Pcr Fingerprinting ◽  
23S Rrna Gene

Comparative study of the genetic characteristics among three Acidithiobacillus caldus strains isolated from different typical environments in China was performed using a combination of molecular methods, namely sequencing analysis of PCR-amplified 16S rRNA genes and 16S-23S rRNA gene intergenic spacers (ITS), repetitive element PCR (rep-PCR), arbitrarily primed PCR (AP-PCR) fingerprinting and random amplified polymorphic DNA (RAPD). Both of the 16S rRNA gene and 16S-23S rRNA gene intergenic spacers sequences of the three strains exhibited small variations, with 99.9-100%, 99.7-100% identity respectively. In contrast, according to the analysis of bacterial diversity based on rep-PCR and AP-PCR fingerprinting, they produced highly discriminatory banding patterns, and the similarity values between them varied from 61.97% to 71.64%. RAPD analysis showed that banding profiles of their genomic DNA exhibited obvious differences from each other with 53.44-75% similarity. These results suggested that in contrast to 16S rRNA genes and 16S-23S rRNA gene intergenic spacers sequencing analysis, rep-PCR, AP-PCR fingerprinting and RAPD analysis possessed higher discriminatory power in identifying these closely related strains. And they could be used as rapid and highly discriminatory typing techniques in studying bacterial diversity, especially in differentiating bacteria within Acidithiobacillus caldus.

Halosimplex halophilum sp. nov. and Halosimplex salinum sp. nov., isolated from saline soil and a salt mine

2021 ◽  
Vol 71 (4) ◽  
Author(s):  
Xiao-Yan Yang ◽  
Xue-Meng Yin ◽  
Jing Hou ◽  
Lin Zhu ◽  
Heng-Lin Cui
Keyword(s):  
16S Rrna ◽  
In Silico ◽  
Saline Soil ◽  
Novel Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Threshold Values ◽  
Content Type ◽  
Link Type ◽  
Sequence Similarities

A polyphasic study was undertaken to determine the taxonomic position of two halophilic archaeal strains, TH32T and YPL4T, isolated from saline soil and a salt mine in PR China, respectively. Strains TH32T and YPL4T both have two dissimilar 16S rRNA genes. The two strains exhibited sequence similarities of 91.5–95.5 % for 16S rRNA genes and 90.9 % for the rpoB′ gene. Sequence similarities of 16S rRNA genes and the rpoB′ gene between the two strains and the current four members of Halosimplex were 90.6–97.4 % and 91.4–93.5 %, respectively. Phylogenetic analysis revealed that the two strains formed different branches separating them from the current Halosimplex members. Several phenotypic characteristics differentiate strains TH32T and YPL4T from current Halosimplex members. The polar lipids of the two strains are phosphatidic acid, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and four glycolipids. Two of the glycolipids are chromatographically identical to disulfated mannosyl glucosyl diether and sulfated mannosyl glucosyl diether, respectively, and the remaining two glycolipids are unidentified. The average nucleotide identity (ANI) and in silico DNA–DNA hybridization (DDH) values between the two strains and the current members of Halosimplex (ANI 80.4–89.2 % and in silico DDH 24.0–41.8 %) were much lower than the threshold values proposed as a species boundary, suggesting that the two strains represent novel species of Halosimplex . The values between the two strains (ANI 81.3 % and in silico DDH 24.9 %) were also much lower than the recommended threshold values, which revealed that the two strains represent two genomically different species of Halosimplex . These results showed that strains TH32T (=CGMCC 1.15190T=JCM 30840T) and YPL4T (=CGMCC 1.15329T=JCM 31108T) represent two novel species of Halosimplex , for which the names Halosimplex halophilum sp. nov. and Halosimplex salinum sp. nov. are proposed.

scholarly journals Comparative Genetic Diversity of the narG, nosZ, and 16S rRNA Genes in Fluorescent Pseudomonads

2003 ◽  
Vol 69 (2) ◽  
pp. 1004-1012 ◽  
Author(s):  
Sandrine Delorme ◽  
Laurent Philippot ◽  
Veronique Edel-Hermann ◽  
Chrystel Deulvot ◽  
Christophe Mougel ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Pairwise Comparison ◽  
Fluorescent Pseudomonads ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Good Correspondence ◽  
The 16S Rrna Gene

ABSTRACT The diversity of the membrane-bound nitrate reductase (narG) and nitrous oxide reductase (nosZ) genes in fluorescent pseudomonads isolated from soil and rhizosphere environments was characterized together with that of the 16S rRNA gene by a PCR-restriction fragment length polymorphism assay. Fragments of 1,008 bp and 1,433 bp were amplified via PCR with primers specific for the narG and nosZ genes, respectively. The presence of the narG and nosZ genes in the bacterial strains was confirmed by hybridization of the genomic DNA and the PCR products with the corresponding probes. The ability of the strains to either reduce nitrate or totally dissimilate nitrogen was assessed. Overall, there was a good correspondence between the reductase activities and the presence of the corresponding genes. Distribution in the different ribotypes of strains harboring both the narG and nosZ genes and of strains missing both genes suggests that these two groups of strains had different evolutionary histories. Both dissimilatory genes showed high polymorphism, with similarity indexes (Jaccard) of between 0.04 and 0.8, whereas those of the 16S rRNA gene only varied from 0.77 to 0.99. No correlation between the similarity indexes of 16S rRNA and dissimilatory genes was seen, suggesting that the evolution rates of ribosomal and functional genes differ. Pairwise comparison of similarity indexes of the narG and nosZ genes led to the delineation of two types of strains. Within the first type, the similarity indexes of both genes varied in the same range, suggesting that these two genes have followed a similar evolution. Within the second type of strain, the range of variations was higher for the nosZ than for the narG gene, suggesting that these genes have had a different evolutionary rate.

scholarly journals Weissella jogaejeotgali sp. nov., isolated from jogae jeotgal, a traditional Korean fermented seafood

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4674-4681 ◽  
Author(s):  
Se-Hui Lee ◽  
Hye-Jin Ku ◽  
Min-Ju Ahn ◽  
Ji-Sang Hong ◽  
Se Hee Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Restriction Analysis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Carbohydrate Fermentation ◽  
Genomic Dnas ◽  
Close Relatives

Strain FOL01T was isolated from traditionally fermented Korean jogae jeotgal (fermented clams). Phylogenetic sequence analysis of the 16S rRNA gene from FOL01T revealed that it is closely related to Weissella thailandensis FS61-1T and Weissella paramesenteroides ATCC 33313T with 99.39 % and 98.50 % 16S rRNA gene sequence similarities, respectively. API and VITEK analyses showed that strain FOL01T could be separated from its nearest phylogenetic relatives with respect to carbohydrate fermentation and antibiotic resistance. Subsequent amplified rRNA gene restriction analysis of 16S rRNA genes and HaeIII-restriction enzyme profiling of genomic DNAs revealed different band patterns. In addition, DNA–DNA hybridization of genomic DNAs showed 63.9 % relatedness. Analysis of the composition of cellular fatty acids confirmed that strain FOL01T differs from its close relatives and supports the proposal to assign this organism to a novel species of the genus Weissella. Based on these results, strain FOL01T could be classified as a novel species of the genus Weissella, for which the name Weissella jogaejeotgali sp. nov. is proposed. The type strain is FOL01T ( = KCCM 43128T = JCM 30589T).

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