Isolation, Characterization and Whole-Genome Analysis of Paenibacillus andongensis sp.nov. from Korean Soil

Guan Yong,Li Zhun,Kang Yoon-Ho,Lee Mi-Kyung 한국미생물·생명공학회 2023 Journal of Microbiology and Biotechnology Vol.33 No.6

The genus Paenibacillus contains a variety of biologically active compounds that have potential applications in a range of fields, including medicine, agriculture, and livestock, playing an important role in the health and economy of society. Our study focused on the bacterium SS4T (KCTC 43402T = GDMCC 1.3498T ), which was characterized using a polyphasic taxonomic approach. This strain was analyzed using antiSMASH, BAGEL4, and PRISM to predict the secondary metabolites. Lassopeptide clusters were found using all three analysis methods, with the possibility of secretion. Additionally, PRISM found three biosynthetic gene clusters (BGC) and predicted the structure of the product. Genome analysis indicated that glucoamylase is present in SS4T . 16S rRNA sequence analysis showed that strain SS4T most closely resembled Paenibacillus marchantiophytorum DSM 29850T (98.22%), Paenibacillus nebraskensis JJ-59T (98.19%), and Paenibacillus aceris KCTC 13870T (98.08%). Analysis of the 16S rRNA gene sequences and Type Strain Genome Server (TYGS) analysis revealed that SS4T belongs to the genus Paenibacillus based on the results of the phylogenetic analysis. As a result of the matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF/MS) results, SS4T was determined to belong to the genus Paenibacillus. Comparing P. marchantiophytorum DSM 29850T with average nucleotide identity (ANI 78.97%) and digital DNA-DNA hybridization (dDDH 23%) revealed values that were all less than the threshold for bacterial species differentiation. The results of this study suggest that strain SS4T can be classified as a Paenibacillus andongensis species and is a novel member of the genus Paenibacillus.

Paenibacillus kimchicus sp. nov., an antimicrobial bacterium isolated from Kimchi

박아름,오지성,노동현,Park, A-rum,Oh, Ji-Sung,Roh, Dong-Hyun The Microbiological Society of Korea 2016 미생물학회지 Vol.52 No.3

An antimicrobial bacterium to pathogenic microorganisms, strain $W5-1^T$ was isolated from Korean fermented-food Kimchi. The isolate was Gram-staining-variable, strictly aerobic, rod-shaped, endospore-forming, and motile with peritrichous flagella. It grew at $15-40^{\circ}C$, at pH 6.0-10.0, and in the presence of 0-4% NaCl. Strain $W5-1^T$ could hydrolyze esculin and xylan, and assimilate $\small{D}$-mannose, but not $\small{D}$-mannitol. Strain $W5-1^T$ showed antimicrobial activity against Listeria monocytogens, Pseudomonas aeruginosa, Staphylococcus aureus, and Salmonella typhi. The G+C content of the DNA of strains $W5-1^T$ was 52.6 mol%. The predominant respiratory quinone was menaquinone-7 (MK-7) and the major cellular fatty acids were $C_{16:0}$, antieiso-$C_{15:0}$, $C_{18:0}$, and $C_{12:0}$. The strain contained meso-diaminopimelic acid in cell-wall peptidoglycan. On the basis of 16S rRNA gene sequence and phylogenetic analysis, the strain W5-1 was shown to belong to the family Paenibacillaceae and was most closely related to Paenibacillus pinihumi $S23^T$ (98.4% similarity) and Paenibacillus tarimensis $SA-7-6^T$ (96.4%). The DNA-DNA relatedness between the isolate and Paenibacillus pinihumi $S23^T$ was 8.5%, indicating that strain $W5-1^T$ represented a species in the genus Paenibacillus. On the basis of the evidence from this polyphasic study, it is proposed that strain $W5-1^T$ is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus kimchicus sp. nov. is proposed. The type strain is $W5-1^T$ (=KACC $15046^T$ = $LMG 25970^T$).

Effect of Glucose on Swarming Motility of Paenibacillus sp. CK214

Sung Wan Kang(강성완),Ah Young Yoo(유아영),Ho Young Kang(강호영) 한국생명과학회 2013 생명과학회지 Vol.23 No.2

Paenibacillus는 호기성의 내생포자를 형성하는 그람양성균으로써 이전에는 Bacillus로 분류되었다. Paenibacillus sp. CK214 균주는 LB agar 평판배지에서 높은 swarming 운동 능력을 가지고 Paenibacillus 특유의 집락 형태를 나타내었지만 glucose가 첨가된 평판배지에서는 운동 능력을 상실하였다. 투과전자현미경(TEM)을 이용하여 glucose 조건에 따른 CK214 균주의 편모를 관찰하면 LB agar 평판배지에서 배양한 CK214 균주는 주모성의 편모를 가지는 반면 glucose를 첨가한 평판배지에서 배양한 CK214 균주의 경우 주모성 편모가 나타나지 않는 것을 확인할 수 있었다. 물리적 충격과 원심분리를 통해 분리한 CK214 균주의 filament 구성 단백질을 SDS-PAGE를 통해 확인하였으며, 약 29 kDa 크기의 단일 단백질 밴드가 나타났다. Edwardsiella tarda 균주의 flagellin 단백질에 특이적인 항체를 이용한 immunoblotting 수행 결과, 이 단일 단백질 밴드는 flagellin 단백질임이 확인되었다. Glucose 조건에 따른 CK214 균주의 flagellin 단백질의 발현을 단백질 수준에서 관찰한 결과, glucose가 첨가된 조건에서 생장한 CK214 균주에서의 flagellin 단백질 발현이 glucose가 없는 조건일 때에 비해 감소하는 것을 확인할 수 있었다. Paenibacillus is a gram-positive, spore-forming aerobes that was previously classified as a Bacillus species. Paenibacillus sp. CK214 was highly motile on LB agar plates and showed typical colonial morphology of Paenibacillus. However, its motility was defective in the absence of glucose. Electron microscopic observation revealed that the cells of CK214 cultured on LB agar plates were peritrichously flagellated but not flagellated in the presence of glucose. Flagellar filaments were purified by centrifugation after shearing off from the CK214 cells with vigorous pipetting. The purified protein was composed of a single flagellin with an apparent molecular size of 29 kDa. Recognition of the protein by anti-Edwardsiella tarda flagellin protein antibody demonstrates that the protein is a flagellin protein. A decreased level of flagellin protein was detected in CK214 cells grown under glucose-supplemented media.

Paenibacillus panacihumi sp. nov., a potential plant growth-promoting bacterium isolated from ginseng-cultivated soil

Kim, Chun-Gon,Kang, Jong-Pyo,Huo, Yue,Chokkalingam, Mohan,Kim, Yeon-Ju,Kim, Dong-Hyun,Yang, Deok-Chun Springer-Verlag 2018 Archives of microbiology Vol.200 No.7

<P>A novel bacterium, designated DCY114(T), was isolated from ginseng-cultivated soil in Gochang-gun, Republic of Korea. This isolate was assigned to the genus Paenibacillus and is closely related to Paenibacillus amylolyticus NRRL NRS-290(T) (98.3%), P. dongdonensis KUDC0114(T) (98.0%), P. tylopili MK2(T) (97.9%), P. tundrae A10b(T) (97.8%), and P. xylanexedens B22a(T) (97.5%) based on 16S rRNA gene sequence analysis. Strain DCY114(T) is a Gram-reaction positive, catalase and oxidase positive, facultatively aerobic rod that is motile by peritrichous flagella. Strain DCY114(T) produces siderophores and indole-3-acetic acid (IAA) and is able to solubilize phosphate as a plant growth-promoting bacterium. MK-7 was the diagnostic menaquinone. The major cellular fatty acids were anteiso-C-15:0, C-16:0, and C-18:0, and the major polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), and an unknown amino lipid (AL1,2). The genomic DNA G + C content was 46.0 mol%. Phenotypic and chemotaxonomic results also placed strain DCY114(T) within the genus Paenibacillus. DNA-DNA homology values between strain DCY114(T) and closely related reference strains were lower than 43%. The low DNA relatedness data in combination with phylogenetic and biochemical tests indicated that strain DCY114(T) could not be assigned to a recognized species. The results of this study support that the DCY114(T) strain is a novel species belonging to the genus Paenibacillus, for which the name Paenibacillus panacihumi is proposed. The type strain is DCY114(T) (= KCTC 33915(T) = JCM 32073(T)).</P>

Paenibacillus insulae sp. nov., isolated from soil

조성준,조성훈,김태수,박석환,김승범,이건형 한국미생물학회 2015 The journal of microbiology Vol.53 No.9

A Gram-stain-positive, motile, endospore-forming, and strictly aerobic rod-shaped bacterium designated DS80T was isolated from an island soil. The strain DS80T grew at temperatures between 15 and 40°C (optimum = 30°C) and at pH values ranging from 5.0 to 9.0 (optimum = 7.0). The phylogenetic analysis based on the comparisons of the 16S rRNA gene sequences showed that the isolate was affiliated to the genus Paenibacillus and was mostly related to Paenibacillus assamensis GPTSA11T (with the sequence similarity of 96.33%) and Paenibacillus urinalis 5402403T(95.48%). The G+C content of the genomic DNA was 44.0 mol% and the major fatty acids were anteiso-C15:0, iso-C15:0, iso-C16:0, and C16:1 ω11c. Strain DS80T contained MK-7 as the major menaquinone, and phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol as the major polar lipids. The peptidoglycan contained a major amount of meso-diaminopimelic acid. The chemotaxonomic profile of strain DS80T was consistent with that of Paenibacillus. However, the phenotypic properties clearly separated the strain from other species of the genus. Accordingly, a new species, Paenibacillus insulae sp. nov., is proposed (type strain =DS80T =JCM 17278T =KCTC 13833T).

Purification and Identification of Paenibacillus sp., Isolated from Diseased Larvae of Allomyrina dichotoma (Linnaeus, 1771) (Coleoptera: Scarabaeidae) in Insect Farms

( Tae Hwa Kang ),( Sang Hoon Han ),( Hang Yeon Weon ),( Young Bo Lee ),( Namjung Kim ),( Sung Hee Nam ),( Hae Chul Park ) 한국잠사학회 2012 International Journal of Industrial Entomology Vol.25 No.2

In reared populations of Allomyrina dichotoma, commercial insects, the skin of last instar larvae was changed softer with opaque white, and infested grubs eventually died. To clarify the cause of the symptom, we collected the larvae of A. dichotoma from five farms and examined their intestinal bacterial florae using pyrosequencing technique. From those results, a member of Paenibacillus was found only in the larvae showing the symptom of disease. Through PCR analysis using a Paenibacillus specific primer set, we obtained the partial 16S rRNA gene sequence and confirmed the microbe as Paenibacillus sp. For clear identification, a whole guts was extracted from each larva showing the sign of the disease and incubated at 70oC for 15 min to isolate spore forming bacteria. After then, each content of guts was cultured on MYPGPNAL agar medium(12.5 μg/ml of nalidixic acid) at 30oC. The 16S rRNA gene sequence analysis for the isolated bacteria showed that they were closely related to P. rigui(97.9% similarity), to P. chinjuensis(96.1% similarity), and to P. soli(95.3% similarity). Additional tests including API test and cellular fatty acid composition analysis were performed, but the strain couldn`t be identified at species level, suggesting it may represent novel species of the genus Paenibacillus.

Paenibacillus gyeongsangnamensis sp. nov., Isolated from Soil

Lee Hyosun,Chaudhary Dhiraj Kumar,Kim Dong-Uk 한국미생물·생명공학회 2024 Journal of Microbiology and Biotechnology Vol.34 No.8

A Gram-stain-positive, aerobic, white-coloured, rod-shaped bacteria, designated as a strain dW9T , was isolated from soil. Strain dW9T was catalase-positive and oxidase-negative. Strain dW9T grew at temperature of 20–37°C and at pH of 5.0–7.0. Phylogenetic and 16S rRNA gene analysis indicated that strain dW9T belonged to the genus Paenibacillus with its closest relative being Paenibacillus filicis S4T (97.4% sequence similarity). The genome size of dW9T was 7,787,916 bp with DNA G+C content of 51.3%. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values of dW9T with its closest relatives were found to be <22.0% and <74.0%, respectively. The only respiratory quinone was MK-7, and the major fatty acids were antiso-C15:0 and iso-C16:0. Overall, the comprehensive taxonomic analysis revealed that strain dW9T met all the fundamental criteria to be classified as a novel species within the genus Paenibacillus. Accordingly, we propose the name Paenibacillus gyeongsangnamensis sp. nov., with the type strain dW9T (=KCTC 43431T =NBRC 116022T ).

극소저체중출생아에서 폐 공기낭종이 합병된 Paenibacillus 패혈증 1례

최서경,한명희,배종우,최용성 대한신생아학회 2014 Neonatal medicine Vol.21 No.1

Paenibacillus spp. are gram-positive, rod-shaped, facultative anaerobic bacteria found in nature and rarely cause diseases in humans. We report our experience with Paenibacillus-induced sepsis complicated with pneumatocele in a very low birth weight male infant with a gestational age of 29 weeks and 5 days and a birth weight of 1,380 g, who was born by cesarean section with because of preterm labor and premature rupture of membrane. On day 12 after admission, the patient presented oxygen desaturation without apnea and fever. We identified pleural effusion on chest radiography and diagnosed pneumatocele on low-dose chest computed tomography. An empirical antibiotic was administered to treat the infection. The patient’s blood culture revealed gram-positive rods, and Paenibacillus spp. was identified using16s rRNA sequencing.

Paenibacillus filicis sp. nov., Isolated from the Rhizosphere of the Fern

김병천,Mi Na Kim,Kang Hyun Lee,Sun Beom Kwon,배경숙,신기선 한국미생물학회 2009 The journal of microbiology Vol.47 No.5

A Gram-positive and endospore-forming bacterial strain, designated S4T, was isolated from the rhizosphere of ferns in Daejeon, Republic of Korea. This isolate is strictly aerobic, motile, and rod-like in shape, and it is positive for catalase, oxidase, esterase lipase, and β-galactosidase activities. In addition, this strain grows when cultured at temperatures between 15 and 37°C and at pH values ranging from 5.5 to 9.0. The DNA G+C content was determined to be 53.2 mol%. Strain S4T has meso-diaminopimelic acid in the cell-wall peptidoglycan; it also contains menaquinone 7 (MK-7) as the predominant isoprenoid quinone and anteiso-C15:0 (57.5%), iso-C16:0 (11.3%), and C16:0 (9.4%) as the major cellular fatty acids. Phylogenetic analysis based on alignments of the 16S rRNA gene sequence showed that S4T is affiliated with a cluster of strains within the genus Paenibacillaceae and is most closely related to Paenibacillus chinjuensis WN9T, with 96.8% similarity. Based on the phylogenetic and phenotypic characteristics of strain S4T, we believe that this isolate should be distinguished from all type species of the genus Paenibacillus and should thus represent a novel taxon within the genus Paenibacillus. We propose naming this type species Paenibacillus filicis sp. nov. for the rhizosphere isolate; the type strain will be known as S4T (=KCTC 13693T =KACC 14197T =JCM 16417T).

Paenibacillus woosongensis으로부터 Mannanase 26AT 유전자의 클로닝과 유전자 산물의 분석

윤기홍(Ki-Hong Yoon) 한국생명과학회 2017 생명과학회지 Vol.27 No.9

Paenibacillus woosongensis의 유전체 부분 염기서열로부터 mannanase를 코드하는 것으로 유추되는 open reading frame을 중합효소연쇄반응으로 증폭하여 대장균에 클로닝하고 염기서열을 결정하였다. Mannanase 유전자는 man26AT로 명명하였으며 1,053 아미노산으로 구성된 단백질을 코드하는 3,159 뉴클레오티드로 이루어졌다. 아미노산 잔기배열을 분석한 결과 Man26AT는 glycosyl hydrolase family 26의 mannanase와 상동성이 높은 활성영역, 탄수화물 결합영역 CBM27과 CBM11로 구성되어 있었다. Man26AT의 아미노산 배열은 P. ihumii의 유추된 mannanase와 상동성이 81%이고 다른 Paenibacillus 속 균주의 여러 mannanases와 57% 이하의 상동성을 보였다. man26AT 유전자를 함유한 재조합 대장균의 균체 파쇄상등액은 55℃와 pH 5.5에서 최대의 mannanase 활성을 보였고, 50℃에서 1시간 열처리한 후에 80% 이상의 잔존활성을 보였다. Man26AT는 locust bean gum (LBG) galactomannan과 konjac glucomannan에 대한 분해활성이 유사하였으며, carboxymethylcellulose, xylan과 para-nitrophenyl-β-mannopyranoside는 분해하지 못하였다. Man26AT에 의해 mannotriose, mannotetraose, mannopentaose와 mannohexaose 등의 만노올리고당이나 LBG로부터 공통의 최종 가수분해 산물로 mannose, mannobiose와 mannotriose가 생성되었다. 또한 mannotriose 보다 큰 만노올리고당이 LBG와 guar gum의 분해산물로 각각 생성되었다. 그러나 Man26AT는 mannobiose를 분해하지는 못하였다. 활성염색을 통해 Man26AT는 균체 내에서 3개 이상의 크기가 다른 활성 단백질로 분해된 것이 확인되었다. An open reading frame coding for mannanase predicted from the partial genomic sequence of Paenibacillus woosongensis was cloned into Escherichia coli by polymerase chain reaction amplification, and completely sequenced. This mannanase gene, designated man26AT, consisted of 3,162 nucleotides encoding a polypeptide of 1,053 amino acid residues. Based on the deduced amino acid sequence, Man26AT was identified as a modular enzyme, which included a catalytic domain belonging to the glycosyl hydrolase family 26 and two carbohydrate-binding modules, CBM27 and CBM11. The amino acid sequence of Man26AT was homologous to that of several putative mannanases, with identity of 81% for P. ihumii and identity of less than 57% for other strains of Paenibacillus. A cell-free extract of recombinant E. coli carrying the man26AT gene showed maximal mannanase activity at 55℃ and pH 5.5. The enzyme retained above 80% of maximal activity after preincubation for 1 h at 50℃. Man26AT was comparably active on locust bean gum (LBG), galactomanan, and kojac glucomannan, whereas it did not exhibit activity on carboxymethylcellulose, xylan, or para-nitrophenyl-β-mannopyranoside. The common end products liberated from mannooligosaccharides, including mannotriose, mannotetraose, mannopentaose, and mannohexaose, or LBG by Man26AT were mannose, mannobiose, and mannotriose. Mannooligosacchrides larger than mannotriose were found in enzymatic hydrolyzates of LBG and guar gum, respectively. However, Man26AT was unable to hydrolyze mannobiose. Man26AT was intracellularly degraded into at least three active proteins with different molecular masses by zymogram.