Are Mud and Germs in Military Training a Health Risk for Soldiers?

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i watch some training soldiers in movies, they crawl in a swamp, dirty, and needless to say full of germs
Are there any entering his blood stream or his "lower part via the tube" ?
 
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Bacteria etc. that enter through holes in the head (mouth, nose, ears, etc) or holes elsewhere (ahem...) have to compete with the ginormous number of bacteria already there- bacteria which we coexist with. The blood is sterile, so open cuts are a potential problem.