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Metagenomics Analysis Reveals Compositional and Functional Differences in the Gut Microbiota of Red Swamp Crayfish, Procambarus clarkii, Grown on Two Different Culture Environments

The structure and function of intestinal microorganisms are closely related to host metabolism, development, physiology, and health. The red swamp crayfish, Procambarus clarkii, is an important farmed aquatic species in China, which is grown in aquaculture ponds and rice paddy fields. Since these ar...

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Autores principales: Chen, Xi, Fan, Limin, Qiu, Liping, Dong, Xinxu, Wang, Qing, Hu, Gengdong, Meng, Shunlong, Li, Dandan, Chen, Jiazhang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8558459/
https://www.ncbi.nlm.nih.gov/pubmed/34733252
http://dx.doi.org/10.3389/fmicb.2021.735190
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author Chen, Xi
Fan, Limin
Qiu, Liping
Dong, Xinxu
Wang, Qing
Hu, Gengdong
Meng, Shunlong
Li, Dandan
Chen, Jiazhang
author_facet Chen, Xi
Fan, Limin
Qiu, Liping
Dong, Xinxu
Wang, Qing
Hu, Gengdong
Meng, Shunlong
Li, Dandan
Chen, Jiazhang
author_sort Chen, Xi
collection PubMed
description The structure and function of intestinal microorganisms are closely related to host metabolism, development, physiology, and health. The red swamp crayfish, Procambarus clarkii, is an important farmed aquatic species in China, which is grown in aquaculture ponds and rice paddy fields. Since these are two distinct cultivation environments with important differences in nutrient input and ecological community composition, we hypothesized that they may have different effects on the gut microbiota of the crayfish. Here, we sought to examine this hypothesis. To that aim, metagenomics analyses were applied to unveil the taxonomic composition and functional diversity of the microbiota in the intestines of red swamp crayfish grown in aquaculture ponds and rice-crayfish cultivation environments. The results showed that Firmicutes and Proteobacteria were the two most abundant microbial components. In addition, the relative abundance of bacterial and archaeal communities, but not that of fungal and viral communities, significantly differed between the two environments. The abundance of genes involved in pathways related to genetic information processing and human diseases was lower in the guts of red swamp crayfish grown in rice-crayfish cultivation environments. In particular, the abundance of two gene sets, K13730 and K08303, which are related to epithelial cell invasion by Listeria monocytogenes and Helicobacter pylori, respectively, decreased in this culture environment. In addition, the samples from rice-crayfish cultivation environments tended to have lower relative abundance of glycosyltransferases (GTs), which were the most abundant carbohydrate-active enzymes in the samples from both groups, higher abundance of glycoside hydrolases, and lower abundance of GT2.
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spelling pubmed-85584592021-11-02 Metagenomics Analysis Reveals Compositional and Functional Differences in the Gut Microbiota of Red Swamp Crayfish, Procambarus clarkii, Grown on Two Different Culture Environments Chen, Xi Fan, Limin Qiu, Liping Dong, Xinxu Wang, Qing Hu, Gengdong Meng, Shunlong Li, Dandan Chen, Jiazhang Front Microbiol Microbiology The structure and function of intestinal microorganisms are closely related to host metabolism, development, physiology, and health. The red swamp crayfish, Procambarus clarkii, is an important farmed aquatic species in China, which is grown in aquaculture ponds and rice paddy fields. Since these are two distinct cultivation environments with important differences in nutrient input and ecological community composition, we hypothesized that they may have different effects on the gut microbiota of the crayfish. Here, we sought to examine this hypothesis. To that aim, metagenomics analyses were applied to unveil the taxonomic composition and functional diversity of the microbiota in the intestines of red swamp crayfish grown in aquaculture ponds and rice-crayfish cultivation environments. The results showed that Firmicutes and Proteobacteria were the two most abundant microbial components. In addition, the relative abundance of bacterial and archaeal communities, but not that of fungal and viral communities, significantly differed between the two environments. The abundance of genes involved in pathways related to genetic information processing and human diseases was lower in the guts of red swamp crayfish grown in rice-crayfish cultivation environments. In particular, the abundance of two gene sets, K13730 and K08303, which are related to epithelial cell invasion by Listeria monocytogenes and Helicobacter pylori, respectively, decreased in this culture environment. In addition, the samples from rice-crayfish cultivation environments tended to have lower relative abundance of glycosyltransferases (GTs), which were the most abundant carbohydrate-active enzymes in the samples from both groups, higher abundance of glycoside hydrolases, and lower abundance of GT2. Frontiers Media S.A. 2021-10-18 /pmc/articles/PMC8558459/ /pubmed/34733252 http://dx.doi.org/10.3389/fmicb.2021.735190 Text en Copyright © 2021 Chen, Fan, Qiu, Dong, Wang, Hu, Meng, Li and Chen. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Chen, Xi
Fan, Limin
Qiu, Liping
Dong, Xinxu
Wang, Qing
Hu, Gengdong
Meng, Shunlong
Li, Dandan
Chen, Jiazhang
Metagenomics Analysis Reveals Compositional and Functional Differences in the Gut Microbiota of Red Swamp Crayfish, Procambarus clarkii, Grown on Two Different Culture Environments
title Metagenomics Analysis Reveals Compositional and Functional Differences in the Gut Microbiota of Red Swamp Crayfish, Procambarus clarkii, Grown on Two Different Culture Environments
title_full Metagenomics Analysis Reveals Compositional and Functional Differences in the Gut Microbiota of Red Swamp Crayfish, Procambarus clarkii, Grown on Two Different Culture Environments
title_fullStr Metagenomics Analysis Reveals Compositional and Functional Differences in the Gut Microbiota of Red Swamp Crayfish, Procambarus clarkii, Grown on Two Different Culture Environments
title_full_unstemmed Metagenomics Analysis Reveals Compositional and Functional Differences in the Gut Microbiota of Red Swamp Crayfish, Procambarus clarkii, Grown on Two Different Culture Environments
title_short Metagenomics Analysis Reveals Compositional and Functional Differences in the Gut Microbiota of Red Swamp Crayfish, Procambarus clarkii, Grown on Two Different Culture Environments
title_sort metagenomics analysis reveals compositional and functional differences in the gut microbiota of red swamp crayfish, procambarus clarkii, grown on two different culture environments
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8558459/
https://www.ncbi.nlm.nih.gov/pubmed/34733252
http://dx.doi.org/10.3389/fmicb.2021.735190
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