According to this website Microbiomeprescription, Modafinil decreases over 800 different types of bacteria. Modafinil is quite popular amongst biohackers but I've heard of it described as an antibiotic like penicillin, Clindamycin or Fluoroquinolones (yikes!) The negative side effects that are commonly attributed to Modafinil are histamine related. I've used Modafinil a bunch of times and the main negative is just the effect on sleep for me. I haven't experienced any antibiotic resistance effects from Modafinil, have you? The health conscious tend to avoid antibiotics, is this a good reason not use Modafinil?
Apparently, this comes from this study, Extensive impact of non-antibiotic drugs on human gut bacteria, published in Nature in 2018. From its abstract:
A few commonly used non-antibiotic drugs have recently been associated with changes in gut microbiome composition, but the extent of this phenomenon is unknown. Here, we screened more than 1,000 marketed drugs against 40 representative gut bacterial strains, and found that 24% of the drugs with human targets, including members of all therapeutic classes, inhibited the growth of at least one strain in vitro. Particular classes, such as the chemically diverse antipsychotics, were overrepresented in this group. The effects of human-targeted drugs on gut bacteria are reflected on their antibiotic-like side effects in humans and are concordant with existing human cohort studies. Susceptibility to antibiotics and human-targeted drugs correlates across bacterial species, suggesting common resistance mechanisms, which we verified for some drugs. The potential risk of non-antibiotics promoting antibiotic resistance warrants further exploration.