We deworm and treat for protozoa (flagellates are a group of protozoa- single-celled parasites) for the same reason that we do mites.
In the wild, a snake, lizard, turtle, or any other herp will have a certain amount of parasites. Parasites don't particularly live to kill their hosts- if they did they wouldn't have a home! The parasites will do some amount of damage to the wild animal, but usually not enough to kill it.
This is because the parasites are not usually dense enough to cause serious damage. Parasite loads in wild herps differ greatly from those in captive herps. Why? Because of the environment.
A wild herp has acres of land to roam. If parasite eggs pass in their poop, what are the chances of that animal stepping in them or ingesting them again? Sure, the herp might ingest eggs passed by another animal, but all of those animals might be ingesting eggs as well. The chances are still slimmer than in a different situation... Like captivity.
In captivity, we have herps cramped into these tiny enclosures compared to what they would have in the wild. Say a snake poops out some eggs, and it isn't cleaned right away. He might slither through the poop again accidentally, and then right into his water dish. The next time he drinks- Whoops! Reinfested! But instead of all of those eggs going to many different animals... There's only one snake that the eggs are finding their way to, and because he has a smaller environment, he's bound to run into those eggs again.
The above applies to parasites with a direct life cycle- meaning that they don't need an intermediate host to develop into an adult. Parasites with indirect life cycles need to find their way into a different host before they can become an adult in your herp.
This is more common than you might think. Pinworms are thought to be transmitted by crickets. Some roundworms infesting snakes have been traced back to feeder mice.
And of course, if you have other herps, you may accidentally transmit parasites, yourself.
All of this means that your herps should have fecals done at least once a year (twice would be better) to determine if they need antiparasitics. It's difficult to completely eliminate all sources of parasites, so a regular fecal exam is a good idea.
Christina
www.herptiles.net