| Summary: | The effect of putative probiotic fermented milk (FM) with buriti pulp (FMB) or passion fruit pulp (FMPF) or without fruit pulp (FMC) on the microbiota of healthy humans was evaluated. FM formulations were administered into a simulator of the human intestinal microbial ecosystem (SHIME<sup>®</sup>) to evaluate the viability of lactic acid bacteria (LAB), microbiota composition, presence of short-chain fatty acids (SCFA), and ammonium ions. The probiotic LAB viability in FM was affected by the addition of the fruit pulp. <i>Phocaeicola</i> was dominant in the FMPF and FMB samples; <i>Bifidobacterium</i> was related to FM formulations, while <i>Alistipes</i> was associated with FMPF and FMB, and <i>Lactobacillus</i> and <i>Lacticaseibacillus</i> were predominant in FMC. <i>Trabulsiella</i> was the central element in the FMC, while <i>Mediterraneibacter</i> was the central one in the FMPF and FMB networks. The FM formulations increased the acetic acid, and a remarkably high amount of propionic and butyric acids were detected in the FMB treatment. All FM formulations decreased the ammonium ions compared to the control; FMPF samples stood out for having lower amounts of ammonia. The probiotic FM with fruit pulp boosted the beneficial effects on the intestinal microbiota of healthy humans in addition to increasing SCFA in SHIME<sup>®</sup> and decreasing ammonium ions, which could be related to the presence of bioactive compounds.
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