Chromogenic bacteria, most often
Actinomyces species, are well known to cause stains on teeth. The bacteria produce hydrogen sulfide which reacts with iron in the saliva to form a bacterial plaque that is usually black or has black discoloration to it.
In my research of the topic I found numerous studies confirming the source and how the bacterial plaque is formed. However, I did not find one single article that attempted to find a cure or suggest a prevention method. I find that very odd and, for you I'm sure,very frustrating.
Unfortunately reducing your iron intake will have virtually no effect on the formation of the stains. The amount of iron in human saliva is very low to start with and you can't reduce it low enough without causing iron deficiency.
So, until some smart biologist/chemist/researcher comes up with an agent that can prevent hydrogen sulfide producing bacteria from forming plaque in the mouth, it is up to you to practice extremely vigilant dental hygiene. This means diligent brushing, flossing, and using anti-bacterial rinsed several times a day.
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