I am trying to extract DNA from skin swabs of Salamandra atra but the DNA concentrations I get are very, very low (like < 0,5 ng/µl). I am using the Qiagen QIAamp DNA Micro Kit in combination with Promega DNA IQ Spin Baskets and the Qia Shredder column.

The tip of the swab is first incubated in 180µl Buffer ATL plus 20 µl Proteinase K at 56°C and 500 rpm. After 20 min I remove the swab and put it into a Spin Basket and put the basket back into the tube. Then I centrifuge it to extract the liquid out of the swab. Afterwards the swab is put back into the liquid. This step is repeated after other 20 min at 56°C. It is sort of a re-suspension (Adamowicz et al., 2014). After further 20 min I put the swab into the QIA Shredder column and centrifuge it to get all the liquid out of the swab. Afterwards I follow the normal protocol of the Qiagen Handbook (next step is adding lysis buffer). In the end I elute twice in 20µl Elution Buffer each.

Has anyone experience with skin swabs of S. atra? We are not looking for Bsal but we want to do microsatellite analyses. So I am looking for a way to get more DNA out of it than so far. We have done the same procedures before with the alpine newt and it worked better here (concentrations were 4-50 ng/µl). What could be the reason that it doesn't work as well with S. atra?

Thank you very much!