Intestinal microbiota in rainbow trout,Oncorhynchus mykiss, fed diets with different levels of fish-based and plant ingredients: A correlative approach with some plasma metabolites

Abstract

The shortage of fish meal and fish oil has led to demonstrate the feasibility of omitting marine ingredients from the diet of rainbow trout. This complete suppression was further studied in the present experiment. Plasma markers indicated that the metabolism was deeply affected in trout fed plant ingredients. The pyrosequencing of reverse transcripts of partial 16S ribosomal RNA revealed the composition of the active bacterial community associated with intestinal mucosa. Most differences appeared between trout fed either a marine diet or a commercial‐like diet with large amounts of plant protein sources and oil. One taxonomic unit of Cetobacterium sp. dominated this microbiota, the overall composition of which was highly variable amongst individuals. This variability in trout fed without marine ingredients was less than in the other dietary groups. At the individual level, the relative prevalence of some bacteria correlated with the level of plasma markers, in particular two distinct taxonomic units of the genus Clostridium, which correlated either with plasma glucose or with several spectral regions containing tyrosine and phenylalanine resonances, detected by 1H‐NMR profiling. Such correlations deserve further investigation for identifying the functional roles of intestinal microbiota.

Metabolomics and fish nutrition: a review in the context of sustainable feed development

“…Metabolomic analysis of faeces has been used as a marker of microbiote activity in different fish species fed with different diets (Asakura et al 2014). Indeed, some correlations between plasma metabolites detected by 1 H-NMR and host microbiota species have been observed in rainbow trout fed commercial and plant-based diets by Gatesoupe et al (2018). NMR-based analyses of faeces of convict grouper (Epinephelus septemfasciatus) fed with a natural diet then with a manufactured diet showed an increase in carbohydrates, phospholipids and fatty acids and a decrease in branched-chain amino acids (Asakura et al 2014).…”

Microbial Communities of Culture Water and African Catfish Reared in Different Aquaculture Systems in Nigeria Analyzed Using Culture Dependent Techniques

“…This suggests that the gut microbial communities could as well be as a result of the feed. According to literature diets exert much influence in determining complexities of the gut microbial community starting from first feeding larval stages and its diversities [32,59,60,61,62]. The consortia of microbes like B.subtilis, Salmonella enteritidis and K.pneumoniae and E. coli could have lead to biofilms which were noticeable and could easily form in the earthen ponds and tarpaulin ponds than the concrete ponds due to the cement chemicals.…”

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“…Proteobacteria Aeromonas sp. OTU_23s (Gatesoupe et al, 2018). Similarly, use of high inclusion of bioprocessed soybean meal in the diets of rainbow trout decreased the microbial richness indices taken from distal intestine of the fish when compared to fishmeal (Bruce, Neiger, & Brown, 2018).…”

“…The frequency of feeding has also been noted as a short term deciding factor on the gut microbiome of fish (Parris et al 2018). Moreover, the use of alternative ingredients in feeds could affect gut microbial communities (Zhou, Ringø, Olsen, & Song, 2017;Gatesoupe, Fauconneau, & Deborde, 2018;Miao et al 2018). According to literature, diets exert much influence in determining complexities of the gut microbial community starting from first feeding larval stages and its diversities (Blanch, Alsina, Simon, & Jofre,1997;Reid, Treasurer, Adam, & Birkbeck, 2009;Giatsis, Sipkema, Smidt, Verreth, & Verdegem, 2014).…”

“…In a recent research on the nutrition of northern snake head, it was noted that different inclusions levels of soybean meal in their diets produced different gut microbial communities like Firmicutes, Lactococcus, Proteobacteria, Bacteroidetes and Planctomycetes (Miao et al, 2018). Firmicutes, were also notably present in plant protein diet fed fish (Gatesoupe et al, 2018). Several bacteria have been associated or commonly isolated from fish fed with fishmeal diets compared to plant based diets, for example, Sphingomonas sp.…”