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With increasing demand for the natural substances with sustainable production as pharmaceutical agents, marine microalgae have been recognized to provide chemical and pharmacological novelty and diversity. In this study marine microalga Chlamydomonas sp. was hydrolyzed with the combination of food-grade microbes, Candida utilis and Bacillus subtilis. The microbial hydrolysate of the Chalydomonas sp. was purified. The successful assay guided purification leads to isolation of bioactive peptide ENLDDLE – 846.35 Da (H-P-3). Activation of gastric enteric glial cells (EGC) was found to incur damages to the intestinal epithelial barriers. The isolated peptide H-P-3 showed a protective effect on bacterial lipopolysaccharide (1 μg/ml) and interferone-γ (10 ng/ml) activated enteric glial cells mediated disruption of the intestinal epithelial barriers. The peptide H-P-3 significantly attenuated the activated EGC mediated damage of tight junction proteins ZO-1 (Zonula occludens-1) and occludin with simultaneous suppression of enteric cell mortality. It was observed that the inflammatory cascade of the activated EGC create an oxidative stress condition in intestinal epithelial cells (IEC-6) which leads to DNA damage and cell cycle arrest. The molecular pathway studies showed that the peptide is protecting the intestinal epithelial cells by down-regulating the inflammatory signaling pathway NF-κB in EGC which suppress the activation of ATM/ATR dependent DNA damage in IEC-6 epithelial cells.