With an estimated 514 fish families, marine teleost fish exhibit remarkable diversity and have undergone exceptional adaptive radiation to occupy a range of habitats in the marine environment. The mucosal surfaces of fish (i.e., the skin, gills, and gut) are colonised by microorganisms from their surrounding environment upon birth and soon establish a stable ‘core’ community as they mature – this group of microorganisms and their genomes are collectively known as a microbiome. The gut microbiome is probably the most well-researched mucosal tissue in fish, owing to the significant role it plays in maintaining the overall health and wellbeing of the fish host with direct influences on immune homeostasis and digestive function. Gut microbiomes are complex and shaped by a range of factors including host genetics, ecology, health, nutrition, and environmental conditions. Different host species may thus harbour vastly different microbial communities despite occurring in the same environment or sharing similar evolutionary histories.
Museums contain a wealth of both extant and extinct marine specimens, which can be used to study genetic and microbial diversity. If valid, such specimens also can allow us to explore temporal changes in the gut microbiome of populations to yield insights into their response/adaptation to environmental change. DNA extracted from appropriately collected and stored fish specimens can inform us about the composition of the microbiome and when compared across different taxa residing in similar environmental conditions, can yield insights into patterns of phylosymbiosis. This study aims to explore the utility of frozen archival fish specimens housed within CSIRO’s Australian National Fish Collection (ANFC, Hobart) for microbiome investigations. Specifically, gut bacterial assemblages from historic specimens obtained from northern Australia (representing species belonging to two divergent [110 MYA] fish families - Labridae and Platycephalidae commonly found in the Gulf of Carpentaria) were surveyed by sequencing the V1-V2 region of the 16S rRNA gene on the Illumina MiSeq platform, revealing common (core) and unique constituents. It is anticipated that this data will serve as a baseline for future longitudinal studies investigating microbiome dynamics in these species in response to anthropogenic mediated climate change, and for providing evidence of phylosymbiosis.