The evaluation of the levels of major colon microbiota populations (lactobacilli, bifidobacteria, enterobacteria) was carried out in two 15-days experiments on Wistar rats, exposed to stress factor (electric shock) and fed with different diets with the addition of biologic active micronutrients [extract from the leaves of Serratula coronata L. and Enzymatic hydrolyzate of the mussels meat (EHMM)]. In the first experiment animals were fed with a common vivarium diet. In the experimental group the water extract from leaves of Serratula coronata L. as a phytoecdysteroid source (5 mg per 1 kg body weight) was added to water. In the second experiment rats received balanced semisynthetic diet. In the diet of the experimental group the part of the protein (casein) was replaced by the peptides from EHMM. During the experiment the animal body weight was measured. On the 14th day of the experiment the animals were subjected to stress stimulation [electrodermal stimulation on paws (electric current 0.4 mA for 8 seconds)]. On the last day of the experiment the animals were euthanized by decapitation and micro-ecological research of protective microbiota populations in the cecal contents was carried out. The relative body weight increase was recorded in both experiments. In the second experiment in animals receiving EHMM this index (68.2 ± 3.0%) was considerably higher than in the control group and in the experimental group receiving no EHMM (57.2 ± 4.0 and 59.7 ± 2.8% respectively). The results of the microecological study showed different effect of diets with biologically active micronutrients on the population levels of lactobacilli. In the experiment with common vivarium diet no significant changes of the levels of the studied colon microbiota populations had been recorded in the rats of control group compared with rats of experimental group, exposed to stress factor but received no extract from Serratula coronata L. The decrease of the levels of lactobacilli by the end of the experiment was observed in the experimental group of rats received water extract from the leaves of Serratula coronata L (content of lactobacilli 7.76 ± 0.17 lg CFU/g) compared to those in control group and experimental group of rats received no extract (8.4 ± 0.09 and 8.69 ± 0.07 lg CFU/g respectively). Feeding with the balanced semisynthetic diet with the addition of EHMM or without it had a positive effect on the levels of lactobacilli and their balance with the aerobic component of the Enterobacteriaceae. There was a trend toward increased levels of lactic acid bacteria in the experimental group received EHMM (9.16 ± 0.12 lg CFU/g) compared with the contents in the control group and in the experimental group exposed to stress factor without adding EHMM in the diet (8.74 ± 0.34 and 8.79 ± 0.23 lg CFU/g, respectively). The conclusion about the positive (protective) effect of a semisynthetic diet enriched with peptides from EHMM was made based on the comparison of indicators that reflect the status of non-specific resistance of the organism: the integral criterion of weight gain and the levels of major colon microbiota populations of laboratory animals.