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

병원성 미생물들에 대해 항균활성을 보이는 $W5-1^T$ 균주가 한국의 발효식품인 김치에서 분리되었다. 이 분리주는 그람염색변이성, 절대호기성, 간균, 내생포자형성과 주모성의 편모를 가지고 운동성을 나타내었다. 균주는 $15-40^{\circ}C$, pH 6.0-10.0, 0-4% NaCl 조건에서 생육하였다. 균주는 esculin과 xylan을 가수분해하였고, $\small{D}$-mannose을 동화하였으나 $\small{D}$-mannitol은 동화하지 못하였다. $W5-1^T$ 균주는 Listeria monocytogens, Pseudomonas aeruginosa, Staphylococcus aureus, Salmonella typhi에 항균활성을 보였다. $W5-1^T$ 균주의 DNA의 G+C 함량은 52.6 mol%였다. 주요 호흡성 퀴논은 menaquinone-7 (MK-7)였고, 주요 세포성 지방산은 $C_{16:0}$, antieiso-$C_{15:0}$, $C_{18:0}$, and $C_{12:0}$였다. 균주는 세포벽 펩티도클리칸으로 meso-diaminopimelic acid을 함유하였다. 16S rRNA 유전자서열 분석에 근거하여 $W5-1^T$ 균주는 Paenibacillaceae 과로 분류되었으며 Paenibacillus pinihumi $S23^T$(98.4% similarity), P. tarimensis $SA-7-6^T$(96.4%) 균주와 높은 연관성을 보였다. 분리주와 P. pinihumi $S23^T$는 8.5%의 DNA-DNA 관련성을 보임으로 $W5-1^T$ 균주가 Paenibacillus 속의 한 종임을 보여주었다. 이러한 다각적 연구의 증거로 볼 때 $W5-1^T$ 균주는 Paenibacillus 속의 신종으로 사료되어 Paenibacillus kimchicus로 명명을 제안하며, 표준균주는 $W5-1^T$(=KACC $15046^T$=LMG $25970^T$)이다. 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 $15046^T$ = $LMG 25970^T$).

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.

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. Paenibacillus는 그람 양성 간균으로서 자연에 존재하지만 사람에서의 감염은 드물다. 저자들은 재태주수 29주 5일, 출생체중 1,380 g의 극소저체중출생아에서 Paenibacillus에 의한 패혈증 및 폐 공기낭종을 경험하여 보고하는 바이다. 인공호흡기를 조기 발관하고 경장관 수유 및 총정맥영양을 병행하던 생후 13일의 환아가 갑작스러운 청색증 증상을 보였고 흉부방사선사진에서 늑막 흉수가 관찰되었으며 동시에 패혈증 증세를 동반하였다. 미생물검사에서 Paenibacillus가동정되었으며 정맥 항생제 투여로 증세는 호전되었다. 이후 흉부방사선사진에서 폐 공기낭종 의심 병변이 지속적으로관찰되어 시행한 흉부전산화단층촬영에서 공기낭종을 확진하였다.

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.

Effects of a Soil-Born Paenibacillus spp. Strain KPB3 on Suppression of Bacterial Wilt Disease Caused by Ralstonia solanacearum

Jung Ki Suk(석정기),Nagesh S. Ipper,Seon Hwa Lee(이선화),Anupama Shrestha,Duck Hwan Park(박덕환),Jun Mo Cho(조준모),Jang Hyun Hur(허장현),Byung Sup Kim(김병섭),Chun Keun Lim(임춘근) 한국농약과학회 2006 농약과학회지 Vol.10 No.4

Two hundred bacterial strains were isolated from the soil around healthy tomato plants in a polyvinyl house, where most of the other plants showed bacterial wilt symptoms. The strains were screened in vitro for their antibacterial activity. Among them, a strain, KPB3 showed strong bactericidal activity against bacterial wilt pathogen, Ralstonia solanacearum. The strain KPB3 was identified using physiological and biochemical tests, and 16S rRNA analyses. Based on these tests, the strain was found to be closer to genus Paenibacillus. To control the bacterial wilt caused by R. solanacearum, greenhouse experiments were conducted to determine the effectiveness of the Paenibacillus strain KPB3. Drench application of this strain (4×10? CFU ㎖?¹) into the pots containing tomato plants, post-inoculated with the pathogen, R. solanacearum could drastically reduce the disease severity, compared to the non-treated plants. To evaluate effectiveness of this strain under field conditions, experiments were carried out in polyvinyl houses infested with R. solanacearum, during spring and autumn of the year 2006. It was observed that, during spring, bacterial wilt was more prevalent compared to the autumn. During spring, 50.9% disease incidences occurred in non-treated controls, while, Paenibacillus strain KPB3 treated plants showed 24.6% disease incidences. Similarly, during autumn, around 17.2% plants were infected with bacterial wilt in non- treated polyvinyl houses, compared to the Paenibacillus strain KPB3 treated plants, which showed 7.0% disease incidences. These results demonstrated that, Paenibacillus strain KPB3 is a potential biological control agent against bacterial wilt caused by R. solanacearum, effective under greenhouse as well as field conditions. This is the first report showing biocontrol of R. solanacearum using a Paenibacillus spp. under field conditions. (Received October 23, 2006; accepted December 23, 2006)

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).

Paenibacillus woosongensis의 Xylanase 유전자 클로닝과 특성분석

윤기홍,Yoon, Ki-Hong 한국미생물학회 2012 미생물학회지 Vol.48 No.2

Paenibacillus woosongensis의 유전체 부분 염기서열로부터 유추된 xylanase 유전자를 PCR 증폭하여 대장균에 클로닝하였다. Xylanase 유전자는 211 아미노산으로 구성된 단백질을 코드하며 633 뉴클레오티드로 이루어졌다. 아미노산 잔기배열을 분석한 결과 xylanase는 glycosyl hydrolase family 11에 속하며 Paenibacillus의 xylanase와 85-89% 상동성을 보였다. Xylanase 유전자를 T7 promoter로 과잉발현한 결과 그 발현량이 높지 않았으며, 균체내 외에서 모두 효소활성이 관찰되었다. 재조합 대장균의 균체파쇄상등액을 사용하여 효소 반응특성을 조사한 결과 pH 5.5와 $60^{\circ}C$에서 최대 반응활성을 보였다. 한편 xylanase의 기질로 xylan과 xylooligosaccharides를 사용하였을 때 xylose와 xylotriose가 주된 최종 반응산물로 관찰되었으며 xylobiose는 분해하지 못하였으나 이보다 중합도가 큰 xylooligosaccharides는 분해하였다. A gene encoding the xylanase (XynA) predicted from partial genomic sequence of Paenibacillus woosongensis was cloned into Escherichia coli by PCR. This xynA gene consisted of 633 nucleotides, encoding a polypeptide of 211 amino acid residues. The deduced amino acid sequence exhibited 85-89% identity with those of several Paenibacillus xylanases, belonging to the glycosyl hydrolase family 11. As a results of expression of the structural gene by T7 promoter of a pET23a(+) expression vector, xylanase activity was higher in cell-free extract than culture filtrate of a recombinant Escherichia coli BL21(DE3) CodonPlus. However, the expression level of xylanase was not sufficient be detected by SDS-PAGE. The cell-free extract showed maximal xylanase activity at $60^{\circ}C$ and pH 5.5. The predominant products resulting from xylan and xylooligosaccharide hydrolysis were xylose and xylotriose. The enzyme could hydrolyze xylooligosaccharides larger than xylbiose.

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>

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 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).