Introduction
Understanding the evolutionary relationships between a host and its intestinal resident bacteria can transform how we understand adaptive phenotypic traits. The interplay between hosts and their resident bacteria inevitably affects the intestinal environment and, thereby, the living conditions of both the host and the microbiota. We present the gut metagenome from wild Atlantic salmon (Salmo salar), a new wild organism model with an intestinal microbiota of low complexity and a well-described population structure, making it well-suited for investigating co-evolution.
Methods
Sample collections for Atlantic salmon were taken from five locations across the coast of northern Norway, spanning 700 km. DNA extraction was performed using ZymoBiomics DNA miniPrep , followed by sequencing at Novogene (Cambridge, UK). Reference-based mapping and taxonomy annotation were applied to remove unknown eukaryotic contaminants and analyze eukaryotic gut content using MGmapper . Genome-resolved metagenomics was conducted with t o infer microbiome taxonomy, functionality and population structu . Population structure analysis was done to investigate co-divergence.
Results
Our data reveal a strong host selection of a core gut microbiota dominated by a single Mycoplasma species. We found a clear co-diversification between the population structure of Atlantic salmon and nucleotide variability of the intestinal Mycoplasma populations conforming to expectations from co-evolution between host and resident bacteria. Our results show that the stable microbiota of Atlantic salmon has evolved with its salmonid host populations while potentially providing adaptive traits to the salmon host populations, including defence mechanisms, biosynthesis of essential amino acids, and metabolism of B vitamins.
Conclusions
The case of Atlantic salmon studied here has not only furthered our evolutionary understanding of this species, but the findings also hold potential for further discoveries towards feed or health optimisation resulting in more sustainable aquaculture practices. We envisage that our study may inspire similar investigations in systems previously investigated using amplicon-based markers to reveal the intriguing functional host-microbiota interactions.