The signaling role of tryptophan and its catabolites is well known. However, their effects on the potential microbiota metabolic activity is still poorly understood. The study was aimed to assess concordance between changes in the predicted gut microbiome enzyme-encoding gene abundance and the tryptophan catabolites. The study involved 109 healthy volunteers and 114 obese patients. Quantification of tryptophan catabolites in the feces was performed by HPLC. Bacterial DNA was extracted from fecal samples, and the 16S rRNA gene V3-V4 region was sequenced. Primary processing of the sequencing data was performed using the QIIME v.1.9.1 tool. The alleged metabolic role of microbiota members was explored via reconstruction of unobservable states using PICRUSt. The maximum number of significant correlations between the unobservable states and the predicted gut microbiome enzyme-encoding gene abundance in obese individuals was reported for indole-3-lactate. A significant correlation between indole-3-lactate and the abundance of genes encoding the enzymes involved in metabolism of fructose, amino sugars, nucleotides, amino acids, polyamines, and sulfosaccharides was revealed. It has been found that obese patients show a threefold increase in the indole-3lactate-producing microbiota. It has been shown that in obese individuals microbial population of the intestine is represented by the totally different genera and species of microorganisms. It is concluded that indole-3-lactate has a significant effect on the predicted gut microbiome enzyme-encoding gene abundance in obese patients.