Black Seed Oil Left Overall Gut Microbiome Stable In 8-Person Pilot Study
A pilot trial published in Scientific Reports found that eight healthy adults who took Nigella sativa (black seed) seed oil for 20 days showed no measurable change in overall gut microbiome diversity. A few individual bacterial species shifted, and the oil's active compound, thymoquinone, showed up in urine after repeated dosing.
Researchers at Jena University Hospital in Germany randomized eight healthy adults into two groups of four. The treatment group took two capsules of Nigella sativa seed oil, each with 12.195 milligrams of thymoquinone, three times daily for 20 days; the control group took nothing, and neither group was blinded. Stool samples were collected at five points, 10 and 3 days before starting and 10, 20 and 30 days after, and analyzed with 16S rRNA gene sequencing, which identifies bacteria from their DNA. Overall diversity within and between groups showed no measurable difference tied to the oil. One species, Mediterraneibacter lactaris, increased in relative abundance, and five species, including Terrisporobacter mayombei and Bifidobacterium longum, decreased, though the study did not report how large these shifts were. Urine collected on days 10 and 20 showed thymoquinone or its breakdown product, thymoquinol, in every treatment-group sample.
1 species increased, 5 species decreased after 20 days of black seed oil in 8 adults
The study authors say thymoquinone's antimicrobial and immune-modulating properties may explain why it nudged specific bacteria without shifting the community as a whole. Alpha diversity measures how many bacterial types live in one person's gut; beta diversity compares that mix across people, and both stayed steady here. The species that increased is a known producer of short-chain fatty acids, compounds gut bacteria make from fiber that feed the cells lining the colon. The authors also note that the species which decreased, Terrisporobacter mayombei, has been linked in separate research to primary ovarian insufficiency, a condition involving early loss of normal ovarian function, though this pilot did not measure any reproductive or hormone outcomes.
This was an open-label pilot with four people in each group and no placebo, so ordinary week-to-week shifts in the gut microbiome cannot be fully separated from the oil's effect. Diet was self-reported rather than controlled, and fiber and fermented-food intake differed somewhat between groups, so some taxon changes could reflect diet instead.
Data Panel
- Who
- 8 healthy adults (4 treatment, 4 control), age 18 and older, Jena University Hospital, Germany
- Design
- Prospective, single-center, randomized, open-label pilot trial with no placebo group; stool sampled at 5 time points, urine at 2
- Dose
- 2 capsules of Nigella sativa seed oil (12.195 mg thymoquinone per capsule) 3 times daily for 20 days; controls received no supplement
- Primary result
- No measurable difference in alpha or beta gut microbiome diversity between treatment and control groups; each person's own microbiome pattern was the largest source of variation
- Secondary
- 1 species (Mediterraneibacter lactaris) increased and 5 species (including Terrisporobacter mayombei, Romboutsia timonensis, Bifidobacterium longum) decreased in relative abundance, size not reported; thymoquinone or its metabolite thymoquinol detected in all treatment-group urine samples on day 10 and day 20
- Funding / conflicts
- Funded by the Interdisciplinary Center of Clinical Research of the Medical Faculty Jena (grant ACSP08); open-access fee covered by Projekt DEAL. Authors declare no competing interests.
Dr. Axe's Take
This tells me black seed oil doesn't disrupt the gut microbiome even at repeated doses, which fits centuries of use in Ayurvedic and Unani medicine, but four people in each group and no placebo means I would not call this proof of a gut benefit. The detail I find useful is that a short-chain-fatty-acid producer increased while a species recently linked to primary ovarian insufficiency in other research decreased, though this pilot did not test reproductive or hormone outcomes. I would use black seed oil as a food-based addition alongside real fiber and fermented foods like kefir or sauerkraut, not as a stand-alone fix. Keep taking any prescribed medication as directed and talk with your doctor before adding it.
— Dr. Axe