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Bai L, Paek J, Shin Y, Kim H, Kim SH, Shin JH, Kook JK, Chang YH. Description of an anaerobic actinobacterium, Kribbibacterium absianum gen. nov., sp. nov., a new member of the novel family Kribbibacteriaceae fam. nov., and reclassification of the genera Granulimonas and Leptogranulimonas. Int J Syst Evol Microbiol 2024; 74. [PMID: 38728210 DOI: 10.1099/ijsem.0.006382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024] Open
Abstract
Two rod-shaped, obligate anaerobic, Gram-stain-positive bacteria isolated from the pig faeces were designated YH-ols2216 and YH-ols2217T. Analysis of 16S rRNA gene sequences revealed that these isolates were most related to the members of the family Atopobiaceae, within the order Coriobacteriales, and Granulimonas faecalis KCTC 25474T with 92.0 and 92.5% similarities, respectively. The 16S rRNA gene sequence similarity within isolates was 99.9 %; and those between isolates YH-ols2216 and YH-ols2217T, and Atopobium minutum DSM 20586T, the type species of the type genus Atopobium within the family Atopobiaceae, were 88.5 and 88.7 %, respectively. Those between isolates and Coriobacterium glomerans PW2T, the type species of the type genus Coriobacterium within the family Coriobacteriaceae, were 88.7 and 89.1 %, respectively. The multi-locus sequence tree revealed that the isolates, alongside the genera Granulimonas and Leptogranulimonas, formed a distinct cluster between the families Atopobiaceae and Coriobacteriaceae. The average nucleotide identities and digital DNA-DNA hybridization values for the isolates and their most closely related strains ranged from 67.7 to 76.2 % and from 18.4 to 23.3 %, respectively. The main cellular fatty acids of the isolates were C18 : 0 DMA, C18 : 1 ω9c, C18 : 0 12OH, C18 : 0, and C16 : 0. The cell wall contained the peptidoglycan meso-diaminopimelic acid. Lactate was the main end-product of the isolates. The major polar lipids of isolate YH-ols2217T were aminophospholipid, aminolipids, and lipids. Menaquinones were not identified in the cells of the isolates. The DNA G+C contents of isolates YH-ols2216 and YH-ols2217T were 67.5 and 67.6 mol%, respectively. Considering these chemotaxonomic, phenotypic, and phylogenetic properties, Kribbibacteriaceae fam. nov. is proposed within the order Coriobacteriales. YH-ols2216 (=KCTC 25708=NBRC 116429) and YH-ols2217T (=KCTC 25709T=NBRC 116430T) represent a novel taxon within this new family and the name Kribbibacterium absianum gen. nov., sp. nov. is proposed. In addition, the genera Granulimonas and Leptogranulimonas are transferred to the family Kribbibacteriaceae fam. nov.
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Affiliation(s)
- Lu Bai
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jayoung Paek
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Yeseul Shin
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hongik Kim
- Vitabio, Inc., Daejeon, Republic of Korea
| | - Si Hyun Kim
- Department of Biomedical Laboratory Science, Inje University, Gimhae, Republic of Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Young-Hyo Chang
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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Zepeda-Rivera M, Minot SS, Bouzek H, Wu H, Blanco-Míguez A, Manghi P, Jones DS, LaCourse KD, Wu Y, McMahon EF, Park SN, Lim YK, Kempchinsky AG, Willis AD, Cotton SL, Yost SC, Sicinska E, Kook JK, Dewhirst FE, Segata N, Bullman S, Johnston CD. A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche. Nature 2024; 628:424-432. [PMID: 38509359 PMCID: PMC11006615 DOI: 10.1038/s41586-024-07182-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 02/08/2024] [Indexed: 03/22/2024]
Abstract
Fusobacterium nucleatum (Fn), a bacterium present in the human oral cavity and rarely found in the lower gastrointestinal tract of healthy individuals1, is enriched in human colorectal cancer (CRC) tumours2-5. High intratumoural Fn loads are associated with recurrence, metastases and poorer patient prognosis5-8. Here, to delineate Fn genetic factors facilitating tumour colonization, we generated closed genomes for 135 Fn strains; 80 oral strains from individuals without cancer and 55 unique cancer strains cultured from tumours from 51 patients with CRC. Pangenomic analyses identified 483 CRC-enriched genetic factors. Tumour-isolated strains predominantly belong to Fn subspecies animalis (Fna). However, genomic analyses reveal that Fna, considered a single subspecies, is instead composed of two distinct clades (Fna C1 and Fna C2). Of these, only Fna C2 dominates the CRC tumour niche. Inter-Fna analyses identified 195 Fna C2-associated genetic factors consistent with increased metabolic potential and colonization of the gastrointestinal tract. In support of this, Fna C2-treated mice had an increased number of intestinal adenomas and altered metabolites. Microbiome analysis of human tumour tissue from 116 patients with CRC demonstrated Fna C2 enrichment. Comparison of 62 paired specimens showed that only Fna C2 is tumour enriched compared to normal adjacent tissue. This was further supported by metagenomic analysis of stool samples from 627 patients with CRC and 619 healthy individuals. Collectively, our results identify the Fna clade bifurcation, show that specifically Fna C2 drives the reported Fn enrichment in human CRC and reveal the genetic underpinnings of pathoadaptation of Fna C2 to the CRC niche.
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Affiliation(s)
- Martha Zepeda-Rivera
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Samuel S Minot
- Data Core, Shared Resources, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Heather Bouzek
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Hanrui Wu
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Aitor Blanco-Míguez
- Department of Computational, Cellular and Integrative Biology, University of Trento, Trento, Italy
| | - Paolo Manghi
- Department of Computational, Cellular and Integrative Biology, University of Trento, Trento, Italy
| | - Dakota S Jones
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Ying Wu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Elsa F McMahon
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Soon-Nang Park
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Yun K Lim
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | | | - Amy D Willis
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | | | | | - Ewa Sicinska
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Floyd E Dewhirst
- Forsyth Institute, Cambridge, MA, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Nicola Segata
- Department of Computational, Cellular and Integrative Biology, University of Trento, Trento, Italy
| | - Susan Bullman
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Christopher D Johnston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
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Bai L, Paek J, Shin Y, Kim H, Kim SH, Shin JH, Kook JK, Chang YH. Aerococcus kribbianus sp. nov., a facultatively anaerobic bacterium isolated from pig faeces. Int J Syst Evol Microbiol 2024; 74. [PMID: 38415779 DOI: 10.1099/ijsem.0.006284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024] Open
Abstract
Two cocci-shaped, facultatively anaerobic, Gram-positive bacteria isolated from the faeces of a pig were designated as strains YH-aer221T and YH-aer222. Analysis of the 16S rRNA gene sequences revealed that the isolates were most closely related to Aerococcus suis JCM 18035T with 96.6 % similarity. The multi-locus sequence tree revealed that the isolates formed a sub-cluster adjacent to A. suis JCM 18035T. The average nucleotide identity values for the isolates and their most closely related strains were 71.8 and 71.7 %, respectively; and the digital DNA-DNA hybridization values for the isolates and their most closely related strains were 25.6 and 25.5 %, respectively. The main fatty acids were C18 : 1ω9c, C16 : 0 and C18 : 0. The cell wall contained the meso-diaminopimelic acid-based peptidoglycan. The two isolates shared the same metabolic pathways. Isolates YH-aer221T and YH-aer222 harboured the same CRISPR array with 33 and 46 spacers, respectively. Single-genome vs. metagenome analysis showed that the genomes of the isolates were not found in the available metagenome database. Given their chemotaxonomic, phenotypic and phylogenetic properties, YH-aer221T (= KCTC 25571T=JCM 35699T) and YH-aer222 (=KCTC 25573=JCM 35700) represent a novel taxon. The name Aerococcus kribbianus sp. nov. is proposed.
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Affiliation(s)
- Lu Bai
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jayoung Paek
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Yeseul Shin
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hongik Kim
- Vitabio, Inc., Daejeon, Republic of Korea
| | - Si Hyun Kim
- Department of Biomedical Laboratory Science, Inje University, Gimhae, Republic of Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Young-Hyo Chang
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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Bai L, Paek J, Shin Y, Kim H, Kim SH, Shin JH, Kook JK, Chang YH. Description of Fusibacillus kribbianus gen. nov., sp. nov., a fusiform anaerobe isolated from pig feces. Anaerobe 2023; 84:102792. [PMID: 37925064 DOI: 10.1016/j.anaerobe.2023.102792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/12/2023] [Accepted: 10/25/2023] [Indexed: 11/06/2023]
Abstract
OBJECTIVE The family Lachnospiraceae is affiliated with the order Clostridiales and was originally contained within Clostridial cluster XIVa. The members of Lachnospiraceae inhabiting the gut comprise the chemoorganotrophic genera, generating sundry short-chain fatty acids to supply energy to the host, and are considered to be related to obesity and gut health. METHODS The polyphasic taxonomic approach was used to characterize the isolate YH-rum2234T. A detailed metabolic analysis was conducted to compare the novel isolate with related strains within the family Lachnospiraceae. RESULTS A fusiform, obligately anaerobic, Gram-stain-negative bacterium, YH-rum2234T, was isolated from pig feces. Analysis of the 16S rRNA gene sequence revealed that the similarities between the isolate and the familiarly interrelated strain Lientehia hominis KCTC 25345T was 94.3%. The average nucleotide identities and genome-to-genome distances of YH-rum2234T and its closely related strains were below 85.5% and 32.5%, respectively. The G + C content of the genomic DNA was 49.2 mol%. The main fatty acids were C16:0, C14:0, and C14:0 DMA. The major polar lipids were aminophospholipids. The cell wall did not contain the peptidoglycan meso-diaminopimelic acid. CONCLUSION Given the chemotaxonomic, phenotypic, and phylogenetic properties, YH-rum2234T (=KCTC 25710T = DSMZ 116041T) represents a new genus and species in the family Lachnospiraceae. Fusibacillus kribbianus gen. nov., sp. nov. is the proposed name.
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Affiliation(s)
- Lu Bai
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jayoung Paek
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yeseul Shin
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hongik Kim
- Vitabio, Inc., Daejeon, 305-500, Republic of Korea
| | - Si Hyun Kim
- Department of Clinical Laboratory Science, Semyung University, Jecheon, Republic of Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, 614-735, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, 501-759, Republic of Korea.
| | - Young-Hyo Chang
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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Bai L, Paek J, Kim H, Kim SH, Shin JH, Kook JK, Chang YH. Limosilactobacillus kribbianus sp. nov., isolated from pig faeces. Int J Syst Evol Microbiol 2023; 73. [PMID: 37486340 DOI: 10.1099/ijsem.0.005988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
A rod-shaped, aerotolerant, Gram-stain-positive bacterium isolated from pig faeces was designated as strain YH-lim2214T. Analysis of the 16S rRNA gene sequence revealed that the isolate was most closely related to Limosilactobacillus pontis KCTC 25258T with 98.0 % similarity. The average nucleotide identity and average amino acid identity values between YH-lim2214T and the most closely related strain Lm. pontis KCTC 25258T were 81.4 and 81.3 %, respectively. The major fatty acids were C18 : 1 ω9c, summed feature 7 and C16 : 0. The cell-wall peptidoglycan type was A4α l-Lys-d-Asp. The genomic DNA G+C content was 51.1 mol%. The chemotaxonomic, phenotypic and phylogenetic properties of YH-lim2214T (=KCTC 25572T=JCM 35701T) suggest that it represents a novel taxon, for which the name Limosilactobacillus kribbianus sp. nov. is proposed.
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Affiliation(s)
- Lu Bai
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jayoung Paek
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hongik Kim
- Vitabio, Inc., Daejeon, 305-500, Republic of Korea
| | - Si Hyun Kim
- Department of Clinical Laboratory Science, Semyung University, Jecheon, Republic of Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine, Busan 614-735, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, 501-759, Republic of Korea
| | - Young Hyo Chang
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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Ji S, Kook JK, Park SN, Lim YK, Choi GH, Jung JS. Characteristics of the Salivary Microbiota in Periodontal Diseases and Potential Roles of Individual Bacterial Species To Predict the Severity of Periodontal Disease. Microbiol Spectr 2023; 11:e0432722. [PMID: 37191548 PMCID: PMC10269672 DOI: 10.1128/spectrum.04327-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 04/27/2023] [Indexed: 05/17/2023] Open
Abstract
The purposes of this study were to examine the compositional changes in the salivary microbiota according to the severity of periodontal disease and to verify whether the distribution of specific bacterial species in saliva can distinguish the severity of disease. Saliva samples were collected from 8 periodontally healthy controls, 16 patients with gingivitis, 19 patients with moderate periodontitis, and 29 patients with severe periodontitis. The V3 and V4 regions of the 16S rRNA gene in the samples were sequenced, and the levels of 9 bacterial species showing significant differences among the groups by sequencing analysis were identified using quantitative real-time PCR (qPCR). The predictive performance of each bacterial species in distinguishing the severity of disease was evaluated using a receiver operating characteristic curve. Twenty-nine species, including Porphyromonas gingivalis, increased as the severity of disease increased, whereas 6 species, including Rothia denticola, decreased. The relative abundances of P. gingivalis, Tannerella forsythia, Filifactor alocis, and Prevotella intermedia determined by qPCR were significantly different among the groups. The three bacterial species P. gingivalis, T. forsythia, and F. alocis were positively correlated with the sum of the full-mouth probing depth and were moderately accurate at distinguishing the severity of periodontal disease. In conclusion, the salivary microbiota showed gradual compositional changes according to the severity of periodontitis, and the levels of P. gingivalis, T. forsythia, and F. alocis in mouth rinse saliva had the ability to distinguish the severity of periodontal disease. IMPORTANCE Periodontal disease is one of the most widespread medical conditions and the leading cause of tooth loss, imposing high economic costs and an increasing burden worldwide as life expectancy increases. Changes in the subgingival bacterial community during the progression of periodontal disease can affect the entire oral ecosystem, and bacteria in saliva can reflect the degree of bacterial imbalance in the oral cavity. This study explored whether the specific bacterial species in saliva can distinguish the severity of periodontal disease by analyzing the salivary microbiota and suggested P. gingivalis, T. forsythia, and F. alocis as biomarkers for distinguishing the severity of periodontal disease in saliva.
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Affiliation(s)
- Suk Ji
- Department of Periodontology, Institute of Oral Health Science, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology, Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Soon-Nang Park
- Korean Collection for Oral Microbiology, Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Yun Kyong Lim
- Korean Collection for Oral Microbiology, Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Geum Hee Choi
- Department of Periodontology, Institute of Oral Health Science, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Jae-Suk Jung
- Department of Periodontology, Institute of Oral Health Science, Ajou University School of Medicine, Suwon, Republic of Korea
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Bai L, Paek J, Kim H, Kim SH, Shin JH, Kook JK, Chang YH. Description and comparative genome analysis of Hallella absiana sp. nov., isolated from pig feces. Anaerobe 2023; 81:102735. [PMID: 37201651 DOI: 10.1016/j.anaerobe.2023.102735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/28/2023] [Accepted: 05/01/2023] [Indexed: 05/20/2023]
Abstract
OBJECTIVE The genus Hallella was described within Bacteroidaceae, and then reclassified within Prevotellaceae based on its phenotypic and phylogenetic description. It is associated with degradation of carbohydrate. However, some species of Hallella have pathobiotic properties, and are involved in infections and chronic inflammatory disorders. METHODS Here, we used a polyphasic taxonomic approach to characterize the two strains: YH-C38T and YH-C4B9b. A detailed metabolic analysis was conducted to compare the two novel isolates with related strains within the genus Hallella. RESULT Analysis of 16S rRNA gene sequences revealed that the isolates were most closely related to Hallella mizrahii JCM 34422T with 98.5% and 98.6% similarities, respectively. Analysis of the multi-locus species tree based on whole genome sequences of the isolates and related strains revealed that the isolates formed a sub-cluster adjacent to H. mizrahii JCM 34422T. The average nucleotide identity values for YH-C38T and YH-C4B9b, and the most closely related strain H. mizrahii JCM 34422T, were 93.5% and 93.8%, respectively. The main fatty acids were iso C17:0 3OH and anteiso C15:0. The predominant menaquinones were MK-12, MK-11, and MK-13. The cell wall contained the peptidoglycan of meso-diaminopimelic acid. Analysis of comparative metabolic analysis revealed that isolates YH-C38T and YH-C4B9b each contained 155 carbohydrate-active enzymes, and glycoside hydrolase was the largest family. CONCLUSION Two rod-shaped, obligately anaerobic, Gram-stain-negative bacteria, isolated from pig feces, were designated as strains YH-C38T and YH-C4B9b. Based on the chemotaxonomic, phenotypic, and phylogenetic properties, YH-C38T (=KCTC 25103T = JCM 35423T) and YH-C4B9b (=KCTC 25104 = JCM 35609) represent a novel taxon. The name Hallella absiana sp. nov. is proposed.
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Affiliation(s)
- Lu Bai
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jayoung Paek
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hongik Kim
- Vitabio, Inc., Daejeon, 305-500, Republic of Korea
| | - Si Hyun Kim
- Department of Clinical Laboratory Science, Semyung University, Jecheon, Republic of Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, 614-735, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, 501-759, Republic of Korea.
| | - Young-Hyo Chang
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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Bai L, Paek J, Shin Y, Kim H, Kim SH, Shin JH, Kook JK, Chang YH. Lacticaseibacillus parakribbianus sp. nov., isolated from a pig farm faeces dump. Int J Syst Evol Microbiol 2023; 73. [PMID: 36943347 DOI: 10.1099/ijsem.0.005758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
A lactic acid bacterium isolated from pig faeces was characterized using a polyphasic approach. The strain was Gram-stain-positive, rod-shaped, and facultative anaerobic. Phylogenetic analysis of the 16S rRNA gene sequence indicated that the isolate belonged to the genus Lacticaseibacillus. The multi-locus sequence tree revealed that the strain formed a sub-cluster adjacent to Lacticaseibacillus kribbianus. The main fatty acids were C16 : 0 and C18 : 1ω9c. The average nucleotide identity value, average amino acid identity, and genome-to-genome distance for YH-lacS6T and its most closely related strain, L. kribbianus, were 85.4, 85.2 and 29.2 %, respectively. The G+C content of the genomic DNA was 61.6 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, aminophospholipids and phospholipids. The cell-wall peptidoglycan did not contain meso-diaminopimelic acid. Thus, YH-lacS6T (=KCTC 21186T=JCM 34954T) represents a novel species. The name Lacticaseibacillus parakribbianus sp. nov. is proposed.
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Affiliation(s)
- Lu Bai
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jayoung Paek
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Yeseul Shin
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hongik Kim
- Vitabio, Inc., Daejeon, 305-500, Republic of Korea
| | - Si Hyun Kim
- Department of Clinical Laboratory Science, Semyung University, Jecheon, Republic of Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine, Busan 614-735, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, 501-759, Republic of Korea
| | - Young Hyo Chang
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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Lee CM, Jeong YIL, Lim YK, Kook JK, Yang SW, Kook MS, Kim BH. The effect of cold atmospheric plasma (CAP) on the formation of reactive oxygen species and treatment of Porphyromonas gingivalis biofilm in vitro for application in treatment of peri-implantitis. KOREAN J CHEM ENG 2023. [DOI: 10.1007/s11814-022-1337-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Yun SY, Lee Y, Hong J, Kim DC, Lee H, Yong D, Lim YK, Kook JK, Lee K. Identification of Fusobacterium Species Using Matrix-Assisted Laser Desorption/Ionization-Time-of-Flight Mass Spectrometry by Updating ASTA CoreDB. Yonsei Med J 2022; 63:1138-1143. [PMID: 36444550 PMCID: PMC9760896 DOI: 10.3349/ymj.2022.0271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/14/2022] [Accepted: 10/20/2022] [Indexed: 11/22/2022] Open
Abstract
PURPOSE Fusobacterium species can cause infections, and associations with cancer are being increasingly reported. As their clinical significance differs, accurate identification of individual species is important. However, matrix-assisted laser desorption/ionization-time of flight mass spectrometry has not been found to be effective in identifying Fusobacterium species in previous studies. In this study, we aimed to improve the accuracy and efficacy of identifying Fusobacterium species in clinical laboratories. MATERIALS AND METHODS In total, 229 Fusobacterium isolates were included in this study. All isolates were identified at the species level based on nucleotide sequences of the 16S ribosomal RNA gene and/or DNA-dependent RNA polymerase β-subunit gene (rpoB). Where necessary, isolates were identified based on whole genome sequences. Among them, 47 isolates were used for updating the ASTA database, and 182 isolates were used for the validation of Fusobacterium spp. identification. RESULTS Fusobacterium isolates used for validation (182/182) were correctly identified at the genus level, and most (180/182) were correctly identified at the species level using the ASTA MicroIDSys system. Most of the F. nucleatum isolates (74/75) were correctly identified at the subspecies level. CONCLUSION The updated ASTA MicroIDSys system can identify nine species of Fusobacterium and four subspecies of F. nucleatum in good agreement. This tool can be routinely used in clinical microbiology laboratories to identify Fusobacterium species and serve as a springboard for future research.
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Affiliation(s)
- Shin Young Yun
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Yunhee Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Juwon Hong
- R&D Center, NOSQUEST Inc., Yongin, Korea
| | | | - Hyukmin Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea.
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Yun Kyong Lim
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Korea.
| | - Kyungwon Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
- Seoul Clinical Laboratories Academy, Yongin, Korea
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11
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Paek J, Bai L, Shin Y, Kim H, Kook JK, Kim SH, Shin JH, Chang YH. Lacticaseibacillus kribbianus sp. nov., isolated from pig farm faeces dump. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748483 DOI: 10.1099/ijsem.0.005617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
A lactic acid bacteria isolated from pig faeces was characterized using a polyphasic approach. Cells of the strain were Gram-stain-positive, rod-shaped and facultative anaerobic. Phylogenetic analysis of 16S rRNA gene sequence indicated that the isolate belonged to the genus Lacticaseibacillus; however, the similarity to other homologues within the genus was <98 %. Analysis of housekeeping gene sequences (pheS and recA) revealed that the strain formed a sub-cluster adjacent to Lacticaseibacillus absianus and Lacticaseibacillus daqingensis. The main fatty acids of the strain is the C18 : 1ω9c and C16 : 0. The G+C content of the genomic DNA was 62.8 mol %. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, aminophospholipids and phospholipids. The cell-wall peptidoglycan did not contain meso-diaminopimelic acid. Thus, YH-lac21T (=KCTC 21185=JCM 34953) represents a novel species. The name Lacticaseibacillus kribbianus sp. nov. is proposed.
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Affiliation(s)
- Jayoung Paek
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Lu Bai
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Yeseul Shin
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hongik Kim
- Vitabio Inc., Daejeon, 305-500, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, 501-759, Republic of Korea
| | - Si Hyun Kim
- Department of Clinical Laboratory Science, Semyung University, Jecheon, Republic of Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine, Busan 614-735, Republic of Korea
| | - Young Hyo Chang
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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12
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Shin Y, Paek J, Kim H, Kook JK, Chang YH. Faecalicatena absiana sp. nov., an obligately anaerobic bacterium from a pig farm faeces dump. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005238] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An obligately anaerobic, Gram-stain-positive, spore-forming, short-rod-shaped bacterium, designated strain YH-C36aT, was isolated from a pig farm faeces dump. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the genus
Faecalicatena
and is most closely related to
Faecalicatena contorta
KCTC 5831T,
Faecalicatena fissicatena
KCTC 15010T and
Faecalicatena orotica
KCTC 15331T, with 96.3, 96.2, and 96.0 % sequence similarity, respectively. The average nucleotide identity values for strain YH-C36aT and the closest related strains were lower than 72 %. The G+C content of the isolate was 43.0 mol%. The cell-wall peptidoglycan was A1γ type and contained meso-diaminopimelic acid. The predominant fatty acids were C16 : 0, C18 : 1
cis 9, C16 : 0 DMA, C18 : 0 DMA and C18:0. The major end products of glucose fermentation were lactate, formate and acetate. Based on its phenotypic, phylogenetic and chemotaxonomic properties, a novel species, named Faecalicatena absiana sp. nov., is proposed for strain YH-C36aT (=KCTC 25106T=NBRC 114768T).
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Affiliation(s)
- Yeseul Shin
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jayoung Paek
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hongik Kim
- Vitabio Inc., Daejeon, 305-500, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, 501-759, Republic of Korea
| | - Young-Hyo Chang
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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Ko YJ, Lee OJ, Lee SB, Kim CM, Lee J, Kook JK, Park SN, Shin JH, Kim SH, Won EJ, Park G, Kang SH, Jang SJ. Accuracy of ASTA MicroIDSys, a New Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry System, for the Identification of Korean Reference and Clinical Bacterial and Yeast Strains. Diagn Microbiol Infect Dis 2022; 103:115658. [DOI: 10.1016/j.diagmicrobio.2022.115658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/17/2022] [Accepted: 01/22/2022] [Indexed: 11/03/2022]
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14
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Kook JK, Park SN, Lim YK, Cho E, Jo E, Roh H, Shin Y, Paek J, Kim HS, Kim H, Shin JH, Chang YH. Correction to: Genome-Based Reclassification of Fusobacterium nucleatum Subspecies at the Species Level. Curr Microbiol 2021; 79:2. [PMID: 34878597 DOI: 10.1007/s00284-021-02680-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Joong-Ki Kook
- Korean Collection for Oral Microbiology, Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
- Oral Biology Research Institute, Chosun University, Gwangju, Republic of Korea
| | - Soon-Nang Park
- Korean Collection for Oral Microbiology, Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Yun Kyong Lim
- Korean Collection for Oral Microbiology, Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Eugene Cho
- Korean Collection for Oral Microbiology, Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Eojin Jo
- Korean Collection for Oral Microbiology, Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | | | - Yeseul Shin
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
| | - Jayoung Paek
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
| | - Hwa-Sook Kim
- Department of Dental Hygiene, Chunnam Techno University, Gokseong-gun, Chunnam, Republic of Korea
| | - Hongik Kim
- Vitabio, Inc., Daejeon, Republic of Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Republic of Korea
| | - Young-Hyo Chang
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea.
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15
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Lee OJ, Ko YJ, Lee SB, Kim CM, Jang SJ, Kook JK, Lim YK, Shin JH, Shin MG, Kee SJ, Jeong SH, Kang SH, Park G. Performance assessment of ASTA MicroIDSys, a new matrix assisted laser desorption ionization-time of flight mass spectrometry system, for identification of viridans group streptococci. Microbiol Immunol 2021; 65:566-574. [PMID: 34516008 DOI: 10.1111/1348-0421.12942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/30/2021] [Accepted: 09/10/2021] [Indexed: 11/29/2022]
Abstract
The performance of the ASTA MicroIDSys system (ASTA, Suwon, South Korea), a new matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) system, was evaluated for the identification of viridans group streptococci (VGS) and compared with the results obtained with the Bruker Biotyper system (Bruker Daltonics, Hamburg, Germany). A total of 106 Streptococcus reference strains belonging to 24 species from the bacterial strain bank was analyzed using the two MALDI-TOF MS systems. Of the 106 reference strains tested, ASTA MicroIDSys and Bruker Biotyper correctly identified 84.9% and 81.1% at the species level, 100% and 97.2% at the group level and 100% and 98.1% at the genus level, respectively. The difference between the two systems was not statistically significant (P = 0.289). Out of 24 species, 13 species were accurately identified to the species level with 100% accurate identification rates with both systems. The accurate identification rates at the species level of ASTA MicroIDSys and Bruker Biotyper were 100% and 87.5% for the S. anginosus group; 78.4% and 73.5% for the S. mitis group; 91.7% and 91.7% for the S. mutans group; and 100% and 100% for the S. salivarius group, respectively. The ASTA MicroIDSys showed an identification performance equivalent to that of the Bruker Biotyper for VGS. Therefore, it would be useful for the identification of VGS strains in clinical microbiology laboratories. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- O-Jin Lee
- Department of Laboratory Medicine, Green Cross Laboratories, Yongin, Republic of Korea
| | - Young Jin Ko
- Department of Laboratory Medicine, School of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Seul-Bi Lee
- Department of Laboratory Medicine, School of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Choon Mee Kim
- Premedical Science, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Sook-Jin Jang
- Department of Laboratory Medicine, School of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, College of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Yun Kyong Lim
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, College of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Jong Hee Shin
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Myung Geun Shin
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Republic of Korea
| | - Seung Jung Kee
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Republic of Korea
| | - Seong-Ho Kang
- Department of Laboratory Medicine, School of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Geon Park
- Department of Laboratory Medicine, School of Medicine, Chosun University, Gwangju, Republic of Korea
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Bae CH, Lim YK, Kook JK, Son MK, Heo YR. Evaluation of antibacterial activity against Candida albicans according to the dosage of various denture cleansers. J Adv Prosthodont 2021; 13:100-106. [PMID: 34025958 PMCID: PMC8110740 DOI: 10.4047/jap.2021.13.2.100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/16/2021] [Accepted: 04/23/2021] [Indexed: 01/18/2023] Open
Abstract
PURPOSE The purpose of this study is to compare the antibacterial activity of currently purchasable denture cleansers against Candida albicans. MATERIALS AND METHODS This study used tablet-type denture cleansers, Polident®, Coolingdent® and Fittydent®, along with liquid denture cleansers, Hexamedine®, Listerine® and Apple vinegar®. The antibacterial activities of denture cleansers were evaluated based on the number of C. albicans and concentrations of the denture cleansers. RESULTS In the 0.5 × 106 cfu/ml culture medium, the C. albicans' death rate of Polident® was significantly lower than those of Fittydent®, Hexamedine®, Listerine®, and Apple vinegar®(P<.05). In the 0.5 × 107 cfu/, the C. albicans' death rates of Polident® and Coolingdent® were significantly lower than those of Fittydent®, Hexamedine®, Listerine® and Apple vinegar®(P<.05). The C. albicans' death rates of Polident® and Coolingdent® were significantly decreased at 0.02 g and 0.01 g. The C. albicans' death rate of Fittydent® was significantly decreased at 0.005 g (P<.05). The C. albicans' death rate of Hexamedine® was significantly decreased at 1/16 dilution. The C. albicans' death rate of Listerine® was decreased at 1/8 dilution, and the antibacterial activity of Apple vinegar® was decreased at 1/4 dilution (P<.05). CONCLUSION As the number of C. albicans
increased, the antibacterial activities of the denture cleansers decrease. In the tablet-type denture cleanser, all denture cleansers showed 100% C. albicans' death rate when used at a dose of 1 tablet. One denture cleanser showed the same antibacterial effect with only 1/3 of a tablet. In the liquid type denture cleanser, the level of dilution required was different for each denture cleanser.
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Affiliation(s)
- Cha-Hwan Bae
- Department of Prosthodontics, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Yun-Kyong Lim
- Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Joong-Ki Kook
- Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Mee-Kyoung Son
- Department of Prosthodontics, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Yu-Ri Heo
- Department of Prosthodontics, School of Dentistry, Chosun University, Gwangju, Republic of Korea
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17
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Paek J, Bai L, Shin Y, Kim H, Kook JK, Chang YH. Description of Paenibacillus dokdonensis sp. nov., a new bacterium isolated from soil. Int J Syst Evol Microbiol 2021; 71. [PMID: 33595431 DOI: 10.1099/ijsem.0.004707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains isolated from soil samples were designated as YH-JAE5T and YH-JAE2. The isolates were facultative anaerobic, Gram-stain-variable, motile, rod-shaped bacteria. Phylogenetic analysis indicated that the isolates belonged to the genus Paenibacillus, but the 16S rRNA gene sequence similarities were <98 % when compared with other species within the genus. Analysis of rpoB gene revealed the isolates formed a sub-cluster with P. chibensis. The only menaquinone identified was MK-7. The two isolates contained meso-diaminopimelic acid within their cell wall peptidoglycan. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phospholipid, aminophospholipids, and lipids. The major fatty acids were C15 : 0 anteiso and C15 : 0 iso. The average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization values between isolate YH-JAE5T and the most closely related reference strain (Paenibacillus chibensis KCTC 3758T) were 81.7, 84.8 and 23.4 %, respectively. The G+C content of the genomic DNA was 47.4 mol%. Thus, the polyphasic data revealed that YH-JAE2 (=KCTC 43239=JCM 34435) and YH-JAE5T (=KCTC 43059=JCM 33533) represent a new species. The name Paenibacillus dokdonensis sp. nov. is proposed.
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Affiliation(s)
- Jayoung Paek
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Lu Bai
- Industrial bio-Materials Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.,Department of Biotechnology, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Yeseul Shin
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hongik Kim
- Vitabio, Inc., Daejeon, 305-500, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, 501-759, Republic of Korea
| | - Young-Hyo Chang
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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18
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Abstract
An obligately anaerobic, Gram-stain-negative, spore-forming, short rod-shaped bacterium, designated strain YH- T4B42T, was isolated from the large intestine of a mini-pig. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the genus Clostridium and is most closely related to Clostridium aminophilum KCTC 5424T, Clostridium symbiosum KCTC 15329T and Clostridium butyricum KCTC 1871T, with 95.5, 92.4 and 83.0 % sequence similarity, respectively. The average nucleotide identity values for strain YH-T4B42T and the closest related strains were lower than 72 %. The G+C content of the isolate was 55.8 mol%. The cell-wall peptidoglycan was A1γ type and contained meso-diaminopimelic acid. The predominant fatty acids were C16 : 0, C18 : 1 cis 9, C14 : 0 and C18 : 0. The major end products of glucose fermentation were lactate, formate and acetate, with a minor amount of butyrate. Based on its phenotypic, phylogenetic and chemotaxonomic properties, a novel species, Clostridium vitabionis sp. nov., is proposed for strain YH-T4B42T (=KCTC 25105T=NBRC 114767T).
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Affiliation(s)
- Yeseul Shin
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jayoung Paek
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hongik Kim
- Vitabio Inc., Daejeon, 305-500, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, 501-759, Republic of Korea
| | - Young Hyo Chang
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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Kim AR, Lim YK, Kook JK, Bak EJ, Yoo YJ. Lipopolysaccharides of Fusobacterium nucleatum and Porphyromonas gingivalis increase RANKL-expressing neutrophils in air pouches of mice. Lab Anim Res 2021; 37:5. [PMID: 33407938 PMCID: PMC7789191 DOI: 10.1186/s42826-020-00080-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 11/27/2020] [Indexed: 11/10/2022] Open
Abstract
Increases of neutrophils and osteoclasts are pathological changes of periodontitis. RANKL is an osteoclast differentiation factor. The effect of periodontopathogen LPS on RANKL-expressing neutrophils has not been clarified yet. We evaluated numerical changes of RANKL-expressing neutrophils in air pouches of mice injected with LPSs of Fusobacterium nucleatum and Porphyromonas gingivalis. Mice with air pouches were assigned into saline (C)-, E. coli LPS- (Ec LPS)-, F. nucleatum LPS (Fn LPS)-, P. gingivalis LPS (Pg LPS)-, and Fn LPS and Pg LPS (Fn + Pg LPS)-injected groups. CD11b+Ly6G+ neutrophils and CD11b+Ly6G+RANKL+ neutrophils in blood and air pouch exudates were determined by flow cytometry. In blood, compared to the C group, the Fn LPS group showed increases of CD11b+Ly6G+ neutrophils and CD11b+Ly6G+RANKL+ neutrophils whereas the Pg LPS group showed no significant differences. These increases in the Fn LPS group were not different to those in the Ec LPS group. In exudates, Fn LPS and Pg LPS groups showed increases of CD11b+Ly6G+ neutrophils and CD11b+Ly6G+RANKL+ neutrophils compared to the C group. Increased levels in the Fn LPS group were not different to those in the Ec LPS group, but Pg LPS group was lower than those in the Ec LPS group. In blood and exudates, the Fn + Pg LPS group showed no difference in levels of these neutrophils compared to the Ec LPS group. LPSs of F. nucleatum and P. gingivalis increased RANKL-expressing neutrophils although the degrees of increases were different. These suggest that periodontopathogen LPS can act as a stimulant to increase RANKL-expressing neutrophils.
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Affiliation(s)
- Ae Ri Kim
- Department of Oral Biology, College of Dentistry, Yonsei University, Seoul, Republic of Korea
- Department of Applied Life Science, The Graduate School, Yonsei University, Seoul, Republic of Korea
- BK21 PLUS Project, College of Dentistry, Yonsei University, Seoul, Republic of Korea
| | - Yun Kyong Lim
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Eun-Jung Bak
- Department of Oral Biology, College of Dentistry, Yonsei University, Seoul, Republic of Korea.
| | - Yun-Jung Yoo
- Department of Oral Biology, College of Dentistry, Yonsei University, Seoul, Republic of Korea.
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Ko YJ, Kook JK, Lee CK. In-house method for direct bacterial identification in positive blood culture broths using microfiltration, bead beating, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J Microbiol Methods 2020; 180:106065. [PMID: 32961240 DOI: 10.1016/j.mimet.2020.106065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 10/23/2022]
Abstract
Rapid identification of bacterial pathogens facilitates earlier optimization of antibiotic treatment and reduces morbidity and mortality in sepsis patients. The aim of this research was to design an in-house chemical-free method for direct bacterial identification in positive blood culture (BC) broths and to compare the performance of this method with that of the commercial Sepsityper® kit. The overall species identification rates for the in-house and Sepsityper methods were 88.4% and 85.8%, respectively (n = 190). Among 146 facultative anaerobes, 92.5% and 95.9% were identified to the species level using the in-house and Sepsityper methods, respectively. For 32 anaerobic bacteria, the in-house method showed a higher species identification rate (75.0%) than the Sepsityper method (53.1%). The in-house method correctly identified more Bacteroides species (100.0%) than the Sepsityper method (18.2%). Our novel in-house method and the Sepsityper method showed a high accuracy for direct bacterial identification in positive BC broths using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.
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Affiliation(s)
- Young Jin Ko
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Republic of Korea; Department of Laboratory Medicine, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, College of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Chang Kyu Lee
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Republic of Korea.
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Shin Y, Paek J, Kim H, Kook JK, Kim JS, Kim SH, Chang YH. Absicoccus porci gen. nov., sp. nov., a member of the family Erysipelotrichaceae isolated from pig faeces. Int J Syst Evol Microbiol 2020; 70:732-737. [DOI: 10.1099/ijsem.0.003803] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yeseul Shin
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Jayoung Paek
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Hongik Kim
- Vitabio, Inc., Daejeon, 305-500, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, 501-759, Republic of Korea
| | - Joong-Su Kim
- Jeonbuk Branch Institute, Molecular Bioprocess Research Center, KRIBB, 1404 Sinjeong-dong, Jeongeup-si, Jeonbuk 580-185, Republic of Korea
| | - Si Hyun Kim
- Department of Clinical Laboratory Science, Semyung University, Jecheon, Republic of Korea
| | - Young-Hyo Chang
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
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22
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Kim UJ, Kim CM, Jang SJ, Lee SB, Cho SS, Jeong SH, Ko YJ, Kang SH, Park G, Kim DM, Yoon NR, Ahn YJ, Lim DH, Kook JK. Evaluation of Synergistic Effect of Combined Treatment with Linalool and Colistin on Multidrug-Resistant Acinetobacter baumannii to Expand Candidate for Therapeutic Option. Ann Clin Microbiol 2020. [DOI: 10.5145/acm.2020.23.1.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Ung-Jun Kim
- Department of Laboratory Medicine, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Choon-Mee Kim
- Premedical Science, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Sook-Jin Jang
- Department of Laboratory Medicine, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Seul-Bi Lee
- Department of Laboratory Medicine, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Seong-Sik Cho
- Department of Laboratory Medicine, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Seok-Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Antimicrobial Resistance, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Young-Jin Ko
- Department of Laboratory Medicine, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Seong-Ho Kang
- Department of Laboratory Medicine, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Geon Park
- Department of Laboratory Medicine, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Dong-Min Kim
- Department of Internal Medicine, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Na-Ra Yoon
- Department of Internal Medicine, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Young-Joon Ahn
- Department of Medical Education, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Dong-hoon Lim
- Department of Urology, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, College of Dentistry, Chosun University, Gwang-Ju, Republic of Korea
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Park SN, Lim YK, Shin JH, Jo E, Chang YH, Shin Y, Paek J, Kim H, Kook JK. Paenibacillus oralis sp. nov., Isolated from Human Subgingival Dental Plaque of Gingivitis Lesion. Curr Microbiol 2019; 77:509-515. [PMID: 31832844 DOI: 10.1007/s00284-019-01843-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 12/06/2019] [Indexed: 11/29/2022]
Abstract
A Gram-stain-negative, facultative anaerobic, spore-forming, motile, and rod-shaped bacterium, strain ChDC PVNT-B20T, was isolated from the human subgingival dental plaque of a gingivitis lesion. Phylogenetic analysis based on the 16S ribosomal RNA gene (16S rDNA) showed that the strain belonged to the genus Paenibacillus. BLAST analysis of 16S rDNA sequence of the strain displayed high identity to those of Paenibacillus faecis DSM 23593T (97.7% similarity) and Paenibacillus macerans ATCC 8244T (97.6% similarity). Draft genome of strain ChDC PVNT-B20T was composed of 8,112,407 bp. The DNA G+C content of the strain was 51.3 mol%. Average nucleotide identity values between strain ChDC PVNT-B20T and P. faecis DSM 23593T or P. macerans ATCC 8244T were 75.71% and 91.5%, respectively. Genome-to-genome distance values between strain ChDC PVNT-B20T and P. faecis DSM 23593T or P. macerans ATCC 8244T were 21.6% (19.3-24.0%) and 44.9% (42.3-47.4%), respectively. Major cellular fatty acids of strain ChDC PVNT-B20T were anteiso-C15:0 (43.4%), C16:0 (16.6%), iso-C16:0 (14.4%), and anteiso-C17:0 (12.4%). The sole respiratory quinone of the strain was menaqinone-7. Major polar lipids of the strain were phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), and one unidentified glycolipid (GL). Minor polar lipids were one unidentified aminolipid (AL), one unidentified phospholipid (PL), and three unidentified lipids (L1-L3). Based on these results, strain ChDC PVNT-B20T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus oralis sp. nov. is proposed. Type strain is ChDC PVNT-B20T (= KCOM 3021T = JCM 33462 T).
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Affiliation(s)
- Soon-Nang Park
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Yun Kyong Lim
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Republic of Korea
| | - Eojin Jo
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Young-Hyo Chang
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
| | - Yeseul Shin
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
| | - Jayoung Paek
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
| | - Hongik Kim
- Vitabio, Inc, Daejeon, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea.
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Lim YK, Park SN, Shin JH, Ji S, Jo E, Chang YH, Shin Y, Paek J, Kim H, Kook JK. Streptococcus koreensis sp. nov., Isolated from Human Subgingival Dental Plaque of Periodontitis Lesion. Curr Microbiol 2019; 76:1531-1536. [PMID: 31570960 DOI: 10.1007/s00284-019-01778-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 09/18/2019] [Indexed: 01/29/2023]
Abstract
A novel facultative anaerobic, Gram-stain-positive coccus, strain JS71T, was isolated from the human subgingival dental plaque of a periodontitis lesion. Phylogenetic analysis based on the 16S ribosomal RNA gene (16S rDNA) revealed that the strain belonged to the genus Streptococcus. The 16S rDNA sequence had high similarity with Streptococcus rubneri DSM 26920T (98.6%), Streptococcus parasanguinis ATCC 15912T (98.5%), and Streptococcus australis CCUG 45919T (98.3%). The genome of strain JS71T was 2,009,592 bp in length. The DNA G+C content of the strain was 42.1 mol%. Average nucleotide identity values between strain JS71T and S. rubneri DSM 26920T, S. parasanguinis ATCC 15912T, and S. australis CCUG 45919T were 88.9%, 80.8%, and 92.4%, respectively. Genome-to-genome distance values between strain JS71TS. rubneri DSM 26920T, S. parasanguinis ATCC 15912T, and S. australis CCUG 45919T were 36.5% (34-39%), 26.3% (23.9-28.7%), and 48.0% (45.4-50.6%), respectively. The major fatty acids of the strain were C16:0 (39.7%), C18:1 ω6c/C18:1 ω7c (15.5%), and C18:0 (10.4%). Based on these results, strain JS71T (= KCOM 2890T = JCM 33454T) should be a novel species of the genus Streptococcus, for which the name Streptococcus koreensis sp. nov. is proposed.
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Affiliation(s)
- Yun Kyong Lim
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Soon-Nang Park
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Republic of Korea
| | - Suk Ji
- Department of Periodontics, Institute of Oral Health Science, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Eojin Jo
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Young-Hyo Chang
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
| | - Yeseul Shin
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
| | - Jayoung Paek
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
| | - Hongik Kim
- Vitabio, Inc., Daejeon, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea.
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25
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Lim YK, Park SN, Lee WP, Shin JH, Jo E, Shin Y, Paek J, Chang YH, Kim H, Kook JK. Lautropia dentalis sp. nov., Isolated from Human Dental Plaque of a Gingivitis Lesion. Curr Microbiol 2019; 76:1369-1373. [PMID: 31446477 DOI: 10.1007/s00284-019-01761-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/13/2019] [Accepted: 08/16/2019] [Indexed: 12/01/2022]
Abstract
A novel Gram-stain-negative, motile, and facultative anaerobic coccus, strain ChDC F240T was isolated from human subgingival dental plaque of a gingivitis lesion. The phylogenetic analysis based on the 16S ribosomal RNA gene (16S rDNA) sequence showed that the strain belonged to the genus Lautropia. 16S rDNA of strain ChDC F240T had the highest similarity to that of Lautropia mirabilis ATCC 51599T (98.8%). Major cellular fatty acids of strain ChDC F240T were C16:0 (43.9%) and C16:1ω6C/C16:1ω7C (38.1%). Draft genome of the strain was 3,834,139 bp in length and the G+C content was 65.0 mol%. Average nucleotide identity and genome-to-genome distance values between strain ChDC F240T and L. mirabilis ATCC 51599 T were 81.99% and 28.50% (26.1-30.9%), respectively. These results reveal that strain ChDC F240T is a novel species within the genus Lautropia, for which the name Lautropia dentalis sp. nov. is proposed; type strain is ChDC F240T (= KCOM 2505T = JCM 33297T).
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Affiliation(s)
- Yun Kyong Lim
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Soon-Nang Park
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Won-Pyo Lee
- Korean Collection for Oral Microbiology and Department of Periodontology, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Republic of Korea
| | - Eojin Jo
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Yeseul Shin
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
| | - Jayoung Paek
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
| | - Young-Hyo Chang
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
| | - Hongik Kim
- Vitabio, Inc., Daejeon, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea.
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26
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Lim YK, Park SN, Jo E, Shin JH, Chang YH, Shin Y, Paek J, Kim H, Kook JK. Lachnoanaerobaculum gingivalis sp. nov., Isolated from Human Subgingival Dental Plaque of a Gingivitis Lesion. Curr Microbiol 2019; 76:1147-1151. [PMID: 31350572 DOI: 10.1007/s00284-019-01747-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/19/2019] [Indexed: 11/30/2022]
Abstract
A novel Gram-stain-positive, obligately anaerobic, spore-forming rod, designated strain ChDC B114T, was isolated from a human dental plaque of a gingivitis lesion. The strain was characterized by polyphasic taxonomic analysis to identify it at the species level. The 16S ribosomal RNA gene (16S rDNA) sequence analysis revealed that the strain belongs to the genus Lachnoanaerobaculum. The percent similarity of the 16S rDNA of the strain was closest to the homologous gene sequence of Lachnoanaerobaculum orale N1T (98.5%) and Lachnoanaerobaculum saburreum CCUG 28089T (97.6%). The major fatty acids of strain ChDC B114T were C16:0 (30.7%), C14:0 (17.7%), iso-C19:0 (14.9%), and C17:0 2OH (12.0%). The draft genome of strain ChDC B114T was 3,097,953 bp in length. The G+C content of the strain was 35.9 mol %. Average nucleotide identity values between strain ChDC B114T and L. orale N1T and L. saburreum CCUG 28089T were 83.2% and 82.0%, respectively. Genome-to-genome distance values between strain ChDC B114T and L. orale N1T and L. saburreum CCUG 28089T were 26.8% (24.5-29.3%) and 26.30% (24.0-28.8%), respectively. Based on these results, strain ChDC B114T (= KCOM 2030T = JCM 33452T) should be classified as a novel species of genus Lachnoanaerobaculum, for which the name Lachnoanaerobaculum gingivalis sp. nov. is proposed.
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Affiliation(s)
- Yun Kyong Lim
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Soon-Nang Park
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Eojin Jo
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Republic of Korea
| | - Young-Hyo Chang
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
| | - Yeseul Shin
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
| | - Jayoung Paek
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
| | - Hongik Kim
- Vitabio, Inc, Daejeon, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea.
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Park D, Kim SH, Bae IK, Kim NY, Kook JK, Park YH, Shin JH. Evaluation of Modified Sequential Multiplex PCR for Streptococcus pneumoniae Serotyping. Jpn J Infect Dis 2019; 72:224-227. [PMID: 30814459 DOI: 10.7883/yoken.jjid.2018.422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The aims of this study were to develop modified sequential multiplex PCR (SM-PCR) primer sets and to evaluate their ability and efficiency for serotype determination. We selected target serotypes for SM-PCR testing according to serotype prevalence as reported in Asian publications. The modified SM-PCR consisted of 6 groups of PCR reactions, and each reaction was performed using 5 primer pairs. We evaluated the efficiency and performance of this modified multiplex PCR using 378 pneumococcal strains by comparing the findings with the results of the Quellung reaction. A total of 30 primer pairs were used in a consecutive set of 6 reactions. All results were concordant with those of the Quellung reaction and there was no cross-reactivity to unintended serotypes. We could identify the final serotypes of 370 isolates (97.9%). The coverage rates of modified SM-PCR were 42.6%, 65.9%, and 79.4% in reactions1, 2, and 3, respectively. The modified SM-PCR showed acceptable performance for detecting pneumococcal serotypes and can serve as useful alternative to the Quellung reaction.
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Affiliation(s)
- Dongchul Park
- Department of Laboratory Medicine, Inje University College of Medicine
| | - Si Hyun Kim
- Department of Clinical Laboratory Science, Semyung University
| | - Il Kwon Bae
- Department of Dental Hygiene, College of Medical and Life Science, Silla University
| | - Na Young Kim
- Department of Laboratory Medicine, Inje University College of Medicine.,Paik Institute for Clinical Research, Inje University College of Medicine
| | - Joong-Ki Kook
- Department of Oral Biochemistry, School of Dentistry, Chosun University
| | - Yo-Han Park
- Department of Surgery, Inje University College of Medicine
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine.,Paik Institute for Clinical Research, Inje University College of Medicine
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Lim YK, Park SN, Shin JH, Chang YH, Shin Y, Paek J, Kim H, Kook JK. Streptococcus periodonticum sp. nov., Isolated from Human Subgingival Dental Plaque of Periodontitis Lesion. Curr Microbiol 2019; 76:835-841. [PMID: 31053905 DOI: 10.1007/s00284-019-01695-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/24/2019] [Indexed: 11/29/2022]
Abstract
A novel facultative anaerobic and Gram-stain-positive coccus, designated strain ChDC F135T, was isolated from human subgingival dental plaque of periodontitis lesion and was characterized by polyphasic taxonomic analysis. The 16S rRNA gene (16S rDNA) sequence of strain ChDC F135T was closest to that of Streptococcus sinensis HKU4T (98.2%), followed by Streptococcus intermedia SK54T (97.0%), Streptococcus constellatus NCTC11325T (96.0%), and Streptococcus anginosus NCTC 10713T (95.7%). In contrast, phylogenetic analysis based on the superoxide dismutase gene (sodA) and the RNA polymerase beta-subunit gene (rpoB) showed that the nucleotide sequence similarities of strain ChDC F135T were highly similar to the corresponding genes of S. anginosus NCTC 10713T (99.2% and 97.6%, respectively), S. constellatus NCTC11325T (87.8% and 91.4%, respectively), and S. intermedia SK54T (85.8% and 91.2%, respectively) rather than those of S. sinensis HKU4T (80.5% and 82.6%). The complete genome of strain ChDC F135T consisted of 1,901,251 bp and the G+C content was 38.9 mol %. Average nucleotide identity value between strain ChDC F135T and S. sinensis HKU4T or S. anginosus NCTC 10713T were 75.7% and 95.6%, respectively. The C14:0 composition of the cellular fatty acids of strain ChDC F135T (32.8%) was different from that of S. intermedia (6-8%), S. constellatus (6-13%), and S. anginosus (13-20%). Based on the results of phylogenetic and phenotypic analysis, strain ChDC F135T (= KCOM 2412T = JCM 33300T) was classified as a type strain of a novel species of the genus Streptococcus, for which we proposed the name Streptococcus periodonticum sp. nov.
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Affiliation(s)
- Yun Kyong Lim
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Soon-Nang Park
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Republic of Korea
| | - Young-Hyo Chang
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
| | - Yeseul Shin
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
| | - Jayoung Paek
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
| | - Hongik Kim
- Vitabio, Inc, Daejeon, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea.
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Park SN, Lim YK, Shin JH, Kim HS, Jo E, Lee WP, Shin Y, Paek J, Chang YH, Kim H, Kook JK. Fusobacterium pseudoperiodonticum sp. nov., Isolated from the Human Oral Cavity. Curr Microbiol 2019; 76:659-665. [PMID: 30937514 DOI: 10.1007/s00284-019-01675-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 03/20/2019] [Indexed: 11/25/2022]
Abstract
In the present study, three strains (ChDC F213T, ChDC F251, and ChDC F267) were classified as novel species of genus Fusobacterium based on average nucleotide identity (ANI) and genome-to-genome distance (GGD) analysis and chemotaxonomic characterization. 16S rDNA sequences of strains ChDC F213T, ChDC F251, and ChDC F267 were highly similar to that of F. periodonticum ATCC 33693T (99.6, 99.4, and 99.4%, respectively). ANI and GGD values of the three isolates with F. periodonticum ATCC 33693T ranged from 92.5 to 92.6% and 47.7 to 48.2%, respectively. Considering that threshold of ANI and GGD values for bacterial species discrimination are 95-96% and 70%, respectively, these results indicate that the three isolates represent a novel Fusobacterium species. DNA G + C contents of the three isolates were 28.0 mol% each. Cellular fatty acid analysis of these strains revealed that C14:0, C16:0, and C16:1 ω6c/C16:1 ω7c were major fatty acids. Therefore, these three strains are novel species belonging to genus Fusobacterium. Strain ChDC F213T (= KCOM 1259T = KCTC 5677T = JCM 33009T) is the type strain of a novel species of genus Fusobacterium, for which a name of Fusobacterium pseudoperiodonticum sp. nov. is proposed.
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Affiliation(s)
- Soon-Nang Park
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Yun Kyong Lim
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Republic of Korea
| | - Hwa-Sook Kim
- Department of Dental Hygiene, Chunnam Techno University, Chunnam, Republic of Korea
| | - Eojin Jo
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Won-Pyo Lee
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Yeseul Shin
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
| | - Jayoung Paek
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
| | - Young-Hyo Chang
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
| | - Hongik Kim
- Vitabio, Inc., Daejeon, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea.
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Puth S, Hong SH, Na HS, Lee HH, Lee YS, Kim SY, Tan W, Hwang HS, Sivasamy S, Jeong K, Kook JK, Ahn SJ, Kang IC, Ryu JH, Koh JT, Rhee JH, Lee SE. A built-in adjuvant-engineered mucosal vaccine against dysbiotic periodontal diseases. Mucosal Immunol 2019; 12:565-579. [PMID: 30487648 DOI: 10.1038/s41385-018-0104-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 09/27/2018] [Accepted: 10/15/2018] [Indexed: 02/04/2023]
Abstract
Periodontitis is associated with a dysbiotic shift in the oral microbiome. Vaccine approaches to prevent microbial shifts from healthy to diseased state in oral biofilms would provide a fundamental therapeutic strategy against periodontitis. Since dental plaque formation is a polymicrobial and multilayered process, vaccines targeting single bacterial species would have limited efficacy in clinical applications. In this study, we developed a divalent mucosal vaccine consisting of a mixture of FlaB-tFomA and Hgp44-FlaB fusion proteins targeting virulence factors of inflammophilic bacteria Fusobacterium nucleatum and Porphyromonas gingivalis, respectively. Introduction of peptide linkers between FlaB and antigen improved the stability and immunogenicity of engineered vaccine antigens. The intranasal immunization of divalent vaccine induced protective immune responses inhibiting alveolar bone loss elicited by F. nucleatum and P. gingivalis infection. The built-in flagellin adjuvant fused to protective antigens enhanced antigen-specific antibody responses and class switch recombination. The divalent vaccine antisera recognized natural forms of surface antigens and reacted with diverse clinical isolates of Fusobacterium subspecies and P. gingivalis. The antisera inhibited F. nucleatum-mediated biofilm formation, co-aggregation of P. gingivalis and Treponema denticola, and P. gingivalis-host cell interactions. Taken together, the built-in adjuvant-engineered mucosal vaccine provides a technological platform for multivalent periodontitis vaccines targeting dysbiotic microbiome.
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Affiliation(s)
- Sao Puth
- Clinical Vaccine R&D Center, Chonnam National University, Hwasun-gun, Jeonnam, 58128, Republic of Korea.,Department of Microbiology, Chonnam National University Medical School, Hwasun-gun, Jeonnam, 58128, Republic of Korea
| | - Seol Hee Hong
- Clinical Vaccine R&D Center, Chonnam National University, Hwasun-gun, Jeonnam, 58128, Republic of Korea.,Department of Pharmacology and Dental Therapeutics, School of Dentistry, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Hee Sam Na
- Department of Oral Microbiology, School of Dentistry, Pusan National University, Yangsan, 50612, Republic of Korea
| | - Hye Hwa Lee
- Clinical Vaccine R&D Center, Chonnam National University, Hwasun-gun, Jeonnam, 58128, Republic of Korea.,Department of Microbiology, Chonnam National University Medical School, Hwasun-gun, Jeonnam, 58128, Republic of Korea
| | - Youn Suhk Lee
- Clinical Vaccine R&D Center, Chonnam National University, Hwasun-gun, Jeonnam, 58128, Republic of Korea.,Department of Pharmacology and Dental Therapeutics, School of Dentistry, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Soo Young Kim
- Clinical Vaccine R&D Center, Chonnam National University, Hwasun-gun, Jeonnam, 58128, Republic of Korea.,Department of Microbiology, Chonnam National University Medical School, Hwasun-gun, Jeonnam, 58128, Republic of Korea
| | - Wenzhi Tan
- Clinical Vaccine R&D Center, Chonnam National University, Hwasun-gun, Jeonnam, 58128, Republic of Korea.,Department of Microbiology, Chonnam National University Medical School, Hwasun-gun, Jeonnam, 58128, Republic of Korea
| | - Hye Suk Hwang
- Clinical Vaccine R&D Center, Chonnam National University, Hwasun-gun, Jeonnam, 58128, Republic of Korea.,Department of Microbiology, Chonnam National University Medical School, Hwasun-gun, Jeonnam, 58128, Republic of Korea
| | - Sethupathy Sivasamy
- Clinical Vaccine R&D Center, Chonnam National University, Hwasun-gun, Jeonnam, 58128, Republic of Korea.,Department of Microbiology, Chonnam National University Medical School, Hwasun-gun, Jeonnam, 58128, Republic of Korea
| | - Kwangjoon Jeong
- Clinical Vaccine R&D Center, Chonnam National University, Hwasun-gun, Jeonnam, 58128, Republic of Korea.,Department of Microbiology, Chonnam National University Medical School, Hwasun-gun, Jeonnam, 58128, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, 61452, Republic of Korea
| | - Sug-Joon Ahn
- Dental Research Institute and Department of Orthodontics, School of Dentistry, Seoul National University, Seoul, 03080, Republic of Korea
| | - In-Chol Kang
- Department of Oral Microbiology, School of Dentistry, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Je-Hwang Ryu
- Department of Pharmacology and Dental Therapeutics, School of Dentistry, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Jeong Tae Koh
- Department of Pharmacology and Dental Therapeutics, School of Dentistry, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Joon Haeng Rhee
- Clinical Vaccine R&D Center, Chonnam National University, Hwasun-gun, Jeonnam, 58128, Republic of Korea. .,Department of Microbiology, Chonnam National University Medical School, Hwasun-gun, Jeonnam, 58128, Republic of Korea.
| | - Shee Eun Lee
- Clinical Vaccine R&D Center, Chonnam National University, Hwasun-gun, Jeonnam, 58128, Republic of Korea. .,Department of Pharmacology and Dental Therapeutics, School of Dentistry, Chonnam National University, Gwangju, 61186, Republic of Korea.
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Shin Y, Paek J, Son AY, Kim H, Kook JK, Paek WK, Chang YH. Clostridium composti sp. nov., a new anaerobic bacteria isolated from compost. Int J Syst Evol Microbiol 2018; 68:3869-3873. [DOI: 10.1099/ijsem.0.003074] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Yeseul Shin
- 1ABS Research Support Center/Korean Collection for Type Cultures, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Jayoung Paek
- 1ABS Research Support Center/Korean Collection for Type Cultures, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Ah Young Son
- 2Vitabio, Inc., Daejeon, 305-500, Republic of Korea
| | - Hongik Kim
- 2Vitabio, Inc., Daejeon, 305-500, Republic of Korea
| | - Joong-Ki Kook
- 3Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, 501-759, Republic of Korea
| | - Woon Kee Paek
- 4National Science Museum, 32-2 Guseong-dong, Yuseong-gu, Daejeon 305-705, Republic of Korea
| | - Young Hyo Chang
- 1ABS Research Support Center/Korean Collection for Type Cultures, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
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Abstract
Two isolates of a Gram-positive, non-motile, coccoid or oval-shaped anaerobic bacterium, designated strains N6H1-15T and YH1_16, were isolated from faecal samples obtained from a mature dog. Analysis of 16S rRNA gene sequences indicated that the isolates belonged to the Blautia coccoidesrRNA gene group (cluster XIVa) and were closely related to Blautia hansenii KCTC 5951T, Blautia stercoris KCTC 5981T, Blautia producta producta KCTC 3695T and B. coccoides DSM 15327T, with 96.7, 94.4, 94.2 and 93.9 % sequence similarity, respectively. The two isolates contained m-diaminopimelic acid within their peptidoglycans. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol, and the major fatty acids were C16 : 0 (18.5 %), C16 : 0 (18.0 %) and C18 : 1cis 9 (16.2 %). The predominant metabolic end products of glucose fermentation were acetic and lactic acids, and the G+C content was 44.2 mol%. Thus, the polyphasic data suggest that the two new isolates represent a new species, proposed as Blautia argi sp. nov. The type strain is N6H1-15T (=KCTC 15426=JCM 31394).
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Affiliation(s)
- Jayoung Paek
- 1ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Yeseul Shin
- 1ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Joong-Ki Kook
- 2Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju 501-759, Republic of Korea
| | - Young-Hyo Chang
- 1ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
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Park SN, Lim YK, Choi MH, Cho E, Bang IS, Kim JM, Ahn SJ, Kook JK. Antimicrobial Mechanism of Oleanolic and Ursolic Acids on Streptococcus mutans UA159. Curr Microbiol 2018; 75:11-19. [PMID: 28852850 DOI: 10.1007/s00284-017-1344-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 08/17/2017] [Indexed: 11/26/2022]
Abstract
Triterpenoid saponin derivatives oleanolic acid (OA) and ursolic acid (UA), but not betulinic acid (BA), were previously found to have strong antimicrobial activity against Streptococcus mutans. OA and UA inhibited the transcription of genes related to peptidoglycan biosynthesis, thereby preventing bacterial growth. However, it is not clear whether this is the only pathway involved in the antimicrobial activity of these compounds against S. mutans. Therefore, we used quantitative real-time PCR (qPCR) and microarray analyses to examine the expression of genes related to essential metabolic pathways in S. mutans UA159 following incubation with OA, UA, or BA. An oligonucleotide array consisting of 5363 probes was designed to survey 1928 of the 1963 genes in the genome of S. mutans UA159. Genes that showed >2-fold changes in expression in response to the treatment conditions were annotated, and selected target genes involved in central metabolism were analyzed by qPCR. Microarray analysis confirmed that the gene expression patterns of the OA- and UA-treated cells differed from that of the BA-treated culture, indicating differences in the antimicrobial mechanism. In particular, the expression of pfk and pykF, coding for glycolysis regulatory proteins phosphofructokinase and pyruvate kinase, respectively, were significantly decreased in the OA and UA groups (P < 0.05), as were genes involved in fatty acid and amino acid synthesis. In addition, the microarray analysis confirmed previous qPCR results showing that peptidoglycan synthesis is down-regulated in the OA- and UA-treated groups. OA and UA also appear to decrease the generation of organic acids by S. mutans UA159, which would have an anticaries effect. Overall, these findings suggest that OA and UA affect multiple genes involved in the central metabolism of S. mutans, with inhibition of glycolysis, fatty acid synthesis, amino acid synthesis, and peptidoglycan synthesis, all contributing to their antimicrobial activity.
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Affiliation(s)
- Soon-Nang Park
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, 61452, Republic of Korea
| | - Yun Kyong Lim
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, 61452, Republic of Korea
| | - Mi-Hwa Choi
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, 61452, Republic of Korea
| | - Eugene Cho
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, 61452, Republic of Korea
| | - Iel Soo Bang
- Department of Oral Microbiology, School of Dentistry, Chosun University, Gwangju, 61452, Republic of Korea
- Oral Biology Research Institute, Chosun University, Gwangju, 61452, Republic of Korea
| | - Jung Min Kim
- Genoplan Korea, Inc. and NAR Center, Inc., Seoul, 06221, Republic of Korea
| | - Sug-Joon Ahn
- Dental Research Institute and Department of Orthodontics, School of Dentistry, Seoul National University, Seoul, 03080, Republic of Korea.
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, 61452, Republic of Korea.
- Oral Biology Research Institute, Chosun University, Gwangju, 61452, Republic of Korea.
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Paek J, Shin Y, Kim JS, Kim H, Kook JK, Paek WK, Chang YH. Description of Absiella argi gen. nov., sp. nov., and transfer of Eubacterium dolichum and Eubacterium tortuosum to the genus Absiella as Absiella dolichum comb. nov. and Absiella tortuosum comb. nov. Anaerobe 2017; 48:70-75. [DOI: 10.1016/j.anaerobe.2017.07.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 07/13/2017] [Accepted: 07/24/2017] [Indexed: 12/01/2022]
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Shin Y, Park SJ, Paek J, Kim JS, Rhee MS, Kim H, Kook JK, Chang YH. Bacteroides koreensis sp. nov. and Bacteroides kribbi sp. nov., two new members of the genus Bacteroides. Int J Syst Evol Microbiol 2017; 67:4352-4357. [PMID: 28945536 DOI: 10.1099/ijsem.0.002226] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Three bacterial isolates from human faeces, YS-aM39T, R2F3-3-3T and R2F3-5-1, were characterized as Gram-negative, strictly anaerobic, non-spore-forming, non-motile, and rod-shaped. Isolate YS-aM39T formed a distinct line of descent, showing greatest 16S rRNA gene sequence relatedness with R2F3-3-3T (97.5 %), R2F3-5-1 (97.5 %), Bacteroides ovatus (98.8 %) and Bacteroides xylanisolvens (97.2 %). Isolates R2F3-3-3T and R2F3-5-1 also formed a distinct line of descent, sharing greatest 16S rRNA gene sequence relatedness with B. ovatus (98.2 %) and B. xylanisolvens (97.2 %). The DNA G+C content of YS-aM39T was 44.8 mol%, that of R2F3-3-3T was 42.4 mol% and that of R2F3-5-1 was 42.6 mol%. The respiratory quinone of all three isolates was menaquinone MK-10. Polar lipid analysis identified phosphatidylethanolamine as the major lipid. The predominant fatty acids in all three isolates were anteiso-C15 : 0, iso-C15 : 0, C16 : 0 3-OH and iso-C17 : 0 3-OH. The major end products of glucose fermentation were acetic acid, lactic acid and formic acid. DNA-DNA hybridization data indicated that two isolates, YS-aM39T and R2F3-3-3T, represent a species distinct from B. ovatus and B. xylanisolvens. Finally, in this study, the two isolates represented two new species in the genus Bacteroides, for which we propose the names Bacteroides koreensis sp. nov. (type strain, YS-aM39T=KCTC 15520T=JCM 31393T) and Bacteroides kribbi sp. nov. (type strain, R2F3-3-3T=KCTC 15460T=JCM 31391T).
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Affiliation(s)
- Yeseul Shin
- ABS Research Support Center/Korean Collection for Type Cultures, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Soo-Je Park
- Department of Biology and Research Institute for Basic Sciences, Jeju National University, 102 Jejudaehak-ro, Jeju 650-756, Republic of Korea
| | - Jayoung Paek
- ABS Research Support Center/Korean Collection for Type Cultures, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Joong-Su Kim
- Jeonbuk Branch Institute, Molecular Bioprocess Research Center, KRIBB, 1404 Sinjeong-dong, Jeongeup-si, Jeonbuk 580-185, Republic of Korea
| | - Moon-Soo Rhee
- ABS Research Support Center/Korean Collection for Type Cultures, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Hongik Kim
- Vitabio, Inc., Daejeon, 305-500, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, 501-759, Republic of Korea
| | - Young-Hyo Chang
- ABS Research Support Center/Korean Collection for Type Cultures, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
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Kim SH, Song SA, Urm SH, Kook JK, Kim HR, Yong D, Choi JY, Shin JH. Evaluation of the Cobas u 701 microscopy analyser compared with urine culture in screening for urinary tract infection. J Med Microbiol 2017; 66:1110-1113. [PMID: 28771134 DOI: 10.1099/jmm.0.000553] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Purpose. A new automated Cobas u 701 microscopy analyser for urine sediment examination was introduced. The aim of this study was to evaluate the analyser in comparison with urine culture in screening for urinary tract infection (UTI).Methodology. A total of 852 urine specimens submitted for culture were included in this study. Urine sediment examination was performed using the Cobas u 701 microscopy analyser. The results of the bacteria (BAC) and yeast (YEA) analyses were compared with the results from urine culture as a method for UTI screening. In addition, we compared the BAC results with white blood cells (WBCs) and leukocyte and nitrite measurement in the Cobas u 601 system.Results. Of the 852 urine specimens, 16.1 % (N=137) were positive by urine culture, yielding 130 bacteria from 124 specimens and 14 yeasts from 14 specimens. The Cobas u 701 microscopy analyser provided no result for 52 specimens because of their high turbidity. The sensitivity, specificity, positive predictive value and negative predictive value were 85.8, 69.4, 33.1 and 96.5 %, respectively. For YEA, these figures were 100, 91.9, 15.8 and 100 %, respectively. The areas under the curve for BAC and WBCs were 0.827 [95 % confidence interval (CI) 0.799, 0.852] and 0.727 (95 % CI 0.695, 0.757), respectively. The sensitivity of the leukocyte and nitrite was 63.5 and 54.6 %, respectively.Conclusion. The Cobas u 701 microscopy analyser showed good diagnostic performance. It can be used for rapid screening for UTI and can reduce the number of cultures required.
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Affiliation(s)
- Si Hyun Kim
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Republic of Korea.,Paik Institute for Clinical Research, Inje University College of Medicine, Busan, Republic of Korea
| | - Sae Am Song
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Republic of Korea
| | - Sang-Hwa Urm
- Department of Preventive Medicine, Inje University College of Medicine, Busan, Republic of Korea
| | - Joong-Ki Kook
- Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Hye Ran Kim
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Republic of Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Antimicrobial Resistance, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jun Yong Choi
- Division of Infectious Disease, Department of Internal Medicine and AIDS Research Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Republic of Korea.,Paik Institute for Clinical Research, Inje University College of Medicine, Busan, Republic of Korea
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Kook JK, Park SN, Lim YK, Cho E, Jo E, Roh H, Shin Y, Paek J, Kim HS, Kim H, Shin JH, Chang YH. Genome-Based Reclassification of Fusobacterium nucleatum Subspecies at the Species Level. Curr Microbiol 2017; 74:1137-1147. [PMID: 28687946 DOI: 10.1007/s00284-017-1296-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 06/29/2017] [Indexed: 10/19/2022]
Abstract
Fusobacterium nucleatum is classified as four subspecies, subsp. nucleatum, polymorphum, vincentii, and animalis, based on DNA-DNA hybridization (DDH) patterns, phenotypic characteristics, and/or multilocus sequence analysis (MLSA). The gold standards for classification of bacterial species are DDH and 16S ribosomal RNA gene (16S rDNA) sequence homology. The thresholds of DDH and 16S rDNA similarity for delineation of bacterial species have been suggested to be >70 and 98.65%, respectively. Average nucleotide identity (ANI) and genome-to-genome distance (GGD) analysis based on genome sequences were recently introduced as a replacement for DDH to delineate bacterial species with ANI (95-96%) and GGD (70%) threshold values. In a previous study, F. hwasookii was classified as a new species based on MLSA and DDH results. 16S rDNA similarity between F. hwasookii type strain and F. nucleatum subspecies type strains was higher than that between F. nucleatum subspecies type strains. Therefore, it is possible that the four F. nucleatum subspecies can be classified as Fusobacterium species. In this study, we performed ANI and GGD analyses using the genome sequences of 36 F. nucleatum, five F. hwasookii, and one Fusobacterium periodonticum strain to determine whether the four F. nucleatum subspecies could be classified as species using OrthoANI and ANI web-based softwares provided by ChunLab and Kostas lab, respectively, and GGD calculator offered by German Collection of Microorganisms and Cell Cultures. ANI values calculated from OrthoANI and ANI calculators between the type strains of F. nucleatum subspecies ranged from 89.80 to 92.97 and from 90.40 to 91.90%, respectively. GGD values between the type strains of F. nucleatum subspecies ranged from 42.3 to 46.0%. ANI and GGD values among strains belonging to the same F. nucleatum subspecies, subsp. nucleatum, subsp. polymorphum, subsp. vincentii, and subsp. animalis were >96 and >68.2%, respectively. These results strongly suggest that F. nucleatum subsp. nucleatum, subsp. polymorphum, subsp. vincentii, and subsp. animalis should be classified as F. nucleatum, F. polymorphum, F. vincentii, and F. animalis, respectively.
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Affiliation(s)
- Joong-Ki Kook
- Korean Collection for Oral Microbiology, Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea. .,Oral Biology Research Institute, Chosun University, Gwangju, Republic of Korea.
| | - Soon-Nang Park
- Korean Collection for Oral Microbiology, Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Yun Kyong Lim
- Korean Collection for Oral Microbiology, Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Eugene Cho
- Korean Collection for Oral Microbiology, Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Eojin Jo
- Korean Collection for Oral Microbiology, Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | | | - Yeseul Shin
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
| | - Jayoung Paek
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
| | - Hwa-Sook Kim
- Department of Dental Hygiene, Chunnam Techno University, Gokseong-gun, Chunnam, Republic of Korea
| | - Hongik Kim
- Vitabio, Inc., Daejeon, Republic of Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Republic of Korea
| | - Young-Hyo Chang
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea.
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Kim YJ, Kim SH, Park HJ, Park HG, Park D, Song SA, Lee HJ, Yong D, Choi JY, Kook JK, Kim HR, Shin JH. Corrigendum to "MALDI-TOF MS is more accurate than VITEK II ANC card and API Rapid ID 32 A system for the identification of Clostridium species" [Anaerobe 40 (2016) 73-75]. Anaerobe 2017; 47:238. [PMID: 28668254 DOI: 10.1016/j.anaerobe.2017.06.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Young Jin Kim
- Department of Laboratory Medicine, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Si Hyun Kim
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Republic of Korea; Paik Institute for Clinical Research, Inje University College of Medicine, Busan, Republic of Korea
| | - Hyun-Jung Park
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Republic of Korea
| | - Hae-Geun Park
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Republic of Korea
| | - Dongchul Park
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Republic of Korea
| | - Sae Am Song
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Republic of Korea
| | - Hee Joo Lee
- Department of Laboratory Medicine, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Antimicrobial Resistance, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jun Yong Choi
- Division of Infectious Disease, Department of Internal Medicine and AIDS Research Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Joong-Ki Kook
- Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Hye Ran Kim
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Republic of Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Republic of Korea; Paik Institute for Clinical Research, Inje University College of Medicine, Busan, Republic of Korea.
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Ahn SH, Song JE, Kim S, Cho SH, Lim YK, Kook JK, Kook MS, Lee TH. NOX1/2 activation in human gingival fibroblasts by Fusobacterium nucleatum facilitates attachment of Porphyromonas gingivalis. Arch Microbiol 2016; 198:573-83. [PMID: 27071620 DOI: 10.1007/s00203-016-1223-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 03/22/2016] [Accepted: 04/06/2016] [Indexed: 10/22/2022]
Abstract
Periodontal diseases are infectious polymicrobial inflammatory diseases that lead to destruction of the periodontal ligament, gingiva, and alveolar bone. Sequential colonization of a broad range of bacteria, including Fusobacterium nucleatum and Porphyromonas gingivalis, is an important phenomenon in this disease model. F. nucleatum is a facultative anaerobic species thought to be a key mediator of dental plaque maturation due to its extensive coaggregation with other oral bacteria, while P. gingivalis is an obligate anaerobic species that induces gingival inflammation by secreting various virulence factors. The formation of a bacterial complex by these two species is central to the pathogenesis of periodontal disease. Reactive oxygen species (ROS) are produced during bacterial infections and are involved in intracellular signaling. However, the impact of oral bacteria-induced ROS on the ecology of F. nucleatum and P. gingivalis has yet to be clarified. In the present study, we investigated ROS production induced in primary human oral cells by F. nucleatum and P. gingivalis and its effect on the formation of their bacterial complexes and further host cell apoptosis. We found that in primary human gingival fibroblasts (GFs), two NADPH oxidase isoforms, NOX1 and NOX2, were activated in response to F. nucleatum infection but not P. gingivalis infection. Accordingly, increased NADPH oxidase activity and production of superoxide anion were observed in GFs after F. nucleatum infection, but not after P. gingivalis infection. Interestingly, in NOX1, NOX2, or NOX1/NOX2 knockdown cells, the number of P. gingivalis decreased when the cells were coinfected with F. nucleatum. A similar pattern of host cell apoptosis was observed. This implies that F. nucleatum contributes to attachment of P. gingivalis by triggering activation of NADPH oxidase in host cells, which may provide an environment more favorable to strict anaerobic bacteria and have a subsequent effect on apoptosis of host cells.
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Affiliation(s)
- Sun Hee Ahn
- Department of Oral Biochemistry, Dental Science Research Institute, Medical Research Center for Biomineralization Disorders, School of Dentistry, Chonnam National University, Gwangju, Republic of Korea
| | - Ji-Eun Song
- Department of Molecular Medicine (BK21plus), Graduate School, Chonnam National University, Gwangju, Republic of Korea
| | - Suhee Kim
- Department of Molecular Medicine (BK21plus), Graduate School, Chonnam National University, Gwangju, Republic of Korea
| | - Sung-Hyun Cho
- Department of Molecular Medicine (BK21plus), Graduate School, Chonnam National University, Gwangju, Republic of Korea
| | - Yun Kyong Lim
- Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Joong-Ki Kook
- Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Min-Suk Kook
- Department of Oral and Maxillofacial Surgery, Medical Research Center for Biomineralization Disorders, School of Dentistry, Chonnam National University, Gwangju, Republic of Korea
| | - Tae-Hoon Lee
- Department of Oral Biochemistry, Dental Science Research Institute, Medical Research Center for Biomineralization Disorders, School of Dentistry, Chonnam National University, Gwangju, Republic of Korea. .,Department of Molecular Medicine (BK21plus), Graduate School, Chonnam National University, Gwangju, Republic of Korea.
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Park G, Jin WY, Jang SJ, Kook JK, Choi JA, Park GC, Lee MJ, Park SN, Li XM, Cho SS, Jang CH, Kang SH, Moon DS. Evaluation of four methods of assigning species and genus to medically important bacteria using 16S rRNA gene sequence analysis. Microbiol Immunol 2016; 59:285-98. [PMID: 25786669 DOI: 10.1111/1348-0421.12254] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 03/03/2015] [Accepted: 03/04/2015] [Indexed: 01/08/2023]
Abstract
The four methods for assigning bacterial species are the Clinical and Laboratory Standards Institute (CLSI), modified CLSI (mCLSI), phylogenetic analysis (PA) and closest match (CM) methods, these are used to identify the genus and species using 16S rRNA gene sequence results. In this study, the results of identification by these four methods of 37 aerobic reference strains, 30 anaerobic reference strains, 15 Acinetobacter reference strains and 167 Acinetobacter clinical strains were compared. The rates of accurate identification to the species level using the CLSI, mCLSI, PA and CM methods were as follows: 24.3, 86.5, 86.5 and 89.2%, respectively, for the 37 aerobic reference strains; 73.3%, 96.7%, 90.0% and 93.3%, respectively, for the 30 anaerobic reference strains; 40.0%, 93.3%, 100% and 93.3%, respectively, for the 15 Acinetobacter reference strains; and 53.9%, 90.4%, 95.8% and 90.4%, respectively, for the 167 Acinetobacter clinical strains. The rates of accurate identification to the genus level using the CLSI, mCLSI, PA, and CM methods were as follows: 91.9%, 91.9%, 94.6% and 91.9%, respectively, for the 37 aerobic reference strains; 100%, 100%, 100% and 100%, respectively, for all of the 30 anaerobic reference strains, 15 Acinetobacter reference strains and the 167 Acinetobacter clinical strains. The mCLSI is the most practical and pragmatic method for identification of species based on 16S rRNA sequences for hospital, research or industry laboratories because it performs well and involves a simple procedure.
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Affiliation(s)
- Geon Park
- Department of Laboratory Medicine, College of Medicine, Chosun University, Gwang-Ju, Republic of Korea
| | - Won-Young Jin
- Department of Laboratory Medicine, College of Medicine, Chosun University, Gwang-Ju, Republic of Korea
| | - Sook-Jin Jang
- Department of Laboratory Medicine, College of Medicine, Chosun University, Gwang-Ju, Republic of Korea.,Research Center for Resistant Cells, College of Medicine, Chosun University, Gwang-Ju, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, College of Dentistry, Chosun University, Gwang-Ju, Republic of Korea
| | - Ji Ae Choi
- Research Center for Resistant Cells, College of Medicine, Chosun University, Gwang-Ju, Republic of Korea
| | - Gyun Cheol Park
- Department of Laboratory Medicine, College of Medicine, Chosun University, Gwang-Ju, Republic of Korea
| | - Min-Jung Lee
- Research Center for Resistant Cells, College of Medicine, Chosun University, Gwang-Ju, Republic of Korea
| | - Soon-Nang Park
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, College of Dentistry, Chosun University, Gwang-Ju, Republic of Korea
| | - Xue Min Li
- Department of Internal Medicine, Yantaishan Hospital, Yantai, China
| | - Seong-Sig Cho
- Department of Laboratory Medicine, Chosun University Hospital, Gwang-Ju, Republic of Korea
| | - Chul Ho Jang
- Department of Otolaryngology, Chonnam National University Medical School, Gwangju, 501-757, Republic of Korea
| | - Seong-Ho Kang
- Department of Laboratory Medicine, College of Medicine, Chosun University, Gwang-Ju, Republic of Korea
| | - Dae-Soo Moon
- Department of Laboratory Medicine, College of Medicine, Chosun University, Gwang-Ju, Republic of Korea
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Park YM, Lee HJ, Jeong JH, Kook JK, Choy HE, Hahn TW, Bang IS. Branched-chain amino acid supplementation promotes aerobic growth of Salmonella Typhimurium under nitrosative stress conditions. Arch Microbiol 2015; 197:1117-27. [PMID: 26374245 DOI: 10.1007/s00203-015-1151-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 09/03/2015] [Accepted: 09/11/2015] [Indexed: 12/31/2022]
Abstract
Nitric oxide (NO) inactivates iron-sulfur enzymes in bacterial amino acid biosynthetic pathways, causing amino acid auxotrophy. We demonstrate that exogenous supplementation with branched-chain amino acids (BCAA) can restore the NO resistance of hmp mutant Salmonella Typhimurium lacking principal NO-metabolizing enzyme flavohemoglobin, and of mutants further lacking iron-sulfur enzymes dihydroxy-acid dehydratase (IlvD) and isopropylmalate isomerase (LeuCD) that are essential for BCAA biosynthesis, in an oxygen-dependent manner. BCAA supplementation did not affect the NO consumption rate of S. Typhimurium, suggesting the BCAA-promoted NO resistance independent of NO metabolism. BCAA supplementation also induced intracellular survival of ilvD and leuCD mutants at wild-type levels inside RAW 264.7 macrophages that produce constant amounts of NO regardless of varied supplemental BCAA concentrations. Our results suggest that the NO-induced BCAA auxotrophy of Salmonella, due to inactivation of iron-sulfur enzymes for BCAA biosynthesis, could be rescued by bacterial taking up exogenous BCAA available in oxic environments.
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Affiliation(s)
- Yoon Mee Park
- Department of Microbiology and Immunology, Chosun University School of Dentistry, Gwangju, 501-759, Republic of Korea
| | - Hwa Jeong Lee
- Department of Microbiology and Immunology, Chosun University School of Dentistry, Gwangju, 501-759, Republic of Korea
| | - Jae-Ho Jeong
- Department of Microbiology, Chonnam National University Medical School, Gwangju, 501-746, Republic of Korea
| | - Joong-Ki Kook
- Department of Oral Biochemistry, Chosun University School of Dentistry, Gwangju, 501-759, Republic of Korea
| | - Hyon E Choy
- Department of Microbiology, Chonnam National University Medical School, Gwangju, 501-746, Republic of Korea
| | - Tae-Wook Hahn
- College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon, 200-701, Republic of Korea
| | - Iel Soo Bang
- Department of Microbiology and Immunology, Chosun University School of Dentistry, Gwangju, 501-759, Republic of Korea.
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Park SN, Ahn SJ, Kook JK. Oleanolic acid and ursolic acid inhibit peptidoglycan biosynthesis in Streptococcus mutans UA159. Braz J Microbiol 2015; 46:613-7. [PMID: 26273281 PMCID: PMC4507558 DOI: 10.1590/s1517-838246246220130209] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Accepted: 10/29/2014] [Indexed: 11/22/2022] Open
Abstract
In this study, we revealed that OA and UA significantly inhibited the expression of most genes related to peptidoglycan biosynthesis in S. mutans UA159. To the best of our knowledge, this is the first report to introduce the antimicrobial mechanism of OA and UA against S. mutans.
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Affiliation(s)
- Soon-Nang Park
- Korean Collection for Oral Microbiology and
Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, >Republic of Korea, Korean Collection for Oral Microbiology and
Department of Oral Biochemistry, School of Dentistry, Chosun University,
Gwangju, Republic of Korea
| | - Sug-Joon Ahn
- Seoul National University, School of Dentistry, Seoul National University, Seoul, >Republic of Korea, Dental Research Institute, School of Dentistry,
Seoul National University, Seoul, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and
Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, >Republic of Korea, Korean Collection for Oral Microbiology and
Department of Oral Biochemistry, School of Dentistry, Chosun University,
Gwangju, Republic of Korea
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Park GC, Jang SJ, Lee MJ, Kook JK, Kim MJ, Kim YS, Yang NW, Lee HS, Kang SH, Park G, Moon DS. Comparison of the Vitek 2, API 20A, and 16s rRNA Gene Sequencing for the Identification of Anaerobic Bacteria. Ann Clin Microbiol 2015. [DOI: 10.5145/acm.2015.18.1.20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Gyun Cheol Park
- Department of Laboratory Medicine, Chosun University College of Medicine, Gwangju, Korea
| | - Sook Jin Jang
- Department of Laboratory Medicine, Chosun University College of Medicine, Gwangju, Korea
- Research Center for Resistant Cells, Chosun University College of Medicine, Gwangju, Korea
| | - Min Jung Lee
- Research Center for Resistant Cells, Chosun University College of Medicine, Gwangju, Korea
| | - Joong-Ki Kook
- Department of Oral Biochemistry, College of Dentistry, Chosun University, Gwangju, Korea
| | - Min Jung Kim
- Department of Oral Biochemistry, College of Dentistry, Chosun University, Gwangju, Korea
| | - Young Sook Kim
- Department of Radiology, Chosun University College of Medicine, Gwangju, Korea
| | - Nam Woong Yang
- Department of Microbiology, College of Medicine, Chosun University, Gwangju, Korea
| | - Hye Soo Lee
- Department of Laboratory Medicine, Chonbuk National University Medical School, Jeonju, Korea
- Chonbuk National University Hospital Branch of National Culture Collection of Pathogens, Jeonju, Korea
| | - Seong Ho Kang
- Department of Laboratory Medicine, Chosun University College of Medicine, Gwangju, Korea
| | - Geon Park
- Department of Laboratory Medicine, Chosun University College of Medicine, Gwangju, Korea
| | - Dae Soo Moon
- Department of Laboratory Medicine, Chosun University College of Medicine, Gwangju, Korea
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Ko YM, Myung SW, Kook JK, Jung SC, Kim BH. In Vitro Antibacterial Activity of Nano Silver Ion Substituted Poly Acrylic Acid Films on Titanium by Plasma Polymerization. J Nanosci Nanotechnol 2015; 15:463-466. [PMID: 26328382 DOI: 10.1166/jnn.2015.8371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Antibacterial activity of oral pathogens such as Streptococcus mutans, Streptococcus sobrinus when silver ion immobilized on commercially pure (CP) titanium (Ti) surface was investigated in this study. Plasma-polymerized acrylic acid to have carboxyl group was deposited on CP-Ti surface and then ion-exchanged with Ag+ ions in 0.1 N AgNO3. In anti-adherent experiment, antibacterial activity was tested using broth culture methods. The biofilm formation assay was performed using semi-defined biofilm medium with sucrose. The silver coated CP-Ti completely inhibited the growth of S. mutans and S. sobrinus. In addition, the biofilm formation was significantly inhibited in silver-coated CP-Ti group.
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Ahn SJ, Park SN, Lee YJ, Cho EJ, Lim YK, Li XM, Choi MH, Seo YW, Kook JK. In vitro antimicrobial activities of 1-methoxyficifolinol, licorisoflavan A, and 6,8-diprenylgenistein against Streptococcus mutans. Caries Res 2014; 49:78-89. [PMID: 25531232 DOI: 10.1159/000362676] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 04/02/2014] [Indexed: 11/19/2022] Open
Abstract
The objective of the study was to investigate the antimicrobial effects of purified single compounds from ethanol-extracted licorice root on Streptococcus mutans. The crude licorice root extract (CLE) was obtained from Glycyrrhiza uralensis, which was subjected to column chromatography to separate compounds. Purified compounds were identified by mass spectrometry and nuclear magnetic resonance. Antimicrobial activities of purified compounds from CLE were evaluated by determining the minimum inhibitory concentration and by performing time-kill kinetics. The inhibitory effects of the compounds on biofilm development were evaluated using crystal violet assay and confocal microscopy. Cell toxicity of substances to normal human gingival fibroblast (NHGF) cells was tested using a methyl thiazolyl tetrazolium assay. Chlorhexidine digluconate (CHX) was used in the control group. Three antimicrobial flavonoids, 1-methoxyficifolinol, licorisoflavan A, and 6,8-diprenylgenistein, were isolated from the CLE. We found that the three flavonoids and CHX had bactericidal effects on S. mutans UA159 at the concentration of ≥4 and ≥1 µg/ml, respectively. The purified compounds completely inhibited biofilm development of S. mutans UA159 at concentrations over 4 μg/ml, which was equivalent to 2 μg/ml of CHX. Confocal analysis showed that biofilms were sparsely scattered in the presence of over 4 μg/ml of the purified compounds. However, the three compounds purified from CLE showed less cytotoxic effects on NHGF cells than CHX at these biofilm-inhibitory concentrations. Our results suggest that purified flavonoids from CLE can be useful in developing oral hygiene products, such as gargling solutions and dentifrices for preventing dental caries.
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Affiliation(s)
- Sug-Joon Ahn
- Dental Research Institute, School of Dentistry, Seoul National University, Jongro-Gu, Seoul, Republic of Korea
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Paek J, Shin JH, Shin Y, Park IS, Jin TE, Kook JK, Wie SH, Cho HG, Park SJ, Chang YH. Myroides injenensis sp. nov., a new member isolated from human urine. Antonie van Leeuwenhoek 2014; 107:201-7. [DOI: 10.1007/s10482-014-0317-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 10/24/2014] [Indexed: 11/28/2022]
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Cho E, Park SN, Lim YK, Shin Y, Paek J, Hwang CH, Chang YH, Kook JK. Fusobacterium hwasookii sp. nov., Isolated from a Human Periodontitis Lesion. Curr Microbiol 2014; 70:169-75. [PMID: 25257648 DOI: 10.1007/s00284-014-0692-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 08/12/2014] [Indexed: 10/24/2022]
Abstract
In this study, we classified the five strains (ChDC F128(T), ChDC F145, ChDC F174, ChDC F206, and ChDC F300) as a novel species of genus Fusobacterium by DNA-DNA hybridization and multi-locus phylogenetic analysis (MLPA), based on a single sequence (24,715 bp) of 22 concatenated housekeeping genes, with morphological and chemotaxonomic characteristics. DNA-DNA hybridization data showed that the values of genomic relatedness between ChDC F128(T) and each of the other novel strains were ranged from 79.0 to 82.6 %, while those of genomic relatedness between ChDC F128(T) and type strain of each of subspecies of F. nucleatum or Fusobacterium periodonticum were ranged from 40.9 to 54.4 %. MLPA revealed that the 5 strains were clustered as one group and clearly discriminated with F. nucleatum and F. periodonticum with 100 % bootstrap value. The DNA G+C content of the five novel strains were ranged from 26.9 to 27.0 mol%. The cellular fatty acid analysis of clinical isolates and type strains revealed C14:0, C16:0, and cis-9 C16:1 as the major fatty acids. The cell wall peptidoglycan of the 5 strains was comprised of meso-lanthionine. These results show that the 5 strains are novel species and belong to the genus Fusobacterium. Strain ChDC F128(T) (=KCOM 1249(T) = KCTC 5108(T) = JCM 30218(T)) is suggested to be the type strain of a novel species of genus Fusobacterium, for which the name Fusobacterium hwasookii sp. nov. is proposed.
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Affiliation(s)
- Eugene Cho
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
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Ahn SJ, Song YD, Mah SJ, Cho EJ, Kook JK. Determination of optimal concentration of deglycyrrhizinated licorice root extract for preventing dental caries using a bacterial model system. J Dent Sci 2014. [DOI: 10.1016/j.jds.2014.03.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Park SN, Kook JK. Development of Streptococcus gordonii-specific quantitative real-time polymerase chain reaction primers based on the nucleotide sequence of rpoB. Microbiol Immunol 2014; 57:583-8. [PMID: 23647321 DOI: 10.1111/1348-0421.12063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 03/19/2013] [Accepted: 04/26/2013] [Indexed: 12/01/2022]
Abstract
In this study, Streptococcus gordonii-specific quantitative real-time polymerase chain reaction (qPCR) primers, RTSgo-F2/RTSgo-R2, were developed based on the nucleotide sequences of RNA polymerase β-subunit gene (rpoB). The specificity of the RTSgo-F2/RTSgo-R2 primers was assessed by conventional PCR on 99 strains comprising 63 oral bacterial species, including the type strain and eight clinical isolates of S. gordonii. PCR products were amplified from the genomic DNAs of only S. gordonii strains. The qPCR primers were able to detect as little as 40 fg of S. gordonii genomic DNA at a cycle threshold value of 33. These findings suggest that these qPCR primers detect S. gordonii with high specificity and sensitivity.
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Affiliation(s)
- Soon-Nang Park
- Korean Collection for Oral Microbiology, Department of Oral Biochemistry, School of Dentistry, Chosun University, 375 Seosuk-Dong, Dong-Gu, Gwangju, 501-759, Korea
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Kook JK, Sakamoto T, Nishi K, Kim MK, Seong JH, Son YN, Kim DK. Detection ofTannerella forsythiaand/orPrevotella intermediaMight Be Useful for Microbial Predictive Markers for the Outcome of Initial Periodontal Treatment in Koreans. Microbiol Immunol 2013; 49:9-16. [PMID: 15665448 DOI: 10.1111/j.1348-0421.2005.tb03634.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A proportion of diseased sites in periodontal disease do not respond to the initial treatment, which might be due in part to the presence of specific microbial pathogens. The aim of this study was to clarify the value of microbial screening for predicting the outcome of periodontal treatment in Koreans using a polymerase chain reaction (PCR). This study enrolled 32 adults with periodontal disease. Microbial and clinical examinations were performed at the baseline and after the initial treatment (professional toothbrushing, scaling, and root planing). Subgingival plaque samples were taken from four sites in each subject (total 128 samples). PCR was used to detect the four putative pathogenic bacteria. There was an improvement in the average of each clinical measurement after the initial treatment. However, approximately half of the sites exhibiting bleeding upon probing (BOP) at the baseline still exhibited bleeding after treatment. There was a close association between the presence of BOP and the presence of Tannerella forsythia (formerly Bacteroides forsythus) and/or Prevotella intermedia. Furthermore, the sites harboring both T. forsythia and P. intermedia at the baseline had a poorer response to treatment than the sites where these two species were not detected. Therefore, microbial screening for T. forsythia and P. intermedia might be useful for predicting the treatment outcome in Koreans.
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Affiliation(s)
- Joong-Ki Kook
- Department of Biochemistry, College of Dentistry, Chosun University, Seo-Suk Dong, Dong-ku, Gwang-ju, Republic of Korea
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