Next generation sequencing for gut microbiome characterization in rainbow trout (Oncorhynchus mykiss) fed animal by-product meals as an alternative to fishmeal protein sources

Abstract

Animal by-product meals from the rendering industry could provide a sustainable and commercially viable alternative to fishmeal (FM) in aquaculture, as they are rich in most essential amino acids and contain important amounts of water-soluble proteins that improve feed digestibility and palatability. Among them, poultry by-product meal (PBM) have given encouraging results in rainbow trout (Oncorhynchus mykiss). However, the introduction of new ingredients in the diet needs to be carefully evaluated since diet is one of the main factors affecting the gut microbiota, which is a complex community that contributes to host metabolism, nutrition, growth, and disease resistance. Accordingly, we investigated the effects of partial replacement of dietary FM with a mix of animal by-product meals and plant proteins on intestinal microbiota composition of rainbow trout in relation to growth and feeding efficiency parameters. We used 1540 trout with an initial mean body weight of 94.6 ± 14.2 g. Fish were fed for 12 weeks with 7 different feed formulations. The growth data showed that trout fed on diets rich in animal by-product meals grew as well as fish fed on control diet, which was rich in FM (37.3%) and PBM-free. High-throughput 16S rRNA gene amplicon sequencing (MiSeq platform, Illumina) was utilised to study the gut microbial community profile. After discarding Cyanobacteria (class Chloroplast) and mitochondria reads a total of 2,701,274 of reads taxonomically classified, corresponding to a mean of 96,474 ± 68,056 reads per sample, were obtained. Five thousand three hundred ninety-nine operational taxonomic units (OTUs) were identified, which predominantly mapped to the phyla of Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria. The ratio between vegetable and animal proteins proved to play a central role in determining microbiome profiles and Firmicutes and Proteobacteria phyla were particularly discriminatory for diet type in trout. Plant ingredients favoured a higher Firmicutes:Proteobacteria ratio than animal proteins. Acceptable abundance of Firmicutes was guaranteed by including at least 25% of vegetable proteins in the diet regardless of animal protein source and percentage. In summary animal by-product meals, as replacements to FM, gave good results in terms of growth performances and did not induce significant changes in gut microbial richness, thus proving to be a suitable protein source for use in rainbow trout aqua feed.

Alternative dietary protein and water temperature influence the skin and gut microbial communities of yellowtail kingfish (Seriola lalandi)

“…The relative abundance of OTUs assigned to Photobacterium and Lawsonella were increased in the skin mucosa of fish fed SPC at both 22 C and 26 C when compared to the control treatment. Lawsonella belongs to the family Corynebacteriaceae and increases in the abundance of this family have also been previously reported in response to altered diet (Rimoldi et al, 2018). Rimoldi et al (2018) noted that the relative abundance of Corynebacteriaceae was increased in the gut of rainbow trout fed diets containing high proportions of animal by-product compared to FM diets, indicating that alternative feeds may specifically impact this family.…”

“…Lawsonella belongs to the family Corynebacteriaceae and increases in the abundance of this family have also been previously reported in response to altered diet (Rimoldi et al, 2018). Rimoldi et al (2018) noted that the relative abundance of Corynebacteriaceae was increased in the gut of rainbow trout fed diets containing high proportions of animal by-product compared to FM diets, indicating that alternative feeds may specifically impact this family. Low levels of Photobacterium have been noted in past microbiome surveys of the skin of marine fish; however, this genus showed higher relative abundance in this study than previously reported (Legrand et al, 2018;Minniti et al, 2017;Chiarello et al, 2015;Siriyappagouder et al, 2018).…”

Habitat and seasonality shape the structure of tench (Tinca tinca L.) gut microbiome

“…Because the fish-gut microbiome is important for host health, it is generally accepted that identification of the gastrointestinal microbiota is undoubtedly important for understanding the functional interactions between the microbes and the host 11 . Although there have been some studies on the gastrointestinal microbiome of various fish species 10,12,13 , to the best of our knowledge, there is a lack of studies on the gut microbiome of tench (T. tinca L.).…”

Gut microbiome analysis of fast- and slow-growing Rainbow Trout (Oncorhynchus mykiss)

“…These bacteria produce microbial metabolites such as short-chain fatty acids during glucose fermentation [37]. Such fatty acids can improve growth rate of rainbow trout [3]. These bacteria, perhaps, can be used as probiotics since they produce enzymes for fatty acid degradation, help in breakdown of food and produce valuable nutrients and energy [38][39][40][41].…”

“…Selective breeding is one strategy that can be used to improve important phenotypic traits and help in understanding the genetic architecture and the role of molecular factors causing genetic variation among different fish [2]. Family-based selection procedures have been undertaken by the United States Department of Agriculture (USDA), National Center for Cool and Cold-Water Aquaculture (NCCCWA) to improve growth rate, fillet quality and disease resistance of rainbow trout [3]. A growth-selected line was developed starting in 2002, and since then yielded a genetic gain of approximately 10% in improved growth performance per generation [4].…”