16S rRNA as an applied tool in the molecular characterization of genera and species of bacteria
ARNr 16S como herramienta aplicada en la caracterización molecular de géneros y especies de bacterias
Article Sidebar
Ver / Descargar
PDF (Español (España))
FLIP
HTML (Español (España))
How to Cite
Suárez-Contreras, L. Y. ., & Yañez-Meneses , L. F. . (2020). 16S rRNA as an applied tool in the molecular characterization of genera and species of bacteria. Respuestas, 25(1), 127–137. https://doi.org/10.22463/0122820X.2430
More Citation Formats
Issue
Section
Investigation articles
License Terms
(SEE)
Main Article Content
Abstract
Bacterial identification is carried out by conventional methods based on phenotypic characteristics, since their implementation and costs are more easily accessible. However, molecular identification allows us to know the true identity of the genus and species. The molecular identification of 24 bacterial strains preserved in the Strain Bank of the University Francisco de Paula Santander, Campos Eliseos Experimental Center, identified under macroscopic and microscopic phenotypic criteria, was carried out. Initially, the strains preserved in saline solution were reactivated and characterized macro- and microscopically, then DNA extraction was performed and PCR was done to amplify the 16S rRNA region allowing access to the DNA sequence of interest; the samples were sent to be sequenced and through bioinformatic tools the identity of each bacterium was known. The strains: BLB003, BLB009, BLB011, BLB012, BLB014, BLB016, BLB018, BLB022, BLB023, BLB024, BLB033, were identified as Bacillus cereus; BLB010 as Bacillus thurigiensis; while BLB030, BLB031, BLB032, as Bacillus pumilus; BLB020 as Bacillus amyloliquefaciens; BLB001, BLB004, BLB007, and BLB037, formed the group of Bacillus subtilis; and it is possible that there are divergent ramifications between species of Bacillus in phylogenetic trees. Another grouping that was observed in the phylogenetic tree are the strains BLB019 and BLB029 that correspond to Achromobacter xylosoxidans and Alcaligenes faecalis respectively. Also another group BLB013 and BLB017, were identified as Stenotrophomonas maltophilia. It is important to take into account that sometimes 16S rRNA presents a low discrimination capacity for some genera and species due to recent divergences, it is necessary to complement the identification with the study of other genes.
Keywords
Downloads
Download data is not yet available.
Article Details
References
C. Pizano, R. González, R. López, R. Jurado, H. Cuadros, A. Castaño, A. Rojas, K. Pérez, H. Vergara, A. Idárraga, P. Isaacs-Cubides and H. García, “El bosque seco tropical en Colombia: Distribución y estado de conservación”, 2016.
G. Bou, A. Fernández, C. Garcia, J. Sáenz and S. Valdezcate, “Métodos de identificación bacteriana en el laboratorio de microbiología”, Enfermedades infecciosas y microbiología clínica, vol. 29, no. 8, pp. 601-608, 2011.
M. Godoy, L. Orozco, C. Hernández, O. DaMatac, J. De Waard and S. González, “Identificación de micobacterias no tuberculosas: comparación de métodos bioquímicos y moleculares”, Revista de la Sociedad Venezolana de Microbiología, vol. 28, no. 2, pp. 96-104, 2008.
J. Clarridge, “Impact of 16S rRNA Gene Sequence Analysis for Identification of Bacteria on Clinical Microbiology and Infectious Diseases”, Clinical Microbiology Reviews, vol. 17, no. 4, 840-862, 2004.
O. Fernández, C. García de la Fuente, J. Saéz Nieto and S. Valdezate, “Metodos de identificación bacteriana en el laboratorio de Microbiología”. España: SEIMC. 2010.
F. Rohwer, M. Breitbart, J. Jara, F. Azam and N. Knowlton, “Diversity of bacteria associated with the Caribbean coral Montastraea franksi”, Coral Reefs, vol. 20, 85-91, 2001.
M. Peña-Hidalgo, C. Dávila-Flores, Á. Tresierra-Ayala and J. Castro-Gómez, “Identificación molecular de Escherichia coli enterotoxigénica en niños con infecciones diarreicas agudas mediante la Reacción en Cadena de la Polimerasa”, Ciencia Amazonica, vol. 4, no. 2, pp. 117-122, 2014.
R. Devereux and S. Willis, “Amplification of ribosomal RNA sequences. En A. Akkermans, J. Van Elsas, & F. De Bruijn”, Molecular Microbial Ecology Manual, pp. 277-287, 2004.
L. Márquez, A. Serrato and R. Cerritos, “Secuenciación de fragmentos de ADN”, Herramientas moleculares aplicadas en ecología: Aspectos teóricos y prácticos, 2014. http://www2.inecc.gob.mx/publicaciones/libros/710/se cuenciacion.pdf.
Baker, G., S. J., & Cowan, D. Review and re-analysis of domain-specific 16S primers. Journal of Microbiological Methods, 541-555. doi:https://doi.org/10.1016/j.mimet.2003.08.009. (2003).
Carter, I., Schuller, M., James, G., S. T., & Halliday, C. PCR for Clinical Microbiology. En I. Carter, M. Schuller, G. James, S. T., & C. Halliday, PCR for Clinical Microbiology: An Australian and International Perspective (págs. 1-438). Springer. doi:10.1007/978-90-481-9039-3. (2010).
Priest, F., Barker, M., Baillie, L., Holmes, E., & Maiden, M. Population Structure and Evolution of the Bacillus cereus Group. Journal of Bacteriology, 7959-7970. (2004).
Schoen, J., & Wong, A. l. Bacillus cereus Food Poisoning and Its Toxins. Journal food protection. 2005.
Lechner, S., Mayr, R., Francis, K., Prüss, B., Kaplan, T., Wiessner-Gunkel, E., . . . Scherer, S. Bacillus weihenstephanensis sp. nov. is a new psychrotolerant species of the Bacillus cereus group. International journal of systematic bacteriology. 1998.
Klenk, H., Lapidus, A., Chertkov, O., Copeland, A., Rio, D., M, T. N., . . .otros., &. y. Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Raine. Standards in Genomic Sciences, 121-34. (2011).
Bhandari, V., Ahmod, N., Shah, H., & Gupta, R. Molecular signatures for Bacillus species: demarcation of the Bacillus subtilis and Bacillus cereus clades in molecular terms and proposal to limit the placement of new species into the genus Bacillus. International Journal of Systematic and Evolutionary Microbiology, 2712–2726. (2013).
Gordon, R., Haynes, W., & Pang, C. The genus Bacillus. En R. Gordon, W. Haynes, & C. Pang, Agriculture handbook (págs. 36-41). Agricultural Research Servic. (1973).
Rooney, A., Price, N., Ehrhardt, C., Swezey, J., & Bannan, J. Phylogeny and molecular taxonomy of the Bacillus subtilis species complex and description of Bacillus subtilis subsp. inaquosorum subsp. nov. Internationa Journal of Systematic and Evolutionary Microbiology, 2429-2436. (2009).
Jeyaram, K., Romi, W., Singh, T., Adewumi, G., Basanti, K., & Oguntoyinbo, F. Distinct differentiation of closely related species of Bacillus subtilis group with industrial importance. Journal of Microbiology Methods, 161-164. (2011).
Wang, L., Lee, F., Tai, C., & Kasai, H. Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA-DNA hybridization in the Bacillus subtilis group. International Journal of Systematic and Evolutionary Microbiology, 1846-1850. (2007).
Sicuia, A., Florica, C., & Cornea, C. Biodiversity of Bacillus subtilis group and beneficial traits of Bacillus species useful in plant protection. Romanian Biotechnological Letters , 10737-50. (2015).
De Ley, J., Segers, P., Kersters, K., Mannheim, W., & Lievens, A. Intra- and Intergeneric Similarities of the Bordetella Ribosomal Ribonucleic Acid Cistrons: Proposal for a New Family, Alcaligenaceae. International Journal of Systematic and Evolutionary Microbiology, 405-414. (1986).
Blümel, S., Mark, B., Busse, H., Kämpfer, P., & Stolz, A. Pigmentiphaga kullae gen. nov., sp. nov., a novel member of the family Alcaligenaceae with the ability to decolorize azo dyes aerobically. International Jorunal of Systematic and Evolutionary Microbiology, 1867-1871. (2001).
Brenner, D., Krieg, N., & Staley, J. Genus II. Achromobacter Yabuuchi and Yano 1981, 477VP emend. In Bergey’s Manual of Systematic Bacteriology, (pp. 658-662). Springer. 2005.
Yabuuchi, E., Kawamura, Y., Kosako, Y., & Ezaki, T. Emendation of genus Achromobacter and Achromobacter xylosoxidans (Yabuuchi and Yano) and proposal of Achromobacter ruhlandii (Packer and Vishniac) comb. nov., Achromobacter piechaudii comb. nov., and Achromobacter xylosoxidans subsp. dedenitrificans. Microbiology and Immunology, 429.438. (1998).
Coenye, T., Vancanneyt, M., Falsen, E., Swings, J., & Vandamme, P. Achromobacter insolitus sp. nov. and Achromobacter spanius sp. nov., from human clinical samples. International Journal of Systematic and Evolutionary Microbiology, 1819-1824. (2003).
Gomila, M., Prince-Manzano, C., Svensson-Stadler, L., Busquets, A., Erhard, M., Martínez, D., . . . Moore, E. Genotypic and Phenotypic Applications for the Differentiation and Species-Level Identification of Achromobacter for Clinical Diagnoses. PloS One, 1-22. (2014).
Vandamme, P., Moore, E., Cnockaert, M., De Brandt, E., Svensson-Stadler, L., Houf, K., & Spilker, T. L. Achromobacter animicus sp. nov., Achromobacter mucicolens sp. nov., Achromobacter pulmonis sp. nov. and Achromobacter spiritinus sp. nov., from human clinical samples. Systematic and applied Microbiology, 1-10. (2013).
Vandamme, P., Moore, E., Cnockaert, M., Peeters, C., Svensson-Stadler, L., Houf, K., .. . JJ., L. Classification of Achromobacter genogroups 2, 5, 7 and 14 as Achromobacter insuavis sp. nov.,. Systematic and applied Microbiology, 474-81. (2014).
Hugh, R., & Leifson, E. A description of the type strain of Pseudomonas maltophilia. International Journal of Systematic and Evolutionary Microbiology, 133-138. (1963).
Swings, J., De vos, P., Van Den Mooter, M., & & De Ley, J. Transfer of Pseudomonas rnaltophilia Hugh 1981 to the Genus Xanthomonas as Xanthomonas maltophilia (Hugh 1981) comb. nov. International Journey of Systematic and Evolutionary Microbiology, 409-413. (1983).
Palleroni, N., & Bradbury, J. Stenotrophomonas, a new bacterial genus for Xanthomonas maltophilia (Hugh 1980) Swings et al. 1983. International Journal of Systematic Bacteriology, 606-609. (1993).
Finkmann, W., Altendorf, K., Stackebrandt, E., & Lipski, A. Characterization of N20-producing Xanthomonas like isolates from biofilters as Stenotrophomonas nitritireducens sp. nov., Luteimonas mephitis gen. nov., sp. nov. and Pseudoxanthomonas broegbernensis gen. nov., sp. nov. International Journal of Systematic and Evolutionary Microbiology, 273-282. (2000).
Wolf, A., Fritze, A., Hagemann, M., & Berg, G. Stenotrophomonas rhizophila sp. nov., a novel plant-associated bacterium with antifungal properties. International Journal of Systematic and Evolutionary Microbiology, 1937-1944. (2002).
Yang, H., Im, W., Kang, M., Shin, D., & Lee, S. Stenotrophomonas koreensis sp. nov., isolated from compost in South Korea. International Journal of Systematic and Evolutionary Microbiology, 81-4. (2006).
Heylen, K., Vanparys, B., Peirsegaele, F., Lebbe, L., & De Vos, P. Stenotrophomonas terrae sp. nov. and Stenotrophomonas humi sp. nov., two nitrate-reducing bacteria isolated from soil. International Journal of Systematic and Evolutionary Microbiology, 2056-61. (2007).
Kaparullina, E., Doronina, N., Chistyakova, T., & Trotsenko, Y. Stenotrophomonas chelatiphaga sp. nov., a new aerobic EDTA-degrading bacterium. Systematic and Applied Microbiology, 157-62. (2009).
Kim, H., Srinivasan, S., Sathiyaraj, G., Quan, L., Kim, S., Bui, T., . . . Yang, D. Stenotrophomonas ginsengisoli sp. nov., isolated from a ginseng field. international Journal of Systematic and Evolutionary Microbiology, 1522-6. (2010).
Pinot, C., Deredjian, A., Nazaret, S., Brothier, B., Cournoyer, B., Segonds, C., & S. Favre-Bonte, S. Identification of Stenotrophomonas maltophilia strains isolated from environmental and clinical samples: a rapid and efficient procedure. Journal of Applied Microbiology, 1185-1193. (2011).
G. Bou, A. Fernández, C. Garcia, J. Sáenz and S. Valdezcate, “Métodos de identificación bacteriana en el laboratorio de microbiología”, Enfermedades infecciosas y microbiología clínica, vol. 29, no. 8, pp. 601-608, 2011.
M. Godoy, L. Orozco, C. Hernández, O. DaMatac, J. De Waard and S. González, “Identificación de micobacterias no tuberculosas: comparación de métodos bioquímicos y moleculares”, Revista de la Sociedad Venezolana de Microbiología, vol. 28, no. 2, pp. 96-104, 2008.
J. Clarridge, “Impact of 16S rRNA Gene Sequence Analysis for Identification of Bacteria on Clinical Microbiology and Infectious Diseases”, Clinical Microbiology Reviews, vol. 17, no. 4, 840-862, 2004.
O. Fernández, C. García de la Fuente, J. Saéz Nieto and S. Valdezate, “Metodos de identificación bacteriana en el laboratorio de Microbiología”. España: SEIMC. 2010.
F. Rohwer, M. Breitbart, J. Jara, F. Azam and N. Knowlton, “Diversity of bacteria associated with the Caribbean coral Montastraea franksi”, Coral Reefs, vol. 20, 85-91, 2001.
M. Peña-Hidalgo, C. Dávila-Flores, Á. Tresierra-Ayala and J. Castro-Gómez, “Identificación molecular de Escherichia coli enterotoxigénica en niños con infecciones diarreicas agudas mediante la Reacción en Cadena de la Polimerasa”, Ciencia Amazonica, vol. 4, no. 2, pp. 117-122, 2014.
R. Devereux and S. Willis, “Amplification of ribosomal RNA sequences. En A. Akkermans, J. Van Elsas, & F. De Bruijn”, Molecular Microbial Ecology Manual, pp. 277-287, 2004.
L. Márquez, A. Serrato and R. Cerritos, “Secuenciación de fragmentos de ADN”, Herramientas moleculares aplicadas en ecología: Aspectos teóricos y prácticos, 2014. http://www2.inecc.gob.mx/publicaciones/libros/710/se cuenciacion.pdf.
Baker, G., S. J., & Cowan, D. Review and re-analysis of domain-specific 16S primers. Journal of Microbiological Methods, 541-555. doi:https://doi.org/10.1016/j.mimet.2003.08.009. (2003).
Carter, I., Schuller, M., James, G., S. T., & Halliday, C. PCR for Clinical Microbiology. En I. Carter, M. Schuller, G. James, S. T., & C. Halliday, PCR for Clinical Microbiology: An Australian and International Perspective (págs. 1-438). Springer. doi:10.1007/978-90-481-9039-3. (2010).
Priest, F., Barker, M., Baillie, L., Holmes, E., & Maiden, M. Population Structure and Evolution of the Bacillus cereus Group. Journal of Bacteriology, 7959-7970. (2004).
Schoen, J., & Wong, A. l. Bacillus cereus Food Poisoning and Its Toxins. Journal food protection. 2005.
Lechner, S., Mayr, R., Francis, K., Prüss, B., Kaplan, T., Wiessner-Gunkel, E., . . . Scherer, S. Bacillus weihenstephanensis sp. nov. is a new psychrotolerant species of the Bacillus cereus group. International journal of systematic bacteriology. 1998.
Klenk, H., Lapidus, A., Chertkov, O., Copeland, A., Rio, D., M, T. N., . . .otros., &. y. Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Raine. Standards in Genomic Sciences, 121-34. (2011).
Bhandari, V., Ahmod, N., Shah, H., & Gupta, R. Molecular signatures for Bacillus species: demarcation of the Bacillus subtilis and Bacillus cereus clades in molecular terms and proposal to limit the placement of new species into the genus Bacillus. International Journal of Systematic and Evolutionary Microbiology, 2712–2726. (2013).
Gordon, R., Haynes, W., & Pang, C. The genus Bacillus. En R. Gordon, W. Haynes, & C. Pang, Agriculture handbook (págs. 36-41). Agricultural Research Servic. (1973).
Rooney, A., Price, N., Ehrhardt, C., Swezey, J., & Bannan, J. Phylogeny and molecular taxonomy of the Bacillus subtilis species complex and description of Bacillus subtilis subsp. inaquosorum subsp. nov. Internationa Journal of Systematic and Evolutionary Microbiology, 2429-2436. (2009).
Jeyaram, K., Romi, W., Singh, T., Adewumi, G., Basanti, K., & Oguntoyinbo, F. Distinct differentiation of closely related species of Bacillus subtilis group with industrial importance. Journal of Microbiology Methods, 161-164. (2011).
Wang, L., Lee, F., Tai, C., & Kasai, H. Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA-DNA hybridization in the Bacillus subtilis group. International Journal of Systematic and Evolutionary Microbiology, 1846-1850. (2007).
Sicuia, A., Florica, C., & Cornea, C. Biodiversity of Bacillus subtilis group and beneficial traits of Bacillus species useful in plant protection. Romanian Biotechnological Letters , 10737-50. (2015).
De Ley, J., Segers, P., Kersters, K., Mannheim, W., & Lievens, A. Intra- and Intergeneric Similarities of the Bordetella Ribosomal Ribonucleic Acid Cistrons: Proposal for a New Family, Alcaligenaceae. International Journal of Systematic and Evolutionary Microbiology, 405-414. (1986).
Blümel, S., Mark, B., Busse, H., Kämpfer, P., & Stolz, A. Pigmentiphaga kullae gen. nov., sp. nov., a novel member of the family Alcaligenaceae with the ability to decolorize azo dyes aerobically. International Jorunal of Systematic and Evolutionary Microbiology, 1867-1871. (2001).
Brenner, D., Krieg, N., & Staley, J. Genus II. Achromobacter Yabuuchi and Yano 1981, 477VP emend. In Bergey’s Manual of Systematic Bacteriology, (pp. 658-662). Springer. 2005.
Yabuuchi, E., Kawamura, Y., Kosako, Y., & Ezaki, T. Emendation of genus Achromobacter and Achromobacter xylosoxidans (Yabuuchi and Yano) and proposal of Achromobacter ruhlandii (Packer and Vishniac) comb. nov., Achromobacter piechaudii comb. nov., and Achromobacter xylosoxidans subsp. dedenitrificans. Microbiology and Immunology, 429.438. (1998).
Coenye, T., Vancanneyt, M., Falsen, E., Swings, J., & Vandamme, P. Achromobacter insolitus sp. nov. and Achromobacter spanius sp. nov., from human clinical samples. International Journal of Systematic and Evolutionary Microbiology, 1819-1824. (2003).
Gomila, M., Prince-Manzano, C., Svensson-Stadler, L., Busquets, A., Erhard, M., Martínez, D., . . . Moore, E. Genotypic and Phenotypic Applications for the Differentiation and Species-Level Identification of Achromobacter for Clinical Diagnoses. PloS One, 1-22. (2014).
Vandamme, P., Moore, E., Cnockaert, M., De Brandt, E., Svensson-Stadler, L., Houf, K., & Spilker, T. L. Achromobacter animicus sp. nov., Achromobacter mucicolens sp. nov., Achromobacter pulmonis sp. nov. and Achromobacter spiritinus sp. nov., from human clinical samples. Systematic and applied Microbiology, 1-10. (2013).
Vandamme, P., Moore, E., Cnockaert, M., Peeters, C., Svensson-Stadler, L., Houf, K., .. . JJ., L. Classification of Achromobacter genogroups 2, 5, 7 and 14 as Achromobacter insuavis sp. nov.,. Systematic and applied Microbiology, 474-81. (2014).
Hugh, R., & Leifson, E. A description of the type strain of Pseudomonas maltophilia. International Journal of Systematic and Evolutionary Microbiology, 133-138. (1963).
Swings, J., De vos, P., Van Den Mooter, M., & & De Ley, J. Transfer of Pseudomonas rnaltophilia Hugh 1981 to the Genus Xanthomonas as Xanthomonas maltophilia (Hugh 1981) comb. nov. International Journey of Systematic and Evolutionary Microbiology, 409-413. (1983).
Palleroni, N., & Bradbury, J. Stenotrophomonas, a new bacterial genus for Xanthomonas maltophilia (Hugh 1980) Swings et al. 1983. International Journal of Systematic Bacteriology, 606-609. (1993).
Finkmann, W., Altendorf, K., Stackebrandt, E., & Lipski, A. Characterization of N20-producing Xanthomonas like isolates from biofilters as Stenotrophomonas nitritireducens sp. nov., Luteimonas mephitis gen. nov., sp. nov. and Pseudoxanthomonas broegbernensis gen. nov., sp. nov. International Journal of Systematic and Evolutionary Microbiology, 273-282. (2000).
Wolf, A., Fritze, A., Hagemann, M., & Berg, G. Stenotrophomonas rhizophila sp. nov., a novel plant-associated bacterium with antifungal properties. International Journal of Systematic and Evolutionary Microbiology, 1937-1944. (2002).
Yang, H., Im, W., Kang, M., Shin, D., & Lee, S. Stenotrophomonas koreensis sp. nov., isolated from compost in South Korea. International Journal of Systematic and Evolutionary Microbiology, 81-4. (2006).
Heylen, K., Vanparys, B., Peirsegaele, F., Lebbe, L., & De Vos, P. Stenotrophomonas terrae sp. nov. and Stenotrophomonas humi sp. nov., two nitrate-reducing bacteria isolated from soil. International Journal of Systematic and Evolutionary Microbiology, 2056-61. (2007).
Kaparullina, E., Doronina, N., Chistyakova, T., & Trotsenko, Y. Stenotrophomonas chelatiphaga sp. nov., a new aerobic EDTA-degrading bacterium. Systematic and Applied Microbiology, 157-62. (2009).
Kim, H., Srinivasan, S., Sathiyaraj, G., Quan, L., Kim, S., Bui, T., . . . Yang, D. Stenotrophomonas ginsengisoli sp. nov., isolated from a ginseng field. international Journal of Systematic and Evolutionary Microbiology, 1522-6. (2010).
Pinot, C., Deredjian, A., Nazaret, S., Brothier, B., Cournoyer, B., Segonds, C., & S. Favre-Bonte, S. Identification of Stenotrophomonas maltophilia strains isolated from environmental and clinical samples: a rapid and efficient procedure. Journal of Applied Microbiology, 1185-1193. (2011).
