The short answers is yes. But there are remedies. If you want to maintain a healthy gut full of rich microbiome content while taking antidepressants, take desipramine or take a Ruminococcus flavefaciens supplement along with the antidepressant. . . . and maybe a healthy daily dose of your favorite probiotic. In addition to keeping a balanced gut when taking antidepressants, ruminococcus flavefaciens is essential to the digestion of cellulose.

There has been a held belief that antidepressants can suppress microbiome diversity. Research confirms this. Antidepressants do reduce the richness and increased diversity of gut bacteria. Except for desipramine, analyses of alpha diversity revealed that all antidepressants reduced the richness of microbial communities. (See Nature.com, Translation Psychiatry, April 09, 2019; Antidepressants affect gut microbiota and Ruminococcus flavefaciens is able to abolish their effects on depressive-like behavior. https://www.nature.com/articles/s41398-019-0466-x).

In addition to the effects of antidepressants on microbiota, microbiota may also effect depressive-like behaviors through influence on neurotransmitters, production of serotonin (the “happy” chemical), and other key molecules. Microbiota can produce neuroactive substances, including neurotransmitters, that may influence host physiology and behavior. Microbiota can also influence the production of serotonin by enterochromaffin cells in the host gut. Serotonin is primarily produced in the gut.

However, anti-depressive effects can be attenuated by simultaneous treatment with Ruminococcus flavefaciens. Abstracts from this study found that supplementing your use of antidepressants with R. flavefaciens, by affecting gene networks in the brain, can decrease depressive-like behavior.