In this large study of 2593 individuals profiled for depressive symptoms and microbiome, we identified 12 genera and 1 microbial family associated with depression. These include genus 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 more severe 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 depression in earlier studies. Eggerthella has been reported to be consistently found to be increased in depression and anxiety cases in 8 studies [26, 27, 39], which is in line with the findings of our study. MR analysis suggests that increase abundance of Eggerthella in depression is more likely to be a consequence of the disease rather than a cause. Also in line with our findings Subdoligranulum and Coprococcus were consistently found to be depleted in individuals with generalized anxiety disorder and depression several studies . Both Subdoligranulum and Coprococcus are involved in the production of butyrate  and Subdoligranulum was found to be increased in omega 3 rich diet . Ruminococcaceae at genus and family levels have been found to be depleted in cases of both uni- and bipolar depression [26, 27, 39, 41–43].
Novel findings of this study include genera Sellimonas, Lachnoclostridium, Hungatella, Eubacterium ventriosum, Subdoligranulum, LachnospiraceaeUCG001, and Ruminococcusgauvreauiigroup. Sellimonas 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 found to be increased in inflammatory diseases including ankylosing spondylitis, atherosclerosis and liver cirrhosis . Further, increased abundance of Sellimonas have been observed after dysbiosis . Lachnoclostridium, which also belongs to the family Lachnospiraceae, appeared as the topmost important predictor of depressive symptoms in random forest analysis. Higher levels of Lachnoclostridium were associated with increased depressive symptoms in our study. Lachnoclostridium has previously found to be depleted in other psychiatric disorders including schizophrenia  and autism  and in patients with gastrointestinal tract neoplasms . Hungatella was found to be associated with paleolithic diet and is known to produce the precursor molecule for trimethylamine-N-oxide (TMAO) . TMAO has been implicated in cardio-vascular and neurological diseases including depression [50, 51]. Eubacterium ventriosum belongs to the family Eubacteriaceae and has been found to be significantly depleted after traumatic brain injury in mice . Major depression is a frequent complication of traumatic brain injury . 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 individuals [54, 55]. Obesity is one of the most prevalent somatic comorbidities of major depressive disorder [56, 57] and is partly attributed to a side effect of selective serotonin reuptake inhibitors (SSRI). However, in our study we excluded those using antidepressant and adjusted for BMI in the linear regression analysis thus our finding is independent of the association with body weight. Subdoligranulum belongs to the family Ruminococcaceae. LachnospiraceaeUCG001, at species level, was found to be associated with anhedonia in mice . Ruminococcusgauvreauii belongs to the family Ruminococcaceae and at species level was found to be increased in atherosclerotic conditions .
Most identified microbiota in our study show potential involvement in the synthesis of glutamate and butyrate (see Supplementary Table 12 of Valles-Colomer et al. 2019) . Eggerthella is further involved in the synthesis of serotonin and gamma aminobutyric acid (GABA). Glutamate is widely distributed in the brain and a major excitatory synaptic neurotransmitter. It is known to be involved in regulating neuroplasticity, learning and memory . Glutamate levels in plasma, serum, cerebrospinal fluid and brain tissue have been associated with mood and psychotic disorders and suicide [61–66]. With increasing evidence of its role in the etiology of depressive disorders, glutamate is rapidly becoming the novel therapeutic target for depressive disorders. Ketamine, for instance, has been shown to increase glutamate signaling in rodents and humans [67, 68] and has shown to reduce depressive symptoms rapidly . Glutamate plays a role as a neurotransmitter in the enteric nervous system, which sustains the reciprocal influence between the gastrointestinal tract and the central nervous system [8, 70]. Butyrate on the hand is a short chain fatty acid and modulates biological responses of host gastrointestinal health by acting as a histone deacetylase inhibitor and binding to specific G protein-coupled receptors (GPCRs) . Butyrate can affect the gut-brain axis by enhancing the cholinergic neurons via epigenetic mechanisms  and can cross the blood brain barrier and activate the vagus nerve and hypothalamus [73, 74]. Sodium butyrate has shown anti-depressant effects in animal models of depression and mania [75, 76]. Serotonin and GABA are both important neurotransmitters relevant to depression. Evidence suggests that serotonin may be the key neurotransmitter to the gut-brain axis . Enteric nervous system accounts for > 90% of the body’s serotonin production where it is produced by enterochromaffin cells and in the neurons of the enteric nervous system . The neuronal production of serotonin is most critical for the development and motility of the enteric nervous system, affecting neurogenesis and guiding development of neurons expressing dopamine and GABA [78–80]. Although serotonin produced by the gut cannot cross the blood-brain barrier , it can affect the blood-brain barrier permeability, which can lead to inflammation of the brain . Further, vagus nerve stimulation by the gut microbiota can alter concentration of serotonin, GABA and glutamate within the brain in animals and humans [51, 83] and germ-free male mice exhibit anxiety-like behaviors and altered serotonin abundance in the brain . GABA is the main inhibitory neurotransmitter of the central nervous system that counterbalances the action of glutamate . Low levels of GABA are linked to depression and mood disorders . Animal studies show that gut microbiota can alter GABA activity in the brain through the vagus nerve . While each of the metabolites mentioned above are highly relevant for depression, most are known to be unable to cross the blood-brain barrier. However, an increasing number of animal studies show that the peripheral production of neurotransmitters by the gut microbiome can alter brain chemistry and therefore influence mood and behavior .
In the current study, we aimed to identify gut microbiota associated with depression in the general population to overcome the bias of reversed causation. The strengths of our study include a large sample, controlling for most known confounders including comorbid conditions, performing analysis in individuals free of anti-depressive medication and finally the use of quantitative depression scales. A large study consisting of 252,503 individuals from 68 countries showed that subthreshold depressive disorders produce significant decrements in health and do not qualitatively differ from full-blown episodes of depression . Use of rating scales is thus more powerful in omics association studies . There may have been a loss of statistical power as the depression assessment scales were different in the discovery and replication cohorts. Further, despite the use of the largest GWAS for both microbiome and depression, the MR analysis lacked power. There are 87 SNPs identified for depression, however, their effect on depression is small (individual odds ratio < 1.05, combined odds ratio < 2.0), which makes unlikely that the individual genetic variants show association with microbiome. For microbiome, there were no SNPs significantly associated at the genome-wide level and we had to lower the threshold to 10− 05 to identify at least more than one independent instrument for the identified microbiota. This limits the value of the MR.
To summarize, we have identified several bacteria at genera level that might influence depression in humans. We confirm the association of Eggerthella, Coprococcus, Subdoligranulum and family Ruminococcaceae and identify novel bacteria including Sellimonas, Lachnoclostridium, Hungatella, Ruminococcus, Subdoligranulum, LachnospiraceaeUCG001, Eubacterium ventriosum and Ruminococcusgauvreauiigroup. These bacteria are involved in the synthesis of glutamate, butyrate, serotonin and GABA, which are the key neurotransmitters relevant for depression.