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What happens if you compost with waste that has E. coli? Will it infect food grown in that compost?

Thanks to the organic acids produced in the fermentation process, the chances of pathogens such as E.coli surviving in the fermented matter are practically zero.

The byproduct during the process of fermentation with lactic acid bacteria (included in EM) are metabolites (organic acids) that help inhibit the growth of pathogens [Rattanacaikunsopon in Phumkhachorn, 2010], such as Salmonella and E.coli. Anaerobic acidic environment and the naturally occurring antibiotics produced by fungi have a detrimental effect on E.coli.

The chances of these types of bacteria surviving are very low, meaning that food is safe from contamination.