The pellet concentration is simply not sufficient for you to see with the unaided eye. It follows that you need some form of magnifying aid if you are so particular about that concentration.

Hi, Marine Makoa Meng

I do agree with Maurice Ekpenyong but you need to give me a few more data in order to give you my thoughts back on it.

Tell me: What xg force you have used? Too much may be lysing your bacterial cells (although not that easy) and too little may have left it loosen, and then, it got free to go during your washings. Ok? Lastly, Have you checked your DNA by spectrophotometry or a gel or any other technique?

An option, you may do a few tests with any DNA staining, such as, SYBR safe/ETBR and look at the transilluminator to check for presence of a stain on the tube, for instance.

I hope it helps you.

Thank you for your answers Adriano Costa de Alcantara and Maurice Ekpenyong .

I have used 5000 xg during 15 minutes and I have also tried 13 000 xg and 16 000 xg during 10 minutes. Everytime, I have a visible pellet for 108 CFU/mL. I had the same hypothesis and I kept the surnatant for the other concentrations and put 10 µL on agar and I saw some colonies grow in 24h.

I checked my DNA by a Qubit measure and I always have less than 0,50 ng/mL for my concentrations ranging from 102 CFU/mL to 105 CFU/mL (without dilution of the DNA elution).