The Microbiota–Gut–Brain Axis and Neurological Disorders: A Comprehensive Review

Rett syndrome is a rare X-linked neurodevelopmental disorder, primarily affecting young girls. It is characterized by developmental delay, which manifests as a progressive loss of motor skills and language, accompanied by the development of repetitive hand movements. Neurologically, Rett syndrome is associated with a reduction in brain volume, particularly in the frontal and temporal lobes, as well as abnormalities in the function and structure of synapses [24,25]. The most significant biomarkers include loss-of-function mutations of the X-linked methyl-CpG binding protein 2 (MeCP2) gene, and decreased levels of the brain-derived neurotrophic factor (BDNF) in the cerebrospinal fluid [24,26]. Recent studies have also identified alterations in mitochondrial function and oxidative stress as contributing factors to the disease pathology [27,28]. Several studies have demonstrated that individuals with Rett syndrome exhibit alterations in the composition and richness of their gut microbiome when compared to a control group (Figure 2). These studies have indicated the presence of a potential dysbiosis, which can be defined as an imbalance in microbial diversity relative to the control group. Nevertheless, further research, including larger cohort studies, is necessary to confirm these results. The studies have observed the most notable alterations in the abundance of bacterial taxa within the Firmicutes and Bacteroidetes phyla, followed by the Actinobacteria phylum in Rett syndrome patients. Notably, a significant increase in potentially pathogenic bacteria has been identified, including taxa belonging to genera such as Bifidobacterium, Clostridium, Erysipelotrichaceae, Actinomyces, Lactobacillus, Enterococcus, Eggerthella, Escherichia, and Shigella in Rett syndrome. The currently available evidence on the genus Bacteroides is inconclusive. The available evidence on this topic is inconclusive, with studies yielding conflicting data [26,29]. In contrast, beneficial bacteria crucial for gut health, including Ruminococcus spp., Faecalibacterium spp., genera from the Oscillospiraceae family (Oscillibacter, Sporobacter), and several Bacteroidetes genera (Prevotella, Barnesiella, Alistipes, Odoribacter, Butyricimonas), were found to be decreased in Rett syndrome [26,29,30]. Furthermore, the fungal genus Candida was observed to be increased in Rett syndrome subjects compared to the control group [29]. Collectively, these studies indicate that Rett syndrome is associated with dysbiosis in the gut microbiome, characterized by an overabundance of potentially harmful bacteria relative to beneficial species. This microbial imbalance may potentially contribute to the pathophysiology of Rett syndrome. Nevertheless, further investigation is required to determine the relationship between bacterial composition and the severity of Rett syndrome [30]. A list of the bacteria involved in Rett syndrome are listed in (Table 1).

ASD is a neurological condition that presents challenges in speech, social interaction, and repetitive behaviours. Additionally, individuals with ASD exhibit differences in movement, learning, and attention [32]. Studies on brain imaging have revealed variations in the morphology of the brain, including changes in the amygdala and prefrontal cortex (PFC) size and connectivity. Although studies have indicated potential candidates, such as aberrant levels of specific neurotransmitters and genetic abnormalities linked to synaptic function, the development of biomarkers for ASD is still being investigated [33]. The current research on the gut–brain axis emphasizes the importance of the ENS to play in establishing a vital communication channel known as the gut–brain axis, which links the gut and the CNS via the vagus nerve. This axis affects emotions and behaviour by facilitating communication through immunological reactions, hormones, and neurotransmitters. The human gut microbiome comprises trillions of bacterial cells, which are essential for the proper functioning of the gut–brain axis. The beneficial bacteria such as Clostridium sporogenes and Bifidobacterium infantis produce metabolites and neurotransmitters that regulate emotions and protect neurological function. However, pathogenic microorganisms like Clostridium bolteae and Clostridium tetani alter behaviour and neurotransmitter function. They have also been linked to GI problems and an increased severity and risk of ASD. An understanding of these interplays provides valuable insights into potential diagnostic and therapeutic approaches for neurological conditions associated with intestinal dysbiosis. Dysbiosis is associated with a range of disorders, including ASD. This imbalance can lead to disturbances in the host–microbiota equilibrium, with potential consequences for the immune system and the gut barrier. Patients with ASD may have dysbiosis gut microbiota that affects their immune system, causing proinflammatory chemicals to be secreted and changes in gut permeability. Potent proinflammatory endotoxins, such as lipopolysaccharide (LPS), can enter the circulation through this “leaky gut” phenomenon and alter CNS activity, which in turn can impact behaviour, emotions, and neurodevelopment. Research has indicated that individuals with ASD exhibit alterations in certain microbial taxa, including elevated levels of Proteobacteria, Lactobacillus, Bacteroides, and Clostridium, accompanied by decreased levels of Bifidobacterium, which are good bacteria. These microbiome imbalances underscore the complex link between gut microbiota dysbiosis and ASD pathogenesis, whereby they promote immunological dysregulation, neurotransmitter production, and gut barrier integrity [34].

In patients with ASD, alterations in gut microbiota composition are evident when compared to control groups. Notably, the phylum Firmicutes exhibits a decrease, while Actinobacteria, Bacteroidetes, and Proteobacteria show increases. At the family level, Ruminococcaceae, Sutterellaceae, Clostridiaceae, and Enterobacteriaceae are increased, whereas Prevotellaceae and Veillonellaceae decrease. Among genera, Blautia experiences a decrease, whereas Bacteroides, Faecalibacterium, Ruminococcus, Akkermansia, Lactobacillus, Clostridium, and Bifidobacterium show alterations, with varying increases or decreases. These changes highlight the potential role of gut microbiota dysbiosis in the pathogenesis of ASD.

ADHD is a complex brain disorder characterized by persistent problems with attention, hyperactivity, and impulsivity. These challenges affect various behaviours and cognitive repertoires. Some researchers propose that children with ADHD experience a delay in maturation because synaptic pruning lags behind normal development [35,36,37]. The decrease in size in various parts of ADHD brains is frequently linked to a decrease in synaptic density rather than a loss of neurons themselves [38]. The delay in cortical maturation, particularly in the lateral PFC, is evident in children with ADHD. Tasks such as controlling inappropriate responses, directing attention, evaluating rewards, and managing working memory are governed by this region of the brain [36,39]. Conversely, in children diagnosed with ADHD, the motor cortex exhibits a peak in maturation four months ahead of control children. This accelerated development in the motor cortex could lead to the impulsivity often observed in individuals with ADHD [36].

The gut microbiome has been implicated in the pathophysiological mechanisms of ADHD through the MGBA. Alterations in the MGBA contribute to neuroinflammation and oxidative stress, leading to ADHD core symptoms and associated comorbidities such as sleep disturbances. There is some evidence indicating maternal stress and the use of acetaminophen, which is a common pain reliever and fever reducer, may increase the risk of ADHD in offspring during pregnancy [40]. Studies suggest a potential therapeutic role for probiotics in children with ADHD. Probiotic supplementation has shown some promising results in reducing ADHD symptoms and improving cognitive function [41]. Furthermore, the gut microbiome may impact dopaminergic metabolic pathways in individuals with ADHD, suggesting a potential genetic influence on ADHD pathophysiology [42]. The previous study demonstrated that an imbalance in the omega-3/omega-6 PUFA ratio can lead to neuroinflammation and dopaminergic dysfunction, contributing to ADHD symptoms. Pyridoxal phosphate, the active form of vitamin B6, acts as a cofactor for glutamic acid decarboxylase. Glutamic acid decarboxylase converts glutamate into gamma aminobutyric acid (GABA), an inhibitory neurotransmitter, and is involved in the metabolism of tryptophan, which serves as the precursor for serotonin, kynurenic, and xanthurenic acids. Research on tryptophan metabolism revealed that B6 deficiencies are central to the biochemical disturbances seen in ADHD [43].

Bacterial species such as Bacteroides spp. and Clostridiae spp. are known for their activity in producing short-chain fatty acids (SCFAs). SCFAs can influence neuroinflammation, oxidative stress, and neurogenesis, potentially affecting ADHD symptoms [44]. Prehn-Kristensen and colleagues discovered a higher presence of the Bacteroidaceae family in adolescents diagnosed with ADHD [45]. This finding was supported by Wang et al., who identified an increase in certain Bacteroides species within the ADHD cohort. However, there were discrepancies in the alpha and beta diversity metrics: Prehn-Kristensen et al. observed reduced alpha diversity and significant variances in beta diversity within the ADHD group, while Wang et al. did not find significant beta diversity differences between groups [46]. These inconsistencies might stem from differences in ADHD medication usage, ethnic composition, and dietary patterns. Probiotics, such as strains of Lactobacillus and Bifidobacterium, have been investigated for their potential benefits in ADHD. Also, promoting a diet rich in fibre, fruits, vegetables, and omega-3 fatty acids while reducing processed foods and sugars may promote a healthier gut microbiome, which may benefit individuals with ADHD. However, ongoing research shows inconsistent results because of significant methodological differences in factors like sample size, participant selection criteria, the identification of potential confounders, taxonomic composition changes, and potential alterations in synaptic plasticity in ADHD patients, as depicted in (Table 2).

MS is a chronic, inflammatory, demyelinating, and degenerative disease that affects the CNS [139]. This autoimmune condition affects approximately 2.8 million individuals worldwide [140]. Individuals of all age groups may be affected by this condition; however, it is more frequently observed in young adults and is particularly prevalent among females, compared to males. The precise aetiology of the disease remains elusive, although research indicates that genetic and environmental factors may play a role. Its underlying pathophysiology is widely believed to be autoimmune [141]. The primary pathological hallmark of MS is the formation of inflammatory plaques, focal areas of demyelination in the brain and spinal cord as illustrated in Figure 6. This inflammation destroys myelin and oligodendrocytes, leading to neuronal loss [142]. Demyelination is caused by an altered selectivity of the blood–brain barrier (BBB), which allows a wide range of immune cells to infiltrate the CNS lymphocytes that recognize the myelin antigen (CD4+ or CD8+ T cells) cross the BBB and interact with antigen-presenting cells, triggering a cascade of inflammatory events. This process leads to the formation of demyelinating lesions, which are characterized by myelin loss, oligodendrocyte damage, and subsequent neuronal impairment.

MS has traditionally been regarded as a CD4 T-cell-mediated disease. This perspective is largely due to the observation that the major histocompatibility complex (MHC) class II locus constitutes the most significant genetic risk factor for MS [143]. MHC Class II molecules are a subset MHC molecule that are typically found on professional antigen-presenting cells like dendritic cells, macrophages, some endothelial cells, thymic epithelial cells, and B cells. These cells play a critical role in initiating immune responses by presenting antigens to CD4+ T cells, thereby activating them and triggering the adaptive immune response [144]. Even though the aetiology of MS is unknown, one of the key regions associated with MS risk is the major MHC, also known as the human leukocyte antigen. The MHC class II region plays a pivotal role in the immune response. It is involved in interactions with CD4+ (helper) T cells [145]. Moreover, IFN-γ orchestrates a number of protective functions that enhance immune responses. These include the promotion of macrophage activation, the mediation of antiviral and antibacterial immunity, the enhancement of antigen presentation, and the regulation of cellular proliferation and apoptosis [146]. However, the role of IFN-γ has remained paradoxical, with some studies attributing it to a pro-inflammatory and pathogenic function in MS. In particular, CD4+ T helper 1 (Th1) lymphocytes are responsible for secreting interferon-gamma, a cytokine that activates macrophages and stimulates the release of their enzymes. IFN-γ also triggers the production of reactive oxygen and nitrogen intermediates, contributing to tissue damage in the vicinity. Conversely, Th17 cells produce cytokines including IL-17, IL-21, and IL- 22, which are implicated in the inflammatory response and the progression of the disease [147]. Teriflunomide and fingolimod, are two oral disease-modifying drugs used in the treatment of relapsing forms of MS. Fingolimod exerts its effects predominantly on CD4+ T cells, resulting in a reduction in lymphocyte counts in the peripheral blood of MS patients [148]. It is noteworthy that B-cells (which produce antibodies) are reduced, and T helper cells (which control immune cell activity) are also affected, with the exception of natural killer cells, which play a pivotal role in the immune responses against viruses and tumours and are involved in killing the target cells by secreting and delivering perforins and granzymes.

ALS is a multi-system disorder with progressive atrophy of skeletal muscles, dysphagia, dyspnoea, dysarthria, cognitive dysfunction, and emotional incoherence. The sporadic and familiar cases of ALS are associate with different mutations that trigger an accumulation of transaction response DBA-binding-protein-43 and superoxide dismutase 1 [76]. In ALS, the neurological symptoms come after GU symptoms such as emptying delay and reduced colonic transit timing [174,175]. Meanwhile, the information on the microbial profiles of ALS patients varies across studies. One study showed decreased microbiota diversity in ALS patients [175]. Another study did not justify any significant variation in the gut microbiota as a hallmark of ALS [176]. Yet another publication revealed a profound difference between ALS patients and healthy controls in the microbial profiles [177]. An animal study elucidated the pathophysiological mechanisms of microbiome disbalance in ALS. Those include an increased gut permeability and reduced integrity of membranes constituting the brain–blood and brain–spinal barriers [178]. Despite contradicting findings of previous studies, some research teams are still enthusiastic about the causative and modulating effects of MGBA on ALS pathogenesis [76].

Both the generation of new neurons in the adult hippocampus (known as adult hippocampal neurogenesis or and the composition of the gut microbiome have been suggested to play a key role in controlling neuroinflammatory mechanisms. The dysregulation of neuroinflammation is a common feature of epilepsy, and interactions between AHN and the gut microbiome may influence inflammatory responses in the brain, contributing to the pathogenesis of TLE []. The gut microbiome can influence neurotransmitter production and signalling in the brain. Changes in neurotransmitter levels, such as GABA and glutamate, have been linked to epileptogenesis in the temporal lobe E [,]. AHN may also play a role in modulating neurotransmitter systems, potentially affecting neuronal excitability and seizure susceptibility. However, the extent to which gut microbiome–AHN interactions are relevant in the context of epilepsy and seizures remains unclear. Disruptions in adult hippocampal neurogenesis and alterations in the gut microbiome composition could influence the balance between excitation and inhibition in the hippocampus, contributing to hyperexcitability and seizure generation in TLE. ^{179 180 181}

The impaired synaptosomal transport of GABA and glutamate, which is critical for the termination of neurotransmission by the rapid removal of extracellular transmitters has also been implicated in the mechanisms underlying temporal lobe epileptogenesis []. Acetylcholine is a neurotransmitter that has been implicated in the pathophysiology of epilepsy, including TLE. Research indicates that cholinergic neurotransmission, involving ACh, is implicated in epileptic activity. However, the biological correlation between ACh and TLE is complex and not fully understood. Additionally, this section discusses the neurotransmitters originating from the dysfunction of the gut–brain axis via the vagus nerve in various neurological and psychiatric disorders. The dysregulation of gut–brain axis signalling has been implicated in conditions such as depression, anxiety disorders, ASD, and NDDs. ¹⁸²

Various studies were conducted to investigate the relationship between gut microbiota dysbiosis and TLE in addition to anxiety (). An analysis was carried out to distinguish differences in the gut microbiota, dissecting them from the broad phylum level down to the more specific genus level []. Epilepsy is a persistent neurological condition in which clusters of nerve cells, known as neurons, transmit incorrect signals in the brain, resulting in seizures. Seizure triggers include stress, alcohol consumption, hormonal changes associated with the menstrual cycle, and sleep deprivation. There are two types of seizures: focal seizures and generalized seizures. Temporal lobe TLE is one of the several types of focal seizures. According to Seid et al. (2022), up to 60% of people diagnosed with epilepsy encounter symptoms of anxiety or depression []. TLE, recognized as one of the most prevalent forms of epilepsy, affects approximately 65 million people worldwide [,]. This condition is characterized by recurrent seizures due to abnormal neuronal activity in the temporal lobes of the brain, resulting in cognitive abnormalities that can adversely influence the overall physical performance in diverse private and public settings. The study hypothesized that various types of epilepsy may lead to distinct prognoses and impacts on the composition of the intestinal flora []. According to Munger Clary (2022), anxiety emerges as a prominent psychiatric comorbidity among individuals with epilepsy, showcasing a multifaceted nature encompassing a diverse array of manifestations []. These manifestations range from paroxysmal symptoms that have a sudden onset and last only for a short time to anxiety specifically linked to epilepsy itself. Nevertheless, the precise mechanisms that underlie the co-occurrence of epilepsy and anxiety remain unclear at present. The neurotransmitters GABA, norepinephrine, and dopamine neurotransmitters have been identified as key players in the pathogenesis of TLE with anxiety disorder. These neurotransmitters are known to regulate various neuronal functions, including excitability and inhibition in the development and progression of TLEA [,]. This study also compares the gut bacteria of individuals with TLEA and patients with TLE but without anxiety disorder. In pathological states like inflammatory bowel disease, T helper 17 cells release pro-inflammatory cytokines that can exacerbate intestinal inflammation. This suggests that Candida albicans may potentially contribute to the development of anxiety in individuals with TLE. Table 4 ^{183 184 185 186 183 187 188 189}

The myenteric plexus creates a continuous network spanning from the upper oesophagus to the internal anal sphincter, as illustrated in. Submucosal ganglia and fibre bundles form plexuses in the small and large intestines, but not in the stomach and oesophagus. Communication between the ENS and CNS occurs through the vagus and pelvic nerves, as well as sympathetic pathways. In the context of the ENS, neuroplasticity occurs because of inflammation and other perturbations. Changes associated with inflammation-induced neuroplasticity include the increased availability of serotonin in the epithelial cells, the hyperexcitability of intrinsic primary afferent neurons, the facilitation of synaptic activity among enteric neurons, and attenuated purinergic neuromuscular transmission, resulting in dysfunctional motility observed in conditions like colitis, which refers to the inflammation of the large intestine and autoimmune diseases. The hypothesis is that reduced levels ofandmay play a role in dysfunctional gut function and increased gut mucosal inflammation in individuals with TLEA []. Gut inflammation, whether triggered by abnormal immune responses or gut infections, has been shown to induce neuroplasticity, which includes structural, synaptic, or intrinsic alterations affecting neuronal function. Consequently, neuroplastic changes contribute to irregular secretion, motility, and sensation, ultimately leading to the onset of discomfort and pain []. Chen found a higher presence ofin individuals with anxiety and noted a positive correlation between the abundance of Escherichia-Shigella and the severity of anxiety symptoms []. Additionally, other bacterial groups like Proteobacteria andshowed increased levels not only in patients with anxiety disorders but also in those with TLE with anxiety (TLEA), underscoring the link between gut pathogens and anxiety once again []. Moreover, a single-strain probiotic——may decrease seizure susceptibility and this effect can be mediated, at least in part, by increased production of SCFAs [].encompasses bacteria known for their pro-inflammatory properties that induce gut inflammation through bacterial structural components such as lipopolysaccharides and bacterial metabolism [,]. Figure 9 ^{183 196 197 198 199 200 201} Lachnospiraceae Ruminococcaceae Escherichia-Shigella Bifidobacterium L. helveticus R0052 Escherichia-Shigella

Depression is a major mental illness that affects 10% to 15% of the general population [202]. The World Health Organization defines depression as a common mental disorder characterized by recurrent episodes of profound sadness, loss of interest and pleasure in activities, disturbed sleep patterns, and suicidal ideation. In addition, depression has a profound effect on interpersonal relationships and the ability to function effectively in daily life. A significant proportion of the world’s population, particularly in low- and middle-income countries, lacks access to mental health care, despite the availability of effective treatments, due to barriers such as stigma and lack of funding [203]. Depression is characterized by changes in brain morphology, including reduced volume in areas such as the hippocampus and PFC, and abnormal neural circuitry involved in mood regulation. The dysregulation of neurotransmitter systems such as dopamine and serotonin, as well as high levels of stress hormones such as cortisol and inflammatory indicators such as C-reactive protein, are biomarkers associated with depression. These physiological changes underscore the importance of multifaceted approaches to diagnosis and treatment, as they contribute to the complex aetiology and symptoms of depression. Brain imaging studies have identified structural changes in brain areas associated with mood regulation and emotional processing, including the hippocampus, amygdala, and PFC. Potential biomarkers of depression include changes in neuroplasticity-related proteins, such as BDNF, and abnormalities in neurotransmitter levels, including serotonin and dopamine [202]. The gut microbiome plays a central role in the pathogenesis of depression. Alterations in its composition can trigger inflammatory responses that influence behaviour through a variety of pathways, including the HPA. For example, studies have shown that changes in the gut microbiota can lead to an increase in the synthesis of microbial lipopolysaccharides, which trigger inflammatory responses and may be involved in the development of depressive symptoms. In addition, research has shown that the composition and diversity of gut microbes differ between people with depression and those who are not depressed. For example, the gut microbiota of individuals with depression often shows an excess of Firmicutes, Bacteroides, and Actinobacteria, illustrating how dysbiosis can affect mood and behaviour. Furthermore, altered neurobiological states associated with depression, such as elevated neurotransmitter concentrations and inflammation, highlight the function of the gut microbiome in controlling mood and bodily functions. It is therefore essential to understand these interactions if we are to develop targeted strategies to alleviate the symptoms of depression [204].

There is a robust correlation between the brain and gut microbiome in major depressive disorder (MDD). Stressful circumstances can disrupt the delicate balance of the gut microbiota, resulting in dysbiosis characterized by elevated levels of proinflammatory cytokines, particularly interleukin-6 (IL-6) and interferon gamma, and reduced levels of SCFAs. This inflammatory state can lead to a weakening of the integrity of the gut, facilitating the migration of bacteria (leaky gut). An imbalance in the kynurenine pathway results from increased levels of inflammatory cytokines that stimulate the action of indoleamine 2, 3-dioxygenase, which interferes with the synthesis of protective metabolites such as kynurenic acid. As a result, the toxic metabolites and inflammatory cytokines from this pathway have the potential to compromise the BBB, increasing inflammation in brain tissue and causing astrocyte atrophy and microglial activation. Anxiety and MDD are two examples of mood disorders that may be exacerbated by this chain of events (Figure 10). Conversely, therapies such as probiotics and prebiotics have been shown to modify the gut microbiota and improve intestinal barrier function, which in turn indirectly reduces BBB permeability, toxic metabolites from the kynurenine pathway, and inflammatory cytokines [205].

Taxonomic changes in the gut microbiota have been observed in individuals with depressive disorders compared to controls. These include increased levels of Firmicutes, Actinobacteria, Bacteroidetes, and Proteobacteria at the phylum level, decreased levels of Ruminococcaceae and increased levels of Prevotellaceae at the family level. In addition, specific genera such as Blautia, Faecalibacterium, and Coprococcus show decreases, while Bacteroides, Streptococcus, Prevotella, Lactobacillus, Clostridium, Bifidobacterium, Eggerthella, and Lachnoclostridium show increases. These findings suggest a potential link between gut microbiota composition and depressive disorders and highlight the need for further research into the role of the gut–brain axis in neurodevelopmental disorders.

Clinical and experimental research suggests that FMT has the potential to reduce symptoms associated with mental illness. Transferring microbiota from a donor with a compromised microbiota to a recipient with a healthy microbiota can cause the recipient to develop symptoms. Conversely, it can alleviate symptoms in recipients who are ill. This suggests that the gut microbiota plays an important role in mental illness. Although FMT from healthy donors regularly reduces symptoms, the duration of relief varies, usually lasting only three to six months. This limitation raises the possibility that FMT may not be a sustainable treatment for mental illness in clinical settings [206].

The MGBA has a bidirectional effect on depression, as evidenced by research showing that introducing microbiota or their metabolites can both cause and treat depression-like symptoms. For FMT, many studies have used faecal samples from depressed humans or mice with depressive-like characteristics. Rats exhibited depressive-like behaviours when exposed to these “depression-related microbiomes” at higher frequencies than controls [207]. On the other hand, it was shown that feeding mice a combination of SCFAs, such as acetate, butyrate, and propionate, could reduce stress-induced depressive-like behaviours [208]. Significant protein changes were found in the serum, prefrontal brain, cecum, and liver of a mouse model of depression induced by FMT from depressed patients, according to a recent proteomics investigation using isobaric tagging for relative and absolute quantitation [209]. These changes in protein profiles were associated with metabolic control and inflammatory immune responses, raising the possibility that the gut–brain axis plays a role in depression. Stronger evidence for the involvement of the MGBA in depression may come from understanding these changes that occur from the gut to the brain or vice versa [210,211,212,213,214].

SCZ is a debilitating psychiatric disorder, classified into three primary categories: cognitive symptoms, such as inattention and impaired working memory; negative symptoms, including social withdrawal, reduced motivation, and slowness; and positive symptoms, such as delusions, hallucinations, and disorganized thoughts [215]. The exact cause of SCZ remains unclear, resulting from a combination of genetic, epigenetic, and environmental factors. Numerous neurotransmitters have been linked to the main positive, negative, and cognitive symptoms of SCZ; nonetheless, subcortical dopamine deficiency continues to be the primary cause of psychotic symptoms. Post-mortem studies have shown altered metabolites in the brains of schizophrenic patients, and psychosis in SCZ appears to be mediated by presynaptic dopamine deficiency [216]. However, recent research has indicated that glutamate, GABA, acetylcholine, and serotonin alterations are also involved in the pathology of SCZ [217]. Negative and cognitive symptoms in SCZ are less responsive to antipsychotics and cause significant disability. Importantly, the heterogeneity of antipsychotic responses across individuals, key symptom domains, and biomarker variables require personalized medicine to alleviate the negative, positive, and cognitive aspects of SCZ. Recently, there has been significant focus on the link between human physiology and the microbiome in mental illnesses, especially SCZ.

SCZ gut microbiota differed significantly from those of healthy control subjects and individuals with metabolic syndrome in terms of global composition. Common GI comorbidities in SCZ include irritable bowel syndrome, inflammatory bowel disease, and celiac disease, which is an immune reaction to gluten that damages the small intestine, preventing nutrient absorption [218]. Studies suggest SCZ is associated with gut microbiome disturbances, chronic GI inflammation, and oxidative stress [219]. SCZ gut microbiota were notably enriched in Flavonifractor plautii, Collinsella aerofaciens, Bilophila wadsworthia, and Sellimonas intestinalis, while depleted in Faecalibacterium prausnitzii, Ruminococcus lactaris, Ruminococcus bicirculans, and Veillonella rogosae [220]. Another study showed changes in the diversity, with associations noted between the microbiome and metabolic and immune pathways, and reported that prebiotics and probiotics can be used as adjunctive strategies in the management of microbiome alterations in patients with SCZ [221]. At the phylum level, Proteobacteria and Firmicutes showed significant variations in SCZ, as did taxa within the class Clostridia, despite one study indicating an overall enrichment of Clostridia in SCZ [219]. Schwarz and collaborators suggest a potential connection between Lactobacilli levels and SCZ progression, correlating with symptom severity [222]. Due to conflicting and limited studies, Further investigation is required to fully understand the microbiome alterations in SCZ, their impact, and potential therapeutic applications.

Moreover, emerging evidence suggests that immune dysregulation, including altered memory T cell function, may contribute to SCZ pathogenesis. A study found an inverse correlation between alpha diversity and a specific subset of memory T cells (CD8+ CD28− CD45RA− cells) in patients with SCZ, highlighting the intricate interplay between the immune system, the microbiome, and the disease process [221]. Dysbiosis may worsen inflammation through increased intestinal permeability. There is a connection between the immune system and the conversion of tryptophan to kynurenate, and the kynurenine pathway plays a role in metabolizing tryptophan, an essential amino acid. The dysregulation of this pathway has been linked to various psychiatric disorders. Kynurenate acts as a broad-spectrum glutamate receptor antagonist, and NMDAR hypofunction is implicated in SCZ [223]. More work is needed to increase the understanding of microbiota–gut–brain axis contributions in SCZ, including increasing sample sizes, excluding potential confounders, accounting for intrinsic variations in microbiome profiles, and ensuring methodological consistency.

The evidence is mounting that the gut microbiome affects brain morphology, function, and behaviour, including depression, psychosis, and neurological disorders [18,20,21,224]. For instance, recently, the psychobiotics Bifidobacterium longum Rosell^®-175 and Lactobacillus rhamnosus JB-1 enhances the expression of proteins involved in the activation and maturation of nerve cells, as well as myelination and homeostatic regulation of neurogenesis in mice [225]. It is therefore reasonable to hypothesize that drugs used to treat these conditions may act, at least in part, by modifying the gut microbiome as a potential therapeutic target. Furthermore, some side effects of these medications may be mediated by the effect of these drugs on the gut microbiome. Alternatively, these alterations may serve as a biomarker for the response to various drugs. The following section presents a review of the bidirectional relationship between different CNS drugs and the gut microbiome, based on preclinical and clinical evidence.

Given the well-established relationship between the gut microbiome and CNS disorders, there has been a suggestion that the alteration of the gut microbiota could be a new therapeutic modality for managing the signs and symptoms of various CNS disorders. These strategies may include the use of prebiotics, probiotics, or FMT (discussed elsewhere in this review). In accordance with the definitions provided by the Food and Agriculture Organization of the United Nations, the World Health Organization, and the International Scientific Association for Probiotics and Prebiotics, probiotics are live microorganisms that provide health benefits to the host when administered in adequate amounts [262]. Species of Lactobacillus, Bifidobacteria, and Saccharomyces are the most used [263], which can be found as additives in various food products, dairy items, and as stand-alone dietary supplements [263]. Probiotics, particularly strains of lactic acid bacteria, are recognized for their ability to alter human gut microbiota by inhibiting the growth of opportunistic bacteria [264]. Hence, using probiotics to stimulate the growth and activity of beneficial strains in the gut is seen as a strategy to manage food-borne enteric pathogens. The health benefits of probiotics extend beyond the gut, as they can exert immunomodulatory, anti-inflammatory, and anticarcinogenic effects [264]. Additionally, there is a category known as prebiotics, which are substrates selectively used by host microorganisms that confer health benefits [265]. While most prebiotics are carbohydrate-based, other compounds like phenolic compounds and conjugated fatty acids also meet prebiotic criteria. Prebiotics are known for their health effects, such as inhibiting pathogens and modulating the immune system [265].

In the context of brain disorders, probiotics exert their mechanisms of action by ameliorating many of the pathogenic processes that are involved in CNS disorders. The positive effect of these “beneficial bacteria/precursors” includes improving the balance of affected neurotransmitters and enhancing the metabolism of lipids and short-chain fatty acid production, in addition to their anti-inflammatory, antioxidative effect [266]. The role of probiotics in ameliorating molecular and behavioural aspect of neuro/psychologic diseases is well studied in animals and human [266]. In the preclinical animal models of AD, the administration of prebiotics and probiotics have been shown to improve memory and decrease Aβ deposition. An 8- to 10-week administration of combined Lactobacilli and bifidobacteria spp. (1 × 10¹⁰ CFU/g) increased acetylcholine, ameliorated oxidative stress, inflammation, and improved different aspects of memory in AD models of rats [267,268,269].

A probiotic formulation, SLAB51, which is a formulation consisting of nine live bacterial strains (Streptococcus thermophilus, bifidobacteria (Bifidobacterium longum, B. breve, B. infantis), lactobacilli (Lactobacillus acidophilus, L. plantarum, L. paracasei, L. delbrueckii subsp. bulgaricus, L. brevis), at a dose of 200bn bacteria/Kg/day, has shown to offset brain oxidative-related damages in transgenic AD mice (3xTg-AD) by triggering SIRT1-dependent mechanisms [270]. Human studies in AD patients have shown that after 12-week treatment with probiotic mix (2 × 10⁹ CFU/g of L. acidophillus, L. casei, L. fermentum, and B. bifidum) improved sugar and lipid metabolism and had favourable metabolic, anti-inflammatory effects [271], while patients on 1 × 10¹⁰ of B. breve showed improved various aspects of memory including short-term, visuospatial, and delayed memory in geriatric AD patients in a 16-week follow up [272]. Clinically, a large, long-term prospective study showed that a prebiotic intake (fructan), was associated with significantly less risk of developing AD in geriatrics that was not altered by smoking, alcohol intake, gender, race, or APOE genotype.

In Parkinson’s disease, the evidence is still emerging and comes from a few preclinical and clinical studies. A mouse model of PD that received a 10¹⁰ CFU probiotic mix over 16 weeks displayed less degeneration of dopamine neurons and thus less worsening of motor dysfunctions. PD patients who received high-CFU probiotics had favourable changes in their disease scales and few metabolic profiles. Moreover, a multi-strain probiotic improved non-motor symptoms of PD such as bowel movement and constipation. Sun et al. (2022) conducted a randomized-controlled trial to investigate the effect of add-on probiotic formulation [Bifidobacterium animalis subsp. lactis Probio-M8 (Probio-M8)] in 42 patients with PD on therapeutic outcomes. After a 3-month follow-up, it was observed that the group receiving Probio-M8 exhibited a significantly higher number of species-level genome bins for Bifidobacterium animalis, Ruminococcaceae, and Lachnospira, but a reduced presence of Lactobacillus fermentum and Klebsiella oxytoca. Notably, there was a positive association between Lactobacillus fermentum and the scores and disease progression assessment score. Conversely, Klebsiella oxytoca showed a negative correlation with the firmness of the stool. Additionally, when Probio-M8 was used alongside traditional treatments, there was an increase in SGBs associated with the breakdown of tryptophan, the production of GABA, SCFAs, and secondary bile acid production, as well as higher levels of serum acetic acid and dopamine. Interestingly, a prebiotic powder [Bimuno™ galactooligosaccharides (B-GOS^®)] ameliorated olanzapine-mediated negative metabolic consequences and weight gain in Spraque-Dwaley rats, but no concomitant changes in gut microbiome were observed. Similarly, several types of gut anaerobic bacteria, such as Clostridium, Eubacterium, and Bacteroides, have been shown to possess nitroreductase activity, an enzyme known of its ability to reduction benzodiazepines, including clonazepam. In studies involving human subjects, consuming L. acidophillus notably decreased the levels of faecal ß-glucuronidase, nitroreductase, and azoreductase by two to four times. Consequently, combining a probiotic with clonazepam could potentially lessen its toxicity [273].

To date, there is no definitive cure through psychologic/neurologic treatments; therefore, in these settings, pre/probiotics are recommended as adjunctive therapy, which is added to pharmacotherapeutic regimens. However, the effect of pre/probiotics on drug response to CNS disease is still an emerging area of research. How this mechanism is translated into response in these diseases is not well-investigated. Potential indirect pathways can be related to their effects on drug disposition and metabolism; the amelioration of pharmacotherapeutic agent side effects; immune system modulation; the alteration of the levels of neurotransmitters, such as serotonin, GABA, and dopamine, involved in these diseases; immune system modulation; and/or by having direct effects on the brain.

There is emerging evidence that suggests a bidirectional relationship between antibiotic-induced dysbiosis and changes in brain functions and structures in animal models and humans through various mechanisms. In mice, the variation in various neurologic functions and structures was evaluated in pups who were exposed to antibiotics in utero [274]. Maternal antibiotics administration is among the most widely used therapeutic approaches in pregnancy. Although published evidence discussed later in this review demonstrates that infants were exposed to antibiotics immediately after birth and while weaning have altered behavioural changes later in life [12], there is a paucity of knowledge regarding the in utero effects of antibiotics on the neuronal function and behaviour of children after birth. The study by Shepilov et al. (2023) aimed to evaluate the impact of MAA at different periods of pregnancy on memory decline and brain structural alterations in young mouse offspring after their first month of life. This study involved pregnant 2–3-month-old C57BL/6J mice. The study consisted of three groups: one control group and two antibiotic-treated groups. The control group (group 1) was provided with sterile drinking water throughout the entire period of gestation, which lasted three weeks. The first antibiotic-treated group (group 2) was exposed to a mixture of amoxicillin and azithromycin in drinking water starting from the second week of pregnancy, with daily administration for seven days. Thereafter, they were provided with only sterile drinking water until birth. The second experimental group (group 3) received the same mixture of antibiotics, but in the third week of pregnancy until delivery. Following delivery, behavioural tests were conducted on the offspring mice during their fifth week of life. These tests were designed to evaluate behavioural changes. The Morris water maze test, a test for spatial learning in rodents [275], and the novel object recognition test, a test commonly used for the investigation of various aspects of learning and memory in mice [276], were employed. The Morris water maze test demonstrated that the administration of antibiotics to pregnant mice in both experimental groups, groups 2 and 3, resulted in a notable reduction in spatial reference memory and learning abilities in their offspring when compared to the offspring of the control group. In contrast, no significant difference in long-term associative memory was observed between the offspring groups in the novel object recognition test. Regarding the structure of the brain and the use of antibiotics, the study employed a histological evaluation of brain samples from the offspring. The researchers employed conventional immunofluorescence and electron microscopy assays, which revealed alterations in hippocampal CA1 pyramidal neurons. These neurons are responsible for processing sensory and motor cues to form a cognitive map encoding spatial, contextual, and emotional information [277]. Additionally, the researchers observed changes in the corpus callosum. The reduction in hippocampal CA1 pyramidal neurons was observed in the groups of mice that were exposed to antibiotics in utero, while the hypomyelination of the corpus callosum was observed in the offspring of treated mice. In addition, both groups of treated mice exhibited a reduction in astrocyte cell surface area and astrocyte territories, respectively, as well as a depletion of neurogenesis in the dentate gyrus and hippocampal synaptic loss. Although this study does not provide evidence that dysbiosis has occurred, it does demonstrate that MAA at different times during pregnancy can pathologically alter cognitive behaviour and brain development in offspring at an early age after weaning [274].

It is well established in the scientific literature that adolescence and early adulthood represent crucial periods in terms of brain development. In a 2015 study, Desbonnet and colleagues assessed the effects of gut dysbiosis on adult cognitive, social, and emotional behaviours in weaned mice. The study used antibiotics to induce gut dysbiosis in the mice. The mice in this study were administered a combination of antibiotics, including ampicillin, vancomycin, ciprofloxacin, imipenem, and metronidazole, beginning at weaning. Both control and antibiotic-treated mice in this study received the same autoclaved pelleted diet. Subsequently, at a later stage of adulthood, between 55 and 80 days postnatal, the researchers assessed the potential neuromodulators of the gut–brain axis, which included tryptophan, monoamines, and neuropeptides, as well as the expression of BDNF. The results of the assessment indicated that depletion of the gut microbiota resulted in reduced anxiety, cognitive deficits, alterations in the dynamics of the tryptophan metabolic pathway, and a significant reduction in BDNF, oxytocin, and vasopressin expression in the adult brain [12]. The alteration in the dynamics of the tryptophan metabolic pathway observed in this study has been demonstrated to affect cognitive performance. Studies have indicated that alterations in the tryptophan metabolic pathway may be associated with specific neurological deficits. These deficits have been observed to be associated with poor cognitive performance and an increased risk of AD and related dementias (ADRDs) [278]. There is a relationship between BDNF and neuronal growth and synaptic plasticity. It has been demonstrated that a reduction in BDNF levels is associated with stress susceptibility, which in turn is linked to a reduction in the synaptic expression of glutamate receptors. This ultimately results in a decrease in excitatory signalling from layer V pyramidal neurons and working memory deficits [279]. In terms of BDNF, it plays a pivotal role in stimulating neuronal growth and synaptic plasticity. Its depletion has been linked to stress susceptibility, which is associated with a reduction in the synaptic expression of glutamate receptors. This ultimately leads to decreased excitatory signalling from layer V pyramidal neurons and working memory deficits [279]. Recent research indicates that oxytocin and vasopressin play a role in cognitive functioning and are involved in the formation of social, working, spatial, and episodic memory [280]. In this study, it was also demonstrated that the severity and longevity of the behavioural abnormalities are associated with the duration of gut dysbiosis during adolescence. The results of the study further elucidate the significant association between gut dysbiosis and brain structure and function.

In the study by Ceylani et al. (2018), 21-day-old male BALB/c mice were administered an antibiotic mixture comprising ampicillin and cefoperazone [281]. The mice were randomly assigned to one of four groups: a control group and three experimental groups that received the antibiotic treatment. The experimental groups were divided based on the orderly or mixed fashion in which they received their treatment. The administration of antibiotics was conducted via drinking water, which each group had free access to. The treatment lasted for a week and was repeated three times, with a one-week interval between each repetition. Following the conclusion of the treatment regimen, at two months of age, behavioural assessments were conducted on the mice. The behavioural tests included the open field test, elevated plus maze test, forced swim test, and novel object recognition test. The open-field test is a commonly employed methodology for the assessment of general locomotor activity and anxiety in rodents [282]. The results of the open-field test demonstrated a significantly reduced locomotor activity in the antibiotic-treated groups in comparison to the control group. The elevated plus maze test is a widely used behavioural test validated to assess anxiety levels in small rodents [283]. The results of this test revealed that most of the treated mice spent a greater amount of time in different areas of the maze than the control group, which confirmed that the treated mice exhibited increased anxiety levels. The forced swim test, a widely utilized procedure for investigating depressive-like behaviours in rodents [284], demonstrated that treated mice exhibited a greater duration of immobility than the control group, thereby substantiating the presence of behavioural despair in the treated mice. Regarding the results obtained within the experimental groups, the ampicillin-treated groups exhibited elevated anxiety levels as evidenced by the open field and elevated pulse maze tests, as well as an increased behavioural despair in the forced swim test. The control group in the novel object recognition test demonstrated a greater propensity to explore novel objects, resulting in lower learning scores for the treated groups. Following the completion of the behavioural tests, blood biochemical markers were evaluated. This included the assessment of BDNF and corticosterone concentrations. The treated mice exhibited lower BDNF levels, which have been associated with changes in affective-like behaviours. Regarding corticosterone levels, no significant difference was observed between the control and experimental groups.

Adult neurogenesis has been linked to hippocampus-dependent cognitive function and is required for memory resolution and proper pattern separation in the dentate gyrus of the hippocampus. Hippocampal neurogenesis may be negatively impacted in various ways, including chronic stress [285] and social isolation [286]. Kempermann investigated the potential association between antibiotic-related gut dysbiosis and its consequences on hippocampal neurogenesis. The study was conducted on adult C57BL/6 mice that were treated with broad-spectrum antibiotics for seven weeks. The antibiotic compounds were administered via drinking water and consisted of ampicillin plus sulbactam, vancomycin, ciprofloxacin, imipenem plus cilastatin, and metronidazole [287]. The researchers employed antibody stains against neuronal progenitor cells and mature neurons to analyse hippocampal sections by immunofluorescence. Their findings indicated that cells in the subgranular zone (SGZ) of the dentate gyrus, the area from which adult neurogenesis originates, were significantly lower in the brains of antibiotic-treated mice.

The impact of dysbiosis on the innate immune system was also examined, given evidence that it serves as an additional link between the brain and gut, in addition to the well-known neuronal association [288]. The evidence for such a connection was established in studies indicating that immune cells play a role in maintaining neurogenesis [289]. Thus, by analysing the infiltrating immune cell populations in single-cell preparations from one brain hemisphere of antibiotic-treated mice, the researchers concluded that the proportions of Ly6Chi monocytes decreased. To further connect the depletion to a decrease in neurogenesis, they employed various strategies to alter monocyte number. One strategy involved the genetic deletion of a chemokine receptor, which deters Ly6Chi monocytes from exiting the bone marrow. The results of the deletion indicated that Ly6Chi monocytes are indeed necessary for neurogenesis. The impact of antibiotic treatment on the gut microbiota of 10-week-old male rats was also evaluated [290]. Following the treatment, the investigators conducted behavioural assessments to evaluate changes in spatial learning and depressive behaviour. The spatial learning assessment employed the Morris water maze, a test widely used to assess spatial learning in rodents [275]. The depressive behaviour assessment utilized the forced swim test, a well-validated method for assessing depressive-like behaviour in rodents [284]. The Morris water maze test demonstrated that mice with depleted gut microbiota in adulthood exhibited deficits in spatial memory. In the forced swim test, the mice exhibited increased visceral sensitivity and a greater display of depressive-like behaviours. The molecular hallmarks of gut–brain communication were also investigated by monitoring CNS serotonin concentration along with changes in the mRNA levels of corticotrophin-releasing hormone receptor 1, glucocorticoid receptor, and BDNF, which is considered a hallmark of altered microbiota–gut–brain axis signalling [290]. CNS serotonin levels modulate higher brain functions, including cognition and emotional behaviour. A deficiency of this neurotransmitter is linked with numerous psychiatric disorders [291]. CRH is the principal regulator of the HPA axis and is critical for the adaptation of the organism to environmental changes. A disruption of the normal HPA axis represents a significant risk factor for neuropsychiatric disorders, with the decreased expression of the glucocorticoid receptor having been documented in numerous cases [292]. Regarding BDNF, the depletion of which was previously highlighted, it is involved in numerous activities that are modulated by the HPA axis. The analysis of behavioural investigations and molecular hallmarks indicates that alterations in the gut microbiota of adult mice may still result in the disruption of cognitive functions. It has been demonstrated that antibiotic treatment can result in alterations to brain structure and function, irrespective of the age at which the treatment is initiated. A review of the literature revealed that studies conducted on mice at different ages have demonstrated that antibiotic treatments do indeed cause changes to the brain’s structure and function. These changes have been shown to manifest as alterations in behaviour and the development of neural diseases.

As previously demonstrated in this review and in other studies [], the evidence on the correlations between GI disorders and neuropsychiatric disorders is overwhelming, with clear implications for the gut–brain axis. Consequently, genetic links have been suspected between some pairs of the two types of disorders, and in fact, have been demonstrated using genome-wide association studies and linkage disequilibrium score regression [,,]. For instance, Wu et al. (2021) [] demonstrated genetic similarity across several GI diseases, including peptic ulcer disease (PUD), gastroesophageal reflux disease (GERD), and irritable bowel syndrome (IBS), with psychiatric disorders, with a particular focus on major depression. Furthermore, significant positive SNP-based genetic correlations (rg) have been observed between PUD, GORD, IBS, depressive symptoms, neuroticism [], major depression [], ADHD [], and insomnia [,]. Pouget et al. (2019) employed GWAS data for SCZ and 19 immune diseases, including some GI autoimmune conditions, and identified genetic variation at rs1734907 that modulates the risk of SCZ and Crohn’s disease via the altered methylation and expression of EPHB4. They also observed genetic correlations between SCZ and IBS, Crohn’s disease, ulcerative colitis, and primary biliary cirrhosis []. ^{351 352 353 354 354 355 356 357 358 359 360}

More recently, a pleiotropic analysis of large-scale genome-wide association studies of 24 pairs comprising four GI diseases (inflammatory bowel disease, IBS, PUD, and GORD) and six neuropsychiatric disorders (SCZ, bipolar disorder, MDD, ADHD, posttraumatic stress disorder, and anorexia nervosa) revealed significant common genetic determinants between 22 of the 24 evaluated GI-psychiatric conditions trait pairs. Of these, 19 pairs showed 2910 significant pleiotropic single nucleotide variants (SNVs) under a composite null hypothesis []. A significant number of common genetic determinants were identified between 22 of the 24 evaluated GI-psychiatric conditions trait pairs. Of these, 19 pairs were found to potentially exhibit 2910 significant pleiotropic single nucleotide variants (SNVs) under a composite null hypothesis []. Furthermore, this led to the identification of 83 pleiotropic loci, 24 colocalized loci, and 158 unique candidate pleiotropic genes. Notably, several of the identified pleiotropic loci share causal variants with gut microbiomes, and many of those loci are common among multiple trait pairs. Several trait pairs were identified, including those involving the loci on 1q32.1 (), 19q13.33 (), 11q23.2 (), and 1p32.3 (). For instance, variants in the FUT2 gene are shared between peptic ulcer disease, SCZ, and ADHD. The associations between peptic ulcer and ADHD, however, are variant-dependent. ^{361 361} INAVA FUT2 NCAM1 LRP8

Despite the significant efforts and progress that have been made, several questions remain unanswered. These include whether the genetic links indicate shared susceptibility genes between the two types of phenotypes [,] or whether the relationships between the pairs are of the causal types [,]. Another crucial question that has emerged is whether it is feasible to simultaneously target those disease pairs for treatment or intervention. ^{362 363 364 365}