Most of the analysis to determine the composition and diversity of the intestinal microbiota in living beings is carried out from stool samples or directly from the intestine. However, the applications of these methods are limited by the need for fresh, unfixed tissues that allow high-quality DNA extraction. Fixed, paraffin-embedded tissue is an invaluable resource for retrospective molecular genetic studies, but high-quality genomic DNA extraction can be problematic1 . Bouin’s solution, a compound fixative, is used in the histological evaluation of cells, due to the nuclear morphological preservation obtained1. Fixation facilitates obtaining images of cell localization and morphology2. however, it is unknown how bouin fixation affects the quality of DNA from the distal intestine of Atlantic Salmon. To tap into this potentially huge resource, it is imperative to develop methods to isolate high-quality, abundant DNA from fixed, paraffin-embedded tissue sections3.
DNA extraction from Salmo salar distal intestine samples embedded in paraffin, fixed with Bouin’s solution, was evaluated. For this, we use a DNA extraction kit that includes the combination of proteinase K digestion and column purification. By means of PCR using primers, we amplified the 16s and 23s gene. Amplified fragments of the expected sizes for the 16s gene were obtained, indicating that this method is suitable for the isolation of high-quality DNA.
Bibliography
1. Tang R-L, Fan L-Q. PLZFposc-KITpos-delineated A1–A4-differentiating spermatogonia by subset and stage detection upon Bouin fixation. Asian J Androl. 2019;21(3):309. doi:10.4103/AJA.AJA_103_18
2. Zhu L, Rajendram M, Huang KC. Effects of fixation on bacterial cellular dimensions and integrity. iScience. 2021;24(4). doi:10.1016/J.ISCI.2021.102348
3. Gloghini A, Canal B, Klein U, et al. RT-PCR Analysis of RNA Extracted from Bouin-Fixed and Paraffin-Embedded Lymphoid Tissues. J Mol Diagn. 2004;6(4):290. doi:10.1016/S1525-1578(10)60524-7