Gut microbiome-wide association study of depressive symptoms

Nature Communications volume 13, Article number: 7128(2022) Cite this article


Depression is one of the most poorly understood diseases due to its elusive pathogenesis. There is an urgency to identify molecular and biological mechanisms underlying depression and the gut microbiome is a novel area of interest. Here we investigate the relation of fecal microbiome diversity and composition with depressive symptoms in 1,054 participants from the Rotterdam Study cohort and validate these findings in the Amsterdam HELIUS cohort in 1,539 subjects. We identify association of thirteen microbial taxa, including genera Eggerthella, Subdoligranulum, Coprococcus, Sellimonas, Lachnoclostridium, Hungatella, Ruminococcaceae (UCG002, UCG003 and UCG005), LachnospiraceaeUCG001, Eubacterium ventriosum and Ruminococcusgauvreauiigroup, and family Ruminococcaceae with depressive symptoms. These bacteria are known to be involved in the synthesis of glutamate, butyrate, serotonin and gamma amino butyric acid (GABA), which are key neurotransmitters for depression. Our study suggests that the gut microbiome composition may play a key role in depression.


Depression is one of the most common mental disorders experienced worldwide with an average lifetime prevalence of 11–15%1. The prevalence has doubled and, in some countries, even tripled during the COVID-19 pandemic2. Yet, depression is also one of the most common and poorly understood diseases courtesy of its elusive pathogenesis. Treatment options are sub-optimal with most antidepressants performing only marginally better than placebo3,4 with additional costs of having side effects ranging from minor cognitive complaints to even suicide5. The low to moderate heritability6 and the small effects of genetic variants (odds ratio <1.05) identified in large genome-wide association studies (GWAS) of depression7entails the need to go beyond genetics in the search of molecular biomarkers of depression.

Evidence is accumulating that gut microbiota may influence brain activity and behavior via neural and humoral pathways8,9 and may have translational applications in the treatment of neuropsychiatric disorders10,11,12. Several animal studies suggest that gut microbiota might have impact on the neurobiological features of depression13,14,15,16,17,18,19,20,21. Fecal microbiota transplantation of either stressed or obese animals to control animals showed significant alteration of anxiety22. Kelly et al.23 showed that transferring gut microbiota of depressed human patients to germfree rats induces behavioral and physiological features characteristic of depression in the recipient animals suggesting that gut microbiota may be involved in causal pathways leading to depression. Another study showed that pre- and probiotic consumption positively affects mood and anxiety in humans24. There have been very few studies systematically exploring the association between gut microbiome and depression in humans25. Further, the existing studies are based on very small samples (<60 cases), lacking statistical power to detect robust and reproducible associations. The most recent study including 121 cases reported depletion of butyrate producing bacteria (Coprococcus and Dialister) in individuals with depression26. However, these studies did not adjust for confounders including life style factors and medication use25, which are known to modify the gut microbiome27. A parallel study investigated the association of the gut microbiome with depressive symptoms in the multiethnic HELIUS cohort comprising of six different ethnic groups. This study has identified genera/species belonging to the families ChristensencellaceaeLachnospiraceae, and Ruminococcaceae consistently associated with depressive symptoms across ethnicities, taking a wide range of confounders into account [NCOMMS-21-20669B]. Thus far, most consistent associations have been reported for genera EggerthellaCoproccocusSubdoligranulumMitsuokellaParaprevotellaSutterella and family Prevotellaceae28. However, the results of existing studies are conflicting with little overlap asking for larger and more carefully designed studies28.

Here, we study the effect of gut microbiome diversity and composition on depression scores in 1,133 individuals from the Rotterdam Study while controlling for lifestyle factors and medication use. The analyses were replicated in the native Dutch participants of the HELIUS cohort (N = 1,539). Finally, we performed Mendelian Randomization (MR) to elucidate causal relationships between the identified microbiota and major depression.


Microbiome association analysis reveals association of thirteen taxa with depressive symptoms

The cohort characteristics are provided in Table 1. After exclusion of individuals using antidepressants and non-European subjects, 1,054 samples from RS and 1,539 samples from the HELIUS-study were included in the analyses (Table 1). The resulting microbiome data consisted of 17 phyla (for both cohorts), 33 classes for RS and 36 classes for HELIUS, 59 orders in RS and 61 orders for HELIUS, 116 families for RS and 108 families for HELIUS, and 439 genera for RS and 418 genera for HELIUS. In both cohorts, microbiome was dominated by phyla Firmicutes (77% in RS and 70% in HELIUS), Bacteroidetes (13% in RS and 21% in HELIUS), Actinobacteria (0.42% in RS and 0.42% in HELIUS) and Proteobacteria (0.48% in RS and 0.22% in HELIUS).

Table 1 Descriptive statistics of the study populations
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Alpha diversity was negatively associated with depressive symptoms in both RS (Shannon index; beta = −1.57, p value = 1.5 × 10−03) and HELIUS cohorts (Shannon index; beta = −0.64, pvalue = 2.84 × 10−02). Beta diversity showed significant association with depressive symptoms in RS (Permanova; R2 = 0.003, p value = 0.001) but not in the HELIUS cohort (R2 = 0.0005, p value = 0.51).

At taxonomic level, 24 genera, three microbial families, one class, two orders and a phylum were significantly (false discovery rate (FDR) < 5%) associated with depressive symptoms in the Rotterdam Study (Table 2, Source Data). We replicated these results in the HELIUS cohort for 12 genera, which were associated with depressive symptoms scores in the same direction (Table 2, Fig. 1). These include Sellimonas, Eggerthella, Ruminococcaceae (UCG002, UCG003, UCG005), Coprococcus3, Lachnoclostridium, Hungatella, LachnospiraceaeUCG001, Ruminococcusgauvreauiigroup, Eubacterium ventriosum and Subdoligranulum. Of the three microbial families significantly associated with depressive symptoms in RS, only family Ruminococcaceae was significantly associated with depressive symptoms in the HELIUS cohort. The direction of association was consistent for all associated taxa across both cohorts and the meta-analysis of results from both cohorts improved association p-values (Table 2). Of the 12 significantly associated genera 10 belong to the families Ruminococcaceae and Lachnospiraceae. All significantly associated genera belonging to the family Ruminococcaceae were depleted in those with higher depressive symptoms (Fig. 1). While most of the significantly associated genera within family Lachnospiraceae were increased in those reporting higher depressive symptoms (Fig. 1).

Table 2 Microbiota significantly associated with depressive symptoms
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Fig. 1: The taxonomic tree showing the 13 genera associated with depressive symptoms.
figure 1

Red dots depict negatively associated genera with depressive symptoms and blue ones depict positively associated genera with depressive symptoms. The outer most layer depicts the phylum level followed by class, order, family and genus levels.

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Random forest analysis with RS as the training cohort and HELIUS as the testing cohort revealed RuminococcaceaeUCG005 as the most important genus in predicting depressive symptoms (Source Data), showing the highest percentage increase in mean squared error (%incMSE) in out of bag analysis. Other important predictors of depressive symptoms include ChristensenellaceaeR7group, Lachnoclostridium, Eggerthella, Sellimonas, and Hungatella, which overlap with the findings of the linear regression analysis in this study (Source Data). Further, important predictors identified by random forest analysis include RoseburiaStreptococcusBacteroidesAnaerotruncusDoreaBlautiaVeillonellaDesulfovibrioAnaerostipes and Bifidobacterium, which replicate associations reported earlier28.

Mendelian Randomization (MR) analysis identifies a causal link between major depression and Eggerthella

Results of MR analysis are provided in the Source Data. With major depression as the exposure, Eggerthella, showed significant MR results under the IVW method (effect = 0.237, p value = 0.027) (Source Data). Tests for heterogeneity and horizontal pleiotropy were negative for Eggerthella (Supplementary Data 1, Supplementary Data 2). Further the effect estimates for Eggerthella was also consistent with the findings of this study, i.e., increase in the abundance of Eggerthella in those with higher depressive symptoms. Interestingly, the Steiger test for directionality suggests that Eggerthella is more likely to be causally associated with MDD (Supplementary Data 3). With microbiome as exposure, significant MR was observed for genus Sellimonas under the IVW method (effect = −0.046, p-value = 5.5*10−04) but effect estimate was inconsistent with the findings of our study (Supplementary Data 3).

Among the 87 depression-associated SNPs7significant association was observed for one SNP rs17641524 with the genus Acidaminococcus after correction for multiple testing (Supplementary Data 4). No significant association was observed for the MDD GRS (Supplementary Data 5).


In this large study of 2593 individuals profiled for depressive symptoms and fecal microbiome, we identified 12 genera and 1 microbial family associated with depressive symptoms. These include genera Sellimonas, Eggerthella, Ruminococcaceae (UCG002, UCG003, UCG005), Lachnoclostridium, Hungatella, Coprococcus, LachnospiraceaeUCG001, Ruminococcusgauvreauiigroup, Eubacterium ventriosum, Subdoligranulum and family Ruminococcaceae. Sellimonas, Eggerthella, Lachnoclostridium and Hungatella were more abundant in individuals with higher depressive symptoms. All other taxa were depleted in depression. Alpha diversity was significantly associated with depressive symptoms in both discovery and replication cohorts.

The intestinal bacterial strains Eggerthella, Subdoligranulum, Coprococcus and Ruminococcaceae have been reported to be associated with major depression in earlier studies. Eggerthella has been consistently found to be increased in depression and anxiety cases in 8 studies25,26,28, which is in line with the findings of our study. MR analysis suggests a causal link between MDD and Eggerthella, which requires further investigation. Also in line with our findings Subdoligranulum and Coprococcuswere consistently found to be depleted in individuals with generalized anxiety disorder and depression in several studies28. In a recent study Coproccocus was depleted in rats that exhibited depressed behavior upon fecal transplantation from depressed human subjects29, suggesting that Coproccocus may have a causal impact on depression. Both Subdoligranulum and Coprococcus are involved in the production of butyrate26 and Subdoligranulum was found to be increased in omega 3 rich diet30. A previous meta-analysis shows that omega 3 fatty acids, more specifically eicosapentaenoic acid (EPA) supplementation are beneficial for depression31Ruminococcaceaeat genus and family levels have been found to be depleted in cases of both uni- and bipolar depression25,26,28,32,33,34. A similar pattern is observed in the study by Bosch et al. [NCOMMS-21-20669B] with several genera belonging to the family Ruminococcaceae depleted in those reporting higher depressive symptoms, which is again consistent with the results of our study.

Other findings of this study that have previously not been reported include association with genera SellimonasLachnoclostridiumHungatellaEubacterium ventriosumLachnospiraceaeUCG001, and RuminococcusgauvreauiigroupSellimonas and Hungatella were positively associated with depressive symptoms. Sellimonas is the most significant finding of this study. It belongs to the family Lachnospiraceae and phylum Firmicutes. Species belonging to Sellimonas have been reported to be increased in inflammatory diseases including ankylosing spondylitis, atherosclerosis and liver cirrhosis35. Further, increased abundance of Sellimonas have been observed after dysbiosis36Lachnoclostridiumbelongs to the family Lachnospiraceae. Higher levels of Lachnoclostridium were associated with increased depressive symptoms in our study and also consistent with the findings of the Bosch et al. study [NCOMMS-21-20669B]. Lachnoclostridium has previously found to be depleted in other psychiatric disorders including schizophrenia37 and autism38 and in patients with gastrointestinal tract neoplasms39Hungatella belongs to the family Clostridiaceae and phylum Firmicutes. It has previously been associated with paleolithic diet and is known to produce the precursor molecule for trimethylamine-N-oxide (TMAO)40. TMAO has been implicated in cardio-vascular and neurological diseases including depression41,42Eubacterium ventriosum belongs to the family Eubacteriaceae and has been found to be significantly depleted after traumatic brain injury in mice43. Major depression is a frequent complication of traumatic brain injury44. In our study we also observed depletion of Eubacterium ventriosum with the increase in depressive symptoms, which fits well with association with traumatic brain injury. In human studies Eubacterium ventriosum was found to be slightly more abundant in obese individuals45,46. Obesity is one of the most prevalent somatic comorbidities of major depressive disorder47,48and is partly attributed to a side effect of selective serotonin reuptake inhibitors (SSRI). However, in our study we excluded those using antidepressants and adjusted for BMI in the linear regression analysis thus our finding is independent of the association with body weight. LachnospiraceaeUCG001, at species level, was found to be associated with anhedonia in mice49Ruminococcusgauvreauii belongs to the family Ruminococcaceae and at species level was found to be increased in atherosclerotic conditions35. Interestingly depression is known to be causally associated with atherosclerosis50. It may be worth to investigate the genera Sellimonas and Ruminococcusgauvreauii as potential mediators in the relationship between depression and atherosclerotic conditions.