Paenibacillus roseus sp. nov., a ginsenoside-transforming bacterium isolated from forest soil

Akter, Shahina; Wang, Xiaoqing; Lee, Sun-Young; Rahman, Mizanur; Park, Jong‐Hyun; Ṣiddiqi, Muḥammad Zubair; Balusamy, Sri Renukadevi; Nam, Ki Hong; Rahman, Syed Azizur; Huq, Md. Amdadul

doi:10.1007/s00203-021-02389-1

Cited by 7 publications

(4 citation statements)

References 41 publications

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“…Briefly, bacterial cells were dissolved in PCR lysis buffer (Takara, Japan). The genomic DNA was extracted using a commercial genomic DNA extraction kit, and the 16S rRNA gene was amplified using the universal bacterial primers 27F and 1492R [ 31 ]. The PCR product was sequenced, and the 16S rRNA gene sequence was compared with sequences available in GenBank by the nucleotide BLAST to determine an approximate phylogenetic affiliation.…”

Section: Methodsmentioning

confidence: 99%

Genome mining reveals polysaccharide-degrading potential and new antimicrobial gene clusters of novel intestinal bacterium Paenibacillus jilinensis sp. nov.

Chen

Yan

et al. 2022

BMC Genomics

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Background Drug-resistant bacteria have posed a great threat to animal breeding and human health. It is obviously urgent to develop new antibiotics that can effectively combat drug-resistant bacteria. The commensal flora inhabited in the intestines become potential candidates owing to the production of a wide range of antimicrobial substances. In addition, host genomes do not encode most of the enzymes needed to degrade dietary structural polysaccharides. The decomposition of these polysaccharides mainly depends on gut commensal-derived CAZymes. Results We report a novel species isolated from the chicken intestine, designated as Paenibacillus jilinensis sp. nov. and with YPG26T (= CCTCC M2020899T) as the type strain. The complete genome of P. jilinensis YPG26T is made up of a single circular chromosome measuring 3.97 Mb in length and containing 49.34% (mol%) G + C. It carries 33 rRNA genes, 89 tRNA genes, and 3871 protein-coding genes, among which abundant carbohydrate-degrading enzymes (CAZymes) are encoded. Moreover, this strain has the capability to antagonize multiple pathogens in vitro. We identified putative 6 BGCs encoding bacteriocin, NRPs, PKs, terpenes, and protcusin by genome mining. In addition, antibiotic susceptibility testing showed sensitivity to all antibiotics tested. Conclusions This study highlights the varieties of CAZymes genes and BGCs in the genome of Paenibacillus jilinensis. These findings confirm the beneficial function of the gut microbiota and also provide a promising candidate for the development of new carbohydrate degrading enzymes and antibacterial agents.

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Section: Methodsmentioning

confidence: 99%

Genome mining reveals polysaccharide-degrading potential and new antimicrobial gene clusters of novel intestinal bacterium Paenibacillus jilinensis sp. nov.

Chen

Yan

et al. 2022

BMC Genomics

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“…The colony morphology of MAHUQ-68 T was investigated using a microscope (Olympus). Gram-staining reaction was conducted as described previously [18]. The cell motility test was performed using both sulphide indole motility medium (Oxoid) and microscopy.…”

Section: Phenotypic and Chemotaxonomic Characterizationmentioning

confidence: 99%

Solitalea agri sp. nov., a new member of the genus Solitalea isolated from rhizospheric soil of a jujube tree

Huq

Lee

Moon

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

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A Gram-stain negative, aerobic, rod-shaped and creamy pink-coloured bacterium, designated MAHUQ-68T, was isolated from rhizospheric soil of a jujube tree. Colonies grew at 10–40 °C (optimum, 28 °C), pH 6.0–9.0 (optimum pH, 7.0) and in the presence of 0–1.5 % NaCl (optimum 0–0.5 %). Positive for both catalase and oxidase activity. Strain MAHUQ-68T hydrolysed casein, starch, aesculin and l-tyrosine. Based on the results of phylogenetic analysis using 16S rRNA gene and genome sequences, strain MAHUQ-68T clustered together within the genus Solitalea . The closest members were Solitalea longa HR-AVT (98.8 % sequence similarity), Solitalea canadensis DSM 3403T (96.9 %) and Solitalea koreensis R2A36-4T (94.0 %). The genome of strain MAHUQ-68 T was 4 250 173 bp long with 68 scaffolds and 3 570 protein-coding genes. The genomic DNA G+C content of the type strain was 38.0 mol%. The average nucleotide identity and in silico DNA–DNA hybridization values between strain MAHUQ-68T and its closest relatives were 72.0–81.4% and 19.8–24.3 %, respectively. The major cellular fatty acids were iso-C15 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). The main respiratory quinone was menaquinone-7. The polar lipids comprised phosphatidylethanolamine, an unidentified aminolipid and four unidentified lipids. Based on these data, strain MAHUQ-68T represents a novel species in the genus Solitalea , for which the name Solitalea agri sp. nov. is proposed. The type strain is MAHUQ-68T (=KACC 22249T=CGMCC 1.19062T).

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“…Biotransformation or bioconversion is a procedure by which an organism (bacterial or fungi) or their derived enzymes carry out structural modifications or chemical changes in a compound that is not part of their metabolism [1][2][3]. Therefore, this conversion process results in the formation of novel or useful products [1][2][3] that are often difficult or impossible to obtain by chemical or heat transformation. Thus, bioconversion signifies a hopeful and environmentally friendly substitution for well-established chemical processes and other commercial products.…”

Section: Introductionmentioning

confidence: 99%

Isolation and characterization of a novel glycoside hydrolase positive bacterial strain named Terrimonas ginsenosidimutans sp. nov. with ginsenoside-converting activity

Ṣiddiqi

Lee

Jun

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

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A novel yellow-pigmented catalase- and oxidase-positive bacterial strain (designated NA20T) was isolated from wetland soil and characterized. Results of 16S rRNA and draft genome sequence analysis placed strain NA20T within the genus Terrimonas of the family Chitinophagaceae . Strain NA20T showed ≤97.1 % sequence similarity to members of the genus Terrimonas and the highest sequence similarity was found to Terrimonas lutea DYT (97.1%). The draft genome of strain NA20T had a total length of 7 144 125 base pairs. A total of 5659 genes were identified, of which 5613 were CDS and 46 RNA genes were assigned a putative function. Mining the genomes revealed the presence of 225 carbohydrate genes out of 1334 genes. Strain NA20T contained iso-C15 : 0, iso-C15 : 0 G, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) as major fatty acids. The predominant quinone was MK-7. The major polar lipids were phosphatidylethanolamine, one unknown polar lipid and one unknown aminophospholipid. Additionally, the functional analysis of NA20T showed the conversion of protopanaxatriol-mix type major ginsenosides (Rb1, Rc and Rd) to minor ginsenosides F2 and weak conversion of Rh2 and C-K within 24 h. As a result, the genotypic, phenotypic and taxonomic analyses support the affiliation of NA20T within the genus Terrimonas , for which the name Terrimonas ginsenosidimutans sp. nov. is proposed. The type strain is NA20T (=KACC 22218T=LMG 32198T).

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Paenibacillus roseus sp. nov., a ginsenoside-transforming bacterium isolated from forest soil

Cited by 7 publications

References 41 publications

Genome mining reveals polysaccharide-degrading potential and new antimicrobial gene clusters of novel intestinal bacterium Paenibacillus jilinensis sp. nov.

Genome mining reveals polysaccharide-degrading potential and new antimicrobial gene clusters of novel intestinal bacterium Paenibacillus jilinensis sp. nov.

Solitalea agri sp. nov., a new member of the genus Solitalea isolated from rhizospheric soil of a jujube tree

Isolation and characterization of a novel glycoside hydrolase positive bacterial strain named Terrimonas ginsenosidimutans sp. nov. with ginsenoside-converting activity

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