Caracterización de bacterias ruminales en novillos Nelore en pastoreo
DOI:
https://doi.org/10.17533/udea.rccp.v32n4a01Palabras clave:
bacterias ruminales, Cynodon spp, diversidad bacteriana, Firmicutes, Nelore, novillos, microorganismos ruminales, rumiante, secuenciación genética, secuenciación de última generación, ZebúResumen
Antecedentes: Los microorganismos ruminales han desarrollado una serie de interacciones complejas que representan uno de los mejores ejemplos de simbiosis entre microorganismos en la naturaleza. Los métodos taxonómicos tradicionales basados en técnicas de cultivo están siendo reemplazados por técnicas moleculares debido a su mayor velocidad y precisión. Objetivo: Caracterizar la diversidad bacteriana ruminal de novillos Nelore mantenidos en pasturas tropicales mediante la secuenciación del gen 16S RNA utilizando la plataforma de secuenciación Illumina. Métodos: Se utilizaron tres novillos Nelore fistulados en el rumen. Las fracciones líquida y sólida del contenido ruminal fueron procesadas para la extracción del DNA meta genómico y las regiones hipervariables VI y V2 del gen 16S rRNA fueron secuenciadas usando la plataforma Illumina. Resultados: En total, se generaron 11.407.000 lecturas de calidad adecuada, y en el nivel de especie se encontraron 812 unidades taxonómicas operacionales (OTUs). Se identificaron veintisiete filos, predominantemente Firmicutes (23%), Bacteroidetes (14%), Proteobacteria (10%), Spirochaetes (9%), Fibrobacteres (7%), Tenericutes (5%) y Actinobacteria (2%), los cuales representaron el 70% de los filos identificados en el contenido ruminal. Conclusión: El ambiente ruminal de novillos Nelore en pastoreo presenta una alta diversidad de bacterias, con dominancia de los filos Firmicutes, Bacteroidetes, Proteobacteria, Spirochaetes y Fibrobacteres.
Descargas
Citas
Amann RI, Ludwig W, Schleifer KH. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 1995; 59:143–149.
Attwood GT, Reilly K. Identification of proteolytic rumen bacteria isolated from New Zealand cattle. J Appl Bacteriol 1995; 79(1):22-29. doi:10.1111/j.1365-2672.1995.tb03119.x
Attwood GT, Reilly K, Patel BK. Clostridium proteoclasticum sp. nov., a novel proteolytic bacterium from the bovine rumen. Int J Syst Bacteriol 1996; 46(3):753-758. doi:10.1099/00207713-46-3-753
Briesacher SL, May T, Grigsby KN, Kerley MS, Anthony RV, Paterson JA. Use of DNA probes to monitor nutritional effects on ruminal prokaryotes and Fibrobacter succinogenes S85. J Anim Sci 1992; 70(1):289-295. doi:10.2527/1992.701289x
Bryant MP, Small N. The anaerobic monotrichous butyric acid-producing curved rod-shaped bacteria of the rumen. J Bacteriol 1956; 72(1):16-21.
Carvalho IPC, Fiorentini G, Castagnino PS, Jesus RB, Messana JD, Granja-Salcedo YT, Detman E, Padmanabha J, McSweeney CS, Berchielli TT. Supplementation with lipid sources alters the ruminal fermentation and duodenal flow of fatty acids in grazing Nellore steers. Anim Feed Sci Technol 2017; 227:142-153. doi:10.1016/j.anifeedsci.2017.02.017
Chao A. Estimating the population size for capture-recapture data with unequal catchability. Biometrics 1987; 43(4):783-791.
Cirne DG, Delgado OD, Marichamy S, Mattiasson B. Clostridium lundense sp. nov., a novel anaerobic lipolytic bacterium isolated from bovine rumen. Int J Syst Evol Microbiol 2006; 56(Pt3):625-628. doi:10.1099/ijs.0.63730-0
Cole JR, Wang Q, Fish JA, Chai B, McGarrel DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 2014; 42:633-642. doi:10.1093/nar/gkt1244
Coppi MV, Leang C, Sandler SJ, Lovley DR. Development of a Genetic System for Geobacter sulfurreducens. Appl Environ Microbiol 2001; 67(7):3180-3187. doi:10.1128/AEM.67.7.3180-3187.2001
Cotta MA. Interaction of ruminal bacteria in the production and utilization of maltooligosaccharides from starch. Appl Environ Microbiol 1992; 58(1):48-54.
Deng W,Xi D, Mao H, Wanapat M. The use of molecular techniques based on ribosomal RNA and DNA for rumen microbial ecosystem studies: a review. Mol Biol Rep 2008; 35(2):265-74. doi:10.1007%2Fs11033-007-9079-1
Flint HJ, Scott KP, Duncan SH, Louis P, Forano E. Microbial degradation of complex carbohydrates in the gut. Gut Microbes 2012; 3(4):289-306. doi:10.4161/gmic.19897
Gillis M, Vandamme P, Vos PD, Swings J, Kersters K. Polyphasic taxonomy. In: Boone DR, Castenholz RW, Garrity GM, editors. The archaea and the deeply branching and phototrophic bacteria. New York: Springer-Verlag 2001:43-47.
Granja-Salcedo YT, Ramirez-Uscategui RA, Machado EG, Duarte Messana J, Takeshi Kishi L, Lino Dias AV, Berchielli TT. Studies on bacterial community composition are affected by the time and storage method of the rumen content. PLoS ONE 2017; 12(4): e0176701. doi:10.1371/journal.pone.0176701
Henderson G, Cox F, Ganesh S, Jonker A, Young W, Global Rumen Census Collaborators, Janssen P. Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Sci Rep 2015; 5: 14567. doi:10.1038/srep14567
Hill GM, Gates RN, Burton GW. Forage quality and grazing steer performance from Tifton 85 and Tifton 78 bermudagrass pastures. J Anim Sci 1993; 71(12):3219–3225. doi:10.2527/1993.71123219x
Kim M, Morrison M, Yu Z. Status of the phylogenetic diversity census of ruminal microbiomes. FEMS Microbiol Ecol 2011; 76(1):49-63. doi:10.1111/j.1574-6941.2010.01029.x
Kobayashi Y, Shinkai T, Koike S. Ecological and physiological characterization shows that Fibrobacter succinogenes is important in rumen fiber digestion - review. Folia Microbiol (Praha). 2008; 53(3):195-200. doi:10.1007%2Fs12223-008-0024-z
Li RW, Wu S, Baldwin RLT, Li W, Li C. Perturbation dynamics of the rumen microbiota in response to exogenous butyrate. Plos One 2012; 7(1):e29392. doi:10.1371/journal.pone.0029392
Ling LY, Zhang Z, Wu M, Wu Y, Xun FJ. Isolation, screening, and identification of cellulolytic bacteria from natural reserves in the subtropical region of China and optimization of cellulase production by Paenibacillus terrae ME27-1. Biomed Res Int 2014;13. doi:10.1155/2014/512497
Lovley DR. Fe(III)- and Mn(IV)-reducing prokaryotes. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E, editors. The prokaryotes, in press. New York: Springer-Verlag, Inc.; 2000.
MAPA—Ministério da Agricultura, Pecuária e Abastecimento, 2016; [access date: Jan 2016] URL:http://www.agricultura.gov.br/animal/especies/bovinos-e-bubalinos/
Magurran AE. Measuring biological diversity. Oxford, UK: Blackwell Publishing; 2004.
McAllister TA, Cheng KJ, Rode LM, Forsberg CW. Digestion of barley, maize, and wheat by selected species of ruminal bacteria. Appl Environ Microbiol 1990;56(10):3146-3153.
McCann JC, Wiley LM, Forbes TB, Rouquette Jr FM, Tedeschi LO. Relationship between the Rumen Microbiome and Residual Feed Intake-Efficiency of Brahman Bulls Stocked on Bermudagrass Pastures. Plos One 2014; 9:3 e91864. doi:10.1371/journal.pone.0091864
Murray RGE. Bacterial diversity. In: Atlas RM, editors. Principles of Microbiology. New York: Mc Graw-Hill; 1997:1056-1097.
Neto AJ, Messana JD, Granja-Salcedo YT, Castagnino PS, Fiorentini G, Reis RA, Berchielli TT. Effect of starch level in supplement with or without oil source on diet and apparent digestibility, rumen fermentation and microbial population of Nellore steers grazing tropical grass. Liv Sci 2017; 202:171-179. doi:10.1016/j.livsci.2017.06.007
Oliveira MN, Jewell KA, Freitas FS, Benjamin LA, Toâtola MR, Borges AC, Moraes CA, Suen G. Characterizing the microbiota across the gastrointestinal tract of a Brazilian Nelore steer. Vet Microbiol 2013; 28(3-4):307-314. doi:10.1016/j.vetmic.2013.02.013
Pandya PR, Singh KM, Parnerkar S, Tripathi AK, Mehta HH, Rank DN, Kothari RK, CG Joshi. Bacterial diversity in the rumen of Indian Surti buffalo (Bubalus bubalis), assessed by 16S rDNA analysis. J Appl Genet 2010; 51(3):395-402. doi:10.1007/2FBF03208869
Pittman KA, MP Bryant. Peptides and Other Nitrogen Sources for Growth of Bacteroides Ruminicola. J Bacteriol 1964; 88:401-410.
Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glockner FO. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 2007; 35(21):7188-7196. doi:10.1093/nar/gkm864
Reis RA, Ruggieri AC, Casagrande DR, Pascoa AG. Suplementação como estratégia do manejo das pastagens. Brazilian journal of animal science 2009; 38 Suppl: 147-159. doi/10.1590/S1516-35982009001300016
Russell JB. Fermentation of peptides by Bacteroides ruminicola B14. Appl Environ Microbiol 1983; 45:1566-1574.
San Vito E, Messana JD, Castagnino PS, Granja-Salcedo YT, Dallantoina EE, Berchielli TT. Effect of crude glycerin in supplement on the intake, rumen fermentation, and microbial profile of Nellore steers grazing tropical grass. Liv Sci 2016; 192:17-24. doi:10.1016/j.livsci.2016.08.011
Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 2011; 27(6):863+864. doi:10.1093/bioinformatics/btr026
Sijpestejin AK. Cellulose-decomposing bacteria from the rumen of cattle. Antonie Van Leeuwenhoek 1949; 15(1949):49-52.
Stanton TB, Canale-Parola E. Treponema bryantii sp. nov., a rumen spirochete that interacts with cellulolytic bacteria. Archives of Microbiology 1980; 127(2):145-156.
Sylvester JT, Karnati SK, Yu Z, Morrison M, Firkins JL. Development of an assay to quantify rumen ciliate protozoal biomass in cows using real-time PCR. Nutr J 2004; 134(12):3378-3384. doi:10.1093/jn/134.12.3378
Tajima K, Aminov RI, Nagamine T, Ogata K, Nakamura M, Matsui H, Benno Y. Rumen bacterial diversity as determined by sequence analysis of 16S rDNA libraries.FEMS Microbiol Ecol 1999; 29(2):159-169. doi:10.1016/S0168-6496(99)00008-2
Van Gylswyk NO. Enumeration and presumptive identification of some functional groups of bacteria in the rumen of dairy cows fed grass silage-based diets. FEMS Microbiol Lett 1990; 73:243-253.
Vandamme P, Pot B, Gillis M, Vos PD, Kersters K, Swings J. Polyphasic taxonomy, a consensus approach to bacterial systematic. Microbiol Rev 1996; 60:407-438.
Wallace RJ, McKain N, Broderick GA. Breakdown of different peptides by Prevotella (Bacteroides) ruminicola and mixed microorganisms from the sheep rumen. Curr Microbiol 1993; 26(6):333-336.
Wu S, Ransom L, Baldwin RL, Li W, Li CE, Connor E, Li RW. The bacterial community composition of the bovine rumen detected using pyrosequencing of 16S rRNA genes. Metagenomics 2012; 1(11):1-11. doi:10.1128/AEM.00720-15
Yang WZ, Beauchemin KA. Physically effective fiber: method of determination and effects on chewing, ruminal acidosis, and digestion by dairy cows. J Dairy Sci 2006; 89(7):2618–2633. doi:10.3168/jds.S0022-0302(06)72339-6
Young JP, Downer HL, Eardly BD. Phylogeny of the phototrophic rhizobium strain BTAi1 by polymerase chain reaction-based sequencing of a 16S rRNA gene segment. J Bacteriol 1991; 173(7):2271-2277.
Descargas
Publicado
Cómo citar
Número
Sección
Licencia
Derechos de autor 2019 Revista Colombiana de Ciencias Pecuarias
Esta obra está bajo una licencia internacional Creative Commons Atribución-NoComercial-CompartirIgual 4.0.
Los autores permiten a RCCP reimprimir el material publicado en él.
La revista permite que los autores tengan los derechos de autor sin restricciones, y permitirá que los autores conserven los derechos de publicación sin restricciones.
