Diet is known to influence intestinal microbiota in fish, but the specifics of these impacts are still poorly understood. Different protein/fibre ratio diets may result in differing structures and activities of gut microbiota. We examined the hindgut

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.

Herbivorous grass carp (Ctenopharyngodon idellus) has a powerful capability to digest cellulose from aquatic plants, depending on the cellulase complex produced by the cellulolytic bacterial community in the gastrointestinal (GI) tract. However, it remains uncertain which bacteria taxa may actively participate in the digestion of food fibre. In this study, a total of 499 cellulolytic bacteria from the gut content of grass carp fed on Sudan grass (242 strains) and artificial feedstuffs (257 strains) were randomly isolated and characterized using carboxymethyl-cellulose, microcrystalline cellulose and cellobiose agar media. The results showed that more than half of the isolates were capable of degrading carboxymethyl-cellulose and cellobiose, while the remaining isolates were restricted to microcrystalline cellulose decomposition, exclusively. The cellulolytic bacterial community was dominated by Aeromonas, followed by Enterobacter, Enterococcus, Citrobacter, Bacillus, Raoultella, Klebsiella, Hydrotalea, Pseudomonas, Brevibacillus and some unclassified bacteria, as revealed by 16S rDNA sequence analysis. Notably, grass carp fed on grass with high-fibre content harboured a higher diversity of cellulolytic bacteria than the ones fed on low-fibre feedstuffs. Our results provided evidence for a positive correlation between the content of food fibre and the diversity of cellulolytic bacteria in grass carp intestines. Thus, improving growth conditions and cellulase activities for GI cellulolytic microorganisms in grass carp intestines are critical for effective utilization of feedstuffs containing high fibre levels.

Traditional culture-based technique and 16S rDNA sequencing method were used to investigate the mucosa-associated autochthonous microbiota of grass carp (Ctenopharyngodon idellus). Twenty-one phylotypes were detected from culturable microbiota, with Aeromonas, Shewanella, Lactococcus, Serratia, Brevibacillus, Delftia, Pseudomonas, Pantoea, Enterobacter, Buttiauxella and Yersinia as their closest relatives. Genomic DNA was directly extracted from the gut mucosa of C. idellus originating from six different geographical regions, and used to generate 609 random bacterial clones from six clone libraries and 99 archaeal clones from one library, which were grouped into 67 bacterial and four archaeal phylotypes. Sequence analysis revealed that the intestinal mucosa harboured a diversified bacterial microbiota, where Proteobacteria, Firmicutes and Bacteroidetes were dominant, followed by Actinobacteria, Verrucomicrobia and DeinococcusThermus. The autochthonous bacterial communities in the gut mucosa of fish from different aquatic environments were not similar (C s < 0.80), but c-Proteobacteria was a common bacterial class. In comparison to bacterial communities, the archaeal community obtained from one library consisted of Crenarchaeota and Euryarchaeota. These results demonstrate that molecular methods facilitate culture-independent studies, and that fish gut mucosa harbours a larger bacterial diversity than previously recognized. The grass carp intestinal habitat selects for specific bacterial taxa despite pronounced differences in host environments.

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Fish meal (FM) is the major protein source in diet of aquaculture animal, especially carnivorous species, like turbot (Scophthalmus maximus). Turbot is a native European seawater fish and has now been introduced to the worldwide. Aquaculture production of turbot becomes increasingly important due to its high commercial value (FAO, 2014). As a typical carnivorous fish, turbot requires high amounts of dietary crude protein (about 50% of dry dietary matter), which mainly relies on FM