GM play a role in the metabolism of nutrients and support immunity. The intestinal mucosa plays a vital role in resisting pathogens [37]. More and more evidence suggests a complex relationship between the gut and the CNS. Visceral signals from the gut affect the CNS via the vagus nerve; in turn, the brain directs signals to regulate the function of the gut. This two-way communication is termed the MGB axis [38]. GM significantly affect the physiological function and behavior of the brain through three pathways of the MGB axis (immune, neuroendocrine and vagal pathways) [15]. The enteric nervous system (ENS) is made up of various types of neurons. The brain receives information from neurons near the spine and intestine that is transferred by spinal and vagal afferent nerves [39]. As the ENS is the communication channel between the GM and the CNS, there is a vital connection between the GM and the physiological activity of the brain [40]. GM develop and regulate the body’s immune system; at the same time, the immune system also affects the composition of the GM. Normal physiological functions in the brain, such as the development of the nervous system, the transmission of signals between nerves, and the activation of the CNS immune system, are affected by the GM through changes in microglia and astrocytes. The integrity and permeability of the BBB are also related to the GM [41]. The immune system plays a role in the formation of the brain’s physical structure and its response to inflammation [32]. Intestinal inflammation and leakage of the intestinal barrier may be caused by the imbalance of the GM. The efflux of incompletely digested food, microorganisms, endotoxins, and immune factors may be the cause of chronic systemic inflammation. The intestinal barrier is permeated mainly by incompletely digested food molecules [42]. The development of a majority of chronic diseases is accompanied by an overactive immune system, which is often associated with immune system overload. The overloading of the immune system can be caused by a chronic inflammatory reaction of the intestinal mucosa, such as neurodegenerative diseases [43]. However, the effect of probiotics on A$\beta$ plaque load is minimal. There is also little association between glial proliferation and probiotic-regulated GM. Most evidence supports an important manifestation of extra-encephalic diseases in biological abnormalities mediated by intestinal dysfunction [44]. Increased AD-related neuroinflammation has been associated with GM-induced activation of peripheral inflammasome. An increase in inflammasomes in the brain has been found to result in an imbalance in the GM of young and old AD mice [45].

Microglia are non-neuronal cells. The maturation and function of microglia are influenced by host intestinal microbes [46]. When the GM decrease, microglia develop defects and cannot mature [47]. Acetate is an important GM metabolite that stimulates microglia to mature [48]. Microglia activation increased after SCFAs supplementation in germ-free (GF) mice [49]. LPS produced by the GM increased the inflammatory response of microglia and promoted the activation of microglia [50]. The increase of Clostridium and Bacillus in the intestinal tract decreased the expression of IB4 binding and $\beta$3 tubulin, damaged the vagal afferent pathway, and activated microglia [51].

The production of pro-inflammatory cytokine/chemokine microglia is the main manifestation of advanced AD-related chronic neuroinflammatory pathology. In humans and animal models of AD-like pathology, enhanced levels of associated inflammatory cytokines are detected in the early stages of AD [52]. Microglia are the main source of Complement component 1q in the brain [53]. The innate immune response mediated by CNS-resident microglia plays an important role in neuroinflammation in AD. Therefore, microglia may play an important role in regulating neurodegeneration [54]. In the presence of aging or genetic predisposing factors, tau pathologically induces abnormal activation of microglia, resulting in the accumulation of toxic amyloid proteins; in turn, the activated microglia promote the spread of tau pathology by phagocytic synapses and secreting neurotoxic cytokines [55]. Bacterial products or metabolites from the GM modulate microglia maturation, morphology and function, such as SCFAs [47, 56]. Microglia have an active role in synaptic formation [57]. In addition to plaques, microglia and immune-related pathways are also the focus of interest in AD. They may be early mediators of synaptic loss and dysfunction in AD [58]. GM dominate the development, maturation and activation of microglia. Activated microglia are involved in brain development and homeostasis [59]. However, activated microglia can serve as a source of inflammatory mediators, as well as phagocytosis of regulating synapses that contribute to AD [55]. The number of microglia in cortical gray and white matter was increased in postmortem AD cases. Furthermore, microglial proliferation was increased in AD and correlated with the severity of AD [60]. Microglia also degraded some of the tau species released from the brains of AD patients [61]. Microglia participated in the process of AD. Studies have shown that the decrease of microglia inhibited the proliferation of tau cells. In addition, neuronal death might be related to astrocytes regulated by microglia. In the pathogenesis of AD, activated microglia play a role in the activation of acute microglia that enhanced phagocytosis and clearance, thereby reducing A$\beta$ accumulation. In addition, neurotoxicity and synaptic damage can occur through the triggering of a number of pro-inflammatory cascades, which is often associated with chronic activation of microglia [62]. Reactive microglia can drive the development of tau pathology in mice with the deletion of the microglial fractalkine receptor (CX3CR1) [63]. Microglia play an important role in the spread of tau protein and neurotoxicity in the brain [64]. CX3CR1 deficiency is associated with the deterioration of AD-related neurons and the exacerbation of cognitive deficits. CX3CR1 is thought to be a key pathway by which abnormally activated microglia lead to AD-related cognitive deficits [65]. Older people and mice are more prone to brain damage and even neurodegeneration. This is because microglia grow slowly with age, leading to a reduction in surrounding tissue, impaired synaptic contact, and poor recovery from injury [66]. Studies have found that brain inflammation associated with AD-like pathology could be alleviated in the APPswe/PS1$\mathrm{\Delta }$E9 mouse model by lifelong choline supplementation. This might be related to the fact that choline reduces the expression of activated microglia [67].

Using single-nucleus RNA-seq, a group of disease-associated astrocytes was found in a mouse model of AD [68]. The A1 neurotoxic phenotype describes mouse astrocytes after exposure to a specific cytokine secreted by microglia of LPS [69]. The formation of A1 neurotoxic reactive astrocytes is a fundamental pathological response of the CNS, which is associated with LPS-induced neuroinflammation, acute CNS injury, and all neurodegenerative diseases. A1 reactive astrocytes are induced by classical activated neuroinflammatory microglia. A1 reactive astrocytes have many normal astrocyte functions that are decreased, such as synaptic functions, phagocytic capacity and neurovirulence. A1-activated astrocytes account for a large proportion of AD in central neurodegenerative regions [70]. In AD mouse models, microglia-mediated reactive astrocyte transformation was blocked by repeated subcutaneous administration of NLY01, a long-acting glucagon-like peptide-1 receptor agonist. Neuronal activity was maintained, and spatial learning and memory were improved [71]. Following CNS injury, astrocytes and microglia produced a large number of mutually regulated signaling molecules. More research is needed to understand how microglia and astrocytes act on neurons in AD environments [72].

The BBB is a barrier that separates the CNS from the peripheral blood circulation [73]. The BBB is composed of cerebral vascular endothelial cells, astrocytes of the perivascular foot, basement membrane and perivascular cells [74]. Tight junctions are expressed in the vascular endothelial cells, preventing polar molecules from passing freely between the blood and the brain [75]. The BBB breakdown is thought to be an early biomarker of cognitive dysfunction in humans [76]. It separates nerve cells from immune system cells. BBB dysfunction during AD influences A$\beta$ clearance and activated glial cells, and facilitates the recruitment of leukocytes in the brain. Therefore, the BBB assists in the generation and maintenance of chronic inflammation during AD [77]. Current studies show that intestinal flora can affect the BBB through the vagus [78] and immune system [79]. Metabolic substances produced by intestinal flora, such as SCFAs, also affect the function of the BBB. SCFAs or metabolites produced by the GM affect the BBB permeability. When C. tyrobutyricum or B. thetaiotaomicron were colonized separately in the gut of GF adult mice, the BBB permeability was reduced. C. tyrobutyricum produces butyrate, and B. thetaiotaomicron mainly produces acetate and propionate [80]. Propionate protects the BBB from oxidative stress by inhibiting pathways associated with nonspecific microbial infection through a CD14-dependent mechanism [81]. The antibiotic-treated mice showed intestinal disorders and increased expression of tight junction protein 1 and occludin mRNA in the amygdala. The expression of tight junction proteins in the frontal cortex, striatum and hippocampus of GF mice was decreased [82].

There is evidence that deterioration of the BBB morphology and function occurs in many neurodegenerative diseases and is considered a marker of cognitive decline [83]. One study confirmed greater BBB permeability in GF mice than in GM normal disease-free mice. In addition, SCFAs or metabolites produced by the GM reduced BBB permeability [80]. The basement membranes cover the brain capillary endothelial cells of the BBB, and the pericytes and astrocytes end foot surround the BBB neurovascular unit. The ability of the BBB to regulate the exchange of molecules between blood flow and the brain parenchyma, determines homeostasis of the CNS. Therefore, BBB dysfunction may be involved in the pathogenesis of several neurological diseases, including AD [84]. Researchers observed an approximately 4.2-fold increase in A$\beta$ load in AD individuals. Inadequate coverage of pericapillary cells in the brain led to increased A$\beta$ accumulation in the hippocampus of AD patients compared to controls [85]. The Chinese medicine, Rehmannia, may maintain the integrity of microvessels in the brain, decrease the BBB permeability, increase A$\beta$ clearance in the brain, and improve daily activity and function in AD mice [86]. Increased inflammation in the CNS was associated with damage to the BBB, which led to infiltration of immune cells into the brain [87]. Disruption of the BBB led to the flow of neurotoxic blood debris, cells and microbial pathogens into the brain, secondary to associated inflammation and immune responses, which could lead to a variety of neurodegenerative diseases [88]. There is a close GM- mediated relationship between the intestinal barrier and the BBB. Intestinal disorders could lead to increased permeability of the hippocampus, which is involved in learning and memory processes. Some blood-derived molecules could cross the BBB at this time, further exacerbating intestinal inflammation [89]. The integrity of the BBB was compromised by translocated bacteria and secreted pro-inflammatory cytokines, which also induced neuro-inflammatory cascades [43]. A study showed that the BBB in patients with mild cognitive impairment manifested an increased permeability to small molecules, such as water. The permeability of the BBB to water is related to AD markers in cerebrospinal fluid (CSF) [90]. The breakdown of the BBB begins in the hippocampus and could lead to cognitive impairment [91]. Brain capillary damage was found in older adults with early cognitive impairment and was associated with parietal cell damage and disruption of the BBB in the hippocampus [76].

These studies provide evidence that the human GM influence the development of the immune system through primary immune cells. Brain microglial activation, neuro-inflammation, neuronal apoptosis and A$\beta$ deposition are more severe in older individuals [92]. Dysfunction caused by increased BBB permeability also increases inflammation. GM disorders lead to a diseased state and promote systemic inflammation.

Endotoxins can cause or contribute to neurodegenerative changes. Neurodegenerative diseases can be triggered by the interaction of endotoxins with different aggregators, which is related to the promotion of the aggregation of A$\beta$ and tau proteins by endotoxins [95]. Bacteroides, such as Bacteroides fragilis, are the largest phylum of Gram-negative bacteria in the human GM. They have the potential to secrete pro-inflammatory neurotoxins, including surface LPS [17]. LPS, the major glycolipid of the outer membrane in gram-negative bacteria, are a potent and powerful endotoxin that could bind to cell surface receptors and induce the secretion of pro-inflammatory cytokines [96], resulting in systemic inflammation [18]. The immune system’s response is highly sensitive to LPS. Sepsis and septic shock can be caused by high concentrations of LPS. Sepsis is a risk factor for cognitive impairment and the development of AD [97]. Therefore, LPS are often used to model neuroinflammation associated with neurodegeneration [98]. The gram-negative facultative anaerobe Bacteroides fragilis secrete pro-inflammatory LPS. A$\beta$ levels in the brain and the permeability of the BBB are increased by LPS in an AD mouse model. The increase of LPS is consistent with findings in AD patients [99]. LPS are present in the cell walls of all gram-negative bacteria and may play a role in the development of AD [100]. LPS can bind to some blood proteins and be transported to different parts of the body. LPS can bind to receptors at the blood-brain interface via lipoprotein transport [101]. There is evidence that LPS accumulates gradually in the neuronal parenchyma in AD and appears to preferentially bind to the peripheral nucleus of neurons [102]. Photoelectron microscopy showed that LPS antibody staining and amyloid fibrils might be present in the same location [103]. Compared to age-matched controls, LPS levels were higher in AD patients. LPS and A$\beta$ were co-localized in amyloid plaques and blood vessels in AD patients, suggesting that LPS are associated with AD pathology [22]. Intracellular molecules could be activated by LPS. The expression of a large number of inflammatory mediators was altered by the action of LPS on its receptors. Neurodegenerative processes might be driven by LPS-induced inflammation. Pathological regression of neurodegenerative changes can be induced by activation of cells by stimulating the immune system with low doses of LPS [98].

The loss of connections between synapses could lead to cognitive deficits. During neuroinflammation, synaptic proteins can be altered by co-activated pro-inflammatory markers and associated cytotoxic products. Altered synaptic proteins are harmful to neurons [104]. Peripheral injection of LPS could induce learning and memory impairments in mice, which is attributed to the microglia-induced synapse damage [105]. When hippocampal dysfunction occurs, such as a reduction in the number of contact zones and the size of postsynaptic densities, it results in a decrease in hippocampal-dependent learning and memory performance [106]. LPS could act directly within brain tissue to disrupt synapses in hippocampal slice cultures, which were dependent on microglia and IL1$\beta$ [107].

SCFAs are the main metabolite of mammalian intestinal dietary fiber by microbial anaerobic fermentation. They have important physiological functions for the human body, and are sources of energy and act as signaling molecules. SCFAs are absorbed effectively by the intestinal mucosa and recognized by specific receptors [108]. SCFAs are not digested and absorbed in the small intestine [109]. Acetate, propionate, and butyrate are the most abundant SCFAs in humans [56]. Butyrate is produced mainly by the gram-positive anaerobes Roseburia and Faecalibacterium (previously Fusobacterium) [110]. SCFAs affect the function of the peripheral nervous system and CNS in different ways [111]. In radiation-induced cognitive impairment models, hippocampal phosphorylated cAMP-responsive element binding protein and brain-derived neurotrophic factor expression were reduced by butyrate, and cognitive impairment was subsequently improved [112]. The GM that produced select SCFAs could reduce the formation of toxic soluble A$\beta$ aggregates. Lap Ho et al. [113] also found that SCFAs interfered with the formation of toxic soluble A$\beta$ aggregates. These results suggest that SCFAs in the gut are likely to protect against the development of AD. In a prospective observational study, the composition of the fecal microbiome in patients with encephalitis was compared with that of healthy controls. They observed GM disruption in encephalitis patients and decreased levels of fecal SCFAs [114].

Butyrate plays an important role in the human gut. It is the primary source of energy for the colonic epithelial cells and maintains the intestinal barrier and regulates intestinal immunity. Haran et al. [115] demonstrated that butyrate producing species were decreased and taxa was increased in elderly individuals with AD compared to those without dementia. Sun et al. [116] found that cognitive impairment in APPswe/PS1dE9 transgenic mice could be improved by fecal microflora transplantation therapy. The brain deposition of A$\beta$ was also reduced in AD mice. We hypothesized that increasing SCFAs butyrate could improve the process of AD. As a histone deacetylase inhibitor, butyrate can improve memory in AD mice by restoring histone acetylation [117].

Functional amyloid peptides and immunogenic mediators, such as LPS, can be produced by the GM. The physiological processes of the bacterial cell surface are closely related to the amyloid peptide in bacteria. The structure and biophysical properties of this amyloid peptide were similar to those of human pathological amyloid [118]. SCFAs can also influence the CNS by modulating microglia [119]. SCFAs are important metabolites secreted by the human GM. SCFAs levels in feces of AD were lower than normal values. The presence of SCFAs has a positive effect on reducing the occurrence of AD.

GABA is the main inhibitory neurotransmitter. Studies have shown that GABA can be produced by the human GM, such as Lactobacillus and Bifidobacterium [125]. Lactobacillus brevis and Bifidobacterium dentium are the most efficient GABA producers among the strains that have been tested [125]. Both lactobacillus inoculation and lactic acid treatment significantly increase the GABA level in the hippocampus of mice [126]. Commensal Bifidobacterium dentium produces GABA through glutamate decarboxylase catalyzed by the decarboxylation of glutamate [127]. GABA is a non-protein amino acid synthesized by dependent glutamic acid decarboxylase (GAD) through irreversible $\alpha$-decarboxylation of l-glutamate [128]. The changes of intestinal microbiota are related to the changes of glutamate metabolism in the gastrointestinal tract. Campylobacter jejuni can activate glutamate synthesis, and then affect the metabolism of glutamate [129]. Glutamic acid decarboxylation synthesizes GABA, which is stored in synaptic vesicles by vesicular GABA transporters. GABA transaminase is a key substance responsible for eliminating and metabolizing GABA [130].

Studies have shown that GABA is not only present in neurons, but also in astrocytes. GABA in astrocytes can release and activate GABA receptors in neighboring neurons [131]. However, GABA is not present in normal astrocytes. Diseased astrocytes become reactive and produce GABA around amyloid plaques [132]. The mode of GABAergic glial cell delivery is altered in the AD mouse model. The upregulation of GABA released by astrocytes can bind to extra-synaptic associated GABA receptors and strongly inhibit synaptic function, ultimately leading to memory and cognitive impairments in AD [133]. Recent evidence indicates that the primary inhibitory neurotransmitter GABA in the brains of AD patients was different from that of a group of non-AD patients, and was mainly distributed in the frontal, parietal, temporal cortex and hippocampus regions [134]. High GABA levels of reactive astrocytes in the dentate gyrus were associated with the development of AD in mouse models (5xFAD), and increased the incidence of tension suppression and memory deficits [135]. Early neuropathological changes from AD were mostly confined to the loss of excitatory glutamatergic pyramidal neurons and synaptic connections in the hippocampus and temporal cortex. The balance between excitatory and inhibitory signals was important for normal cognitive function and memory formation within the hippocampus and cortex, and was needed to be carefully maintained [136]. Part of the risk of cognitive and memory loss came from loss of excitatory glutamate pyramidal neurons and synaptic connections. The GABA levels of CSF decreased significantly, and synaptic loss correlated with memory loss in AD patients [137]. Both GABA and 5-HT can be synthesized and released by the GM. These molecules have important physiological roles in the brain. They act as neurotransmitters or precursors of neurotransmitters and control neuron activity [124]. Glutamate, acting at N-methyl-d-aspartate receptors primarily in peri-synaptic astrocytes, can impair function in AD. The downregulation of vesicular glutamate transporters is related to the abnormal APP expression in AD patients. Glutamate uptake/recycling mechanisms are disrupted by toxic A$\beta$, and therefore glutamate availability increased. AD-associated excitotoxicity and neurodegeneration might be caused by the increased supply of glutamate. Hippocampal GABA/glutamate ratios are regulated by the human GM [129]. As to why abnormal production and aggregation of A$\beta$ could lead to cognitive dysfunction in AD patients and mice, it may be because the function of GABA inhibitory interneurons was affected, causing abnormalities in the transmission of signals between neurons [138]. These studies strongly suggest that human GM have an important role in AD.

The human GM can determine the production of 5-HT through its metabolites. Entero-endocrine cells are found throughout the intestinal mucosal epithelium. They are specialized hormone-secreting cells, consisting of an array of different cell types that receive stimulation from the luminal and the basolateral surfaces and secrete a combination of more than 20 hormones [139]. Chemical messengers involved in messaging, such as 5-HT, and serotonin, interact with the GM [140]. The rate-limiting enzyme tryptophan hydroxylase 1 (TPH1) found in entero-chromaffin cells of the gut produces more than 90% of the 5-HT in humans [141]. Studies in GF mice have shown that GM is necessary for the development of the central serotonergic system [142]. SCFAs enhance the expression of the enzyme TPH1 mRNA by interacting with EC cells. EC cells use TPH1 to synthesize 5-HT [143]. In human EC cell models, butyrate enhanced Tph1 transcription in mice by inducing ZBP-89, a zinc finger transcription factor [141]. Tryptophan is a central precursor in the synthesis of 5-HT. Tryptophan is produced by the GM. The peripheral tryptophan is able to cross the BBB, where it is involved in 5-HT synthesis [144]. It was found that gut Firmicutes Clostridium sporogenes could decarboxylate tryptophan to tryptamine. Tryptamine enhances the inhibitory response of cells to serotonin [145]. Kynurenine and its metabolites are an important pathway in tryptophan metabolism. Indoleamine 2,3-dioxygenase is a rate-limiting enzyme responsible for the initiation of the Kyn metabolic pathway [146]. L. plantarum treatment can increase 5-HT in the human gut [147]. GM play a key role in enhancing colon and serum 5-HT levels by inducing and reversibly promoting 5-HT in colonic entero-chromaffin cells. Gastrointestinal motility and platelet function are significantly affected by the microbiota-dependent effects on 5-HT [148].

5-HT can affect dopaminergic neurons in several ways, which is vital to the ENS [149]. Studies have found that the occurrence of AD in humans could be delayed and alleviated by most selective serotonin reuptake inhibitors [150]. Serotonin content significantly decreased in the temporal and frontal cortex and was altered in the CSF [151]. A connection between 5-HT and AD showed that citalopram acted as a selective serotonin reuptake inhibitor (SSRI) that increased serotonin levels in AD neurons. Citalopram-treated APP mice exhibited improved cognitive behavior [152].

Memory retention and the ability to learn depend on the serotonergic system. 5-HT-related receptors, such as 5-HT1, 5-HT4, 5-HT6 and 5-HT7 receptor classes, have unique abilities to enhance cognition [150]. In patients with severe AD, the density of the 5-HT2A receptors in the brain was lower than that in the control group, specifically in the frontal and temporal cortex. Despite the effects of choline acetyltransferase activity and the presence of behavioral symptoms, there was an association between the loss of the 5-HT2A receptor and cognitive decline [153]. Burke et al. [154] reinforced the relationship between depression, APOE $ϵ$4, and the development of AD. An emerging theory is that the use of antidepressants, usually SSRIs, such as tetracyclic serotonin antagonists, might reduce the deleterious effects of AD [154]. A$\beta$ levels in mouse interstitial fluid could be reduced by administration of several SSRI antidepressants and by direct injection of 5-HT into the hippocampus [155].

In addition to AD, there is a strong association between the gut-brain axis and neurodegenerative diseases, such as PD and HD.