Serotonin: The Link between Gut Microbiome and Brain

Abstract

Serotonin, as a neurotransmitter plays a key role in regulating mood, sleep, appetite, and various physiological processes. Serotonin is closely linked to the microbiome-gut-brain axis, which is a bidirectional communication between the gut and the brain facilitated by the gut microbiome which consists of trillions of microorganisms that inhabit the digestive tract. This connection is a growing area of research and serotonin produced in the gut is being investigated for its potential impact on human personality, mood, and overall health. Microbiome influences serotonin production, serotonin precursor metabolism, serotonin reuptake, and immune system modulation. A balanced microbiome is crucial for regulating homeostasis and stress response and altered gut microbiota composition has been linked to depression, anxiety, bipolar, schizophrenia, stress-related, and autism spectrum disorders. Microbiome-based interventions might help to regulate the immune response, neuroprotection, and neuroplasticity to reduce neuroinflammation and thus prove crucial to modifying the course of major depressive, bipolar, and related disorders where inflammation is evidenced to lead to the progression of illnesses. Microbiome-based interventions such as probiotic supplementation influence the production of neuroactive compounds and have the potential to bridge the treatment gap for Parkinson’s disease, multiple sclerosis, and Alzheimer’s disease and might prove to be a turning point for the treatment of obesity-associated systemic low-level inflammation, whether psychotropic medication related or otherwise. The gut microbiome offers a novel possibility to employ manipulation of the gut microbiota as a non-invasive measure in health and disease, especially at a time when the clinical field of forthcoming psychotropics looks exhausted.

1. Introduction

Serotonin is a biologically active amine that serves the dual functions of neurotransmitters and hormones by exerting a wide range of physiological and pathological effects through nearly a dozen receptors classified into seven families [1]. Serotonin also known as enteramine or 5-hydroxytryptamine (5-HT) was successfully extracted and purified by Rapport and colleagues in 1948 [2].

1.1 Serotonin in the brain

1.1.1 Anatomy

The distribution of serotonin in CNS consists of the following:

1. Raphe Nuclei (Latin, meaning “midline”): Serotonin within the CNS is almost exclusively produced in neurons originating in the raphe nuclei which are collections of neurons, with poorly defined cytoarchitectonic limits localized to the periaqueductal gray, also known as central gray, and the surrounding reticular formation in the brain.

2. Long and extensively branched axonal processes called projections. Serotonergic neurons from the raphe nuclei project widely throughout the CNS and form classical chemical synapses as well as such synapses that contribute to the so-called paracrine or volume transmission, and this has led to the suggestion that serotonin exerts a major modulatory role throughout the CNS.

3. Multiple cortical and limbic target regions: The raphe nuclei provide projections to the cortex, and many forebrain limbic structures such as the hippocampus and medulla. Projections to the dorsal, intermediate, and ventral columns in the spinal cord regulate pain perception at the level of the dorsal horn. Serotonergic terminals in the cortex are less organized than the noradrenergic cortical projections, however, the two systems are co-localized in most limbic areas of the brain and this might explain the major involvement of these transmitters in the affective disorders [3, 4, 5].

1.1.2 Neurochemistry

Serotonin is synthesized from the essential amino acid L-tryptophan (Trp) which is primarily obtained from dietary sources [6]. After absorption about 85% of tryptophan is bound to plasmatic albumin protein and only 10–20% is unbound and able to cross blood–brain barrier (BBB) and hence available for 5-HT synthesis in the brain. Tryptophan released from plasma proteins becomes available for incorporation into proteins [7] as this is the principal role of tryptophan in the human body [8]. The second most prevalent metabolic pathway of tryptophan, the kynurenine pathway, accounts for the catabolism of approximately 99% of ingested tryptophan not used for protein synthesis and has importance in generating cellular energy in the form of nicotinamide adenine dinucleotide (NAD). The kynurenine pathway produces other pro and antioxidant molecules of neurobiological importance namely, kynurenine, kynurenic acid, and quinolinic acid (QUIN) [9, 10]. Synthesis of B6 and B12 vitamins, required as co-factors for kynurine pathway enzymes are dependent on gut microbiome activity [11]. The third tryptophan metabolic pathway that leads to the synthesis of 5-HT in the periphery (e.g. in blood platelets and the enterochromaffin cells of the gastrointestinal tract) or in the nerve endings in brain is relatively minor. It is estimated that 95% of mammalian serotonin is found within the gastrointestinal tract and while 3% of dietary tryptophan is used for serotonin synthesis throughout the body only 1% of dietary tryptophan is used for the synthesis of this broad-impact neurotransmitter and neuromodulator in the brain. Melatonin and tryptamine are other by-products of the tryptophan/serotonin pathway [12]. In serotonin synthesis from tryptophan, the first step is catalyzed by the enzyme tryptophan hydroxylase which exists in two isoforms tryptophan hydroxylase 1 (Tph1) and tryptophan hydroxylase 2 (Tph 2) and convert tryptophan to 5-hydroxytryptophan. 5-Hydroxytryptophan is then converted by the aromatic amino acid decarboxylase to 5-hydroxytryptamine [13]. After synthesis serotonin (5HT) is transported into synaptic vesicles using vesicular monoamine transporter 2 (VMAT2) to protect serotonin from enzymatic breakdown. Once released from the presynaptic terminal serotonin acts on various presynaptic and postsynaptic receptors which are also targets of numerous drugs. The action of serotonin on its receptors at the synapses is terminated mainly by an active reuptake process mediated by the serotonin transporter (SERT), a sodium and chloride-dependent neurotransmitter transporter [14, 15].

1.2 Role of serotonin in mood regulation and emotional well-being

Speculations about the role of monoamines in affective states began with the serendipitous discovery in the late 1950s that members of two structurally unrelated classes of compounds monoamine oxidase inhibitors (MOAIs) and tricyclic antidepressants (TCAs) were effective in treating severe depression [16]. In the most basic form, Monoamine Theories postulate that depression is related to decreased levels of centrally available monoamines, typically either the catecholamine, noradrenaline (norepinephrine in the United States), or the indoleamine, serotonin [17]. Monoamine theories later evolved into monoamine receptor theories, which associate depression with lesions at the level of monoamine receptors [18]. With the advancement in neurosciences, even receptor theories have come under scrutiny, and contemporary literature has expanded these theories to the non-mutually exclusive neurotrophic and neurogenesis hypotheses which are closely related to a third entity called neurotrophic hypothesis. These hypotheses were proposed as the monoamine theory of depression was too simplistic to explain several conundrums which evidenced that monoamine deficiency cannot be the sole cause of depression [19]. The Neuroplasticity hypothesis postulates that depression may result from environmental contingencies like adverse life experiences that cause neuronal architectural changes and resultant defects in brain processing, the pathophysiology of which is strongly linked to impairments in serotonin (5-HT) neurotransmission [20]. Neurogenesis research suggests that very sophisticated transport systems can allow freshly produced neurons (from lateral subventricular zone (SVZ) and the dentate gyrus (DG) of the hippocampus and the olfactory bulb), called “neuroblasts,” to be migrated long distances across the brain to help regenerate damaged areas or regions which are experiencing neural dilapidation and thus neurogenesis is thought to be important for maintaining brain health. Antidepressants might improve neurogenesis in the hippocampus through activation of the 5-HT1A receptor [21, 22]. The neurotrophic hypothesis of depression posits that major depressive disorder (MDD) is caused partly by decreases in neurotrophic factors such as brain-derived neurotrophic factor (BDNF) and their restoration is critical for the therapeutic efficacy of antidepressant treatment [23]. Emotional and cognitive deficits in bipolar and related mood disorders are linked to changes in neuroplasticity, cell resilience, and connectivity with BDNF as an important contributor to the neuroplasticity changes described among bipolar disorder patients. Thus, evidence from differential lines of research converges to serotonin signaling and 5-HT receptors being involved in regulating the levels of both neurotrophic factors and adult hippocampal neurogenesis thereby mediating a pivotal role in neuroplasticity in both normal and neuropsychiatric conditions [24, 25, 26]. Further, the neuroplasticity theory is not considered exclusive for MDD, and the mechanisms of alterations in neuroplasticity accounting for the significantly different symptomatology of schizophrenia [27] and bipolar disorders [28] are being investigated.

1.3 Other roles of serotonin

1.3.1 Cognition

The role of serotonin in human cognition has been investigated, especially in the context of the growing notion of memory deficits in neuropsychiatric disorders like posttraumatic stress disorder, schizophrenia, depression, and Parkinson’s disease [29]. 5-HT6 antagonists are expected to be effective against learning impairment from anticholinergic and antiglutamatergic models of dementia. It is supposed that the procognitive activity of some marketed antidepressants (Vortioxetine) and antipsychotics (Lurasidone) is caused by potent 5-HT7R affinity, and both 5-HT6 and 5-HT7 receptors represent interesting targets in the search for innovative therapies of AD [30]. Evidence is mounting for the role of 5-HT in human cognition and normalizing 5-HT activity in depression and Alzheimer’s disease (AD) may have specific beneficial effects on cognition, independent of a general relief of mood symptoms, however, as of now, data is not sufficient to comment on emergent use of 5-HT targeting drugs as potential cognition enhancers [31].

1.3.2 Appetite

Brainstem-derived serotonin influences cognitive functions including eating behaviors and regulates homeostatic functions of bone remodeling, appetite, and energy expenditure. Gut-derived serotonin, on the other hand, plays a critical role in feeding activity. Serotonin thus acts as a hormone when made in the gut and a neurotransmitter when made in the brain [32, 33]. Although social and psychological aspects of eating are powerful influences that are independent of or only partially dependent on the physiologic control mechanisms, at the receptor level there is evidence that the 5-HT1B and 5-HT2C receptors are involved in mediating the effects of serotonergic drugs on food intake. Appetite suppression appears to be associated with agonist action at 5-HT2C receptors in the central nervous system. 5-HT2C agonist, lorcaserin, is approved by the FDA for use as a weight-loss medication in monotherapy. While no available pharmacologic therapy has succeeded in maintaining a weight loss of over 10% for 1 year, bariatric (weight-reducing) surgery readily achieves a sustained weight loss of 10–40%, and surgery that bypasses the stomach and upper small intestine rapidly reverses some aspects of the metabolic syndrome. Gastrointestinal flora also influence energy expenditure, and research suggests that altering the microbiome can lead to weight gain or loss [1, 34].

1.3.3 Sleep

Serotonin along with fast-acting non-monoaminergic neurotransmitters (glutamate and GABA) and other monoaminergic neurotransmitters plays a crucial role in regulating the sleep–wake cycle. Earlier it was thought that serotonin might help to produce NREM and possibly REM sleep, however, more recent work indicates that serotonin generally promotes wakefulness and suppresses REM sleep. The role of serotonin in sleep is, however, not straightforward. On one hand, serotonin inhibits the wake-promoting cholinergic neurons and serves as a precursor of melatonin in the pineal gland where 5-HT is Ο-methylated to form melatonin. In humans, melatonin plays a significant role in both inducing and maintaining nocturnal sleep and drives the circadian rhythm which in turn regulates the sleep–wake cycle, and endocrine, immune and neurotransmitter rhythmicity [35]. On the other hand, the firing rates of dorsal raphe neurons and extracellular 5-HT levels are highest during wakefulness, much lower during NREM sleep, and lowest during REM sleep. This wake-promoting role of serotonin is further evidenced by agonists of the 5-HT 1A, 5-HT 1B, 5-HT2, or 5-HT3 receptors that increase wakefulness and 5-HT2 receptor blockers such as ritanserin or agomelatine that promote NREM sleep [36].

1.3.4 Pain

Advances in basic sciences, clinical research and now neuroimaging have established that central sensitization and alterations in neuroplasticity induced by the enhancement of descending pain facilitation and/or the impairment of descending pain inhibition underlie many chronic pain conditions. The descending serotonergic neurons in the raphe nuclei target receptors along the descending pain circuits and exert either pro- or antinociceptive effects, thus, serotonin has a definite role in the pathogenesis of chronic pain conditions like chronic primary pain (CPP), inflammatory bowel disease (IBD), Fibromyalgia syndrome (FMS), etc. [37]. Antidepressants like TCAs, SNRIs, and SSRIs influence the descending pain modulation system by increasing 5-HT at the synaptic junction [5, 38].

1.3.5 Neurological diseases

Migraine, epilepsy, Parkinson’s disease (PD), multiple sclerosis (MS), ALS, and neuropsychiatric disorders (ADHD, ASD) are connected to abnormal 5-HT synthesis and metabolism as the efficiency of 5-HT metabolism is changed in neurodegeneration. Patients with amyotrophic lateral sclerosis (ALS) and multiple sclerosis (MS) present with reduced plasma and CSF levels of tryptophan and subsequently a decreased 5-HT synthesis. In MS, 5-HT synthesis is decreased because of the overactivation of the kynurenine pathway, which drives Tryptophan away from 5-HT synthesis [39]. Migraine is caused by a decreased level of platelet serotonin and its metabolite N-acetylserotonin (NAS) that activate trigeminovascular system (TGVS) and lead to cortical spreading depression (CSD) during an acute attack of migraine. Triptans, acting via 5-HT 1B receptor and serotonin activity at the 5-HT1F receptor on neuronal synapses inhibiting the release of calcitonin gene-related peptide (CGRP) are disease-specific treatments of migraine. It has long been known that serotonin inhibits epileptic activity and because of its crucial role in influencing seizures, regulating sleep and wakefulness, arousal, circadian rhythms, breathing, and cardiac activity, serotonin (5-HT) has been implicated in the pathophysiology of sudden unexpected death in epilepsy (SUDEP) [40]. Apart from other actions, CBZ and VPA release serotonin and LTG inhibits serotonin uptake, however, only a few AEDs, such as the recently approved fenfluramine, act via 5-HT receptors [41]. Progressive dopaminergic denervation is the cardinal pathology in Parkinson’s disease, however, several lines of evidence suggest that a progressive and non-linear loss of serotonergic terminals which is not related to disease duration, disability or dopamine replacement therapy takes place in Parkinson’s disease though at a slower rate. Human PET studies indicate that striatal serotonergic terminals contribute to Levodopa-induced dyskinesias (LIDs) via aberrant processing wherein serotonergic neurons take up, convert exogenous Levodopa into dopamine, and release dopamine as a false neurotransmitter in the denervated striatum of PD patients with LIDs. This study also speculates the development of selective serotonin receptor type 1A agonists for use as antidyskinetic agents in PD [42]. In clinical studies, the nonselective 5-HT 1A agonist buspirone reduced LID without worsening parkinsonian disability. 5-HT 2C receptor antagonism is a potential mechanism whereby clozapine and quetiapine can reduce LID [42, 43]. Abnormalities in SERT and MAO-A activity in various brain regions have been found to be associated with impulsivity and aggressive tendencies in ADHD. 5-HT deficiency leads to a failure of 5-HT-mediated inhibition of aggressive behavior in adults as well as children and decreased levels of 5-HT and its metabolite 5-HIAA, in the blood, urine, and CSF in individuals with ADHD compared with healthy controls. Although precise pathomechanism of ASD has not been elucidated, hyperserotonemia is present in approximately 30% of patients of ASD. One of the consequences of hyperserotonemia is increased catabolism of 5-HT [39].

2. Serotonin in the gut

Nearly 95% of the body’s content of serotonin is found in GIT and only 5% is found in the brain. Within the gut, about 90% of serotonin is in EC cells and about 10% is found in enteric neurons, pancreatic cells and mast cells. Enterochromaffin (EC) cells are excitable, serotonergic neuroendocrine cells located throughout the length of the lining of the gastrointestinal tract. EC cells synthesize 5-HT, in the presence of some cofactors, such as vitamin B6, vitamin B3, and magnesium, from its precursor L-tryptophan in a reaction catalyzed by the enzyme tryptophan hydroxylase, which exists in two isoforms (Tph1 and Tph2). Tph1 is mainly present in EC whereas Tph2 is found in CNS and enteric neurons [44]. EC cells release 5-HT in a regulated manner in response to various mechanical and chemical stimuli. 5-HT thus released from EC cells reaches the blood, surrounding tissues, and gut lumen. Once released, 5-HT is transported into surrounding epithelial cells and platelets by the serotonin reuptake transporter (SERT) and degraded to 5-hydroxyindoleacetic acid (5-HIAA). Platelets are a major source of peripheral 5-HT as they store the 5-HT synthesized by EC cells in the gut and are always present in the circulation. Five (5-HTR1, 5-HTR2, 5-HTR3, 5-HTR4, and 5-HTR7) of the seven 5-HT receptor (5-HTR) families are expressed in the gut smooth muscle, enteric neurons, enterocytes, and immune cells through which serotonin mediates various secretomotor and sensory functions such as nausea, vomiting, intestinal fluid and mucus secretion and peristaltic movement [45].

2.1 Functions of serotonin in the gastrointestinal tract

1. Serotonin as a regulator of gut motility: 5-HT plays a crucial role in the generation of peristaltic reflexes, segmentation, and mucosal stimulation in response to food intake, under normal circumstances and in disorders of GI tract associated with the alteration of motility and sensation like the irritable bowel syndrome (IBS) [44].

2. Serotonin in fluid and mucus secretion: 5-HT inhibits gastric acidity by increasing the gastric mucus and fluid secretion. Mucus in GIT acts as a physical barrier for microorganisms, diffusion of toxins, and as an antioxidant [46].

3. Pain and anxiety: EC cell activation produces persistent visceral hypersensitivity in response to gut distension, even in the absence of inflammation.

4. Serotonin in immune cell function: Serotonin receptors are expressed by nearly all innate immune cells, such as the Langerhans cells or the immature dendrite cells (DCs) in the skin and other epithelial tissues lining the nose, lungs, stomach and intestine, monocytes, mast cells and eosinophils. 5-HT, along with other platelet-derived factors, plays a crucial role in the recruitment of these cells at the site of acute inflammation [47].

5. Serotonin in inflammation: Serotonin evokes divergent pro as well as anti-inflammatory actions and while 5-HTR4-mediated anti-inflammatory action predominates in the basal or normal conditions, 5-HTR7-mediated pro-inflammatory signals predominate under pathological conditions. Inflammatory bowel diseases (IBD) viz., Crohn’s disease (CD) and ulcerative colitis (UC) are believed to result from an abnormal response to self-antigens or the gut resident microbiota and are characterized by activation of both innate and adaptive immune systems in response to enhanced cytokine production in GIT [48].

6. Angiogenesis: 5-HT release from platelets stimulates angiogenesis in many physiological processes, such as organ development, reproduction, wound healing and pathological conditions like IBD, diabetic retinopathy, rheumatoid arthritis, age-related macular degeneration, and tumor growth and metastasis [49].

3. The gut microbiome

Conventionally brain has been considered sealed from microbial influence unless infection occurs, however, evidence in favor of gut microbiota interplays with different systems ultimately impacting the brain has accumulated over the past few decades to the extent that the gut microbiome has earned the name “second brain” from some authors.

3.1 Composition and diversity of gut microbiome

The term microbiome pertains to the community of microorganisms, their structure, activity, metabolites and mobile genetic elements while microbiota is a collection of microbial communities associated with a habitat [11]. This collection of bacteria, viruses, fungi, protozoans, and archaea found in an individual constitutes about 1–3% of total human body mass. Majority of the human microbiome is comprised of bacteria, about 100 trillion bacteria from 500 to 1000 different species, with varying diversity adding over eight million genes to the human genome. The microbiota colonize predominantly the human intestine and to a lesser extent the airways and the skin surface. A simplified taxonomic composition of gut microbiota is presented in Table 1. Most of these microorganisms belong to the phyla Firmicutes and Bacteroidetes [51].

Phylum	Examples
Actinobacteria	Bifidobacterum longum; Bifidobacterium bifidum
Firmicutes	Faecalibacteruim prausnitzii; Clostridium spp.; Roseburia intestinalis; Runinococcus feacis; Dialister invisus; Lactobacillus renteri; Enterococcus faecium; Staphylococcus leei
Bacteriodetes	Bacteriodes fragilis; Bacteriodes vulgaris; Bacteriodes uniformis; Parabacteriodes diastaoms; Alistipes finegoldii; Prevotella spp.
Proteobacteria	Escherichia coli; Shigella flexineria; Desulforibrio intestinalis; Bilophila; Wadsworthia
Fusobacteria	H. Pylori; Fusobacterium nucleatum
Verrucomicrobia	Akkermansia muciniphila

Table 1.

Simplified taxonomic classification of gut microbial composition [50].

3.2 Factors influencing the composition of the microbiome

Gut microbiome is a dynamic with many variables influencing its composition.

3.2.1 Genetics

Twin studies have revealed similar microbiome composition in monozygotic twins and this similarity has been seen to be more in monozygotic twins and dizygotic twins than in other family members [52]. Genetic animal models of 5-HTT deficiency have revealed the presence of altered microbial composition in 5HTT knockout mice such as they had predominance of pathobionts [53].

3.2.2 Early life factors

Microbes colonize the various sites from the first days of life, reach high numbers immediately after birth, and gradually evolve and diversify with the growth of the individual to outnumber somatic cells by a number of ten. Microbiota are shaped in the first few years of life by gut maturation developing from enterotypes, which are functionally harmonious clusters of bacteria that characterize individuals and are regrouped by functions. The first 2 years of life including the intrauterine period seem to represent the most critical time for microbiome modulation. Other factors modulating this composition of microbiota in early life are birth gestational age, type of delivery, methods of milk feeding, weaning period, maternal diet/weight, pro and prebiotic use, early antibiotic exposure, timing and type of complementary feeding, lifestyle, dietary and cultural habits [54, 55, 56].

3.2.3 Gut permeability and inflammation

Gut epithelium serves a protective and structural role in the human body and when this barrier is compromised, the so-called “leaky gut” is associated with pathological conditions that activate gut pain sensory pathways and dysregulate the enteric nervous system. The stress of varying types can impact the developmental trajectory of intestinal barrier by causing significant perturbations in gut permeability as well as gut microbiome [57, 58] and maternal separation has been shown to cause such a shift in the microbial composition in a drastic way [59, 60].

3.2.4 Body mass index (BMI) classes and exercise frequency

Gut microbiota variations are correlated with obesity, anorexia nervosa and exercise as a form of environmental enrichment has been shown to impact the gut microbiome in a positive way [61, 62].

3.2.5 Aging

Microbial changes that occur with Aging have been grouped into two categories; those associated with healthy aging and pathobionts associated with ill health in aging [63].

3.3 Gut-brain axis

It is a complex, firmly established, bidirectional network that connects the microbiota, enteric and central nervous system. The microbiome gut-brain axis (MGBA) can be modulated by endocrine, neural and immune pathways in a bottom-up or top-down approach with multiple feedback loops regulating this network. In top-down approach, the brain uses these mechanisms to influence the composition of microbiota in gut. In the bottom-up approach microbiome signals brain through immune regulation by the production of cytokines and through production of neurotransmitters and neuroactive metabolites like short-chain fatty acids (SCFAs) [11, 64].

3.4 Pathways of the gut-brain axis

3.4.1 Neurologic pathway

The vagus nerve tonically transmits information from the viscera to the brain and vice versa and is considered to be the fastest and most direct way for the microbiota to influence the brain. Specific bacteria within the gut microbiota utilize the vagus nerve to communicate with the brain to alter certain neurocircuits by affecting primary afferent neuronal excitability. Ablation of gut-related vagal communication between lower GI tract and brain, as evidenced by animal studies and surgical procedures like gastrectomies, resulting in changes in adult neurogenesis, stress reactivity, cognition, and increased occurrences of psychiatric-related disorders has been recognized for long [65, 66].

3.4.2 Endocrine pathway

The hypothalamus pituitary adrenal (HPA) axis regulates cortisol secretion in response to stress by directly affecting immune cells and release of cytokines systemically as well as locally in the gut. Cortisol affects gut permeability, its barrier function as well as composition of gut microbiota. Gut microbiome, in a bottom-up fashion, influences the release of cytokines and other immune mediators like interferon-gamma. Serotonin plays a crucial role in recruitment of innate immune cells in response to this cytokine release during time of dysbiosis. Gut microbiome also influences the release of neuropeptides like galanin, leptin and neuropeptide Y (NPY) from enteroendocrine cells which reach the systemic circulation and bind receptors on immune cells and vagus nerve terminals thereby enabling indirect gut-brain communication [67, 68, 69]. Another mechanism of microbiome-gut-brain crosstalk is through tryptophan and its metabolites such as 5-hydroxyindoleacetic acid (5-HIAA). The gut microbiota can alter concentrations of kynurine and disruption of this metabolic pathway has been linked to both GI and brain disorders.

3.4.3 Metabolic/humoral pathway

Bacterial metabolites like short-chain fatty acids [SCFAs] and lipopolysaccharides, which are produced by their fermentation of dietary carbohydrates are important humoral influencers. These metabolites affect the nutrition of the enterocytes, possess hormone-like activity, stimulate the sympathetic nerves of gut and also have immunomodulatory properties. SCFAs also regulate microglial homeostasis which in turn affects brain development, brain tissue homeostasis, and behavior [70].

3.5 Impact of the gut microbiota on serotonin levels in gut and brain

Serotonin is directly synthesized by commensal bacteria from the colonic luminal tryptophan and serotonin biosynthesis is promoted in the colonic ECs by spore-forming bacteria. Gut microbiota promotes enteric 5-HT production through SCFAs as well as phenolic and indolic compounds derived from microbes. Microbiota affects the central serotonin levels through many pathways. It influences availability of the peripheral tryptophan by affecting the metabolism of the gut luminal tryptophan thereby altering the central tryptophan levels and hence the central serotonin levels. The microbial metabolites e.g., SCFAs, especially butyrate have been reported to increase brain serotonin concentration. In addition, inflammatory stimuli, such as LPS, the major components of the outer membrane of Gram-negative bacteria, have been postulated to affect the kynurenine pathway thereby diverting tryptophan away from serotonin synthesis. In gut dysbiosis, as demonstrated by antibiotic studies, central levels of serotonin and its precursor tryptophan has been seen to be reduced and these are posited to be due to increased serotonin metabolism as reflected by increased SERT and MAO expression in the hypothalami of piglets. The microbiome also regulates serotonin transporter (SERT) expression by gut bacteria via posttranslational and transcriptional mechanisms, alterations in SERT surface levels, and epigenetic or immune mechanisms. Gut microbiome metabolites like SCFAs also affect serotonin signaling by regulating 5-HT receptor expression by increasing the mRNA expression of 5-HTR1A, 2B, and 5-HT7. Bacterial extracellular vesicles (EVs) that are hypothesized to permeate the blood–brain barrier (BBB) cause an increase in colonic and hippocampal serotonin levels [71].

4. Influence of microbiome on brain function and behavior

Bacteria within the gut microbiome play crucial roles in the maintenance of gut epithelium integrity, digestion, metabolism, synthesis of beneficial substances including vitamins, combating infection and inflammation and resisting colonization by pathogenic bacteria during conditions of good health [72]. Gut microbiome dysbiosis is being implicated in a myriad of conditions like stress, obesity, and inflammation, however, elucidating the effects of the microbiome on behavior has been especially fascinating. Such research highlights the importance of the complexity and diversity of gut microbiome in both health and disease and underscores the need for further exploration.

4.1 Human personality

Investigation of microbiome composition and diversity with respect to human personality has analyzed bacterial genera linked to human behavior and has revealed that sociability is associated with higher diversity and stress and anxiety are associated with reduced diversity. These results add a new dimension to the evidence that gut microbiome can influence the central nervous system in humans with effects on behavior and stresses the ways in which modern-day living with fewer social interactions, less time spent with nature, processed diets, and oversanitized environments might be contributing to gut dysbiosis [73].

4.2 Cognition

Microbiome mediates the plasticity of cognitive traits by altering protein expression, adult hippocampal neurogenesis and performance on cognitive tasks [74].

4.3 Physical activity

Evidence suggests that aerobic exercise improves the diversity and abundance of genera from the Firmicutes phylum, which may be the link between the positive effects of exercise on the gut and brain [75].

4.4 Autism spectrum disorder (ASD)

Numerous studies, stimulated by frequent gastrointestinal complaints and immune dysregulation in ASD, have suggested microbial dysbiosis in clinical populations of ASD. Increased blood levels of lipopolysaccharides with a corresponding increase in peripheral IL-6 levels have been found in ASD patients. Further, increased intestinal permeability as reported in ASD subjects and their first-degree relatives is posited to be a pathogenetic factor rather than a consequence of autistic behavior. Probiotic supplementation, oral vancomycin treatment and a modified fecal microbiome transfer have been demonstrated to have therapeutic potential in children with ASD [57].

4.5 Major depressive disorder

Serotonin in CNS is synthesized from tryptophan transported from blood and hence, tryptophan availability is critical for serotonin synthesis in brain [76]. Normal gut microbiota buffer extreme fluctuations in serotonin levels by making the serotonergic system less sensitive to variations in its precursor. Gut serotonin, which is under the control of gut microbiota, through neural routes communicates to the brainstem neurons by stimulating serotonin receptors at the terminals of vagal afferents [77]. It has been shown that vagotomy abolishes the antidepressant effects of SSRIs thus implicating the role of peripheral serotonin and vagus nerve stimulation in the regulation of depressive behavior [78] and leading to the postulation that gut microbiome through stimulation of the vagus nerve influences depressive behavior [79]. A few case–control studies have reported differences in the gut microbiome between depressed patients, and healthy controls and preliminary evidence suggests that probiotics might prove to be beneficial in patients with major depressive disorder and in healthy populations as well [80].

4.6 Bipolar disorder

Extensive research has suggested an abnormal inflammatory response in bipolar disorder and evidence is emerging for alterations in gut microbial composition of patients with bipolar disorder suggesting that gut microbial dysbiosis contributes to disease progression and cognitive impairment in bipolar disorder [81]. Gut microbial profiling in bipolar disorder patients revealed some correlation between certain genera and sleep and stress in these patients [82].

4.7 Schizophrenia

High rates of comorbidity reported in schizophrenia with autoimmune and gastrointestinal conditions, systemic low-level inflammation, and increased intestinal permeability suggest the involvement of gut microbiome. Studies that need further investigation, have identified reduced phylum Proteobacteria and Gammaproteobacteria as class-level biomarkers of schizophrenia [57]. Antipsychotic medications have been shown to alter gut microbiome and this alteration is considered to play a crucial role in adverse effects like metabolic syndrome resulting from antipsychotic medication use [83]. A positive correlation was seen between Lactobacillus bacterial group members and the severity of psychotic symptoms in a study in which 70% of subjects showed remission on antipsychotic treatment whereas only 28% subjects with “abnormal” microbiota experienced remission indicating thereby that gut microbiome may moderate treatment response in schizophrenia. The use of probiotics improved gastrointestinal disturbance in psychosis although improvement in symptoms of psychosis has not shown promising results [57].

4.8 Attention deficit hyperactivity disorder (ADHD)

Altered and reduced diversity of gut microbiome in children with ADHD has been reported in studies limited by sample size and concomitant methylphenidate intake [84, 85].

4.9 Anxiety and related disorders

Anxiety and related disorders viz., obsessive-compulsive disorder (OCD) and pediatric autoimmune neuropsychiatric disorder associated with streptococcal infection (PANDAS) are other areas wherein indirect evidence suggests that gut microbiome has a potential causative role and therapeutic potential [57].

5. Recent advances and potential therapeutic targets

Some of the key technologies used to investigate the complex interactions between the gut microbiome and the central nervous system include:

5.1 Multi-omics

Metagenomic sequencing allows researchers to analyze the genetic material of the entire microbial community in the gut, providing insights into the diversity and functional potential of the microbiome. Metatranscriptomics technology focuses on the RNA transcripts of the gut microbiome, revealing which genes are actively expressed and providing information on microbial functions. Metabolomics is used to study the small molecules produced by gut microbes, such as short-chain fatty acids and neurotransmitters, which can influence brain function. Multi-omics integration combining data from genomics, transcriptomics, and metabolomics can provide a comprehensive understanding of the microbiome–gut–brain axis. In microbiota profiling, 16S rRNA sequencing and shotgun metagenomic sequencing are used to identify and characterize the composition of microbial communities in the gut [86].

5.2 Functional neuroimaging

Techniques like fMRI (functional magnetic resonance imaging) can be employed to observe changes in brain activity in response to gut microbiome alterations.

5.3 Animal models

Animal studies, including germ-free and gnotobiotic models, are used to investigate the effects of specific microbial communities on behavior and brain function.

5.4 Germ-free studies

Germ-free animals are the “microbiota free” control group for the animals whose gut is conventionally colonized. They are maintained in gnobiotic units which are sterile, eliminating the chances of postnatal colonization of their GI tracts [87]. Germ-free animals are studied for social, stereotypical, and anxiety-like behaviors on exposure to novel and aversive environments (elevated plus maze, light/dark box, open field), and non-spatial and working memory tasks (novel object recognition and spontaneous alternation assessed in the T-maze) in labs. Germ-free mice have been shown to have lower levels of molecular targets like the N-methyl-daspartate receptors (NMDARs) in the hippocampus, or amygdala and decreased levels of brain-derived neurotrophic factor (BDNF). Apart from other findings, the results have been seen to be dependent on the time of colonization, be it in adolescence or adulthood, positing that there is a critical time period that is neurodevelopmentally sensitive to dysbiosis [88].

5.5 Antibiotics

Both in-vitro and in-vivo experiments [89] have documented the perturbation of gut microbiota with antibiotic treatment that leads to an increase in sensitivity to visceral pain, increase in gut motility and altered BDNF levels in the brain.

5.6 Probiotics and prebiotics

Probiotics are defined as live organisms which when administered in adequate amounts confer a health benefit on the host. Prebiotics are non-digestible food ingredients that selectively stimulate the growth of Lactobacilli and Bifidobacteria in the gut, hence indirectly affecting the brain function. The two main genera which are used as probiotics are Lactobacillus and Bifidobacterium. Several pre- and probiotic studies have demonstrated their beneficial effects on behavior of the host and offer novel therapeutic potential for treating mood and anxiety disorders [90]. Caution is warranted when translating and generalizing the evidence that certain pre- and/or probiotic strains are able to modulate brain function and behavior.

5.7 Microbiome manipulation

Researchers can manipulate the gut microbiome using techniques such as fecal microbiota transplantation (FMT) to assess its impact on brain health and behavior [91].

5.8 Brain-gut communication assays

These assays involve measuring biomarkers like cytokines and neuropeptides to understand how the gut and brain communicate. Finally, researchers may employ psychological tests and behavioral observations to assess the impact of the gut microbiome on mood, cognition, and other brain-related functions [92].

5.9 Potential therapeutic strategies targeting the microbiome gut-brain axis

Efforts are being put to target the vast ecosystem of the gut microbiome for a role in neuropsychiatric disorders.

5.9.1 Psychobiotic

Dinan et al. coined the term “psychobiotic” and defined it as “live organism that, when ingested in adequate amounts, produces a health benefit in patients suffering from psychiatric illness.” This definition has been expanded since then to include “any exogenous influence whose effect on the brain is bacterially-mediated.” Thus, psychobiotics include a range of substances that have the potential to affect microbiota–gut–brain axis signaling, including probiotics, prebiotics, symbiotics, and postbiotics. These substances can be delivered through supplements, functional foods, and improvements to dietary intake. Some microbial therapeutics have been engineered to sense a range of biomarkers and respond accordingly and are currently in clinical trials for the treatment of diabetes, inflammation, and cancers [71].

5.9.2 Probiotics

There is preliminary evidence from human studies wherein Probiotics have demonstrated their efficacy in ameliorating anxiety and depression states [93]. These findings have been supported by systematic reviews of therapeutic potential of probiotics in MDD [94].

5.9.3 Prebiotics

Prebiotics consist of fibers such as resistant starch, fructo-oligosaccharides, galacto-oligosaccharides (GOSs), and inulin which are unabsorbed in the small intestine and are selectively fermented by gut microbes. Prebiotics are also found in human milk. One study which was done in a cohort of patients suffering from IBS demonstrated a significant decrease in anxiety scores with prebiotic administration [95].

5.9.4 Synbiotics

Synbiotics are a combination of both pre- and probiotics, whereby the prebiotics improves the viability of the probiotic, providing a source of fermentable fiber as well as acting as a general prebiotic. In a recent study, a symbiotic comprising galacto-oligosaccharides (GOS) and a dual-strain probiotic (Lactobacillus helveticus and B. longum) was successfully shown to decrease scores on depression scale and positively impacted tryptophan signaling in mild to moderate MDD [96].

5.9.5 Postbiotics

Postbiotics are nonviable entities that are byproducts of bacterial fermentation and include bioactive metabolites such as SCFAs. The use of gut peptides directly as an intervention in gut–brain axis may not be feasible due to technical issues, however, targeting specific microbiota in order to modulate specific gut peptides may be a useful psychobiotic therapy. Para probiotics, or nonviable probiotics, e.g., heat-killed probiotics, can also be included in the category of postbiotics in that they contain structural components that may exert biological activity in the host. In preclinical studies, several heat-killed probiotics have described antidepressant and anxiolytic effects, with heat-killed Lactobacillus paracasei [97].

5.9.6 Fermented foods and diet

Fermented foods contain probiotics, prebiotics, and bacterially derived bioactives. Two of the most common strains used in the fermentation process include Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus. In dairy products, lactic acid-producing Bifido-bacterium and Lactobacillus are commonly used. Studies using fermented food interventions in humans are limited, however, there is some evidence showing ameliorations in anxiety and mood scores. Fermented milk drinks have been found to result in positive benefits in emotional processing. Fermented milk containing Lactobacillus casei strain Shirota prevents the onset of physical symptoms in medical students under academic stress by modulating the gut-brain interaction [98]. Mediterranean diets have well-known mental health benefits. One large-cohort, cross-sectional study in women found healthier dietary patterns to be associated with better general health scores and decreased incidence of anxiety and depression outcomes [99].

6. Ethical considerations and challenges

As with any medical intervention, ethical concerns arise regarding the use of microbiome-based interventions for mental health and neurology. Balancing potential benefits with safety and long-term effects is crucial. It is important to note that while there is promising research in this area, it is still relatively new and complex. More studies are needed to fully understand the mechanisms at play and to establish the effectiveness and safety of microbiome-based interventions for mental health and neurology.

Ethical considerations in microbiome-based treatments include issues related to informed consent, privacy and data security, equitable access, potential conflicts of interest, and the long-term effects of manipulating the microbiome. These treatments involve complex interactions with individual health and the broader ecosystem, requiring careful consideration of both short-term benefits and potential unintended consequences. One of the challenges in this field is the identification of neuroactive compounds originating from the host rather than gut microbiome due to complex communications between these two. Many of the dietary benefits on the microbiome and brain health have been attributed to anti-inflammatory effects mediated by the microbial metabolites of dietary fiber and polyphenols. Overall, it is clear that although animal studies have shown much promise, more progress is necessary before these findings can be translated for diagnostic and therapeutic benefit in patient populations.