The mites and the lung parasites can cause illness if you breathe it in when it is still fresh. The manure may contain salmonella or e.coli which are the contaminants you would worry about in the manures. I know chicks have to consume bacteria to seed their gut. Commercially, they are sprayed with something so that it becomes their resident gut bacteria, they don't want something like salmonella to become resident in their systems.
E. coli pretty much is a common gut bacteria. If you think about it most mammals are technically cylinders with the outer skin being on the outside of the body and the inner skin being the intestinal tract. E. coli in the gut actually helps synthesize Vitamin K and some B vitamins humans cannot make themselves. 90% of humans coexist with the non-virulent strains of this bacteria. In homeostasis there are many species of bacteria that live on us in our gut and on our skin. As long as the host is healthy and the bacteria stay where they are supposed to stay, they are part of our normal flora. There presence can actually keep bad stuff away. This is why when people are on long terms antibiotics that kill off normal flora, they get into trouble.
Killing off the normal bacteria of the gut and the skin can lead to overgrowth of fungi that the bacteria would have eaten. Fungal infections like thrush, are common in babies and immune compromised individuals. People who have had their gut bacteria killed off, have problems eating, and digesting their food. People who have been on TPN, and long term antibiotics are usually given things like yogurt which has live bacteria cultures to jump start the return of the gut bacteria.
The strains of bacteria we live with long term are different from the strains of pathogenic bacteria. All bacteria and fungi are not created equal. The skin and the mucosa of the gut and technically the lungs as well are natural barriers against pathogens as long as they are healthy and their is no inflamation or breaks in the barrier. It is when bacteria or other disease causing organisms find a susceptible host or a way through their normal barriers that they can cause a problem.
https://www.umsl.edu/microbes/files/pdfs/ecoli.pdf