First, I disagree with your selection of hydrolysis conditions. In my opinion, your best bet is cold superconcentrated (i.e. more HCl gas added, possibly under pressure if you can, otherwise make sure it is well chilled) hydrochloric acid. This hydrolyses the glycosidic linkages quite well over time, BUT by and large it does not send sugars down the hydroxymethyl cellulose route. Evaporate off the HCl under vacuum, still cold. Filter

Now, to purify from the sulphuric route, first filter, then make slightly alkaline and absorb the phenol anions on an ion exchange resin, then treat with activated charcoal. That should get you pure enough sugars. It pays to drive off volatile terpenes from your chips before you start.

Acid hydrolysis using concentrated sulfuric acid is the predominant and most efficient chemical method. In general, during acid hydrolysis, the amorphous regions were chopped down to lower molecular sizes such as sugar. Besides that, some other impurities (not cellulose) were also chopped down. The materials will contribute to the color of the suspension.

I agree with Dr @ Balajii Muthusamy

The cold hydrochloric acid route definitely gets the best yield, and was used by the Germans during WW2. I have used it in the lab to make sugars. The yields are better, industrially there is much less to do which is important for costs, the acid is recycled, by and large, and finally there are much fewer degradation products. Note the German chemists and engineers were pretty clever, and they went for the best yields

So your question is not about why E.coli will not grow but why the loss of sugar in the forms xylose and glucose. So, the problem was the method of hydrolysis. The cold hydrochloric acid method mentioned by Ian should serve you better

As previously mentioned by Ian miller, cold hydrochloric acid method is best. Various literature data were available fir reference on topic : cold HCL treatment.

Thanks Ian Miller, Muthusaravanan Sivaramakrishnan , Maurice Ekpenyong

, Balajii Muthusamy , and Karen A. Darbinyan for your kind and valuable suggestions. Unfortunately, I could not change the method of hydrolysis I was using for wood-based lignocellulosic material (Project constraints). However, I worked towards optimizing detoxification strategy using charcoal and E. coli cells were able to grow quite well in the detoxified solution.