Logotipo del repositorio
Logotipo del repositorio
 

Studies on bacterial community composition are affected by the time and storage method of the rumen content

Vista sencilla de ítem
dc.contributor.authorGranja-Salcedo, Yury Tatiana
dc.contributor.authorRamirez-Uscategui, Ricardo Andrés
dc.contributor.authorMachado, Elwi Guillermo
dc.contributor.authorDuarte Messana, Juliana
dc.contributor.authorTakeshi Kishi, Luciano
dc.contributor.authorLino Dias, Ana Veronica
dc.contributor.authorBerchielli, Telma Teresinha
dc.date.accessioned2018-02-05T21:18:49Z
dc.date.available2018-02-05T21:18:49Z
dc.date.issued2017-04-28
dc.description.abstractThe objective of this study was to investigate three storage methods and four storage times for rumen sampling in terms of quality and yield of extracted metagenomic DNA as well as the composition of the rumen bacterial community. One Nellore steer fitted with a ruminal silicone- type cannula was used as a donor of ruminal contents. The experiment comprised 11 experimental groups: pellet control (PC), lyophilized control (LC), P-20: pellet stored frozen at -20ÊC for a period of 3, 6, and 12 months, P-80: pellet stored frozen at -80ÊC for a period of 3, 6, and 12 months, and L-20: lyophilized sample stored frozen at -20ÊC for a period of 3, 6, and 12 months. Metagenomic DNA concentrations were measured spectrophotometrically and fluorometrically and ion torrent sequencing was used to assess the bacterial community composition. The L-20 method could not maintain the yield of DNA during storage. In addition, the P-80 group showed a greater yield of metagenomic DNA than the other groups after 6 months of storage. Rumen samples stored as pellets (P-20 and P-80) resulted in lower richness Chao 1, ACE, and Shannon Wiener indices when compared to PC, while LC and PC were only different in richness ACE. The storage method and storage time influenced the proportions of 14 of 17 phyla identified by sequencing. In the P-20 group, the proportion of Cyanobacteria, Elusimicrobia, Fibrobacteres, Lentisphaerae, Proteobacteria, and Spirochaetes phyla identified was lower than 1%. In the P-80 group, there was an increase in the proportion of the Bacteroidetes phylum (p = 0.010); however, the proportion of Actinobacteria, Chloroflexi, SR1, Synergistetes, TM7, and WPS.2 phyla were unchanged compared to the PC group (p > 0.05). The class Clostridium was the most abundant in all stored groups and increased in its proportion, especially in the L-20 group. The rumen sample storage time significantly reduced the yield of metagenomic DNA extracted. Therefore, the storage method can influence the abundance of phyla, classes, and bacterial families studied in rumen samples and affect the richness and diversity index.eng
dc.identifier.issn19326203
dc.identifier.urihttp://hdl.handle.net/20.500.12442/1604
dc.language.isoengspa
dc.publisherPublic Library of Sciencespa
dc.rights.accessrightsinfo:eu-repo/semantics/openAccess
dc.rights.licenseLicencia de Creative Commons Reconocimiento-NoComercial-CompartirIgual 4.0 Internacionalspa
dc.sourceRevista PLos Onespa
dc.sourceVol. 12, No.4 (2017)spa
dc.source.urihttps://doi.org/10.1371/journal.pone.0176701eng
dc.subjectMicrobioma ruminalspa
dc.subjectAcidosis ruminal subagudospa
dc.titleStudies on bacterial community composition are affected by the time and storage method of the rumen contentspa
dc.typearticlespa
dcterms.referencesZilber-Rosenberg I, Rosenberg E. Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol Rev. 2008; 32(5):723±35. https://doi.org/10.1111/j. 1574-6976.2008.00123.x PMID: 18549407eng
dcterms.referencesPetri RM, Schwaiger T, Penner GB, Beauchemin KA, Forster RJ, McKinnon JJ, McAllister TA. Characterization of the core rumen microbiome in cattle during transition from forage to concentrate as well as during and after an acidotic challenge. PLoS ONE. 2013; 31: 8(12):e83424. https://doi.org/10.1371/ journal.pone.0083424 PMID: 24391765eng
dcterms.referencesMakkar HPS, McSweeney CS. Methods in Gut Microbial Ecology for Ruminants. 1st ed. Dordrecht: Springer: 2005.eng
dcterms.referencesDeng 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. https://doi.org/10. 1007/s11033-007-9079-1 PMID: 17484038eng
dcterms.referencesYu Z, Morrison M. Improved extraction of PCR-quality community DNA from digesta and fecal samples. Biotechniques. 2004; 36(5):808±12. PMID: 15152600eng
dcterms.referencesHenderson G, Cox F, Kittelmann S, Miri VH, Zethof M, Noel SJ, et al. Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities. PLoS One. 2013; 11: 8(9):e74787. https://doi.org/10.1371/journal.pone.0074787 PMID: 24040342eng
dcterms.referencesVillegas-Rivera G, Vargas-Cabrera Y, GonzaÂlez-Silva N, Aguilera-GarcõÂa F, GutieÂrrez-VaÂzquez E, Bravo-Patiño A, et al. Evaluation of DNA extraction methods of rumen microbial populations. World J Microbiol Biotechnol. 2013; 29(2):301±7. https://doi.org/10.1007/s11274-012-1183-2 PMID: 23054703eng
dcterms.referencesGeishauser T., Gitzel A. A comparison of rumen fluid sampled by oro-ruminal probe versus rumen fistula. Small Rumin Res. 1996; 21 (1): 63±69.eng
dcterms.referencesPitta DW, Pinchak E, Dowd SE, Osterstock J, Gontcharova V, Youn E, et al. Rumen bacterial diversity dynamics associated with changing from bermudagrass hay to grazed winter wheat diets. Microb Ecol. 2010; 59(3):511±22. https://doi.org/10.1007/s00248-009-9609-6 PMID: 20037795eng
dcterms.referencesFouts DE, Szpakowski S, Purushe J, Torralba M, Waterman RC, MacNeil MD, et al. Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen. PLoS One. 2012; 7(11): e48289. https://doi.org/10.1371/journal.pone.0048289 PMID: 23144861eng
dcterms.referencesSaro C, Ranilla MJ, Carro MD. Postprandial changes of fiber-degrading microbes in the rumen of sheep fed diets varying in type of forage as monitored by real-time PCR and automated ribosomal intergenic spacer analysis. J Anim Sci. 2012; 90(12):4487±94. https://doi.org/10.2527/jas.2012-5265 PMID: 23100580eng
dcterms.referencesFliegerova K, Tapio I, Bonin A, Mrazek J, Callegari ML, Bani P, et al.Effect of DNA extraction and sample preservation method on rumen bacterial population. Anaerobe. 2014; 29:80±4. https://doi.org/10. 1016/j.anaerobe.2013.09.015 PMID: 24125910eng
dcterms.referencesPetri RM, Mapiye C, Dugan ME, McAllister TA. Subcutaneous adipose fatty acid profiles and related rumen bacterial populations of steers fed red clover or grass hay diets containing flax or sunflowerseed. PLoS One. 2015; 9(8): e104167.eng
dcterms.referencesJiang SZ, Yang ZB, Yang WR, Li Z, Zhang CY, Liu XM, et al. Diets of differentially processed wheat alter ruminal fermentation parameters and microbial populations in beef cattle. J Anim Sci. 2015; 93 (11):5378±85. https://doi.org/10.2527/jas.2015-9547 PMID: 26641057eng
dcterms.referencesShingfield KJ, Kairenius P, AroÈ laÈ A, Paillard D, Muetzel S, AhvenjaÈ rvi S, et al. Dietary fish oil supplements modify ruminal biohydrogenation, alter the flow of fatty acids at the omasum, and induce changes in the ruminal Butyrivibrio population in lactating cows. J Nutr. 2012; 142(8):1437±48. https://doi.org/10. 3945/jn.112.158576 PMID: 22739367eng
dcterms.referencesZhou YW, McSweeney CS, Wang JK, Liu JX. Effects of disodium fumarate on ruminal fermentation and microbial communities in sheep fed on high-forage diets. Animal. 2012; 6(5):815±23. https://doi.org/10. 1017/S1751731111002102 PMID: 22558929eng
dcterms.referencesZhao L, Meng Q, Ren L, Liu W, Zhang X, Huo Y, et al. Effects of Nitrate Addition on Rumen Fermentation, Bacterial Biodiversity and Abundance. Asian-Australas J Anim Sci. 2015; 28(10):1433±41. https:// doi.org/10.5713/ajas.15.0091 PMID: 26194220eng
dcterms.referencesMa T, Chen DD, Tu Y, Zhang NF, Si BW, Deng KD, et al. Effect of dietary supplementation with resveratrol on nutrient digestibility, methanogenesis and ruminal microbial flora in sheep. J Anim Physiol Anim Nutr (Berl). 2015; 99(4):676±83.eng
dcterms.referencesYang SL, Bu DP, Wang JQ, Hu ZY, Li D, Wei HY, et al. Soybean oil and linseed oil supplementation affect profiles of ruminal microorganisms in dairy cows. Animal. 2009; 3(11):1562±9. https://doi.org/10. 1017/S1751731109990462 PMID: 22444989eng
dcterms.referencesFernando SC, Purvis HT 2nd, Najar FZ, Sukharnikov LO, Krehbiel CR, Nagaraja TG, et al. Rumen microbial population dynamics during adaptation to a high-grain diet. Appl Environ Microbiol. 2010; 76 (22): 7482±90. https://doi.org/10.1128/AEM.00388-10 PMID: 20851965eng
dcterms.referencesCherdthong A, Wanapat M, Saenkamsorn A, Supapong C, Anantasook N, Gunun P. Improving rumen ecology and microbial population by dried rumen digesta in beef cattle. Trop Anim Health Prod. 2015; 47(5): 921±6. https://doi.org/10.1007/s11250-015-0809-4 PMID: 25851930eng
dcterms.referencesVargas-Bello-PeÂrez E, Cancino-Padilla N, Romero J, Garnsworthy PC. Quantitative analysis of ruminal bacterial populations involved in lipid metabolism in dairy cows fed different vegetable oils. Animal. 2016; 5:1±8.eng
dcterms.referencesPatel DD, Patel AK, Parmar NR, Shah TM, Patel JB, Pandya PR, et al. Microbial and Carbohydrate Active Enzyme profile of buffalo rumen metagenome and their alteration in response to variation in the diet. Gene. 2014; 545(1):88±94. https://doi.org/10.1016/j.gene.2014.05.003 PMID: 24797613eng
dcterms.referencesRibeiro CS, Granja-Salcedo YT, Messana JD, Neto AJ, Canesin RC, Fiorentini G, et al. Feeding increasing concentrate to Tifton 85 hay ratios modulated rumen fermentation and microbiota in Nellore feedlot steers. J Agric Sci. 2015; 153:1116±1127.eng
dcterms.referencesRibeiro JuÂnior CS, Messana JD, Granja-Salcedo YT, Canesin RC, Fiorentini G, San Vito E, et al. Parameters of fermentation and rumen microbiota of Nellore steers fed with different proportions of concentrate in fresh sugarcane containing diets. Arch Anim Nutr. 2016; 70(5):402±15. https://doi.org/10. 1080/1745039X.2016.1206737 PMID: 27415825eng
dcterms.referencesGranja-Salcedo YT, Ribeiro JuÂnior CS, de Jesus RB, Gomez-Insuasti AS, Rivera AR, Messana JD, et al. Effect of different levels of concentrate on ruminal microorganisms and rumen fermentation in Nellore steers. Arch Anim Nutr. 2016; 70(1): 17±32. https://doi.org/10.1080/1745039X.2015.1117562 PMID: 26654381eng
dcterms.referencesMessana JD, Carvalho ALGF, Ribeiro AF, Fiorentini G, Castagnino PS, Granja-Salcedo YT, et al. Effects of different sources of forage in high-concentrate diets on fermentation parameters, ruminal biohydrogenation and microbiota in Nellore feedlot steers. J Agric Sci. 2016; 154: 928±941.eng
dcterms.referencesSan 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;eng
dcterms.referencesCaporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. PNAS. 2011; 108: supl. 1 4516±4522.eng
dcterms.referencesMartin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal. 2011; 17(1), 10±12.eng
dcterms.referencesSchmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 2011; 27 (6): 863±864. https://doi.org/10.1093/bioinformatics/btr026 PMID: 21278185eng
dcterms.referencesCaporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD et al. QIIME allows analysis of highthroughput community sequencing data. Nat Methods. 2010; 7: 335±336. https://doi.org/10.1038/ nmeth.f.303 PMID: 20383131eng
dcterms.referencesCole JR, Wang Q, Fish JA, Chai B, McGarrel DM et al. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 2014; 42(Database issue): D633±D642. https://doi. org/10.1093/nar/gkt1244 PMID: 24288368eng
dcterms.referencesLozupone C, Hamady M, Knight R. UniFrac±an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics. 2006; 7: 371. https://doi.org/10.1186/1471-2105-7-371 PMID: 16893466eng
dcterms.referencesR version 3.2.2, The R Foundation for Statistical Computing, Austria.eng
dcterms.referencesMinato H, Endo A, Ootomo Y, Uemura T. Ecological treatise of the rumen fermentation. II. The amylolytic and cellulolytic activities of the fractionated bacterial portions attached to the rumen solids. J Gen Appl Microbiol. 1966; 12:53-69eng
dcterms.referencesMcAllister TA, Bae HD, Jones GA, Cheng KJ. Microbial attachment and feed digestion in the rumen. J Anim Sci. 1994; 72(11): 3004-3018. PMID: 7730196eng
dcterms.referencesMorgan CA, Herman N, White PA, Vesey G. Preservation of microorganisms by dryingÐa review. J Microbiol Methods. 2006; 66(2): 183-193. https://doi.org/10.1016/j.mimet.2006.02.017 PMID: 16632005eng
dcterms.referencesKumar S, Kashyap PL, Singh R, Srivastava AK. Preservation and Maintenance of Microbial Cultures. In: Arora DK, Das S, Sukumar M, editors. Analyzing Microbes. Berlin Heidelberg: Springer-Verlag, 2012.eng
dcterms.referencesKirsop BE, Doyle A. Maintenance of microorganisms and culture cells: a manual of laboratory methods, 2nd ed. London: Academic, 1991.eng
dcterms.referencesChen YB, Lan DL, Tang C, Yang XN, Li J. Effect of DNA Extraction Methods on the Apparent Structure of Yak Rumen Microbial Communities as Revealed by 16S rDNA Sequencing. Pol J Microbiol. 2015; 64(1): 29-36. PMID: 26094313eng
dcterms.referencesde Oliveira MN, Jewell KA, Freitas FS, Benjamin LA, ToÂtola MR, Borges AC, et al. Characterizing the microbiota across the gastrointestinal tract of a Brazilian Nelore steer. Vet Microbiol. 2013; 28; 164(3± 4):307-314. https://doi.org/10.1016/j.vetmic.2013.02.013 PMID: 23490556eng
dcterms.referencesMcCann JC, Wiley LM, Forbes TD, Rouquette FM Jr, 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. https://doi.org/10.1371/journal.pone.0091864 PMID: 24642871eng
dcterms.referencesSingh KM, Jakhesara SJ, Koringa PG, Rank DN, Joshi CG. Metagenomic analysis of virulence-associated and antibiotic resistance genes of microbes in rumen of Indian buffalo (Bubalus bubalis). Gene. 2012; 507 (2): 146-151. https://doi.org/10.1016/j.gene.2012.07.037 PMID: 22850272eng
dcterms.referencesSingh KM, Reddy B, Patel AK, Panchasara H, Parmar N, Patel AB, et al., Metagenomic analysis of buffalo rumen microbiome: Effect of roughage diet on Dormancy and Sporulation genes. Meta Gene. 2014; 1 (2): 252-268.eng
dcterms.referencesJalanka-Tuovinen J, Salonen A, Nikkila J, Immonen O, Kekkonen R, Lahti L, et al. Intestinal Microbiota in Healthy Adults: Temporal Analysis Reveals Individual and Common Core and Relation to Intestinal Symptoms. PLoS One. 2011; 6(7): e23035. https://doi.org/10.1371/journal.pone.0023035 PMID: 21829582eng
dcterms.referencesBiddle A, Stewart L, Blanchard J, Leschine S. Untangling the genetic basis of fibrolytic specialization by lachnospiraceae and ruminococcaceae in diverse gut communities. Diversity. 2013; 5: 627-640.eng
dcterms.referencesKobayashi Y, Shinkai T, Koike S.Ecological and physiological characterization shows that Fibrobacter succinogenes is important in rumen fiber digestionÐreview. Folia Microbiol (Praha). 2008; 53(3):195-200.eng
dcterms.referencesRansom-Jones E, Jones DL, McCarthy AJ, McDonald JE. The Fibrobacteres: an important phylum of cellulose-degrading bacteria. Microb Ecol. 2012; 63(2):267-281. https://doi.org/10.1007/s00248-011- 9998-1 PMID: 22213055eng
dcterms.referencesMesapogu S, Jillepalli MC, Arora DK. 2012. Microbial DNA Extraction, Purification, and Quantitation. In: Arora DK, Das S, SukumarM (eds). Analyzing Microbes. Springer-Verlag Berlin Heidelberg 2013. pp 1-16.eng

Archivos

Bloque original
Mostrando 1 - 1 de 1
Miniatura
Nombre:
Studies on bacterial community composition (1).pdf
Tamaño:
3.09 MB
Formato:
Adobe Portable Document Format
Descripción:
Formato Pdf texto completo
Descargar
Bloque de licencias
Mostrando 1 - 1 de 1
No hay miniatura disponible
Nombre:
license.txt
Tamaño:
1.71 KB
Formato:
Item-specific license agreed upon to submission
Descripción:
Descargar

Colecciones

Artículos

Universidad Simón Bolívar: Todos los derechos reservados / Sistema de biblioteca