Enteric infection by faecal contamination of drinking water is a major concern in developing nations contributing to the huge burden of malnutrition and infant mortality. We have developed a holistic approach, named as gut to gutter approach, to treat wastewater treatment, by screening potential probiotic strains from staple food sources. The strains could be potentially used for competing out the enteric pathogens in different applications such as food and wastewater treatment. We focused on two strains isolated from rice water (RS) and lemon pickle (T1), identified as Lactobacillus fermentum and characterized for their probiotic and wastewater treatment capabilities. The strains showed many probiotic properties (tolerance to low pH (pH 3), bile salts up to 0.5% and simulated gastric juice at low pH and binding to extracellular matrix molecules, heparin and gelatin. Auto-aggregation of T1 was in the range of 85% and the strain exhibited significant co-aggregating ability with enteric pathogens, Klebsiella pneumoniae, Salmonella enterica and E. coli (MDR) with 48%, 79% and 65% respectively. Both strains had a higher binding affinity to gelatin and heparin, compared to widely claimed “probiotic” Bacillus clausii and the pathogenic E. coli ET. The strains had high galactosidase activities. Further, the cell free supernatant from RS showed BLIS (bacteriocin like inhibitory substance) activity against Klebsiella pneumoniae, Staphylococcus aureus and Salmonella enterica at 60%, 48% and 30% respectively. T1 strains and B. clausii effectively reduced the coliform count by by 90%(1-log) when immobilized in a biofilter to treat wastewater.