I had a GREAT question from a coffee client, and thought I would share my response to him with everyone (see below). I hope this answers some of your questions and PLEASE feel free to contact us with any other questions!
We do not test specifically for mold levels in our coffee. There are a few reasons behind this:
Yes, high levels of mold are found in "most" coffees today, as the majority of coffees today still tend to be low quality, Robusta, and instant coffees. All of our coffees are of the highest quality--this is an absolute requirement for Direct Trade. If you're thinking of mold like what you get on an orange after its been sitting way too long on the counter? No way, you would totally be able to taste that bitter, dank, and well, moldy flavor. Your taste-buds would tell you it is NOT okay to drink.
Most of the "concerning" molds and bacterias that have been touched on (many of which concerns come from an advertisement from Bulletproof/Upgraded Coffee) are aflatoxins, ochratoxin A, and other fungal toxins. These appear in many of our foods in small amounts. These toxins are found in beer, wine, potatoes, rice, berries, raisins, wheat, coffee (roasted and green beans) and even chocolate, among other things. As part of the food chain, and since it's not possible to irradiate our foods, we expect a small level to be present, but no where near any levels that would make us sick.
Our coffees are also Arabica; Robusta is what Folgers brand and many of the other instant store brand coffees are made of. Robusta is known to have higher levels of molds due to the low-disease/mold-tolerance species of coffee plant that it is. And, it is also known to be a very low quality bean. Incidentally, it has been shown that instant coffees tend to have at least 2 times the amount of mold/toxins present as even medium quality roasted beans!
Coming back to Direct Trade, keep in mind that Direct Trade accepts only the highest quality beans, which is why the price is higher, thereby giving the producers a much larger incentive to produce high quality beans. Fair Trade, on the other hand, combines poor quality, average quality, and high quality beans into one pool, and sells it as a fair quality, fairly traded product. And since all of our beans are single-source, we know EXACTLY where they are coming from, who the farmer is, and any issues that may have surmised during the coffee season prior to harvest. Another reason we love having that close connection.
I apologize for the lengthy response; I have over a decade of experience at top institutions as a Biological Scientist prior to my Business Ops role. This type of stuff still gets me excited! :)