Probiotics as a Tool for Regulating Molecular Mechanisms in Depression: A Systematic Review and Meta-Analysis of Randomized Clinical Trials

Depression remains a major mental disorder with high rates of inadequate response to current treatments. A holistic perspective on mental health has energized research into the gut microbiota and its bidirectional communication with the brain (the gut–microbiota–brain axis). Studies indicate altered gut microbiota composition and abundance in depressed individuals compared with healthy controls, motivating exploration of psychobiotics as adjunctive treatments. This review aimed to systematically summarize, following PRISMA guidelines, the molecular mechanisms linking probiotic administration to changes in depressive symptoms in healthy adults with subclinical symptoms and in patients with depression, with or without somatic comorbidities. The central research question was whether probiotics modulate specific molecular markers (inflammation, neurotrophic factors, endocrine measures, nitric oxide, lipids, oxidative stress) alongside improvements in depressive symptoms.

Emerging literature implicates the gut–microbiota–brain axis in mood disorders, with neuronal, immune, and endocrine pathways mediating communication. Observational studies report altered fecal microbiota in major depressive disorder, and experimental work suggests microbiome-driven metabolic pathways can influence depressive-like behaviors. Prior reviews and meta-analyses have suggested potential benefits of probiotics or prebiotics on depressive symptoms, and proposed mechanisms include modulation of inflammatory cytokines, HPA axis activity, tryptophan–kynurenine metabolism, short-chain fatty acids affecting BDNF expression, nitric oxide signaling, and oxidative stress. However, clinical findings have been heterogeneous, varying by strains, dosing, duration, and participant characteristics, underscoring the need for focused synthesis on molecular outcomes alongside clinical endpoints.

This systematic review followed PRISMA guidelines. Eligibility focused on randomized clinical trials and interventional studies evaluating probiotics (alone or add-on) in adults with depressive symptoms or diagnosed depression (with or without somatic comorbidities), and healthy adults with subclinical depressive/anxiety symptoms, that reported molecular outcomes. Exclusions included nonoriginal articles, non-English language, unavailable full text, nonhuman studies, and studies not addressing prespecified PICO. Two reviewers independently screened titles/abstracts and full texts, resolving disagreements by consensus. Data extracted included study design, sample size, duration, participant characteristics, probiotic type/strains, and outcomes on depressive symptoms and molecular markers. Risk of bias was assessed using RoB 2 for randomized trials and ROBINS-I for nonrandomized studies. Meta-analysis used Review Manager (RevMan) 5.3 with random-effects models. Parameters included only if assessed in at least two studies of low/moderate risk of bias with sufficient data: IL-1β, IL-6, IL-10, TNF-α, CRP, BDNF, cortisol, nitric oxide (NO). Effects were summarized as standardized mean differences (SMD) with 95% CIs. Heterogeneity was evaluated by Tau², χ², and I², with I² ≥50% indicating substantial heterogeneity. Funnel plots were examined for publication bias. Planned subgroup analyses (healthy; depression without comorbidity; depression with somatic comorbidities) were limited by insufficient studies in some subgroups.

- Study selection and characteristics: Of 5819 records identified, 20 clinical trial records met inclusion criteria (19 unique trials after deduplication), comprising 17 double-blind randomized placebo-controlled trials and 2 open-label RCTs. Total participants = 1461; individual study sample sizes 11–156; durations 4–12 weeks. Studies were conducted primarily in Iran (7), with others in Austria (2), China (2), Russia (1), Turkey (1), Korea (1), Poland (1), New Zealand (1), Taiwan (1), Switzerland (1), India (1). Probiotics ranged from single-strain to multi-strain formulations (up to 14 strains), from genera Bacillus, Bifidobacterium, Lacticaseibacillus, Lactobacillus, Lactococcus, and Streptococcus. No serious adverse effects were reported. - Risk of bias: Among 18 randomized studies, 4 were low risk, 9 had some concerns, and 5 were high risk. One nonrandomized open trial had serious risk of bias (ROBINS-I). - Clinical outcomes: In major depression, 7/10 studies reported antidepressant effectiveness (3/5 among good-quality studies). In depression with somatic comorbidities, 6/7 studies showed mood improvement. In healthy participants with subclinical symptoms, results were conflicting (1 positive, 1 null). - Meta-analysis (good-quality studies): • CRP: SMD = −0.47 (95% CI [−0.75, −0.19], p = 0.001), lower with probiotics; significant reductions were observed among depressed patients with somatic comorbidities. • BDNF: SMD = 0.37 (95% CI [0.07, 0.68], p = 0.02), higher with probiotics; observed in depressed patients with and without comorbidities. • Nitric oxide (NO): SMD = 0.97 (95% CI [0.58, 1.36], p < 0.0001), higher with probiotics; confirmed in depressed diabetic patients with coronary artery disease. • IL-1β: SMD = 0.56 (95% CI [−0.14, 1.26], p = 0.11) – not significant. • IL-6: SMD = −0.21 (95% CI [−0.63, 0.21], p = 0.32) – not significant. • IL-10: SMD = 0.20 (95% CI [−0.20, 0.60], p = 0.33) – not significant. • TNF-α: SMD = −0.19 (95% CI [−0.45, 0.08], p = 0.16) – not significant. • Cortisol: SMD = −0.10 (95% CI [−0.36, 0.15], p = 0.43) – not significant. - Subgroup patterns: Associations for CRP and NO were identified only among depressed patients with somatic comorbidities; BDNF increases were seen across depressed populations. Among healthy participants with subclinical symptoms, IL-6 reduction was observed in one of two trials; other markers showed no consistent changes. - Additional molecular insights: No consistent changes in proinflammatory cytokines or cortisol in high-quality MDD trials; one study showed reduced kynurenine and 3HKYN:KYN ratio with Lactobacillus plantarum 299v; two studies in comorbid populations showed improvements in oxidative stress markers (myeloperoxidase; malondialdehyde).

Findings support that probiotics can improve depressive symptoms, particularly in patients with depression and somatic comorbidities, and are associated with specific molecular changes: increased BDNF across depressed populations and reduced CRP and increased NO among those with somatic illnesses. Variability in clinical and molecular outcomes likely reflects differences in probiotic strains (single vs multistrain; specific Lactobacillus/Bifidobacterium combinations), dosing, and treatment duration (studies with only 4 weeks of treatment were more often negative), as well as population heterogeneity (severity, comorbid inflammation, age, sex). While modulation of inflammatory cytokines and HPA-axis cortisol has been hypothesized, high-quality trials generally did not show consistent cytokine or cortisol changes in MDD without somatic comorbidities. In contrast, inflammatory markers (CRP, sometimes IL-6) and oxidative stress markers were more responsive in comorbid conditions, where baseline inflammation may be higher. Increases in BDNF align with mechanistic pathways involving short-chain fatty acids, mTOR signaling, and neuroplasticity, potentially mediating mood improvement. Elevated NO following probiotic supplementation, observed in coronary disease populations, may reflect vascular and metabolic effects tied to microbiota-derived metabolites. Safety signals were favorable across studies. Overall, probiotics appear promising as adjunctive therapy, with molecular effects varying by host context and strain regimen.

This systematic review and meta-analysis support probiotic use in depressed patients with or without somatic comorbidities, with consistent evidence of increased BDNF accompanying symptom improvement. Reductions in CRP and increases in NO were evident only in depressed patients with somatic comorbidities, and oxidative stress markers also improved in this group. Evidence remains inconclusive for healthy individuals with subclinical symptoms. Future research should prioritize larger, high-quality, longer-duration RCTs to define effective strains and doses, clarify mechanisms (inflammation, neurotrophic, metabolic pathways), and evaluate probiotics as add-on therapies to standard antidepressants, including broader somatic comorbidity settings and preventive applications.

- Limited number of eligible trials and heterogeneous outcome measures reduce precision and generalizability. - Many studies assessed molecular outcomes as secondary endpoints with potentially inadequate power. - High heterogeneity across strains, doses, durations, and populations; subgroup meta-analyses were limited by insufficient studies. - Risk of bias was often moderate to high, particularly among MDD-only trials, constraining firm mechanistic conclusions. - Only English-language publications were included, introducing language bias.