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Sphingomonas agri sp. nov., a bacterium isolated from soil
Siddiqi, Muhammad Zubair,Choi, Gyu-Min,Kim, Sang Yong,Choi, Kang Duk,Im, Wan-Taek Society for General Microbiology 2017 International journal of systematic and evolutiona Vol.67 No.11
<P> A Gram-reaction-negative, aerobic, non-motile, white (translucent) and rod-shaped bacterium (designated HKS-06<SUP>T</SUP>) isolated from soil was characterized by a polyphasic approach to clarify its taxonomic position. Strain HKS-06T was observed to grow optimally at 30 °C and at pH 6.5-7.0 on R2A agar medium. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HKS-06<SUP>T</SUP> belongs to the genus Sphingomonas and is most closely related to Sphingomonas lutea JS5<SUP>T</SUP> (97.4% similarity). The G+C content of the genomic DNA was 64.1 mol%. Chemotaxonomic data [major quinone (Q-10), major polar lipids (phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, phosphatidylcholine, unknown polar lipid) and major fatty acids (summed feature 8, comprising C18 : 1ω7c/ω6c and/or C<SUB>18</SUB> : <SUB>1</SUB>ω6c, C<SUB>18 : 0</SUB> 3-OH and C<SUB>16 : 0</SUB>)] supported the affiliation of strain HKS-06<SUP>T</SUP> to the genus Sphingomonas. Moreover, the physiological and biochemical results and low level of DNA-DNA relatedness [between strain HKS06<SUP>T</SUP> and S. lutea JS5<SUP>T</SUP> (20.24±1.2 %)] allowed the phenotypic and genotypic differentiation of strain HKS-06<SUP>T</SUP> from recognized species of the genus Sphingomonas. The new isolate therefore represents a novel species, for which the name Sphingomonas agri sp. nov. is proposed. The type strain is HKS-06<SUP>T</SUP> (=KACC 18880T=LMG 29563<SUP>T</SUP>). </P>
Arthrobacter ginsengisoli sp. nov., isolated from soil of a ginseng field
Siddiqi, Muhammad Zubair,Kim, Yeon-Ju,Hoang, Van-An,Siddiqi, Muhammad Hanif,Huq, Md. Amdadul,Yang, Deok-Chun Springer-Verlag 2014 Archives of microbiology Vol.196 No.12
<P>A Gram-staining-positive, catalase-positive, oxidase-negative, non-motile, non-flagellate and rod-shaped bacterium, was designated as DCY81(T), and isolated from soil of a ginseng field in Pocheon province, Republic of Korea. The 16S rRNA gene sequence analysis revealed that strain DCY81(T) belonged to the genus Arthrobacter. Major fatty acid was anteiso-C15:0, while major polar lipids were diphosphatidyglycerol, phatidyglycerol, phosphatidylinositol, monogalactosyldiacylglycerol (GL1), and dimannosyldiacylglycerol (GL2). The dominant quinone was MK-9(H2). The peptidoglycan type was A3α with an L-Lys-L-Ala-L-Thr-L-Ala interpeptide bridge. The DNA-DNA hybridization relatedness between strain DCY81(T) and Arthrobacter siccitolerans LMG 27359(T) (98.2?%), Arthrobacter sulfonivorans JCM 13520(T) (97.81?%), Arthrobacter scleromae DSM 17756(T) (97.59?%), Arthrobacter oxydans KCTC 3383(T) (97.3?%) was 39.1??0.2, 62.2??1.6, 36.8??1.1 and 48.3??1.6?%, respectively which show that the genotypic separation of strain DCY81(T) from the closest reference strain of the genus Arthrobacter. The DNA G+C content was 65.2?mol%. The genotypic analysis, physiological, and chemotaxonomic results indicate that strain DCY81(T) represents a novel species of the genus Arthrobacter. Therefore, Arthrobacter ginsengisoli sp. nov., is proposed as the type strain (=KCTC 29225(T)?=?JCM 19357(T)).</P>
Siddiqi, Muhammad Hanif,Siddiqi, Muhammad Zubair,Ahn, Sungeun,Kim, Yeon-Ju,Yang, Deok Chun Pharmaceutical Society of Great Britain 2014 Journal of pharmacy and pharmacology Vol.66 No.12
<P>This study aimed to investigate the stimulative and pharmacological effects of ginsenoside Rh1 (hereinafter referred to as: Rh1) on differentiation and mineralization of osteoblast and its possible mechanism of action on the expression of bone morphogenetic protein 2 (BMP-2)/Runt-related gene 2 (Runx2) signalling pathways using mouse preosteoblastic MC3T3-E1 cell line as in-vitro model.</P>
Ginseng saponins and the treatment of osteoporosis: mini literature review
Muhammad Hanif Siddiqi,Muhammad Zubair Siddiqi,Sungeun Ahn,Sera Kang,Yeon-Ju Kim,Natarajan Sathishkumar,Dong-Uk Yang,Deok-Chun Yang 고려인삼학회 2013 Journal of Ginseng Research Vol.37 No.3
The ginseng plant (Panax ginseng Meyer) has a large number of active ingredients including steroidal saponins with a dammarane skeleton as well as protopanaxadiol and protopanaxatriol, commonly known as ginsenosides, which have antioxidant, anticancer, antidiabetic, anti-adipocyte, and sexual enhancing effects. Though several discoveries have demonstrated that ginseng saponins (ginsenosides) as the most important therapeutic agent for the treatment of osteoporosis, yet the molecular mechanism of its active metabolites is unknown. In this review, we summarize the evidence supporting the therapeutic properties of ginsenosides both in vivo and in vitro, with an emphasis on the different molecular agents comprising receptor activator of nuclear factor kappa-B ligand, receptor activator of nuclear factor kappa-B, and matrix metallopeptidase-9, as well as the bone morphogenetic protein-2 and Smad signaling pathways.
Draft genome sequence of silver nanoparticle producing bacterium Paenibacillus anseongense MAH-34
Muhammad Zubair Siddiqi,Sathiyaraj Srinivasan,Ramesh Subramani,Wan-Taek Im,Md. Amdadul Huq 한국미생물학회 2020 미생물학회지 Vol.56 No.4
A bacterial strain MAH-34T was isolated from rhizosphere soil of magnolia flower tree. The isolate can grow on R2A agar/ broth at 10~37°C with optimum growth at 28~30°C and pH 7.0 without NaCl supplement. The MAH-34T was responsible for the silver nanoparticle (AgNP) production via hydrolysis of AgNO3. Thus, to know about the nitrate reductase genes, the genome analysis of Paenibacillus anseongense MAH-34T was carried out. The assembled genome of MAH-34T consists of 42 scaffolds with a total of 8,647,101 bp with N50 and N75 values of 553,491 and 230,930, respectively. The DAN G + C content was 46.0 mol%. Additionally, the genome annotation also shows the nitrate and/or nitrite reductase genes using the Rapid Annotation using Subsystem Technology (RAST), which may be responsible for the production of silver nanoparticle (AgNP) through the hydrolysis of AgNO3.
Siddiqi, Muhammad Zubair,Siddiqi, Muhammad Hanif,Kim, Yeon-Ju,Jin, Yan,Huq, Md. Amdadul,Yang, Deok-Chun Mary Ann Liebert 2015 Journal of medicinal food Vol.18 No.5
<P>In this study, red ginseng extract (RGE) was converted into high-content minor ginsenosides by fermenting with Bgp1 enzymes at 37 degrees C for 5 days. Compared to the RGE, the minor ginsenoside contents were increased in fermented red ginseng extract (FRGE). Moreover, the amount of minor ginsenosides such as Rh1 (11%) and Rg2 (16%) was slightly augmented, while the level of Rg3 (33%) was significantly increased after bioconversion. Furthermore, we also examined and compared the effect of RGE and FRGE on the differentiation and mineralization of preosteoblastic MC3T3-E1 cells. Similarly, the level of mRNA expression of intracellular alkaline phosphatase (ALP) activity, type-1 collagen (Col-I) was also increased. Based on the comparison, it is clear that the FRGE has improved effects on bone formation and differentiation of preosteoblastic MC3T3-E1 cells.</P>
Description of 39 unrecorded bacterial species in Korea, belonging to the class Alphaproteobacteria
Siddiqi, Muhammad Zubair,Kim, Seung-Bum,Cho, Jang-Cheon,Yoon, Jung-Hoon,Joh, Ki-seong,Seong, Chi-Nam,Bae, Jin-Woo,Jahng, Kwang-Yeop,Jeon, Che-Ok,Im, Wan-Taek The National Institute of Biological Resources 2017 Journal of species research Vol.6 No.2
During an investigation of the biodiversity of bacterial species in Korea, we discovered many indigenous prokaryotic species. A total of 39 bacterial strains in the class Alphaproteobacteria were isolated from various environmental samples collected from marine organisms, sea water, fresh water, tap water, mud flats, activated sludge, mineral water, tidal flats, soil and decayed plants. From the high 16S rRNA gene sequence similarity (>98.7%) and formation of robust phylogenetic clades with the most closely related species, it was determined that each strain belonged to each independent and predefined bacterial species. There is no official report that any of these 39 Alphaproteobacteria species have been described in Korea. Specifically, 18 species in 11 genera in the order Sphingomonadales, 11 species in 10 genera in the order Rhizobiales, two species in two genera in the order Caulobacterales, six species in six genera in the order Rhodobacterales and two species in two genera in the order Rhodospirillales were found in Korea. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs are described in the species description section.
A report of 23 unrecorded bacterial species belonging to the class Alphaproteobacteria
Siddiqi, Muhammad Zubair,Kim, Seung-Bum,Cho, Jang-Cheon,Yoon, Jung-Hoon,Joh, Kiseong,Seong, Chi-Nam,Bae, Jin-Woo,Jahng, Kwang-Yeop,Jeon, Che-Ok,Im, Wan-Taek The National Institute of Biological Resources 2021 Journal of species research Vol.10 No.3
To study the biodiversity of bacterial species, here we report indigenous prokaryotic species of Korea. A total of 23 bacterial strains affiliated to the class Alphaproteobacteria were isolated from various environmental sources including seaweeds, seawater, fresh water, wetland/marsh, tidal sediment, plant roots, sewage and soil. Considering higher than 98.8% 16S rRNA gene sequence similarities and formation of a well-defined phylogenetic clade with named species, it was confirmed that each strain belonged to the predefined bacterial species of the class Alphaproteobacteria. There is no official report of these 23 species in Korea; 20 species of 16 genera (Mameliella, Yangia, Paracoccus, Ruegeria, Loktanella, Phaeobacter, Dinoroseobacter, Tropicimonas, Lutimaribacter, Litoreibacter, Sulfitobacter, Roseivivax, Labrenzia, Hyphomonas, Maricaulis, Thalassospira) in the order Rhodobacterales and 3 species of a single genus (Brevundimonas) in the order Caulobacterales. Gram-staining, cell morphology, basic biochemical characteristics, isolation sources, optimum temperature, growth media, and strain IDs are detailed in the species description as well as Table 1.