Impact of Fishmeal Replacement in Diets for Gilthead Sea Bream (Sparus aurata) on the Gastrointestinal Microbiota Determined by Pyrosequencing the 16S rRNA Gene

Abstract

Recent studies have demonstrated the impact of diet on microbiota composition, but the essential need for the optimization of production rates and costs forces farms and aquaculture production to carry out continuous dietary tests. In order to understand the effect of total fishmeal replacement by vegetable-based feed in the sea bream (Sparus aurata), the microbial composition of the stomach, foregut, midgut and hindgut was analysed using high-throughput 16S rDNA sequencing, also considering parameters of growth, survival and nutrient utilisation indices.A total of 91,539 16S rRNA filtered-sequences were analysed, with an average number of 3661.56 taxonomically assigned, high-quality sequences per sample. The dominant phyla throughout the whole gastrointestinal tract were Actinobacteria, Protebacteria and Firmicutes. A lower diversity in the stomach in comparison to the other intestinal sections was observed. The microbial composition of the Recirculating Aquaculture System was totally different to that of the sea bream gastrointestinal tract. Total fishmeal replacement had an important impact on microbial profiles but not on diversity. Streptococcus (p-value: 0.043) and Photobacterium (p-value: 0.025) were highly represented in fish fed with fishmeal and vegetable-meal diets, respectively. In the stomach samples with the vegetable diet, reads of chloroplasts and mitochondria from vegetable dietary ingredients were rather abundant. Principal Coordinate Analysis showed a clear differentiation between diets in the microbiota present in the gut, supporting the presence of specific bacterial consortia associated with the diet.Although differences in growth and nutritive parameters were not observed, a negative effect of the vegetable diet on the survival rate was determined. Further studies are required to shed more light on the relationship between the immune system and sea bream gastrointestinal tract microbiota and should consider the modulation of the microbiota to improve the survival rate and nutritive efficacy when using plant-based diets.

Dietary Butyrate Helps to Restore the Intestinal Status of a Marine Teleost (Sparus aurata) Fed Extreme Diets Low in Fish Meal and Fish Oil

“…In particular, the intestinal inflammatory profile, the antioxidant activation, the imbalance of the genes involved in mucus production, the changes in the epithelial junctions, and the decrease in Rt were returned to the levels of control fish. Recent studies have shown that fish meal replacement also has an impact on fish microbial profile [63]. Thus, further studies are underway to determine the changes induced in the intestinal microbiome and the possible protection of fish against pathogen challenges with this additive.…”

Ontogenetic Characterization of the Intestinal Microbiota of Channel Catfish through 16S rRNA Gene Sequencing Reveals Insights on Temporal Shifts and the Influence of Environmental Microbes

“…Singletons, or OTUs represented by only one sequence read, were removed from analysis. Clusters assigned to the order chloroplast or the family mitochondria were removed from analysis, as they represented reads derived from plant material found in the diets and eukaryotic and host mitochondrial DNA, respectively, and were not considered functional microbiota [47]. We further required OTUs to account for at least 0.0001% of the overall abundance, in order to reduce the incidence of spurious OTUs.…”

Fish intestinal microbiome: diversity and symbiosis unravelled by metagenomics

“…,b; Estruch et al . ; Schmidt et al . ), as concern over the use of fishmeal forces aquaculturists to test new, plant protein‐based formulations.…”

“…Diet is recognized as a primary factor influencing diversity and community structure of fish gut microbiomes. The majority of studies relating diet and microbiome composition alter diet treatments in culture or controlled settings (Desai et al 2012;Ingerslev et al 2014a,b;Estruch et al 2015;Schmidt et al 2016), as concern over the use of fishmeal forces aquaculturists to test new, plant protein-based formulations. As microbial communities play an important role in nutrient acquisition and provide a protective barrier against opportunistic pathogens (Llewellyn et al 2014), gut microbiome manipulation is often tested as a mechanism to increase feed efficiency, growth and disease resistance of fish in aquaculture (Dimitroglou et al 2011).…”