Frozen in time: using museomics to investigate the gut bacteriome of fish from the Gulf of Carpentaria

AbstractArchival fish collections are not only an important resource for informing systematic and taxonomic research, but also for elucidating the diversity of microorganisms that colonise the body surfaces of fish and which interact with the host to drive health and fitness (as the ‘microbiome’). Effectively ‘frozen in time’, these specimens act as potential host–microbiome time capsules, enabling the opportunity to gain valuable insights into their dynamics, although to date they have been underutilised. Here, whole frozen archived specimens from seven well‐represented fish species (belonging to the Labridae and Platycephalidae) collected from the Gulf of Carpentaria off the northern coast of Australia and stored in the Australian National Fish Collection for 11 years were evaluated for determining their suitability for fish gut bacteriome investigations. DNA yield and quality were assessed from extracts obtained from samples of the gastrointestinal tract (from thawed specimens) and the 16S rRNA gene sequenced using the Illumina platform to determine the core and unique gut bacteriome constituents of these fish species. High‐quality bacterial DNA from frozen specimens produced comparable numbers of sequence reads and bacterial amplicon sequence variants to contemporary studies and identified some unique and common constituents across the two fish families, notably members belonging to the Gammaproteobacteria as well as putative symbionts belonging to the genus Epulopiscium. This study highlights for the first time the relevance of frozen specimens for gut bacteriome investigations and provides a baseline for future comparative investigations of contemporary specimens.