Abstract This study was designed to evaluate the changes number of cells of the two selected probiotic bacteria, B. longum TISTR2195 and L. plantarum TISTR1465, and yeast S. cerevisiae TISTR8656. The microorganisms were cultured in two types of media, namely selective media and protein base model. Selective media were divided into 4 sub-groups: with 2% glucose added as a positive control (i), inulin (ii), fructo-oligosaccharide (FOS) (iii), and without added carbon source as negative control (iv). Protein base media had chicken egg and coconut juice, baker’s yeast and potassium chloride (i), with 9% FOS (ii), or inulin (iii), or 7.34% whey protein (iv) to verify growth. All the probiotics were able to utilize inulin and FOS to growth. The numbers of cells increased with incubation time. However, L. plantarum produced an acidic in the selective culture medium significantly. Protein based with FOS and inulin added supported all probiotics growth. In addition, acetic acid content was the highest among short-chain fatty acids (SCFAs) produced. B. longum produced acetic acid very fast within 24 h. L. plantarum cultured in inulin added provided the peak level of acetic acid at 72 h. However, S. cerevisiae tended to decrease the SCFAs with incubation time.