RNA-Seq Analysis on the Microbiota Associated with the White Shrimp (<i>Litopenaeus vannamei</i>) in Different Stages of Development
White leg shrimp (<i>Litopenaeus vannamei</i>) is a widely cultured species along the Pacific coast and is one of the most important crustaceans in world aquaculture. The microbiome composition of <i>L. vannamei</i> has been previously studied in different developmental stage...
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MDPI AG
2022-02-01
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| Series: | Applied Sciences |
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| Online Access: | https://www.mdpi.com/2076-3417/12/5/2483 |
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| author | Raúl Enrique Valle-Gough Blancka Yesenia Samaniego-Gámez Javier Eduardo Apodaca-Hernández Francisco Xavier Chiappa-Carrara Mauricio Rodríguez-Dorantes María Leticia Arena-Ortiz |
| author_facet | Raúl Enrique Valle-Gough Blancka Yesenia Samaniego-Gámez Javier Eduardo Apodaca-Hernández Francisco Xavier Chiappa-Carrara Mauricio Rodríguez-Dorantes María Leticia Arena-Ortiz |
| author_sort | Raúl Enrique Valle-Gough |
| collection | DOAJ |
| description | White leg shrimp (<i>Litopenaeus vannamei</i>) is a widely cultured species along the Pacific coast and is one of the most important crustaceans in world aquaculture. The microbiome composition of <i>L. vannamei</i> has been previously studied in different developmental stages, but there is limited information regarding the functional role of the microbiome during the development of <i>L. vannamei</i>. In this study the metatranscriptome in different developmental stages of <i>L. vannamei</i> (larvae, juvenile and adult) were generated using next generation sequencing techniques. The bacterial phyla found throughout all the stages of development belonged to the <i>Proteobacteria</i>, <i>Firmicutes</i> and <i>Actinobacteria</i>, these bacterial phyla are present in the digestive tract and are capable of producing several hydrolytic enzymes, which agrees with high representation of the primary metabolism and energy production, in both host and the microbiome. In this sense, functional changes were observed as the development progressed, in both host and the microbiome, in stages of larvae the most represented metabolic functions were associated with biomass production; while in juvenile and adult stages a higher proportion of metabolic functions associated to biotic and abiotic stress in <i>L. vannamei</i> and the microbiome were shown. This study provides evidence of the interaction of the microbiome with <i>L. vannamei</i>, and how the stage of development and the culture conditions of this species influences the gene expression and the microbiome composition, which suggests a complex metabolic network present throughout the life cycle of <i>L. vannamei</i>. |
| first_indexed | 2024-03-09T20:48:03Z |
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| id | doaj.art-d46bf3db80da4aaabe2f95ef0e94c9c9 |
| institution | Directory Open Access Journal |
| issn | 2076-3417 |
| language | English |
| last_indexed | 2024-03-09T20:48:03Z |
| publishDate | 2022-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Applied Sciences |
| spelling | doaj.art-d46bf3db80da4aaabe2f95ef0e94c9c92023-11-23T22:41:34ZengMDPI AGApplied Sciences2076-34172022-02-01125248310.3390/app12052483RNA-Seq Analysis on the Microbiota Associated with the White Shrimp (<i>Litopenaeus vannamei</i>) in Different Stages of DevelopmentRaúl Enrique Valle-Gough0Blancka Yesenia Samaniego-Gámez1Javier Eduardo Apodaca-Hernández2Francisco Xavier Chiappa-Carrara3Mauricio Rodríguez-Dorantes4María Leticia Arena-Ortiz5Ecogenomics Laboratory, Autonomous National University of Mexico (UNAM), Sierra Papacal Road, Km. 5.5, Chuburna Port. Sierra Papacal, Merida 97302, MexicoInstitute of Agricultural Sciences, Autonomous University of Baja California, Carretera Blvd., Delta s/n Ejido Nuevo León, Valle de Mexicali, Mexicali 21705, MexicoLaboratory of Genomic Computing, Genomic Libraries (Bibliotecas Genómicas), 3 St, # 404 by 24a. Bugambilias de Chuburna, Merida 97205, MexicoConservation Biology Laboratory, Autonomous National University of Mexico (UNAM), Sierra Papacal Road, Km. 5.5, Chuburna Port. Sierra Papacal, Merida 97302, MexicoOncogenomic Consortium, National Institute of Genomic Medicine (INMEGEN), South Periphery 4809, Arenal Tepepan Tlapan, CDMX 14610, MexicoEcogenomics Laboratory, Autonomous National University of Mexico (UNAM), Sierra Papacal Road, Km. 5.5, Chuburna Port. Sierra Papacal, Merida 97302, MexicoWhite leg shrimp (<i>Litopenaeus vannamei</i>) is a widely cultured species along the Pacific coast and is one of the most important crustaceans in world aquaculture. The microbiome composition of <i>L. vannamei</i> has been previously studied in different developmental stages, but there is limited information regarding the functional role of the microbiome during the development of <i>L. vannamei</i>. In this study the metatranscriptome in different developmental stages of <i>L. vannamei</i> (larvae, juvenile and adult) were generated using next generation sequencing techniques. The bacterial phyla found throughout all the stages of development belonged to the <i>Proteobacteria</i>, <i>Firmicutes</i> and <i>Actinobacteria</i>, these bacterial phyla are present in the digestive tract and are capable of producing several hydrolytic enzymes, which agrees with high representation of the primary metabolism and energy production, in both host and the microbiome. In this sense, functional changes were observed as the development progressed, in both host and the microbiome, in stages of larvae the most represented metabolic functions were associated with biomass production; while in juvenile and adult stages a higher proportion of metabolic functions associated to biotic and abiotic stress in <i>L. vannamei</i> and the microbiome were shown. This study provides evidence of the interaction of the microbiome with <i>L. vannamei</i>, and how the stage of development and the culture conditions of this species influences the gene expression and the microbiome composition, which suggests a complex metabolic network present throughout the life cycle of <i>L. vannamei</i>.https://www.mdpi.com/2076-3417/12/5/2483transcriptomicsRNA-Seqmetatranscriptomicsfunctional analysisdevelopmentmicrobiome |
| spellingShingle | Raúl Enrique Valle-Gough Blancka Yesenia Samaniego-Gámez Javier Eduardo Apodaca-Hernández Francisco Xavier Chiappa-Carrara Mauricio Rodríguez-Dorantes María Leticia Arena-Ortiz RNA-Seq Analysis on the Microbiota Associated with the White Shrimp (<i>Litopenaeus vannamei</i>) in Different Stages of Development Applied Sciences transcriptomics RNA-Seq metatranscriptomics functional analysis development microbiome |
| title | RNA-Seq Analysis on the Microbiota Associated with the White Shrimp (<i>Litopenaeus vannamei</i>) in Different Stages of Development |
| title_full | RNA-Seq Analysis on the Microbiota Associated with the White Shrimp (<i>Litopenaeus vannamei</i>) in Different Stages of Development |
| title_fullStr | RNA-Seq Analysis on the Microbiota Associated with the White Shrimp (<i>Litopenaeus vannamei</i>) in Different Stages of Development |
| title_full_unstemmed | RNA-Seq Analysis on the Microbiota Associated with the White Shrimp (<i>Litopenaeus vannamei</i>) in Different Stages of Development |
| title_short | RNA-Seq Analysis on the Microbiota Associated with the White Shrimp (<i>Litopenaeus vannamei</i>) in Different Stages of Development |
| title_sort | rna seq analysis on the microbiota associated with the white shrimp i litopenaeus vannamei i in different stages of development |
| topic | transcriptomics RNA-Seq metatranscriptomics functional analysis development microbiome |
| url | https://www.mdpi.com/2076-3417/12/5/2483 |
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