The present invention is directed to a process for reducing a population of one, or more than one target pathogen present in animal waste, including livestock manure , comprising administering one, or more than one protected bacteriophage strain to livestock. The one, or more than one bateriophage strain is capable of adsorbing to and killing the target pathogen, is released in vivo, and acts to clear the one or more than one pathogen from livestock gut and waste. The one, or more than one bacteriophage it further reduces the population of the one or more than one target pathogen in the waste or manure. The present invention also relates to a process for reducing a population of one, or more than one target pathogen present in liquid manure comprising treating the animal waste such as liquid manure with one, or more than one protected bateriophage strain, or phage components, or a combination thereof.