Gut microbial dysbiosis is associated with the development of critical clinical conditions of metabolic syndrome (obesity, type II diabetes), and calcium oxalate kidney stones. The human gut microbial eubiosis with functional probiotics and their heat-killed cells of lactic acid bacteria (LAB) is considered the current therapy for metabolic syndrome (MS). In accordance with this, our study aimed to isolate oxalate-degrading, cholesterol-lowering, and anti-adipogenic bacterial strains from raw donkey's milk and homemade fermented pickles. Nine LAB strains with potential in vitro oxalate degrading, α-glucosidase inhibiting, and cholesterol-lowering activities were pre-screened from fourteen isolates. Further, the heat-killed cells of selected strains were evaluated for anti-adipogenic activity in murine 3T3-L1 adipocytes. This activity was examined by studying the lipid storage, gene, and protein expression of adipogenic and lipogenic transcription factors. Subsequently, four potential isolates demonstrated a significant reduction in lipid storage by limiting adipogenesis (reducing C/EBPα, PPARγ expression), lipid transportation (downregulating aP2 expression), and lipogenesis (reducing PLIN-1 expression). These effective isolates were characterized using 16S rRNA molecular sequencing, and were identified as closest relatives to the Enterococcus (RRLA5, RRLA1, and RRLD6) and Lactobacillus (RRLM2) genera. Further, they displayed good survivability under in vitro gastric conditions and non-haemolytic activity. Taken together, the live cells of effective isolates depicted significant in vitro oxalate degradation, and their heat-killed cells demonstrated anti-adipogenic activity through downregulating the adipogenesis and lipogenesis. Moreover, future preclinical animal model studies on the synergistic role of probiotics and their heat-killed cells in disease prevention through gut microbial modulation could provide evidence as a biotherapeutic agent.