Hello,
I sequenced bacterial 16s amplicons from aerial plant parts for the first Time (i only did roots before) and the results give me 99 % of chloroplastic 16S (so from the plant), even 100 % in some samples. Does it usually happens with leaves samples, are there some methods to prevent this ?
Jean Legeay Chloroplast genes are always present in 16S sequencing data for plant samples. If the plant leaves are free of bacteria, you will get mostly chloroplast sequences. + Some endosymbiotic bacteria could be poorly amplified by the universal 16S primers - at least in theory.
@Alex Ignatov
Thank you for your answer,
So, i guess i Can assume that the leaves are either free of bacteria or that the bacteria are not amplified by classical 16S. Thanks.
Jean Legeay Look at Chen, L., Zhang, M., Liu, D., Sun, H., Wu, J., Huo, Y., ... & Zhang, L. (2021). Designing specific bacterial 16S primers to sequence and quantitate plant endo-bacteriome. Science China Life Sciences, 1-14.
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