Studies on bacterial community composition are affected by the time and storage method of the rumen content
| Autor: | Telma Teresinha Berchielli, Luciano Takeshi Kishi, Juliana Duarte Messana, Ana Veronica Lino Dias, Yury Tatiana Granja-Salcedo, Elwi Guillermo Machado, Ricardo Andrés Ramirez-Uscategui |
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| Přispěvatelé: | Universidade Estadual Paulista (Unesp), Universidad Simón Bolívar, Universidade Federal de Viçosa (UFV) |
| Jazyk: | angličtina |
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Time Factors lcsh:Medicine Storage Microbioma ruminal Specimen Storage Freezing Composition of the bacterial community Fluorometry Food science lcsh:Science DNA extraction Data Management Gel Electrophoresis Multidisciplinary biology Ecology Chemistry Biodiversity Genomics Shannon Index Fibrobacteres Spectrophotometry Proteobacteria Acidosis ruminal subagudo Research Article DNA Bacterial Computer and Information Sciences Rumen Ecological Metrics Method ruminal content Bacterial Physiological Phenomena Research and Analysis Methods Cyanobacteria Microbiology Actinobacteria Time 03 medical and health sciences Electrophoretic Techniques Extraction techniques Genetics Animals Taxonomy Cryopreservation Bacteria lcsh:R Ecology and Environmental Sciences Organisms Bacteroidetes Biology and Life Sciences Species Diversity Sequence Analysis DNA biology.organism_classification Gastrointestinal Microbiome 030104 developmental biology Freeze Drying Storage and Handling lcsh:Q Cattle Metagenomics Synergistetes |
| Zdroj: | Revista PLos One Vol. 12, No.4 (2017) Repositorio Digital USB Universidad Simón Bolívar instacron:Universidad Simón Bolívar Scopus Repositório Institucional da UNESP Universidade Estadual Paulista (UNESP) instacron:UNESP PLoS ONE LOCUS Repositório Institucional da UFV Universidade Federal de Viçosa (UFV) instacron:UFV PLoS ONE, Vol 12, Iss 4, p e0176701 (2017) |
| DOI: | 10.1371/journal.pone.0176701 |
| Popis: | Made available in DSpace on 2018-12-11T17:11:29Z (GMT). No. of bitstreams: 0 Previous issue date: 2017-04-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) 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. Department of Animal Science Faculdade de Ciências Agra Rias E Veterinárias (FCAV) UNESP - Univ Estadual Paulista Jaboticabal Department of Clinical and Veterinary Surgery Faculdade de Ciências Agra Rias E Veterinárias (FCAV) UNESP - Univ Estadual Paulista Jaboticabal Grupo de Investigación en Medicina Genómica - GIMEGEN Universidad Simón Bolívar Department of Technology Faculdade de Ciências Agra Rias E Veterinárias (FCAV) UNESP - Univ Estadual Paulista Jaboticabal Department 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 Jaboticabal Department of Clinical and Veterinary Surgery Faculdade de Ciências Agra Rias E Veterinárias (FCAV) UNESP - Univ Estadual Paulista Jaboticabal Department of Technology Faculdade de Ciências Agra Rias E Veterinárias (FCAV) UNESP - Univ Estadual Paulista Jaboticabal FAPESP: 2013/ 23851-6 |
| Databáze: | OpenAIRE |
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