You need to physically break the cells with bead beating using tiny glass beads. We use a "Fastprep" instrument from MP Bio and the corresponding blue kit/matrix (http://www.mpbio.com/product.php?pid=116004500&country=222); works very well for all mycobacteria.

In my opinion, a good kit of total RNA isolation is "RNeasy Mini Kit" from Qiagen. I often use it for RNA isolation from lymphocytes and epithelial cells.

https://www.qiagen.com/us/shop/sample-technologies/rna/total-rna/rneasy-mini-kit/#orderinginformation

By the way, I've find on Qiagen website a specific supplementary protocol for bacteria. So, I'm sending it to you and I hope it may be usuful for your problem.

Regards

In our lab, we regularly use for isolation of RNA from M.smegmatis combination of sonication + phenol/chloroform extraction.

The RNA is after that in good quality, we can also make NGS with it.

Thank you so much for your response