Metabarcoding of museum samples stored in formalin: analysing the prey and microbiome composition of Antarctic fish (Trematomus sp.)
Heindler, F.M. (2018). Metabarcoding of museum samples stored in formalin: analysing the prey and microbiome composition of Antarctic fish (Trematomus sp.). Brilliant Marine Research Idea 2017 – Final Report. KULeuven, Laboratory of Biodiversity and Evolutionary Genomics: Leuven. 7 pp.
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| Abstract |
We present the first study to assess the prey item and microbiome composition of Antarctic fish that have been stored in formalin for prolonged amounts of time. We applied a technique of treatment of the stomachs/hind guts with an alkaline solution and heat in order to extract DNA. We then amplified a region of the COI mitochondrial gene for stomachs and 16S rRNA nuclear gene for the hindgut samples to assess the prey item and microbiome composition, respectively. We employed extensive quality and contamination controls in order to ensure reliable results. We found that stomach samples were characterized strongly by contamination. In contrast, microbiome composition clustered differently from all our quality control samples. Therefore, we have high confidence in the quality of the microbiome composition data. Furthermore, we found a weak correlation between microbiome composition and standard length (size) of the fish. Due to high dropout rates among samples few were left and therefore the results are lacking statistical confidence. Results will be compared with contemporary samples once these have been further analyzed. |
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