Good morning, everyone,
I have a general questions that goes back to the sequencing step, before QIIME2 pipeline.
I work with amphibian samples, that are taken with sterile swabs. My question is: should I also sequence some blanks (new swabs, not used) to check for possible contamination or it is not necessary, since the material is sterile?
I appreciate your feedback!
Thanks
Hi @Cravo_Adri,
It’s a good practice to always include and sequence your negative controls. Generally speaking, it’s sufficient to include negative controls starting from the sample DNA extraction. However, if you’re dealing with low-biomass samples, i.e., the microbial DNA is expected to be very low in your samples, it’s also recommended to include negative controls during the sampling. You can take out a few sterile swabs, pretend to take samples and preserve these swabs as you do for real biological samples.
For more information, you can read this paper by Kim et al., 2017: Optimizing methods and dodging pitfalls in microbiome research
hi, @yanxianl, sorry for the delay, I just forgot to answer. But yes, I’ve done what you suggested and added some blanks, but starting from the dna extraction, since I could not go back to the sampling location.
Thanks a lot!