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Lin WH, Tsai TS. Comparisons of the Oral Microbiota from Seven Species of Wild Venomous Snakes in Taiwan Using the High-Throughput Amplicon Sequencing of the Full-Length 16S rRNA Gene. Biology (Basel) 2023; 12:1206. [PMID: 37759605 PMCID: PMC10525742 DOI: 10.3390/biology12091206] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/26/2023] [Accepted: 09/02/2023] [Indexed: 09/29/2023]
Abstract
A venomous snake's oral cavity may harbor pathogenic microorganisms that cause secondary infection at the wound site after being bitten. We collected oral samples from 37 individuals belonging to seven species of wild venomous snakes in Taiwan, including Naja atra (Na), Bungarus multicinctus (Bm), Protobothrops mucrosquamatus (Pm), Trimeresurus stejnegeri (Ts), Daboia siamensis (Ds), Deinagkistrodon acutus (Da), and alpine Trimeresurus gracilis (Tg). Bacterial species were identified using full-length 16S rRNA amplicon sequencing analysis, and this is the first study using this technique to investigate the oral microbiota of multiple Taiwanese snake species. Up to 1064 bacterial species were identified from the snake's oral cavities, with 24 pathogenic and 24 non-pathogenic species among the most abundant ones. The most abundant oral bacterial species detected in our study were different from those found in previous studies, which varied by snake species, collection sites, sampling tissues, culture dependence, and analysis methods. Multivariate analysis revealed that the oral bacterial species compositions in Na, Bm, and Pm each were significantly different from the other species, whereas those among Ts, Ds, Da, and Tg showed fewer differences. Herein, we reveal the microbial diversity in multiple species of wild snakes and provide potential therapeutic implications regarding empiric antibiotic selection for wildlife medicine and snakebite management.
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Affiliation(s)
- Wen-Hao Lin
- Institute of Wildlife Conservation, National Pingtung University of Science and Technology, Pingtung 912301, Taiwan;
| | - Tein-Shun Tsai
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 912301, Taiwan
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Tapia-García EY, Arroyo-Herrera I, Rojas-Rojas FU, Ibarra JA, Vásquez-Murrieta MS, Martínez-Aguilar L, López-Lara IM, Whitman WB, Estrada de Los Santos P. Paraburkholderia lycopersici sp. nov., a nitrogen-fixing species isolated from rhizoplane of Lycopersicon esculentum Mill. var. Saladette in Mexico. Syst Appl Microbiol 2020; 43:126133. [PMID: 32998072 DOI: 10.1016/j.syapm.2020.126133] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/06/2020] [Accepted: 09/07/2020] [Indexed: 01/29/2023]
Abstract
A survey of our in-house bacterial collection identified a group of six strains isolated from the tomato rhizoplane that possessed 16S rRNA gene sequences with 98.2% sequence similarity to Paraburkholderia pallida, suggesting that these strains represented a novel species. Multilocus sequence analysis using gltB, lepA and recA gene sequences showed the clustering of the strains and the BOX-PCR patterns were similar among these strains. The average nucleotide identity and the DNA-DNA virtual hybridization of strain TNe-862T was <89% and <34%, respectively, to the genomes of any sequenced Paraburkholderia species. The genome of strain TNe-862T possessed all the genes necessary for nitrogen fixation and biosynthesis of indoleacetic acid and antimicrobials terpenes, phosphonates and bacteriocins. It also contained genes for metal resistance, xenobiotic degradation, and hydrolytic enzymes such as a putative chitinase and isoamylase. Even though the strain contained potential genes for degradation of cellulose and starch, the bacterium was unable to utilize these substrates in culture medium. The genome encoded flagella and pili as well as multiple chemotaxis systems. In addition, genes encoding for the type I, II, IV, V and VI secretion systems were also present. The strains grow up to 42°C and 5% NaCl. The optimum growth pH was 8. The major cellular fatty acids were C16:0 and C18:1 ω7c. Based on this polyphasic analysis, these strains represent a novel species in the genus Paraburkholderia, for which the name Paraburkholderia lycopersici sp. nov. is proposed. The type strain is TNe-862T (=LMG 26415T=CIP 110323T).
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Arroyo-Herrera I, Rojas-Rojas FU, Lozano-Cervantes KD, Larios-Serrato V, Vásquez-Murrieta MS, Whtiman WB, Ibarra JA, Estrada-de Los Santos P. Draft genome of five Cupriavidus plantarum strains: agave, maize and sorghum plant-associated bacteria with resistance to metals. 3 Biotech 2020; 10:242. [PMID: 32405446 DOI: 10.1007/s13205-020-02210-8] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/15/2020] [Indexed: 11/27/2022] Open
Abstract
Five strains of Cupriavidus plantarum, a metal-resistant, plant-associated bacterium, were selected for genome sequencing through the Genomic Encyclopedia of Bacteria and Archaea (GEBA) Phase IV project at the Joint Genome Institute (JGI) of the U.S. Department of Energy (DOE). The genome of the strains was in the size range of 6.2-6.4 Mbp and encoded 5605-5834 proteins; 16.9-23.7% of these genes could not be assigned to a COG-associated functional category. The G + C content was 65.83-65.99%, and the genomes encoded 59-67 stable RNAs. The strains were resistant in vitro to arsenite, arsenate, cobalt, chromium, copper, nickel and zinc, and their genomes possessed the resistance genes for these metals. The genomes also encoded the biosynthesis of potential antimicrobial compounds, such as terpenes, phosphonates, bacteriocins, betalactones, nonribosomal peptides, phenazine and siderophores, as well as the biosynthesis of cellulose and enzymes such as chitinase and trehalase. The average nucleotide identity (ANI) and DNA-DNA in silico hybridization of the genomes confirmed that C. plantarum is a single species. Moreover, the strains cluster within a single group upon multilocus sequence analyses with eight genes and a phylogenomic analyses. Noteworthy, the ability of the species to tolerate high concentrations of different metals might prove useful for bioremediation of naturally contaminated environments.
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Affiliation(s)
- Ivan Arroyo-Herrera
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala S/N. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340 Cd. de México, Mexico
| | - Fernando Uriel Rojas-Rojas
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala S/N. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340 Cd. de México, Mexico
- 2Laboratorio de Ciencias AgroGenómicas, Escuela Nacional de Estudios Superiores, Universidad Nacional Autónoma de México, León, Guanajuato, Mexico
| | - Karla Daniela Lozano-Cervantes
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala S/N. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340 Cd. de México, Mexico
| | - Violeta Larios-Serrato
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala S/N. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340 Cd. de México, Mexico
| | - María Soledad Vásquez-Murrieta
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala S/N. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340 Cd. de México, Mexico
| | | | - J Antonio Ibarra
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala S/N. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340 Cd. de México, Mexico
| | - Paulina Estrada-de Los Santos
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala S/N. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340 Cd. de México, Mexico
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Feng T, Kim KH, Oh J, Jeon CO. Cupriavidus lacunae sp. nov., isolated from pond-side soil. Antonie van Leeuwenhoek 2019; 112:543-51. [DOI: 10.1007/s10482-018-1187-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/10/2018] [Indexed: 11/25/2022]
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Ramachandran H, Shafie NAH, Sudesh K, Azizan MN, Majid MIA, Amirul AAA. Cupriavidus malaysiensis sp. nov., a novel poly(3-hydroxybutyrate-co-4-hydroxybutyrate) accumulating bacterium isolated from the Malaysian environment. Antonie van Leeuwenhoek 2017; 111:361-372. [DOI: 10.1007/s10482-017-0958-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 10/04/2017] [Indexed: 10/18/2022]
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Sun LN, Wang DS, Yang ED, Fang LC, Chen YF, Tang XY, Hua RM. Cupriavidus nantongensis sp. nov., a novel chlorpyrifos-degrading bacterium isolated from sludge. Int J Syst Evol Microbiol 2016; 66:2335-2341. [PMID: 27001671 DOI: 10.1099/ijsem.0.001034] [Citation(s) in RCA: 22] [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] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, coccoid to small rod-shaped bacterium, designated X1T, was isolated from sludge collected from the vicinity of a pesticide manufacturer in Nantong, Jiangsu Province, China. Based on 16S rRNA gene sequence analysis, strain X1T belonged to the genus Cupriavidus, and was most closely related to Cupriavidus taiwanensis LMG 19424T (99.1 % 16S rRNA gene sequence similarity) and Cupriavidus alkaliphilus LMG 26294T (98.9 %). Strain X1T showed 16S rRNA gene sequence similarities of 97.2-98.2 % with other species of the genus Cupriavidus. The major cellular fatty acids of strain X1T were C16 : 0, C16 : 1ω7c and/or iso-C15 : 0 2-OH (summed feature 3), C18 : 1ω7c and C17 : 0 cyclo, and the major respiratory quinone was ubiquinone Q-8. The major polar lipids of strain X1T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, aminophospholipid, phospholipid and hydroxyphosphatidylethanolamine. The DNA G+C content was 66.6 mol%. The DNA-DNA relatedness values of strain X1T with the five reference strains C. taiwanensis LMG 19424T, C. alkaliphilus LMG 26294T, Cupriavidus necator LMG 8453T, Cupriavidus gilardii LMG 5886T and 'Cupriavidus yeoncheonense' KCTC 42053 were lower than 70 %. The results obtained from phylogenetic analysis, phenotypic characterization and DNA-DNA hybridization indicated that strain X1T should be proposed to represent a novel species of the genus Cupriavidus, for which the name Cupriavidus nantongensis sp. nov. is proposed. The type strain is X1T (=KCTC 42909T=LMG 29218T).
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Affiliation(s)
- Le-Ni Sun
- School of Life Science, Anhui Agricultural University, Hefei 230036, PR China
| | - Dao-Sheng Wang
- School of Life Science, Anhui Agricultural University, Hefei 230036, PR China
| | - En-Dong Yang
- School of Life Science, Anhui Agricultural University, Hefei 230036, PR China
| | - Lian-Cheng Fang
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, PR China
| | - Yi-Fei Chen
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, PR China
| | - Xin-Yun Tang
- School of Life Science, Anhui Agricultural University, Hefei 230036, PR China
| | - Ri-Mao Hua
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, PR China
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Singh P, Kim Y, Nguyen N, Hoang V, Sukweenadhi J, Farh ME, Yang D. Cupriavidus yeoncheonense sp. nov., isolated from soil of ginseng. Antonie van Leeuwenhoek 2015; 107:749-58. [DOI: 10.1007/s10482-014-0369-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 12/23/2014] [Indexed: 10/24/2022]
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Estrada-de los Santos P, Solano-Rodríguez R, Matsumura-Paz LT, Vásquez-Murrieta MS, Martínez-Aguilar L. Cupriavidus plantarum sp. nov., a plant-associated species. Arch Microbiol 2014; 196:811-7. [DOI: 10.1007/s00203-014-1018-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 07/13/2014] [Accepted: 07/15/2014] [Indexed: 11/25/2022]
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Borewicz K, Pragman AA, Kim HB, Hertz M, Wendt C, Isaacson RE. Longitudinal analysis of the lung microbiome in lung transplantation. FEMS Microbiol Lett 2013; 339:57-65. [PMID: 23173619 PMCID: PMC3546157 DOI: 10.1111/1574-6968.12053] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [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: 09/07/2012] [Revised: 10/27/2012] [Accepted: 11/17/2012] [Indexed: 01/30/2023] Open
Abstract
Lung transplant recipients experience poor long-term survival, largely due to chronic rejection. The pathogenesis of chronic rejection is incompletely understood, but bacterial colonization of the lung is associated with chronic rejection, while antibiotic use slows its progression. The lung harbors a bacterial community, termed the microbiome, which is present both in health and disease. We hypothesize that the lung microbiome will change following transplantation, and these changes may correspond to the development of rejection. Twelve bronchoalveolar lavage fluid (BALF) samples were obtained from four patients at three time points after transplantation, and two BALF samples were obtained from healthy, nontransplant controls. The microbiome of each sample was determined by pyrosequencing the 16S rRNA gene hypervariable 3 region. The data were analyzed using mothur, Ribosomal Database Project Classifier, Fast UniFrac, and Metastats. Transplanted lungs contained more bacterial sequences and demonstrated more microbial diversity than did control lungs. Bacteria in the phyla Proteobacteria (class Betaproteobacteria) predominated in the transplant samples. In contrast, the microbiome of the healthy lung consisted of the phyla Proteobacteria (class Gammaproteobacteria) and Firmicutes. The microbiome of the transplanted lung is vastly different from that of healthy lungs, mainly due to the presence of the family Burkholderiaceae in transplant samples.
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Affiliation(s)
- Klaudyna Borewicz
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN, USA and
| | - Alexa A. Pragman
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Hyeun Bum Kim
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN, USA and
| | - Marshall Hertz
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Christine Wendt
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
- Department of Medicine, VA Medical Center, Minneapolis, MN USA
| | - Richard E. Isaacson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN, USA and
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Estrada-de los Santos P, Martínez-Aguilar L, López-Lara IM, Caballero-Mellado J. Cupriavidus alkaliphilus sp. nov., a new species associated with agricultural plants that grow in alkaline soils. Syst Appl Microbiol 2012; 35:310-4. [DOI: 10.1016/j.syapm.2012.05.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 04/04/2012] [Accepted: 05/25/2012] [Indexed: 11/25/2022]
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