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Obesity caused by a high-fat diet (HFD) affects gut microbiota linked to the risk of type-2 diabetes (T2D). This study evaluates live cells and ethanolic extract (SEL) of <i>Lactobacillus sakei</i> Probio65 and <i>Lactobacillus plantarum</i> Probio-093 as natural anti-diabetic compounds. In-vitro anti-diabetic effects were determined based on the inhibition of α-glucosidase and α-amylase enzymes. The SEL of Probio65 and Probio-093 significantly retarded α-glucosidase and α-amylase enzymes (<i>p</i> < 0.05). Live Probio65 and Probio-093 inhibited α-glucosidase and α-amylase, respectively (<i>p</i> < 0.05). In mice fed with a 45% kcal high-fat diet (HFD), the SEL and live cells of both strains reduced body weight significantly compared to HFD control (<i>p</i> < 0.05). Probio-093 also improved blood glucose level compared to control (<i>p</i> < 0.05). The gut microbiota modulatory effects of lactobacilli on HFD-induced diabetic mice were analyzed with qPCR method. The SEL and live cells of both strains reduced phyla <i>Deferribacteres</i> compared to HFD control (<i>p</i> < 0.05). The SEL and live cells of Probio-093 promoted more <i>Actinobacteria</i> (phyla), <i>Bifidobacterium</i>, and <i>Prevotella</i> (genus) compared to control (<i>p</i> < 0.05). Both strains exerted metabolic-modulatory effects, with strain Probio-093 showing more prominent alteration in gut microbiota, substantiating the role of probiotics in gut microbiome modulations and anti-diabetic effect. Both lactobacilli are potential candidates to lessen obesity-linked T2D.