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Methods: Fifty patients with MetS (sex-matched, aged 42\u201363 years) were randomized to an experimental group (Ap, n = 26) that received autoprobiotics grown in nutritional mix SuproPlus 2640 and a control group (Pl, n = 24) that received SuproPlus 2640 for 20 days. Results: The effects of therapy on anthropometric and biochemical parameters, as well as the gut microbiome, were assessed on days 14 and 28 after the autoprobiotic course. Autoprobiotic treatment reduced the severity of obesity symptoms and led to decreases in serum glucose and glycated hemoglobin (HbAc1) levels and partial normalization of the lipid profile. An intergroup comparison revealed lower concentrations of HbAc1 and triglycerides in blood serum when comparing samples taken from Ap and Pl groups on day 28 after therapy. qPCR showed a reduction in the numbers of Bacteroides fragilis group, Streptococcus spp., and Ruminococcus spp. in the Ap group. The 16S rRNA gene sequencing results provided a longitudinal model for relative abundance analysis of the observed taxa, and comparison between dynamic parameters indicated a more favorable trend in the Ap group, with a decrease in the relative abundance of Oscillospiraceae UCG-003 and an increase in that of \u201cPrevotellamassilia\u201d observed only in this group. Longitudinal microbiota analysis using the coda4microbiome package demonstrated that the most pronounced microbiome shifts occurred in the Ap group, with the genera Senegalimassilia, \u201cPrevotellamassilia\u201d, Streptococcus, Paraprevotella, and Anaerobutyricum contributing substantially. Conclusions: Autoprobiotic Enterococcus spp. may affect the gut microbiome and is potentially effective for treating MetS.<\/jats:p>","DOI":"10.3390\/nu18142324","type":"journal-article","created":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T06:49:36Z","timestamp":1784184576000},"page":"2324","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Autoprobiotic Supplements Attenuate Obesity and Improve Gut Microbiota, Carbohydrate, and Lipid Metabolism in Patients with Metabolic Syndrome: A Pilot Trial"],"prefix":"10.3390","volume":"18","author":[{"given":"Elena","family":"Ermolenko","sequence":"first","affiliation":[{"name":"Institute of Experimental Medicine, St. Petersburg 197376, Russia"},{"name":"Department of Medical Microbiology, North-Western State Medical University Named After I.I. Mechnikov, St. Petersburg 191015, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0331-0963","authenticated-orcid":false,"given":"Stanislav","family":"Sitkin","sequence":"additional","affiliation":[{"name":"Institute of Experimental Medicine, St. Petersburg 197376, Russia"},{"name":"Department of Internal Diseases, Gastroenterology and Dietetics Named After S.M. Ryss, North-Western State Medical University Named After I.I. 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