Analysis of bacterial diversity in the intestine of grass carp (Ctenopharyngodon idellus) based on 16S rDNA gene sequences

Abstract

In the current study, we assessed bacterial diversity in the gut content of pond-reared grass carp (Ctenopharyngodon idellus), in the associated habitat environments (pond water and sediment) and in the ingested food (commercial feed and the reed Phragmites australis) by analysing 16S rDNA sequences from clone libraries. The highest bacterial diversity was observed in the gut content and was determined by the total number of operational taxonomic units, Shannon diversity index (H), Shannon equitability index (E H ), Coverage (C good ) and rarefaction curves calculated from the 16S rDNA gene libraries. Our data indicated that allochthonous gut microbes of grass carp were distinctively di¡erent from the corresponding environmental microbes. The pairwise similarity coe⁄cient (C s ) for microbe communities between gut content and ingested food was higher than for those between the gut content and habitats, indicating that the allochthonous microbiota identi¢ed in the intestines of grass carp were phylogenetically closer to those in the ingested food than to those in the habitat. Based on our study and previous research, we suggest that the digesta of grass carp harbours a microbiota phylogenetic core of Proteobacteria and Firmicutes and this observation deserves further investigations with respect to a potential pool of probiotics to grass carp.

Diversity of autochthonous bacterial communities in the intestinal mucosa of grass carp (Ctenopharyngodon idellus) (Valenciennes) determined by culture-dependent and culture-independent techniques

“…The bacterial communities were slightly different from the results reported by Wu et al (2012), who concluded that Proteobacteria, Firmicutes and Spirochaetes were the most abundant in the gut mucosa of C. idellus fed on ryegrass. However, the results are very similar to those of previous studies, which found that Proteobacteria and Firmicutes were the most common groups, while Bacteroidetes were relatively rare in the gut contents of different species of fish (Han et al 2010;Wu et al 2010Wu et al , 2012Roeselers, Mittge, Stephens, Parichy, Cavanaugh, Guillemin & Rawls 2011). In our study, c-Proteobacteria appeared consistently in the gut microbiota of C. idellus from different aquatic environments, suggesting that the members of this bacterial class are especially well adapted to conditions in the fish intestinal mucosa.…”

“…During this season, the gut mucosal microbiota of the fish will become relatively stable, and can be regarded as autochthonous. Recent studies on the diversity of the microbiota in the intestinal contents of C. idellus have revealed Proteobacteria and Firmicutes as the most common bacterial groups (Han, Liu, Zhou, He, Cao, Shi, Yao & Ringø 2010;Wu, Wang, Angert, Wang, Li & Zou 2012). However, these studies could not test autochthonous microbiota associated with intestinal mucosa exclusively.…”

Intestinal microbiota of gibel carp (Carassius auratus gibelio) and its origin as revealed by 454 pyrosequencing

“…These findings are consistent with the study of Lozupone and Knight (2007), who demonstrated that microbes in sediment are more phylogenetically diverse than any other environment type. However, Han et al (2010) reported that microbiota was more diverse in the gut content than in the samples collected from the rearing environment of grass carp, Ctenopharyngodon idellus. This incongruence may be due to the difference in methodology.…”

Continuous desulfurization and bacterial community structure of an integrated bioreactor developed to treat SO2 from a gas stream

“…Coverage analysis indicated that the bioreactor libraries represented approximately 80%-92% of the total number of clones examined, providing a dependable inventory of the bacterial 16S rRNA gene sequences present in the bioreactor. The C values observed in all the samples were larger than 0.70, which indicates that the clone number analyzed in each sample in this study is valid for microbial diversity analysis (Han et al, 2010). Sequences were assigned to a bacterial phylum according to their position in the phylogenetic tree (Fig.…”