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Factors influencing the grass carp gut microbiome and its effect on metabolism.pdf

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Factors influencing the grass carp gut microbiome and its effect on metabolism

R E S EA RCH AR T I C L E Factors influencing the grass carp gut microbiome and its effect on metabolism Jiajia Ni1,2,3, Qingyun Yan1, Yuhe Yu1 Tanglin Zhang4 1Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; 2Guangdong Institute of Microbiology, Guangzhou, China; 3State Key Laboratory of Applied Microbiology, South China (The Ministry-Province Joint Development), Guangzhou, China; and 4State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China Correspondence: Yuhe Yu, Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuchang District, Wuhan 430072, China. Tel./fax: +86 27 e-mail: yhyu@ Received 11 August 2013; revised 12 November 2013; accepted 14 November 2013. Final version published online 11 December 2013. DOI: 10.1111/1574-6941.12256 Editor: Julian Marchesi Keywords grass carp; gut microbiome; metabolism; metagenome. Abstract Gut microbiota have attracted extensive attention recently because of their important role in host metabolism, immunity and health maintenance. The present study focused on factors affecting the gut microbiome of grass carp (Ctenopharyngodon idella) and further explored the potential effect of the gut microbiome on metabolism. Totally, 43.39 Gb of screened metagenomic sequences obtained from 24 gut samples were fully analysed. We detected 1228 phylotypes (116 Archaea and 1112 Bacteria), most of which belonged to the phyla Firmicutes, Proteobacteria and Fusobacteria. Totally, 41 335 of the detected open reading frames (ORFs) were matched to Kyoto Encyclopedia of Genes and Genomes pathways, and carbohydrate and amino acid metabolism was the main matched pathway deduced from the annotated ORFs. Redun- dancy analysis based on the phylogenetic composition and gene composition of the gut microbiome indicated that gut fullness