In an old experiment dating back to 2014, some 16S libraries from plant samples were prepared, with the aim to identify the microbial community living/contaminating the surface of the fruits.
The primer choice was the couple 27F and 533R.
Sadly, once analyzed with QIIME2 and clustered, out of 12 samples, 10 had chloroplast DNA contaminations percentages up to 99% (80-99%), making them completely useless.
I'd like to run the experiment again, with Illumina technology, addressing the problem of the primers not being specific enough to distinguish between plastid and bacteria DNA.
At the moment, the only scientific paper directly addressing the issue I was able to find was this one, but it's quite an old one.
Any suggestions here? Thanks in advance.