title: Metatranscriptomic discovery of plant biomass-degrading capacity from grass carp intestinal microbiomes.
abstract: Despite the economic importance of fish, the ecology and metabolic capacity of fish microbiomes are largely unknown. Here, we sequenced the metatranscriptome of the intestinal microbiota of grass carp, Ctenopharyngodon idellus, a freshwater herbivorous fish species. Our results confirmed previous work describing the bacterial composition of the microbiota at the phylum level as being dominated by Firmicutes, Fusobacteria, Proteobacteria and Bacteriodetes. Comparative transcriptomes of the microbiomes of fish fed with different experimental diets indicated that the bacterial transcriptomes are influenced by host diet. Although hydrolases and cellulosome-based systems predicted to be involved in degradation of the main chain of cellulose, xylan, mannan and pectin were identified, transcripts with glycoside hydrolase modules targeting the side chains of noncellulosic polysaccharides were more abundant. Predominant 'COG' (Clusters of Orthologous Group) categories in the intestinal microbiome included those for energy production and conversion, as well as carbohydrate and amino acid transport and metabolism. These results suggest that the grass carp intestinal microbiome functions in carbohydrate turnover and fermentation, which likely provides energy for both host and microbiota. Grass carp intestinal microbiome thus reflects its evolutionary adaption for harvesting nutrients for an herbivore with a high-throughput nutritional strategy that is not dominated by cellulose digestion but rather the degradation of intracellular polysaccharides.
authors.affiliation: Institute of Hydrobiology, Chinese Academy of Sciences, and the Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Wuhan, Hubei Province 430072, P. R. China Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, P. R. China.
authors.forename: Shangong
authors.initials: S
authors.lastname: Wu
authors.affiliation: Shanghai Majorbio Bio-Pharm Technology Co., Ltd, Shanghai 201203, P. R. China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Ren
authors.affiliation: Institute of Hydrobiology, Chinese Academy of Sciences, and the Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Wuhan, Hubei Province 430072, P. R. China.
authors.forename: Chun
authors.initials: C
authors.lastname: Peng
authors.affiliation: Institute of Hydrobiology, Chinese Academy of Sciences, and the Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Wuhan, Hubei Province 430072, P. R. China.
authors.forename: Yaotong
authors.initials: Y
authors.lastname: Hao
authors.affiliation: Institute of Hydrobiology, Chinese Academy of Sciences, and the Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Wuhan, Hubei Province 430072, P. R. China.
authors.forename: Fan
authors.initials: F
authors.lastname: Xiong
authors.affiliation: Institute of Hydrobiology, Chinese Academy of Sciences, and the Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Wuhan, Hubei Province 430072, P. R. China gtwang@ihb.ac.cn.
authors.forename: Guitang
authors.initials: G
authors.lastname: Wang
authors.affiliation: Institute of Hydrobiology, Chinese Academy of Sciences, and the Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Wuhan, Hubei Province 430072, P. R. China.
authors.forename: Wenxiang
authors.initials: W
authors.lastname: Li
authors.affiliation: Institute of Hydrobiology, Chinese Academy of Sciences, and the Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Wuhan, Hubei Province 430072, P. R. China.
authors.forename: Hong
authors.initials: H
authors.lastname: Zou
authors.affiliation: Department of Microbiology, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Esther R
authors.initials: ER
authors.lastname: Angert
mesh_terms: D000818:Animals; D002347:Carps / Q000382:microbiology*; D002482:Cellulose / Q000378:metabolism; D045182:Fusobacteria / Q000378:metabolism*; D000069196:Gastrointestinal Microbiome / Q000502:physiology*; D006026:Glycoside Hydrolases / Q000235:genetics / Q000378:metabolism; D008351:Mannans / Q000378:metabolism; D010368:Pectins / Q000378:metabolism; D010944:Plants / Q000378:metabolism*; D020560:Proteobacteria / Q000378:metabolism*; D059467:Transcriptome; D014990:Xylans / Q000378:metabolism
chemical_list: D008351:Mannans; D014990:Xylans; D010368:Pectins; D002482:Cellulose; D006026:Glycoside Hydrolases
keywords: CAZy; grass carp; metatranscriptome; microbiome; plant cell wall polysaccharide