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E. coli is mostly harmless; only a few strains are harmful. I don't believe the route by which gut biota is established has been entirely established for any species but, for example, koala feed their faeces to their offspring to help them establish biota capable of digesting eucalyptus. It seems that a small proportion of ingested bacteria somehow survive ...

This is a bit hard because the usual composition statements are a combination of different types of molecules. Most of faeces are, by dry weight, bacteria (30%), undigested food and fiber (30%), fat (10%-20%), inorganic matter( 10-20%), other protein(2-3%). (reference) As you can see the bacterial portion contains proteins (amino acids) and other types of ...