Studies on bacterial community composition are affected by the time and storage method of the rumen content
Autor(a) principal: | |
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Data de Publicação: | 2017 |
Outros Autores: | , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1371/journal.pone.0176701 http://hdl.handle.net/11449/174511 |
Resumo: | The 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 -20?C for a period of 3, 6, and 12 months, P-80: pellet stored frozen at -80°C for a period of 3, 6, and 12 months, and L-20: lyophilized sample stored frozen at -20°C 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, thestorage method can influence the abundance of phyla, classes, and bacterial families studied in rumen samples and affect the richness and diversity index. |
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Studies on bacterial community composition are affected by the time and storage method of the rumen contentThe 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 -20?C for a period of 3, 6, and 12 months, P-80: pellet stored frozen at -80°C for a period of 3, 6, and 12 months, and L-20: lyophilized sample stored frozen at -20°C 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, thestorage method can influence the abundance of phyla, classes, and bacterial families studied in rumen samples and affect the richness and diversity index.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Department of Animal Science Faculdade de Ciências Agra Rias E Veterinárias (FCAV) UNESP - Univ Estadual Paulista JaboticabalDepartment of Clinical and Veterinary Surgery Faculdade de Ciências Agra Rias E Veterinárias (FCAV) UNESP - Univ Estadual Paulista JaboticabalGrupo de Investigación en Medicina Genómica - GIMEGEN Universidad Simón BolívarDepartment of Technology Faculdade de Ciências Agra Rias E Veterinárias (FCAV) UNESP - Univ Estadual Paulista JaboticabalDepartment of Animal Science INCT CA - Universidade Federal de Viçosa (UFV)Department of Animal Science Faculdade de Ciências Agra Rias E Veterinárias (FCAV) UNESP - Univ Estadual Paulista JaboticabalDepartment of Clinical and Veterinary Surgery Faculdade de Ciências Agra Rias E Veterinárias (FCAV) UNESP - Univ Estadual Paulista JaboticabalDepartment of Technology Faculdade de Ciências Agra Rias E Veterinárias (FCAV) UNESP - Univ Estadual Paulista JaboticabalFAPESP: 2013/ 23851-6Universidade Estadual Paulista (Unesp)Universidad Simón BolívarUniversidade Federal de Viçosa (UFV)Granja-Salcedo, Yury Tatiana [UNESP]Ramirez-Uscategui, Ricardo Andrés [UNESP]Machado, Elwi GuillermoMessana, Juliana Duarte [UNESP]Kishi, Luciano Takeshi [UNESP]Dias, Ana Veronica Lino [UNESP]Berchielli, Telma Teresinha [UNESP]2018-12-11T17:11:29Z2018-12-11T17:11:29Z2017-04-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://dx.doi.org/10.1371/journal.pone.0176701PLoS ONE, v. 12, n. 4, 2017.1932-6203http://hdl.handle.net/11449/17451110.1371/journal.pone.01767012-s2.0-850184588452-s2.0-85018458845.pdfScopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengPLoS ONE1,164info:eu-repo/semantics/openAccess2024-06-07T18:42:33Zoai:repositorio.unesp.br:11449/174511Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T19:09:36.261147Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Studies on bacterial community composition are affected by the time and storage method of the rumen content |
title |
Studies on bacterial community composition are affected by the time and storage method of the rumen content |
spellingShingle |
Studies on bacterial community composition are affected by the time and storage method of the rumen content Granja-Salcedo, Yury Tatiana [UNESP] |
title_short |
Studies on bacterial community composition are affected by the time and storage method of the rumen content |
title_full |
Studies on bacterial community composition are affected by the time and storage method of the rumen content |
title_fullStr |
Studies on bacterial community composition are affected by the time and storage method of the rumen content |
title_full_unstemmed |
Studies on bacterial community composition are affected by the time and storage method of the rumen content |
title_sort |
Studies on bacterial community composition are affected by the time and storage method of the rumen content |
author |
Granja-Salcedo, Yury Tatiana [UNESP] |
author_facet |
Granja-Salcedo, Yury Tatiana [UNESP] Ramirez-Uscategui, Ricardo Andrés [UNESP] Machado, Elwi Guillermo Messana, Juliana Duarte [UNESP] Kishi, Luciano Takeshi [UNESP] Dias, Ana Veronica Lino [UNESP] Berchielli, Telma Teresinha [UNESP] |
author_role |
author |
author2 |
Ramirez-Uscategui, Ricardo Andrés [UNESP] Machado, Elwi Guillermo Messana, Juliana Duarte [UNESP] Kishi, Luciano Takeshi [UNESP] Dias, Ana Veronica Lino [UNESP] Berchielli, Telma Teresinha [UNESP] |
author2_role |
author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) Universidad Simón Bolívar Universidade Federal de Viçosa (UFV) |
dc.contributor.author.fl_str_mv |
Granja-Salcedo, Yury Tatiana [UNESP] Ramirez-Uscategui, Ricardo Andrés [UNESP] Machado, Elwi Guillermo Messana, Juliana Duarte [UNESP] Kishi, Luciano Takeshi [UNESP] Dias, Ana Veronica Lino [UNESP] Berchielli, Telma Teresinha [UNESP] |
description |
The 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 -20?C for a period of 3, 6, and 12 months, P-80: pellet stored frozen at -80°C for a period of 3, 6, and 12 months, and L-20: lyophilized sample stored frozen at -20°C 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, thestorage method can influence the abundance of phyla, classes, and bacterial families studied in rumen samples and affect the richness and diversity index. |
publishDate |
2017 |
dc.date.none.fl_str_mv |
2017-04-01 2018-12-11T17:11:29Z 2018-12-11T17:11:29Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1371/journal.pone.0176701 PLoS ONE, v. 12, n. 4, 2017. 1932-6203 http://hdl.handle.net/11449/174511 10.1371/journal.pone.0176701 2-s2.0-85018458845 2-s2.0-85018458845.pdf |
url |
http://dx.doi.org/10.1371/journal.pone.0176701 http://hdl.handle.net/11449/174511 |
identifier_str_mv |
PLoS ONE, v. 12, n. 4, 2017. 1932-6203 10.1371/journal.pone.0176701 2-s2.0-85018458845 2-s2.0-85018458845.pdf |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
PLoS ONE 1,164 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
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1808129027925344256 |