The malleable gut microbiome of juvenile rainbow trout (Oncorhynchus mykiss): Diet-dependent shifts of bacterial community structures

Abstract

Plant-derived protein sources are the most relevant substitutes for fishmeal in aquafeeds. Nevertheless, the effects of plant based diets on the intestinal microbiome especially of juvenile Rainbow trout (Oncorhynchus mykiss) are yet to be fully investigated. The present study demonstrates, based on 16S rDNA bacterial community profiling, that the intestinal microbiome of juvenile Rainbow trout is strongly affected by dietary plant protein inclusion levels. After first feeding of juveniles with either 0%, 50% or 97% of total dietary protein content derived from plants, statistically significant differences of the bacterial gut community for the three diet-types were detected, both at phylum and order level. The microbiome of juvenile fish consisted mainly of the phyla Proteobacteria, Firmicutes, Bacteroidetes, Fusobacteria and Actinobacteria, and thus fits the salmonid core microbiome suggested in previous studies. Dietary plant proteins significantly enhanced the relative abundance of the orders Lactobacillales, Bacillales and Pseudomonadales. Animal proteins in contrast significantly promoted Bacteroidales, Clostridiales, Vibrionales, Fusobacteriales and Alteromonadales. The overall alpha diversity significantly decreased with increasing plant protein inclusion levels and with age of experimental animals. In order to investigate permanent effects of the first feeding diet-type on the early development of the microbiome, a diet change was included in the study after 54 days, but no such effects could be detected. Instead, the microbiome of juvenile trout fry was highly dependent on the actual diet fed at the time of sampling.

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

“…Such a difference between Chao 1 richness was already noted in intestinal microbiota of rainbow trout fed with or without plant protein sources (Desai et al., ). In a recent study (Michl et al., ), this index was significantly lower in trout fry fed a diet devoid of marine protein sources, compared to fish fed diets including such ingredients, at least from day 54 to day 93 after start feeding. Bioprocessed soybean meal high dietary inclusion decreased richness indices in the faecal samples from the distal intestine of rainbow trout, compared to a control group with fish meal as main protein source (Bruce, Neiger, & Brown, ).…”

“…Despite the strong dominance of the main OTU, the individual bacterial communities were highly variable both in terms of α‐ and β‐diversity. A high variability in intestinal microbiota has been already observed in rainbow trout within the same experiment amongst individuals (Etyemez & Balcazar, ; Lowrey, Woodhams, Tacchi, & Salinas, ; Lyons et al., ,,; Michl et al., ) and families (Navarrete et al., ), or depending on the development stage (Ingerslev, von Gersdorff Jorgensen et al., ; Michl et al., ) and sampling date (Desai et al., ; Ingerslev, Strube et al., ). The individual variability was likely accentuated by the analytical procedures.…”

“…More recently, the next‐generation sequencing methods have brought new insight into microbiota, and several studies dealt with the influence of plant‐based diet on intestinal microbiota in fish (reviewed by Ghanbari, Kneifel, & Domig, ). A recent study investigated the effects of a diet devoid of animal protein sources on the gut microbiome of rainbow trout juveniles during the first 3 months of feeding (Michl et al., ). Most studies showed that the bacterial communities in the intestine of rainbow trout changed significantly, depending on the diet with or without plant protein sources as partial substitute for fish meal (Desai et al., ; Heikkinen et al., ; Ingerslev, Strube et al., ; Ingerslev, von Gersdorff Jorgensen et al., ; Mansfield et al., ; Merrifield, Dimitroglou, Bradley, Baker, & Davies, ; Navarrete et al., ; Wong et al., ).…”

Dietary live yeast and increased water temperature influence the gut microbiota of rainbow trout

“…; Michl et al . ) and Atlantic salmon (Gajardo et al . ) fed diets with higher inclusion levels of FM.…”

Diet and diet‐associated bacteria shape early microbiome development in Yellowtail Kingfish (Seriola lalandi)

“…While this bacterial group is commonly associated with the gastrointestinal tract of freshwater fish, it has also been found in some cultivated marine species (Hennersdorf et al ., ; Tarnecki et al ., ). Although the specific role of Fusobacteriaceae for S. lalandi is yet to be determined, these bacteria have previously been associated with carnivorous fish (Liu et al ., ; Michl et al ., ), indicating that they may assist in the breakdown of the animal protein components of their diet. Interestingly, the pattern of a shift from a Proteobacteria to a Firmicutes in the larval microbiota reflects recent observation of the gut microbiome in adult S. lalandi, where Firmicutes were higher in abundance in aquaculture‐raised kingfish and Proteobacteria more abundant in wild‐caught individuals (Ramirez and Romero, ).…”