Could be sampling error especially if your "new" one is not very common in the environment. Also you have been storing your bacteria in a desiccating environment for 4 months with limited accessible nutrients. Only spore forming species could last in such a hostile environment.

Thank you Robert Adolf Brinzer actually, I'm working with solid-state fermented tea (like Pu-erh tea) and the "old" bacteria were observed spore-forming. I did mix tea bags well when sampling but maybe it's not enough.

I agree with Robert Adolf Brinzer that it could be sampling error but you have changed the environment for 4 months so you may have selected for growth of some different organisms better suited to the new environment.

Thank you @Michael J. Benedik

Storing bacteria in a refrigerator is practical for short periods of time. Bacteria are best preserved by freezing at ultralow to cryogenic temperatures, or by freeze drying. However, some bacterial cultures may be used daily, thus having a readily available active culture can be practical.

Also, changes in the environment/medium can initiate microbial dynamics. Alterations in pH, moisture, nutrients, temperature, oxygen, presence of metabolites as a result of microbial activities, etc, can render some microbes non-culturable, though viable.

To conclude whether an organism is present or not, I suggest molecular identification of viable organisms from the sample. This will capture both the culturable and non-culturable organisms.

Though contamination of the culture can be a source of new organisms.