Influence of the diet on the microbial diversity of faecal and gastrointestinal contents in gilthead sea bream (Sparus aurata) and intestinal contents in goldfish (Carassius auratus)

Abstract

Fish intestinal microbiota changes with the diet and this effect is of particular interest considering the increasing substitution of fish meal by plant protein sources. The objective of this work was to study the effects of partial substitution of fish meal with lupin and rapeseed meals on gut microbiota of the gilthead sea bream (Sparus aurata) and in goldfish (Carassius auratus). Faecal, gastrointestinal and intestinal contents were characterized using culture-based and molecular methods. Vibrionaceae was high in faeces and in the intestine of sea bream, while a more diverse microbiota was retrieved from the stomach, where Bacillales and Flavobacteriaceae appeared to be influenced by the diet. PCR-denaturing gradient gel electrophoresis profiles revealed a high diversity of the microbiota transiting in the sea bream digestive tract, with a shift between gastric and intestinal communities, especially in the group fed with lupin meal. The goldfish was different, with a predominance of Aeromonas spp., Shewanella putrefaciens and Staphylococcus spp. among the aerotolerant-cultivable bacteria. The culture-independent methods revealed the presence of anaerobes like Cetobacterium somerae, and that of Vibrio spp., likely in a viable, but noncultivable state. There was a trend towards decreasing diversity in goldfish microbiota with the partial substitution by lupin, which seemed to inhibit some taxa.

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

“…Roeselers et al (2011) confirmed that Proteobacteria, especially c-Proteobacteria, were dominant in the intestinal microbiota of fishes living in sea and in freshwater, while the abundance of Firmicutes was highly variable in zebrafish, depending on the origin. Asfie et al (2003), Feng et al (2008 and Silva et al (2011) also identified Proteobacteria and Firmicutes as the dominant phyla in the intestine of C. auratus. Although the present study was generally consistent with these findings at the phylum level, the bacterial genera detected by Asfie et al (2003), Feng et al (2008) and Silva et al (2011) accounted for small proportions of the total reads in the present study (less than 0.5 %), except for Streptococcus (3.9 %) and Clostridium (1.0 %).…”

“…Asfie et al (2003), Feng et al (2008 and Silva et al (2011) also identified Proteobacteria and Firmicutes as the dominant phyla in the intestine of C. auratus. Although the present study was generally consistent with these findings at the phylum level, the bacterial genera detected by Asfie et al (2003), Feng et al (2008) and Silva et al (2011) accounted for small proportions of the total reads in the present study (less than 0.5 %), except for Streptococcus (3.9 %) and Clostridium (1.0 %). The high dominance of some genera in the previous studies was likely due to culture-dependent methods of characterization.…”

“…Limited investigations on the intestinal microbiota of goldfish (C. auratus) and gibel carp indicated that members from Proteobacteria and Firmicutes were dominant, and species of the genera Aeromonas, Acinetobacter, Bacillus, Cetobacterium, Clostridium, Lactococcus, Pseudomonas, Shewanella, Staphylococcus, Streptococcus, and Vibrio were common (Asfie et al 2003;Feng et al 2008;Silva et al 2011). However, an in-depth study was still needed to comprehend the microbial diversity in the intestine of this important species for aquaculture.…”

Illumina Based Analysis of Bacterial and Fungal Flora in Foreguts and Hindguts of Crucian Carp (Carassius Aumtus) in Retail Markets

“…Although gut microbiota has become an integral component of the host, and received increasing attention [18], the fungal diversity in fi sh gut fl ora is not still reported [10]. The fi sh gut microbiota is only focused on bacteria [7][8][9][10][11][12][13][14][15][16][17][18][19]. Our results showed that the hindguts contained more diverse fungi than those in foreguts.…”

“…Bacteria recovered from the skin and gills may be transient rather than resident on the fi sh surfaces [7]. The gastrointestinal microbiota in fi sh is constituted of facultative and obligate anaerobes, which may vary among fi sh species with different digestive apparatus [8].…”