Beyond 2020 >> Work packages >> Microbiome

Microbiome

This work package is motivated by studies recently published by University of Glasgow and University College Cork with partners in Canada (University of Laval) and in Wales (University of Bangor) into the biogeography of gut microbiomes of Atlantic salmon sampled in Burrishoole. As the BEYOND 2020 is envisaged as a part of an establishment phase for a longer programme of observations we have planned for samples to be collected throughout.
Environmental and biological samples will be collected on a seasonal basis for microbiome analysis as part of this work package. A non-lethal intestinal wash will be taken for microbial DNA extraction and sequencing from eel and stickleback collected in the Srahrevagh river, Lough Feeagh and Lough Furnace. Water and control samples will also be taken to monitor environmental microbiome fluctuations as well as potential contamination. DNA extraction from faeces will be achieved using a QIAGEN DNA stool kit which improves on both DNA yields and PCR inhibitor removal as compared to other methodologies. Profiling of the gut microbiota will be via amplification and sequencing of the 16S v4 region on an Illumina MiSeq platform. (Direct shotgun sequence is not possible in teleosts due to heavy contamination with host genetic material. Microbial amplicon sequence will be analysed using standard and custom work flows. A sub-set of fish will be euthanized and their alimentary canal (cardiac, stomach, the pyloric caeca, mid- intestine, posterior intestine) removed for epithelial histology (‘villus’ -- salmon have densely folded columnar epithelia rather than villi -- density and folding) and gut morphology measurements. In addition, Stickleback from the common garden experiments will be similarly sampled and screened. This work package will deliver microbiome gut morphology profiles of stickleback in the Burrishoole system and a microbiome profile and gut morphology of European eel in the Burrishoole system.