Bacterial meta-analysis of chicken cecal microbiota
"Chicken production is an industry that generates 90,000 metric tons worldwide. Thus, optimizing chicken growth and production is of great importance. A central factor determining not only food conversion rate but also stability of the immune system is the diversity and variability of the micro...
- Autores:
-
Chica Cárdenas, Luis Alberto
- Tipo de recurso:
- Trabajo de grado de pregrado
- Fecha de publicación:
- 2019
- Institución:
- Universidad de los Andes
- Repositorio:
- Séneca: repositorio Uniandes
- Idioma:
- eng
- OAI Identifier:
- oai:repositorio.uniandes.edu.co:1992/45815
- Acceso en línea:
- http://hdl.handle.net/1992/45815
- Palabra clave:
- Pollos
Aparato digestivo
Bioinformática
Microbiología
- Rights
- openAccess
- License
- http://creativecommons.org/licenses/by-nc-sa/4.0/
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Bacterial meta-analysis of chicken cecal microbiota |
| title |
Bacterial meta-analysis of chicken cecal microbiota |
| spellingShingle |
Bacterial meta-analysis of chicken cecal microbiota Pollos Aparato digestivo Bioinformática Microbiología |
| title_short |
Bacterial meta-analysis of chicken cecal microbiota |
| title_full |
Bacterial meta-analysis of chicken cecal microbiota |
| title_fullStr |
Bacterial meta-analysis of chicken cecal microbiota |
| title_full_unstemmed |
Bacterial meta-analysis of chicken cecal microbiota |
| title_sort |
Bacterial meta-analysis of chicken cecal microbiota |
| dc.creator.fl_str_mv |
Chica Cárdenas, Luis Alberto |
| dc.contributor.advisor.none.fl_str_mv |
Reyes Muñoz, Alejandro |
| dc.contributor.author.none.fl_str_mv |
Chica Cárdenas, Luis Alberto |
| dc.subject.armarc.es_CO.fl_str_mv |
Pollos Aparato digestivo Bioinformática |
| topic |
Pollos Aparato digestivo Bioinformática Microbiología |
| dc.subject.themes.none.fl_str_mv |
Microbiología |
| description |
"Chicken production is an industry that generates 90,000 metric tons worldwide. Thus, optimizing chicken growth and production is of great importance. A central factor determining not only food conversion rate but also stability of the immune system is the diversity and variability of the microbiota present throughout the gastrointestinal tract, mainly in the cecum. To date, several studies have investigated the relationship between bacterial communities and the gut microbiome, with limited data to compare. This study aims to create a bacterial meta-analysis based on Illumina sequences in order to lay a baseline understanding that will be useful for future analyses of the cecum bacterial composition. A total of 276 samples, comprising two different regions within the 16S rRNA gene, were analyzed. Due to the heterogeneity of the data, each region was analyzed independently and an effort for a joint analysis was performed as well. Taxonomic profiling revealed 23 phyla. Firmicutes was the most prevalent phylum, followed by Bacteroidetes and Proteobacteria. At genus level, 137 genera were found. Shannon metric for alpha diversity showed that factors like type of chickens (Commercial or experimental) and 16S rRNA gene subregion have negligible effect on diversity. 29 genera were found to be common for all sets in at least 50% of the samples, which are highly related to cellulose degradation and short chain fatty acids synthesis. Despite the large number of parameters that were taken into account, the identification of common bacteria was achieved. Furthermore, a model of comparison for future studies is presented."--Tomado del Formato de Documento de Grado. |
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2019 |
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Trabajo de grado - Pregrado |
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Al consultar y hacer uso de este recurso, está aceptando las condiciones de uso establecidas por los autores.http://creativecommons.org/licenses/by-nc-sa/4.0/info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2Reyes Muñoz, Alejandrovirtual::8999-1Chica Cárdenas, Luis Alberto7ca49731-5204-4ec2-9851-0a5cb931c5ee5002020-09-03T16:15:14Z2020-09-03T16:15:14Z2019http://hdl.handle.net/1992/45815u826994.pdfinstname:Universidad de los Andesreponame:Repositorio Institucional Sénecarepourl:https://repositorio.uniandes.edu.co/"Chicken production is an industry that generates 90,000 metric tons worldwide. Thus, optimizing chicken growth and production is of great importance. A central factor determining not only food conversion rate but also stability of the immune system is the diversity and variability of the microbiota present throughout the gastrointestinal tract, mainly in the cecum. To date, several studies have investigated the relationship between bacterial communities and the gut microbiome, with limited data to compare. This study aims to create a bacterial meta-analysis based on Illumina sequences in order to lay a baseline understanding that will be useful for future analyses of the cecum bacterial composition. A total of 276 samples, comprising two different regions within the 16S rRNA gene, were analyzed. Due to the heterogeneity of the data, each region was analyzed independently and an effort for a joint analysis was performed as well. Taxonomic profiling revealed 23 phyla. Firmicutes was the most prevalent phylum, followed by Bacteroidetes and Proteobacteria. At genus level, 137 genera were found. Shannon metric for alpha diversity showed that factors like type of chickens (Commercial or experimental) and 16S rRNA gene subregion have negligible effect on diversity. 29 genera were found to be common for all sets in at least 50% of the samples, which are highly related to cellulose degradation and short chain fatty acids synthesis. Despite the large number of parameters that were taken into account, the identification of common bacteria was achieved. Furthermore, a model of comparison for future studies is presented."--Tomado del Formato de Documento de Grado."Gracias a los elevados índices de producción alrededor del mundo, la industria avícola es considerada como la mayor fuente de obtención de proteína animal. Dichas tasas de producción están relacionadas en gran medida con la salud del animal y el tamaño de la superficie de absorción en el tracto gastrointestinal, los que a su vez son altamente influenciados por la microbiota presente en dichas zonas. Dicha microbiota se considera altamente variable y se encuentra influenciada por una gran cantidad de factores externos, por lo que diversos estudios se han enfocado en evaluar las relaciones entre las diferentes condiciones y la composición bacteriana. El objetivo de este estudió radica en hacer un consenso de la composición microbiana del ciego del pollo, con el fin de crear un modelo de compración robusto para nuevos estudios. Las secuencias utilizadas para este análisis fueron obtenidas mediante la secuenciación del gen del 16S rRNA y descargadas de la base de datos del SRA. Mediante la utilización de diversos softwares bioinformáticos se realizó la limpieza de las secuencias, y los análisis de alfa y beta diversidad. A su vez, la asignación taxonómica de las bacterias presentes fue reportada. Finalmente, las bacterias comunes para el 50 y 80% de las muestras fueron reportadas. La asignación taxonómica a nivel de phylum, reveló la predominancia de Firmicutes, Bacteroidetes y Proteobacterias en la mayoría de las muestras analizadas. Después de analizar los valores de alfa diversidad mediante el índice de Shannon, se comprobó que factores como el tipo de pollos y la región del 16S secuenciada tienen una influencia mínima en la diversidad. A nivel de género, 29 bacterias se reportaron como comunes para al menos el 50% de las muestras, las cuales están altamente relacionadas con la degradación de celulosa y la generación de ácidos grasos de cadena corta, involucrados principalmente en el aumento de la superficie de absorción."--Tomado del Formato de Documento de Grado.MicrobiólogoPregrado19 hojasapplication/pdfengUniversidad de los AndesMicrobiologíaFacultad de CienciasDepartamento de Ciencias Biológicasinstname:Universidad de los Andesreponame:Repositorio Institucional SénecaBacterial meta-analysis of chicken cecal microbiotaTrabajo de grado - Pregradoinfo:eu-repo/semantics/bachelorThesishttp://purl.org/coar/resource_type/c_7a1fhttp://purl.org/coar/version/c_970fb48d4fbd8a85Texthttp://purl.org/redcol/resource_type/TPPollosAparato digestivoBioinformáticaMicrobiologíaPublicationhttps://scholar.google.es/citations?user=hbXF8UEAAAAJvirtual::8999-10000-0003-2907-3265virtual::8999-1https://scienti.minciencias.gov.co/cvlac/visualizador/generarCurriculoCv.do?cod_rh=0000395927virtual::8999-1f71489e5-69f6-4e6b-90a6-c6b1d3fecec7virtual::8999-1f71489e5-69f6-4e6b-90a6-c6b1d3fecec7virtual::8999-1TEXTu826994.pdf.txtu826994.pdf.txtExtracted texttext/plain25873https://repositorio.uniandes.edu.co/bitstreams/9848e794-c824-4498-916a-50c912329655/download6d91479f370b8fac17ca6b0438b95903MD54ORIGINALu826994.pdfapplication/pdf759294https://repositorio.uniandes.edu.co/bitstreams/a09747ba-4a47-4c54-a087-f7c3e27d2cc8/download0acb5288fa38fc5df342b79a97adfd24MD51THUMBNAILu826994.pdf.jpgu826994.pdf.jpgIM Thumbnailimage/jpeg20896https://repositorio.uniandes.edu.co/bitstreams/dc5707f5-2015-4173-9c84-726431aad13c/download6d6a7a34ab475c8e6f6c23f579798287MD551992/45815oai:repositorio.uniandes.edu.co:1992/458152024-11-14 14:50:05.725http://creativecommons.org/licenses/by-nc-sa/4.0/open.accesshttps://repositorio.uniandes.edu.coRepositorio institucional Sénecaadminrepositorio@uniandes.edu.co |