For a study, researchers sought to understand that people with various psychiatric disorders, including depression, had altered gut microbiota. However, it is unclear whether the action of psychotropic medication caused these differences. There was no data for patients with borderline personality disorder (BPD), a psychiatric condition that was frequently co-occurring with depression. A total of 24 unmedicated patients and 21 age- and gender-matched healthy controls were included in the study. Within 10 minutes of defecation, stools were frozen at 80°C. On an Illumina platform, the V4 region of the bacterial 16S ribosomal RNA (rRNA) gene was sequenced. OTUs (operational taxonomic units) were used to conduct additional research on community structure and alpha- and beta-diversity. There was no statistically significant difference between patients and controls in alpha- and beta-diversity. The Bacteroidetes/Firmicutes-ratio, on the other hand, was higher in patients, approaching significance (P=0.06,r=0.23). Pseudoflavonifractor phocaensis (P=0.003, r=0.41), Eubacterium coprostanoligenes (P=0.01,r=0.34), Anaerotaenia torta (P=0.01,r=0.35), and (statistically slightly weaker) Parabacteroides chongii (P=0.046,r=0.26) were all significantly less abundant in BPD patients. Differences in taxonomic composition among SCFA-producing bacteria in BPD may indicate a potential dysbiosis. Future research was needed to replicate these findings in larger, independent samples. The findings suggested that microbiota-targeted therapies could be a useful adjunct strategy for BPD if the findings were confirmed.