A prospective randomized controlled pilot study of gut microbiome modulation by Nigella sativa seed oil and thymoquinone metabolism in healthy volunteers: implications for gastrointestinal surgery.
El-Banna A, Junca H, et al. • Scientific reports • 2026
Repeated NSSO intake is feasible for longitudinal microbiome and urinary metabolite sampling and provides preliminary evidence for taxon-specific changes in healthy adults, with urinary detection of TQ/TQ-H₂ confirming detectability following repeated NSSO intake.
Key Findings
Results
No significant differences in alpha or beta diversity were observed between the NSSO treatment group and control group, indicating a stable overall microbiome composition.
Eight healthy adults were randomized into a treatment group (n=4) receiving NSSO capsules or a control group (n=4) without supplementation.
Fecal samples were collected at five time points and analyzed by 16S rRNA gene sequencing.
Alpha and beta diversity analyses were performed as primary measures of overall microbiome composition.
The stable microbiome composition finding suggests NSSO supplementation at this dose and duration did not broadly disrupt gut microbial ecology.
Results
Specific bacterial taxa showed differential abundance associated with NSSO supplementation, including an increase in Mediterraneibacter lactaris and a decrease in Terrisporobacter mayombei.
Exploratory differential abundance and machine learning analyses were performed alongside standard diversity metrics.
These taxon-specific changes occurred in the absence of overall alpha or beta diversity shifts, suggesting selective rather than broad microbiome modulation.
Results
Thymoquinone (TQ) and/or its reduced metabolite TQ-H₂ were qualitatively detected in urine samples from the treatment group following repeated NSSO intake.
Urine samples were obtained at two time points and analyzed using Gas Chromatography Mass Spectrometry (GC-MS).
Detection was qualitative only; the authors explicitly state that findings 'do not permit pharmacokinetic conclusions.'
TQ/TQ-H₂ detectability was confirmed only in the treatment group, not in controls.
The treatment regimen consisted of two NSSO capsules taken three times daily for 20 days.
Results
The study design of repeated NSSO intake over 20 days was found to be feasible for longitudinal microbiome and urinary metabolite sampling in healthy volunteers.
This was a prospective, single-center, randomized open-label pilot study.
The total sample size was eight participants, making this a pilot study with limited statistical power.
Food diaries were reviewed descriptively to contextualize dietary influences on microbiome changes.
The authors describe this as providing a framework to 'guide the design of future blinded, placebo-controlled, diet-controlled perioperative microbiome studies.'
Discussion
The authors propose that NSSO-associated gut microbiome modulation may have implications for gastrointestinal surgery outcomes.
The rationale is based on the premise that 'maintaining gut microbial balance may influence outcomes in gastrointestinal surgery.'
NSSO contains the bioactive compound thymoquinone, which has documented antimicrobial and immunomodulatory properties.
The authors note that 'human data on NSSO-associated gut microbiome changes and urinary TQ detectability after repeated oral exposure remain limited' prior to this study.
The study was retrospectively registered at ClinicalTrials.gov (NCT07450807) on 4 March 2026.
What This Means
This research suggests that taking Nigella sativa seed oil (NSSO) capsules — derived from black seed, which contains an active compound called thymoquinone — for 20 days did not broadly disrupt the overall diversity of gut bacteria in healthy adults. However, the study found that specific bacterial species did change in abundance: one type of bacteria (Mediterraneibacter lactaris) increased, while another (Terrisporobacter mayombei) decreased in the group taking NSSO compared to those who did not. Additionally, thymoquinone and a related compound were detectable in the urine of participants taking NSSO, confirming that the body absorbs and processes these compounds after repeated oral intake.
This was a small pilot study with only four people in each group, so the findings are preliminary and cannot be used to draw firm conclusions about effectiveness or safety. The lack of a placebo, the small sample size, and the absence of strict dietary control are recognized limitations. The qualitative urine detection also means the study cannot say how much thymoquinone was absorbed or how it moves through the body over time.
This research suggests that this type of supplementation study in humans is feasible and that NSSO may selectively alter certain gut bacteria without broadly destabilizing the gut microbial community. The authors propose these findings could help design larger, more rigorous studies investigating whether NSSO supplementation before gastrointestinal surgery might help optimize patients' gut health and potentially improve surgical outcomes.
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El-Banna A, Junca H, Steube A, Wissenbach D, Settmacher U, Schneider C, et al.. (2026). A prospective randomized controlled pilot study of gut microbiome modulation by Nigella sativa seed oil and thymoquinone metabolism in healthy volunteers: implications for gastrointestinal surgery.. Scientific reports. https://doi.org/10.1038/s41598-026-69567-3