A high-resolution map of the gut microbiota in Atlantic salmon (Salmo salar): A basis for comparative gut microbial research

Abstract

Gut health challenges, possibly related to alterations in gut microbiota, caused by plant ingredients in the diets, cause losses in Atlantic salmon production. To investigate the role of the microbiota for gut function and health, detailed characterization of the gut microbiota is needed. We present the first in-depth characterization of salmon gut microbiota based on high-throughput sequencing of the 16S rRNA gene’s V1-V2 region. Samples were taken from five intestinal compartments: digesta from proximal, mid and distal intestine and of mucosa from mid and distal intestine of 67.3 g salmon kept in seawater (12–14 °C) and fed a commercial diet for 4 weeks. Microbial richness and diversity differed significantly and were higher in the digesta than the mucosa. In mucosa, Proteobacteria dominated the microbiota (90%), whereas in digesta both Proteobacteria (47%) and Firmicutes (38%) showed high abundance. Future studies of diet and environmental impacts on gut microbiota should therefore differentiate between effects on mucosa and digesta in the proximal, mid and the distal intestine. A core microbiota, represented by 22 OTUs, was found in 80% of the samples. The gut microbiota of Atlantic salmon showed similarities with that of mammals.

Bacillus sp. QSI-1 Modulate Quorum Sensing Signals Reduce Aeromonas hydrophila Level and Alter Gut Microbial Community Structure in Fish

“…The fish intestine houses a dense and diverse microbial community, studies on fish gut microbiota have been reported by some researchers (Wu et al, 2013; Li et al, 2014; Kashinskaya et al, 2015; Gajardo et al, 2016), the gut microbiota is critical to health, and the microorganisms in the gut use chemical communication to coordinate and synchronize gene expression via the quorum-sensing regulatory pathway. Quorum sensing molecules, such as Autoinducer-2 (AI-2) and N-acyl-homoserine lactones (AHLs) are usually used by the gut microbiota (Borlee et al, 2008; Thompson et al, 2016).…”

Current Advances in Functional Genomics in Aquaculture

“…Gajardo et al [12] analysed the microbiota proile of the digesta and gut mucosal of Atlantic salmon (S. salar L.) fed commercial diets and showed that microbiota richness and diversity difered signiicantly between the digesta and gut. The digesta had a higher and diverse richness than the gut mucosa.…”

“…In terms of assembly, both whole genome shotgun and marker gene guided sequencing have been used on diferent aquatic organisms. The commonly used marker gene in metagenomics analyses is the 16S ribosomal RNA (16S rRNA), which has been widely used to characterize the microbiota of diferent aquatic organisms including rainbow trout [88,89], Atlantic salmon [11,12], turbot (Scophthalmus maximus) [90], lamprey (Lampetra morii) [91] and Baleen whale [92]. Whole genome shotgun sequencing has also been widely used in the study of environmental microbial communities and pathogens infecting diferent aquatic organisms.…”

“…These omics technologies have not only accelerated whole genome sequencing projects of diferent aquatic organisms [7,8], but they also have the capacity to unravel the sequences of entire genomes without prior knowledge of the genes to be sequenced thereby enhancing the discovery and annotation of novel genes in non-model species. And as shown from recent studies, their applications in aquaculture have accelerated our ability to identify emerging pathogens [9], monitor the microbiomes of diferent aquatic environments [10], develop nutritional diets with less side efects [11,12] and understand the cellular networks that regulate diferent biological processes in aquatic organisms [13][14][15]. It is evident from studies carried out this far that an integrated use of different omics technologies is bound to improve our production systems in aquaculture [10,12,[16][17][18].…”

“…And as shown from recent studies, their applications in aquaculture have accelerated our ability to identify emerging pathogens [9], monitor the microbiomes of diferent aquatic environments [10], develop nutritional diets with less side efects [11,12] and understand the cellular networks that regulate diferent biological processes in aquatic organisms [13][14][15]. It is evident from studies carried out this far that an integrated use of different omics technologies is bound to improve our production systems in aquaculture [10,12,[16][17][18]. Hence, this chapter provides an overview of diferent omics technologies currently used in aquaculture mainly focusing on their overall contribution to transforming genomics studies into functional applications.…”