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Qiu X, Ye K, Ma Y, Zhao Q, Wang L, Yang J. Genome sequence-based species classification of Enterobacter cloacae complex: a study among clinical isolates. Microbiol Spectr 2024:e0431223. [PMID: 38687068 DOI: 10.1128/spectrum.04312-23] [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: 12/28/2023] [Accepted: 04/13/2024] [Indexed: 05/02/2024] Open
Abstract
Accurate species-level identification of Enterobacter cloacae complex (ECC) is crucial for related research. The classification of ECC is based on strain-to-strain phylogenetic congruence, as well as genomic features including average nucleotide identity (ANI) and digitalized DNA-DNA hybridization (dDDH). ANI and dDDH derived from whole-genome sequencing have emerged as a reliable metric for assessing genetic relatedness between genomes and are increasingly recognized as a standard for species delimitation. Up to now, there are two different classification methods for ECC. The first one categorizes E. hormaechei, a species within ECC, into five subspecies (E. hormaechei subsp. steigerwaltii, subsp. oharae, subsp. xiangfangensis, subsp. hoffmannii, and subsp. hormaechei). The second classifies E. hormaechei as three species: E. hormaechei, "E. xiangfangensis," "E. hoffmanii." While the former is well-accepted in the academic area, the latter may have a greater ability to distinguish different species of ECC. To assess the suitability of these identification criteria for clinical ECC isolates, we conducted a comprehensive analysis involving phylogenetic analysis, ANI and dDDH value alignment, virulence gene identification, and capsule typing on 256 clinical ECC strains isolated from the bloodstream. Our findings indicated that the method of categorizing E. hormaechei into five subspecies has better correlation and consistency with the molecular characteristics of clinical ECC isolates, as evidenced by phylogenetic analysis, virulence genes, and capsule typing. Therefore, the subspecies-based classification method appears more suitable for taxonomic assignments of clinical ECC isolates. IMPORTANCE Standardizing taxonomy of the Enterobacter cloacae complex (ECC) is necessary for data integration across diverse studies. The study utilized whole-genome data to accurately identify 256 clinical ECC isolated from bloodstream infections using average nucleotide identity (ANI), digitalized DNA-DNA hybridization (dDDH), and phylogenetic analysis. Through comprehensive assessments including phylogenetic analysis, ANI and dDDH comparisons, virulence gene, and capsule typing of the 256 clinical isolates, it was concluded that the classification method based on subspecies exhibited better correlation and consistency with the molecular characteristics of clinical ECC isolates. In summary, this research contributes to the precise identification of clinical ECC at the species level and expands our understanding of ECC.
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Affiliation(s)
- Xuemei Qiu
- Laboratory Medicine Department, First Medical Center of Chinese PLA General Hospital, Beijing, China
- Medical school of Chinese PLA, Beijing, China
| | - Kun Ye
- Laboratory Medicine Department, First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yanning Ma
- Laboratory Medicine Department, First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Qiang Zhao
- Laboratory Medicine Department, First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Lifeng Wang
- Laboratory Medicine Department, First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Jiyong Yang
- Laboratory Medicine Department, First Medical Center of Chinese PLA General Hospital, Beijing, China
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Albert MJ, Al-Hashem G, Rotimi VO. Multiplex gyrB PCR Assay for Identification of Acinetobacter baumannii Is Validated by Whole Genome Sequence-Based Assays. Med Princ Pract 2022; 31:493-496. [PMID: 35944494 PMCID: PMC9801371 DOI: 10.1159/000526402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 03/10/2022] [Accepted: 08/07/2022] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVE A multiplex gyrB PCR assay has been used to diagnose Acinetobacter baumannii. However, this assay has not been validated against the gold standard DNA-DNA hybridization assay, which is a laborious method. DNA-DNA hybridization assay is now replaced by whole genome sequence (WGS)-based methods. Two such methods are a k-mer-based search of sequence reads using the Kraken 2 program and average nucleotide identity (ANI). The objective was to validate the gyrB PCR assay with WGS-based methods. SUBJECTS AND METHODS We cultured 270 sequential A. baumannii isolates from the rectal swabs of 32 adult patients. The identity of the isolates was determined by gyrB PCR. The sequences of 269 isolates were determined by Illumina sequencing and the taxonomy was inferred by the Kraken 2 program and ANI. RESULTS All the 269 isolates were confirmed as A. baumannii by Kraken 2 and ANI. CONCLUSION The gyrB PCR assay is now validated for easy identification of A. baumannii in comparison with gold standard WGS-based assays.
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Nimse SB, Song KS, Warkad SD, Kim T. A Novel Method That Allows SNP Discrimination with 160:1 Ratio for Biosensors Based on DNA-DNA Hybridization. Biosensors (Basel) 2021; 11:bios11080265. [PMID: 34436067 PMCID: PMC8391390 DOI: 10.3390/bios11080265] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/19/2022]
Abstract
Highly sensitive (high SBR) and highly specific (high SNP discrimination ratio) DNA hybridization is essential for a biosensor with clinical application. Herein, we propose a method that allows detecting multiple pathogens on a single platform with the SNP discrimination ratios over 160:1 in the dynamic range of 101 to 104 copies per test. The newly developed SWAT method allows achieving highly sensitive and highly specific DNA hybridizations. The detection and discrimination of the MTB and NTM strain in the clinical samples with the SBR and SNP discrimination ratios higher than 160:1 indicate the high clinical applicability of the SWAT.
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Affiliation(s)
- Satish Balasaheb Nimse
- Department of Chemistry, Institute for Applied Chemistry, Hallym University, Chuncheon 200-702, Korea;
| | - Keum-Soo Song
- Biometrix Technology, Inc. 202 BioVenture Plaza, Chuncheon 200-161, Korea; (K.-S.S.); (S.D.W.)
| | | | - Taisun Kim
- Department of Chemistry, Institute for Applied Chemistry, Hallym University, Chuncheon 200-702, Korea;
- Correspondence:
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Abstract
OBJECTIVE To compare the oral microbiota of Sjögren's syndrome (SS) with that of healthy subjects (HS). METHODS Supragingival and subgingival biofilm samples were collected from the mesial-buccal tooth surfaces of SS patients (n = 57) and age- and sex-matched HS (n = 53). Unstimulated saliva and 8 oral tissue samples were taken using a buccal brush. Caries and periodontal measures were recorded. All supragingival samples and a subgroup of 24 SS and 28 HS subgingival samples, as well as 32 SS and 11 HS saliva and oral tissue samples, were analyzed for their content of 41 bacterial species using checkerboard DNA-DNA hybridization. Mean levels (×105 ± SEM) and percentage of DNA probe counts of each species were determined for each sample site and averaged within subjects in the 2 clinical groups. Kruskal-Wallis tests, adjusting for multiple comparisons and cluster analysis, were used for soft tissue and microbial analysis, and the Mann-Whitney test was used to compare caries and periodontal measures. RESULTS Mean (×105 ± SEM) total DNA probe counts in supragingival samples were significantly lower (P < 0.001) in the SS (13.3 ± .7) compared to the HS (44.1 ± 6.8) group. In supragingival samples, Veillonella parvula, Fusobacterium nucleatum ss vincenti, and Propionibacterium acnes were markedly elevated in the SS compared to the HS group in both mean (×105 ± SEM) and mean (± SEM) percentage DNA probe counts (P < 0.001). In subgingival samples of SS, V. parvula was significantly different compared to HS (P < 0.05). SS was characterized by high levels of purple and low levels of orange and red complexes. Cluster analysis of oral tissues and saliva demonstrated that the mean microbial profiles for SS patients and the HS group clustered separately. Active root caries (P < 0.003) and attachment loss were significantly higher (P < 0.029) in the SS group compared to the HS group. CONCLUSION These findings indicate that saliva is a major controlling factor of intraoral biofilm. V. parvula may be a unique microbial biomarker for Sjögren's syndrome. KNOWLEDGE TRANSFER STATEMENT The microbiome characterized for Sjögren's syndrome in salivary hypofunction is shown to be under stress and reduced. Veillonella parvula can be a possible identification of a biomarker for Sjögren's syndrome.
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Affiliation(s)
- M Singh
- Division of Oral Medicine, School of Dental Medicine, Tufts University, Boston, MA, USA
| | - F Teles
- Department of Basic and Translational Sciences, University of Pennsylvania, School of Dental Medicine, Philadelphia, PA, USA.,Center for Innovation & Precision Dentistry, School of Engineering and Applied Sciences, University of Pennsylvania, School of Dental Medicine, Philadelphia, Pennsylvania, USA
| | - N G Uzel
- Department of Periodontology, School of Dental Medicine, Tufts University, Boston, MA, USA
| | - A Papas
- Division of Oral Medicine, School of Dental Medicine, Tufts University, Boston, MA, USA
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Kwak MJ, Choi SB, Ha SM, Kim EH, Kim BY, Chun J. Genome-based reclassification of Paenibacillus jamilae Aguilera et al. 2001 as a later heterotypic synonym of Paenibacillus polymyxa (Prazmowski 1880) Ash et al. 1994. Int J Syst Evol Microbiol 2020; 70:3134-3138. [PMID: 32375953 DOI: 10.1099/ijsem.0.004140] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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
Paenibacillus is one of the genera that has high species diversity and Paenibacillus polymyxa, the type species of the genus, is mainly isolated from plant-associated environments. Among the plant-associated species, Paenibacillus jamilae B.3T (=CECT 5266T=DSM 13815T=KACC 10925T=KCTC 13919T) was proposed to be a novel species according to 16S rRNA gene similarity and DNA-DNA relatedness with related species, including Paenibacillus polymyxa. Nevertheless, in the description of Paenibacillus jamilae the used strain of Paenibacillus polymyxa was not the type strain of this species. In this work we found that the type strains of both species showed 16S rRNA gene similarity of 99.6 %. Therefore, in this study, we sequenced the genome of Paenibacillus jamilae KACC 10925T and compared it with those of the type strain of Paenibacillus polymyxa ATCC 842T and other phylogenetically related species. Genome relatedness value calculated by DNA-DNA hybridization between type strains of Paenibacillus polymyxa and Paenibacillus jamilae was 73.5 %, which is higher than the threshold value (70 %). For more objective and repeatable results of genome relatedness, we analysed an average nucleotide identity (ANI) between two strains. Our results showed that ANI value between the type strains of Paenibacillus jamilae and Paenibacillus polymyxa is 98.5 %, a phylogenetic distance also higher than the threshold values (95~96 %). These values were proposed by Yoon et al. (2017). In addition, their phylogenetic distance based on 92 bacterial core genes is highly close compared to other species. These mean that Paenibacillus jamilae and Paenibacillus polymyxa should be reclassified as a single species. Based on the results from genomic level comparison as well as reexamination results of physiological and chemotaxonomic features, we propose reclassification of Paenibacillus jamilae as a later heterotypic synonym of Paenibacillus polymyxa.
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Affiliation(s)
- Min-Jung Kwak
- ChunLab, Inc., JW Tower, 2477, Nambusunhwan-ro, Seocho-gu, Seoul 06725, Republic of Korea
| | - Seon-Bin Choi
- ChunLab, Inc., JW Tower, 2477, Nambusunhwan-ro, Seocho-gu, Seoul 06725, Republic of Korea
| | - Sung-Min Ha
- ChunLab, Inc., JW Tower, 2477, Nambusunhwan-ro, Seocho-gu, Seoul 06725, Republic of Korea
| | - Eun Hye Kim
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea.,ChunLab, Inc., JW Tower, 2477, Nambusunhwan-ro, Seocho-gu, Seoul 06725, Republic of Korea
| | - Byung-Yong Kim
- ChunLab, Inc., JW Tower, 2477, Nambusunhwan-ro, Seocho-gu, Seoul 06725, Republic of Korea
| | - Jongsik Chun
- School of Biological Sciences & Inst. of Molecular Biology and Genetics, Seoul National University, Seoul 151-742, Republic of Korea.,ChunLab, Inc., JW Tower, 2477, Nambusunhwan-ro, Seocho-gu, Seoul 06725, Republic of Korea
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Wei M, Wang P, Yang C, Gu L. Molecular identification and phylogenetic relationships of clinical Nocardia isolates. Antonie Van Leeuwenhoek 2019; 112:1755-1766. [PMID: 31350617 DOI: 10.1007/s10482-019-01296-2] [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] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 06/26/2019] [Indexed: 12/17/2022]
Abstract
Species identification of Nocardia is difficult because of a complex and rapidly evolving taxonomy. In this study, gene sequencing (16S rRNA, gyrB, secA1, hsp65, rpoB), single 16S rRNA gene sequence phylogenetic analysis, and MALDI-TOF analysis were used to accurately identify 46 clinical Nocardia isolates to the species level. This provided a basis for establishing a routine method of multi-locus sequence analysis (MLSA) for molecular identification of Nocardia species. Genetic polymorphism analysis showed that MLSA was a powerfully discriminating method compared with the 16S rRNA gene to identify clinical Nocardia isolates. However, five-locus (gyrB-16S rRNA-secA1-hsp65-rpoB) MLSA led to misidentifications of all of the five Nocardia abscessus, which were confirmed by digital DNA-DNA hybridization (DDH) analysis. Interestingly, four strains identified as Nocardia beijingensis by a 16S rRNA gene phylogenetic tree may be novel species as suggested by DDH studies. For the purpose of achieving both accuracy and discrimination, the data of MLSA were reanalyzed. A three-locus MLSA with concatenated gyrB-16S rRNA-secA1 sequences was used to construct the phylogenetic tree with high accuracy and powerful discrimination. Therefore, a routine method of MLSA was developed to identify clinical Nocardia species.
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Affiliation(s)
- Ming Wei
- Department of Infectious Diseases and Clinical Microbiology, Beijing Chao-Yang Hospital, Capital Medical University, 8 Gongren Tiyuchang Nanlu, Chaoyang District, Beijing, 100020, People's Republic of China
| | - Peng Wang
- Department of Infectious Diseases and Clinical Microbiology, Beijing Chao-Yang Hospital, Capital Medical University, 8 Gongren Tiyuchang Nanlu, Chaoyang District, Beijing, 100020, People's Republic of China
| | - Chunxia Yang
- Department of Infectious Diseases and Clinical Microbiology, Beijing Chao-Yang Hospital, Capital Medical University, 8 Gongren Tiyuchang Nanlu, Chaoyang District, Beijing, 100020, People's Republic of China
| | - Li Gu
- Department of Infectious Diseases and Clinical Microbiology, Beijing Chao-Yang Hospital, Capital Medical University, 8 Gongren Tiyuchang Nanlu, Chaoyang District, Beijing, 100020, People's Republic of China.
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Kutsuna R, Miyoshi-Akiyama T, Mori K, Hayashi M, Tomida J, Morita Y, Tanaka K, Kawamura Y. Description of Paraclostridium bifermentans subsp. muricolitidis subsp. nov., emended description of Paraclostridium bifermentans (Sasi Jyothsna et al., 2016), and creation of Paraclostridium bifermentans subsp. bifermentans subsp. nov. Microbiol Immunol 2018; 63:1-10. [PMID: 30549099 DOI: 10.1111/1348-0421.12663] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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: 09/10/2018] [Revised: 11/27/2018] [Accepted: 12/09/2018] [Indexed: 11/29/2022]
Abstract
Taxonomic studies of strain PAGU 1678T , an obligately anaerobic, gram-positive, spore-forming bacterium isolated from biobreeding rat feces, were performed. This strain has been demonstrated to have the ability to exacerbate pathosis in a mouse model of dextran sulfate sodium-induced ulcerative colitis. Phylogenetic analysis based on the 16S rRNA gene showed high homology with Paraclostridium bifermentans. To clarify the correct taxonomic position of strain PAGU 1678T , a comparative taxonomic study using P. bifermentans PAGU 2008T (═JCM 1386T ) and the closely related bacterial species P. benzoelyticum PAGU 2068T (═LMG 28745T ) was carried out. Despite the close similarity of 16S rRNA gene sequences, DNA-DNA hybridization between strain PAGU 1678T and P. bifermentans PAGU 2008T was 60.03% on average, average nucleotide identity was 96.17%, and it was shown to have different genomic sequences. Biochemically, strain PAGU 1678T could be differentiated from P. bifermentans PAGU 2008T by H2 S production. Furthermore, strain PAGU 1678T was characterized by the presence of two phospholipids with different polarity on polar lipid analysis. In addition, strain PAGU 1678T differed from P. bifermentans PAGU 2008T in findings on whole-cell protein analysis and matrix-assisted laser desorption/ionization-time of flight mass spectrometry. On the basis of these biochemical and genetic characteristics, a novel subspecies of P. bifermentans with the name Paraclostridium bifermentans subsp. muricolitidis subsp. nov. is here proposed, with PAGU 1678T (═CCUG 72489T ═NBRC 113386T ) as the type strain, which automatically creates P. bifermentans subsp. bifermentans subsp. nov. JCM 1386T (═ATCC 638T ═DSM 14991T ).
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Affiliation(s)
- Ryo Kutsuna
- Laboratory of Microbiology, Aichi Gakuin University Graduate School of Pharmaceutical Science, Nagoya, Aichi, Japan
| | - Tohru Miyoshi-Akiyama
- Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, Shinjuku, Tokyo, Japan
| | - Koji Mori
- Biological Resource Center, National Institute of Technology and Evaluation, Kisarazu, Chiba, Japan
| | - Masahiro Hayashi
- Division of Anaerobe Research, Life Science Research Center, Gifu University, Gifu, Japan.,Center for Conservation of Microbial Genetic Resource, Gifu University, Gifu, Japan
| | - Junko Tomida
- Laboratory of Microbiology, Aichi Gakuin University Graduate School of Pharmaceutical Science, Nagoya, Aichi, Japan
| | - Yuji Morita
- Laboratory of Microbiology, Aichi Gakuin University Graduate School of Pharmaceutical Science, Nagoya, Aichi, Japan
| | - Kaori Tanaka
- Division of Anaerobe Research, Life Science Research Center, Gifu University, Gifu, Japan.,Center for Conservation of Microbial Genetic Resource, Gifu University, Gifu, Japan.,United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Yoshiaki Kawamura
- Laboratory of Microbiology, Aichi Gakuin University Graduate School of Pharmaceutical Science, Nagoya, Aichi, Japan
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Wang YS, Yan ZF, Lin P, Gao W, Yi TH. Paracoccus pueri sp. nov., isolated from Pu'er tea. Antonie Van Leeuwenhoek 2018; 111:1535-1542. [PMID: 29484518 DOI: 10.1007/s10482-018-1041-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 02/05/2018] [Indexed: 12/01/2022]
Abstract
A Gram-stain negative, aerobic, short rod-shaped, motile by flagella bacterial strain (THG-N2.35T), was isolated from Pu'er tea. Growth occurred at 10-40 °C (optimum 28 °C), at pH 4-7 (optimum 7) and at 0-5% NaCl (optimum 1%). Based on 16S rRNA gene sequence analysis, the near phylogenetic neighbours of strain THG-N2.35T were identified as Paracoccus hibisci KACC 18632T (99.0%), Paracoccus tibetensis CGMCC 1.8925T (98.7%), Paracoccus beibuensis CGMCC 1.7295T (98.2%), Paracoccus aestuarii KCTC 22049T (98.2%), Paracoccus rhizosphaerae LMG 26205T (98.1%), Paracoccus zeaxanthinifaciens ATCC 21588T (97.1%), Paracoccus marcusii DSM 11574T (97.0%). Levels of similarity between strain THG-N2.35T and other Paracoccus species were lower than 97.0%. DNA-DNA hybridization values between strain THG-N2.35T and P. hibisci KACC 18632T, P. tibetensis CGMCC 1.8925T, P. beibuensis CGMCC 1.7295T, P. aestuarii KCTC 22049T, P. rhizosphaerae LMG 26205T, P. zeaxanthinifaciens ATCC 21588T, P.marcusii DSM 11574T were 47.5% (42.3%, reciprocal analysis), 36.1% (32.3%), 24.7% (22.1%), 19.2% (16.3%), 11.3% (8.8%), 11.1% (10.8%), 6.1% (5.8%), respectively. The DNA G+C content of strain THG-N2.35T was 62.3 mol%. The polar lipids were diphosphatidylglycerol, phosphatidyl-N-methylethanolamine, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. The quinone was ubiquinone-10 (Q-10). The major fatty acids were C10:0 3OH, C16:0, C18:0 and C18:1 ω7ϲ. On the basis of the phylogenetic analysis, chemotaxonomic data, physiological characteristics and DNA-DNA hybridization data, strain THG-N2.35T represent a novel species of the genus Paracoccus, for which the name Paracoccus pueri sp. nov. is proposed. The type strain is THG-N2.35T (= KACC 18934T = CCTCC AB 2016177T).
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Affiliation(s)
- Yu-Shuai Wang
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-Si, Gyeonggi-do, 17104, Republic of Korea
| | - Zheng-Fei Yan
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-Si, Gyeonggi-do, 17104, Republic of Korea
| | - Pei Lin
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-Si, Gyeonggi-do, 17104, Republic of Korea
| | - Wei Gao
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-Si, Gyeonggi-do, 17104, Republic of Korea
| | - Tae-Hoo Yi
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-Si, Gyeonggi-do, 17104, Republic of Korea.
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Benn A, Heng N, Broadbent JM, Thomson WM. Studying the human oral microbiome: challenges and the evolution of solutions. Aust Dent J 2017; 63:14-24. [PMID: 28853139 DOI: 10.1111/adj.12565] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2017] [Indexed: 01/06/2023]
Abstract
Since the pioneering work of van Leeuwenhoek in 1684, subsequently built upon by other renowned microbiologists Robert Koch, Willoughby Miller and GV Black, oral microbiology has developed innovative techniques to study the oral microflora (now termed the 'oral microbiome'). The advent of molecular techniques such as DNA-DNA hybridization, polymerase chain reaction and DNA sequencing has created an array of opportunities to construct a comprehensive picture of the diversity and composition of the oral microbiome. Approximately 700 oral bacterial species have been identified, of which 50% have yet to be cultivated, and some of these are known only by their signature DNA sequences. The synergism of ever-evolving culture-based and state-of-the-art culture-independent molecular techniques has facilitated in-depth understanding of the dynamics, acquisition and transfer of oral bacteria, along with their role in oral and general health and disease. Further research is needed to not only analyse but also to make sense of the ever-increasing volumes of data which these molecular techniques (especially high-throughput DNA sequencing) are generating, as well as why particular bacteria are present and what they are 'actually doing' there. This review presents a comprehensive literature search of oral microbiology-related methods currently used to study the oral microbiome.
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Affiliation(s)
- Aml Benn
- Southern District Health Board, Dunedin, New Zealand
| | - Nck Heng
- The University of Otago - Sir John Walsh Research Institute, Dunedin, New Zealand
| | - J M Broadbent
- The University of Otago - Sir John Walsh Research Institute, Dunedin, New Zealand
| | - W M Thomson
- The University of Otago - Sir John Walsh Research Institute, Dunedin, New Zealand
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Abstract
Ethological studies in the 1940s and 1950s, most notably those of Lorenz and Tinbergen, emphasized a historical perspective. By the 1970s, the notion that behavioral traits are too plastic to retain historical information became prevalent, and evolutionary approaches in behavioral studies were largely abandoned. However, several recent studies have demonstrated that behavioral characters are remarkably consistent with phylogenies obtained from other data and not particularly prone to homoplasy. In this study, I coded descriptions of courtship display behaviors in stork species (Aves: Ciconiiformes: Ciconiidae) as a matrix of discrete characters. I mapped each behavioral character onto a phylogeny based on DNA-DNA hybridization distances to test the homology of individual characters. Generally, displays occurring early in courtship were congruent with phylogenetic relationships and showed little homoplasy, while displays occurring late in courtship were more homoplastic. I also performed a phylogenetic analysis of the behavioral data matrix using maximum parsimony. The strict consensus of the 24 most-parsimonious trees was congruent with the DNA-DNA hybridization tree in all nodes having greater than 70% bootstrap support.
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Affiliation(s)
- Beth Slikas
- Biology Department, University of Pennsylvania, Philadelphia, Pennsylvania, 19104-6018.,Academy of Natural Sciences of Philadelphia, 1900 Benjamin Franklin Parkway, Philadelphia, Pennsylvania, 19103-1195
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Abstract
Alkaliphilic Bacillus sp. C-125 was taxonomically characterized by physiological and biochemical characteristics, 16S rDNA sequence similarity, and DNA-DNA hybridization analyses. Phylogenetic analysis of strain C-125 based on comparison of 16S rDNA sequences showed that this strain is closely related to Bacillus halodurans. DNA-DNA hybridization analysis was done comparing C-125 and related Bacillus reference strains. The highest level of DNA-DNA relatedness (86%) was found between strain C-125 and B. halodurans. Our findings demonstrate that strain C-125 is a member of the species B. halodurans.
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Malolina EA, Lebedeva AL, Kulibin AY, Evdokimov VV, Kurilo LF, Sorokina TM, Tulenev JA, Naumenko VA, Kushch AA. [Interaction of herpesviruses with mature human spermatozoa in the model system in vitro]. Vopr Virusol 2016; 61:119-125. [PMID: 36494945 DOI: 10.18821/0507-4088-2016-61-3-119-125] [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: 07/12/2020] [Accepted: 07/12/2020] [Indexed: 12/13/2022]
Abstract
The DNA of human herpesviruses (HHV), including the herpes simplex virus (HSV) and cytomegalovirus (CMV), is often identified in ejaculates of patients with urogenital diseases and infertility. At least a part of viral DNA is associated with cell fraction of ejaculate. However, it remains unclear how the semen is infected by the virus. It can be located in gametes or be capable of infecting mature germ cells, including motile sperm cells. In order to resolve this issue, interactions of the CMV and HSV with human sperm cells were studied using an original optimized model of the herpesviral infection of male gametes in vitro. The analysis of the immunofluorescent staining of gametes for viral antigens has shown that CMV infected 2% gametes, while HSV infected 17.26 ± 2.58% gametes. The fraction of progressively motile sperm cells contained 13.99 ± 4.64% infected cells. Localization of HSV was studied by the confocal microscopy. Sometimes, viral gB protein was found on sperm cell membrane. In addition, optical scanning of other cells has shown the intracellular localization of the viral proteins. In the majority of spermatozoa, the viral proteins were observed in the head and neck. In some cells, they were located in the middle piece or, rarely, in the equatorial segment. In general, after in vitro infection HSV antigens were located in the same areas of the sperm cells as in ejaculates from infected patients. According to DNA-DNA hybridization in situ, gametes containing HSV DNA accounted for 16.94 ± 5.28%, which is consistent with the results obtained in the immunofluorescence assay. It can be concluded that mature male gametes are infected by HHV in the genital tract, where the virus binds to the sperm cell membrane and enters the cell. Interaction of HHV with progressively motile sperm cells implies a vertical viral transmission upon fertilization and points to the necessity of testing ejaculate for herpesviruses infections.
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Affiliation(s)
- E A Malolina
- Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya.,Koltzov Institute of Developmental Biology
| | - A L Lebedeva
- Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya.,Research Center for Medical Genetics
| | | | - V V Evdokimov
- Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya.,Moscow Scientific and Practical Center of Dermatovenereology and Cosmetology, Department of Healthcare of the Government of Moscow
| | | | | | - J A Tulenev
- Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya
| | - V A Naumenko
- Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya
| | - A A Kushch
- Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya
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Fritz ML, Miller JR, Bayoh MN, Vulule JM, Landgraf JR, Walker ED. Application of a reverse dot blot DNA-DNA hydridization method to quantify host-feeding tendencies of two sibling species in the Anopheles gambiae complex. Med Vet Entomol 2013; 27:398-407. [PMID: 24188164 PMCID: PMC3818715 DOI: 10.1111/j.1365-2915.2012.01063.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A DNA-DNA hybridization method, reverse dot blot analysis (RDBA), was used to identify Anopheles gambiae s.s. and Anopheles arabiensis (Diptera: Culicidae) hosts. Of 299 blood-fed and semi-gravid An. gambiae s.l. collected from Kisian, Kenya, 244 individuals were identifiable to species; of these, 69.5% were An. arabiensis and 29.5% were An. gambiae s.s. Host identifications with RDBA were comparable with those of conventional polymerase chain reaction (PCR) followed by direct sequencing of amplicons of the vertebrate mitochondrial cytochrome b gene. Of the 174 amplicon-producing samples used to compare these two methods, 147 were identifiable by direct sequencing and 139 of these were identifiable by RDBA. Anopheles arabiensis bloodmeals were mostly (94.6%) bovine in origin, whereas An. gambiae s.s. fed upon humans more than 91.8% of the time. Tests by RDBA detected that two of 112 An. arabiensis contained blood from more than one host species, whereas PCR and direct sequencing did not. Recent use of insecticide-treated bednets in Kisian is likely to have caused the shift in the dominant vector species from An. gambiae s.s. to An. arabiensis. Reverse dot blot analysis provides an opportunity to study changes in host-feeding by members of the An. gambiae complex in response to the broadening distribution of vector control measures targeting host-selection behaviours.
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Affiliation(s)
- Megan L Fritz
- Department of Zoology, Michigan State University, 48 Giltner, East Lansing, MI, 48824 USA
| | - James R Miller
- Department of Entomology, 203 Center for Integrated Plant Systems, Michigan State University, East Lansing, MI 48824 USA
| | - M Nabie Bayoh
- Centre for Global Health Research, Centers for Disease Control and Prevent/Kenya Medical Research Institute, Box 1578, Kisumu, Kenya
| | - John M Vulule
- Centre for Global Health Research, Centers for Disease Control and Prevent/Kenya Medical Research Institute, Box 1578, Kisumu, Kenya
| | - Jeffrey R Landgraf
- Research Technology Support Facility, S18 Plant Biology Laboratory, Michigan State University, East Lansing, MI 48824 USA
| | - Edward D Walker
- Department of Microbiology and Molecular Genetics, Michigan State University, 6169 Biomedical Physical Sciences Building, East Lansing, MI, 48824, USA
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