Ok, so for years we said we didn't recommend drinking coffee while recovering from candida overgrowth. This is for two reasons. One- coffee is acidic and kills off beneficial bacteria and two- coffee's caffeine could cause an adrenaline and or cortisol surge and result in increased blood sugar levels. Increased blood sugar, adrenaline and cortisol are all hard on the healing process.
Well, now there are enough microbiome-related studies showing that coffee may actually be beneficial to diverse gut ecosystem, that I think we can rule out number one. There may be some truth to the acidity killing off bacteria but there seems to be something about coffee that has a beneficial effect as well. There are also studies that show it can reduce brain decline in older individuals.
As for number two, the increase in cortisol and adrenaline, a study done by US National Laboratory of Medicine showed that the increase in cortisol in response to coffee was limited if the coffee was consumed in the morning, when cortisol levels would naturally be increased, and, if the use of coffee was habitual (i.e. the body got used to it). Coffee later in the day however, when cortisol levels were naturally lowered, would cause a distinct increase in cortisol.
Adrenaline is also triggered further as well through an excitatory response caused by caffeine stimulation.
My conclusion after looking at several reports and studies, is that using coffee in the morning to start the day off, is a decent bet but that it would be more gentle on digestion and on the gut if it were cold brewed. Cold brew coffee (yep- coffee made with cold or room temperature water), is an increasingly common trend. People like it mainly for taste reasons though I also seems to have all the anti-oxidants of coffee (yes it does have some further redeeming qualities), but less of the unhealthy aspects of coffee, including a lower level of acidity.
Here's a link to Livestrong's article about cold brewed coffee.
So you may wish to try cold brew coffee in the morning for yourself. See how you feel. Is caffeine a good thing for you or does it make you jittery or cause a come down. Using very good quality coffee that is free of mold and aflatoxins is another way to get the best out of coffee if you're going to drink it.