The gut microbiome exhibits correlations with the expression of microglial markers. One study identified a connection between the abundance of Bacteroides in individuals with Parkinson’s disease and markers of inflammation in their blood, as well as motor impairment (Bartl et al., 2022). Another investigation demonstrated that the repetitive usage of colony-stimulating factor 1 receptor inhibitor (PLX5622) led to the elimination of microglia in adult mice, resulting in irregularities in the composition of their intestinal flora. Additionally, transcript levels of microglia markers such as tgfb1, aif1, and csflr in the prefrontal cortex of these mice appeared to be positively associated with the relative abundance of Bacteroides caecimuris (Yang et al., 2022). Furthermore, the Enterobacteriaceae genus exhibited an association with a high-fat diet (HFD). Metagenomic analysis revealed an elevated presence of Bacteroides and a reduced presence of S24-7 in the gut of the HFD group. Simultaneously, there was a decline in the claudin-5 protein found in the intestinal tight junctions, while the area occupied by microglia increased. The research revealed that Bacteroides had the ability to generate a fragilysin toxin which disrupted the parietal epithelial barrier by degrading the extracellular structural region of E-cadherin on intestinal cells using proteases, leading to the disassembly of the junction (Chompre et al., 2022). Collectively, studies indicate that Bacteroides may activate microglia through the C/EBPβ/AEP pathway and release pro-inflammatory cytokines including IL-6 and IL-1β (Xia et al., 2023), although the exact mechanism behind this effect is still unknown.

Jang et al. (2018) found that Ruminococcus spp. abundance was significantly elevated in the intestinal flora of immune-tolerant mice, expression of the tight junction protein claudin-5 was significantly elevated, showed lower concentration of IL-1β, and microglia were M2-polarized through a study of an epileptic mouse model. It was also hypothesized that Ruminococcus spp. could reduce intestinal mucosal permeability and promote microglia M2 polarization. However, in another study (Teng et al., 2022), the Ruminococcaceae metabolite isoamylamine (IAA) was found to be enriched in aged mice and the elderly, and young mice given IAA orally exhibited age-related cognitive dysfunction. Further studies revealed that the gastric Ruminococcus metabolite IAA induces microglia apoptosis by recruiting the transcriptional regulator p53 to the S100A8 promoter region and that overexpression of S100A8 induces division of caspase-3, a marker of apoptotic cells. Gut microbes have the potential to impact microglia activation through the generation of diverse metabolites.

Numerous studies have demonstrated that Lactobacillus can stimulate cytokine production in microglia/macrophages and induce the polarization of microglia/macrophages into various phenotypes through multiple pathways (Christensen et al., 2002; Lebovitz et al., 2018). This in turn diminishes the inflammatory response and promotes the generation of anti-inflammatory microglia. Lebovitz et al. (2019) reported that maternal microbiota dysbiosis (MMD) caused microglia activation and the upregulation of cx3cr1. This upregulation was associated with enhanced expression of the senescence-related genes il1β and trp53. Subsequently, they demonstrated that the existence of a new intestinal commensal variant, Lactobacillus murinus (HU-1), reverses microglial activation. In an animal study, it was observed that Lactobacillus rhamnosus (LGG-CM) inhibited the NF-κB pathway by reducing IκBα phosphorylation. This facilitated the polarization of microglia/macrophages toward M2 and suppressed polarization toward M1 (Lin et al., 2021). Another study found that the lifespan of the model organism C. elegans could be regulated by administering Probio-M9, a Lactobacillus rhamnosus bacterium isolated from healthy human breast milk. This regulation was linked to the p38 cascade and the daf-2 signaling pathway (Zhang et al., 2022). Likewise, Duan et al. (2021) discovered that supplementation with Lactobacillus reuteri (L. reuteri) and butyrate reversed the activation of microglia and dendritic spine loss in mice subjected to an HFD. They postulated that Lactobacillus royal might either secrete butyrate or modulate the intestinal flora to enhance butyrate production, thereby influencing microglia activation.

Wang et al. (2021) utilized existing databases to analyze Microbial Metabolite-Gene-Pathway-Phenotype (MGPPN) data, leading to the conclusion that there is a significant correlation between microglial functional and physiological dysfunction and AD. This suggests a strong association between AD, microglia, and gut microbes, particularly emphasizing the significant correlation with SCFAs like acetic acid, propionic acid, and butyric acid. These SCFAs are metabolites produced from the fermentation of dietary fiber by bacteria. In vitro studies have revealed that SCFAs directly impact microglia through a diffusion mechanism, leading to the inhibition of histone deacetylase activities, NF-κB activities, and inflammation induced by lipopolysaccharides (LPS). This impact is independent of the known SCFA receptor and monocarboxylate transporter, Mct1 (Caetano-Silva et al., 2023). However, Colombo et al. (2021) discovered that SCFAs may actually enhance Aβ deposition by activating microglia through the upregulation of apoe gene expression. It seems that the biological effects of SCFAs on microglia are heavily contingent on specific disease conditions. Consequently, the precise mechanisms through which SCFAs regulate microglia remain to be explored, particularly in relation to distinct mouse models of AD or in individuals.

Butyrate, a type of SCFA, is primarily produced through bacterial fermentation of colonic fiber and has been extensively examined as a histone deacetylase inhibitor in pharmacological research. Research has shown that butyrate mitigates the increase in pro-inflammatory cytokine production in microglial cells drived from elderly mice (Matt et al., 2018). Furthermore, administering butyric acid-producing Clostridium butyricum (CB) to APP/PS1 mice prevented microglia activation, cognitive impairments, Aβ deposition, and the release of TNF-α and IL-1β in the cerebrum, while concurrently rectifying dysbiosis in the intestinal flora. Additional research uncovered that butyrate treatment inhibited the activation of microglia by suppressing NF-κB p65 phosphorylation in Aβ-induced BV2 microglia and reducing CD11b and COX-2 levels in cells (Sun et al., 2020). In a study involving mice with chronic alcohol-induced impairment, Wei et al. (2023) discovered that administration of sodium butyrate (NaB) modified the microglial polarity imbalance (M1/M2) by interacting with GPR109A, leading to upregulated expression of PPAR-γ and downregulated activation of TLR4/NF-κB. Furthermore, they conducted sequencing and analysis of mouse gut bacteria, revealing that following NaB administration, there was a reduction in the Bifidobacterium, Bacteroides, and Lactobacillus genera, while the Parvibacter, Faecalibaculum, and Alloprevotella genus experienced an increase at the genus level. In a separate animal experiment, Agathobaculum butyriciproducens (SR79), a severely anaerobic bacterium producing butyric acid, was utilized. SR79 enhanced cognitive function and ameliorated AD pathology in animal models by modulating neuroinflammation and IGF-1 signaling (Go et al., 2021).

Acetic acid, a SCFAs with the capability to cross the blood-brain barrier, influences microglial function within the brain. Acetate regulates microglia’s maturation and metabolic state, thereby impacting their responses to inflammation (Frost et al., 2014). Research has revealed that acetic acid inhibited nitric oxide (NO) generation in the primary rat microglial cells, thus exerting a neuroprotective effect. However, this effect is not observed in BV-2 microglial cells, suggesting differential responses to acetic acid among microglia of varying origins. The authors propose that acetate’s mechanism of action on microglia likely involves the suppression of the mitochondrial respiratory chain complex, which plays a role in regulating iNOS activity (Moriyama et al., 2021). Additionally, in another study, the authors found that acetate exhibited a dual role in microglial TNF-α generation. It could both promote and suppress TNF-α secretion, depending on the acetate concentration and the activation state of the microglial cells. The authors concluded that acetate facilitated access to chromatin, histone acetylation, and TNF-α production in LPS-stimulated microglial cells (Fragas et al., 2022).

During a clinical trial, daily high-dose supplementation of mixed omega-3 polyunsaturated fatty acids (PUFAs) for 8 weeks significantly increased the abundance of Bifidobacterium, Roseburia, and Lachnospira species, while decreasing the presence of Coprococcus and Faecalibacterium (Watson et al., 2018). Another study, focusing on microglial size, revealed that PUFAs reduced the baseline activation state of microglia. This was evidenced by larger cell sizes, reduced cell numbers, and lower labeling intensity. Additionally, the PUFAs diet positively influenced the composition of the intestinal bacterial flora (Hakimian et al., 2019). Moreover, Chen et al. (2022) observed that in 3 × Tg AD transgenic mice, microglia activation and inflammation levels were notably lower than in germ-positive mice. In contrast, transplanting gut microbiota from AD patients exacerbated microglial activation and inflammatory responses in 3 × Tg mice compared to microbiota transplants from healthy donors. The authors further found that the gut flora could influence the levels of PUFAs metabolites and their oxidative enzymes, subsequently modulating the C/EBPβ/aspartate endopeptidase (AEP) signaling pathway within microglia. This modulation led to the promotion of neuronal degenerative changes and cognitive dysfunction through the cleavage of Tau proteins. They also discovered an increase in Bacteroides, which mediate the metabolism of proinflammatory PUFAs, in the gut microbiomes of AD patients. This increase plays a role in regulating the activation of microglia in the brain. The administration of PGE2-G, a metabolite produced from AA by the bacterial strain Bacteroides, has been found to restore AD pathologies and microglial activation in GF mice, especially in the presence of SCFA. Additionally, the gut lactic acid bacterium, Lactobacillus plantarum, produces two long-chain fatty acids: 10-oxo-trans-11-octadecenoic acid (KetoC) and 10-hydroxy-cis-12-octadecenoic acid (HYA), derived from linoleic acid. These compounds possess anti-inflammatory properties by inhibiting the production of nitric oxide (NO) and the expression of iNOS in BV2 microglia when stimulated by LPS. This anti-inflammatory mechanism potentially functions by inhibiting ERK phosphorylation, with a hypothesis that this inhibition might be associated with a decrease in iNOS transcription, which is facilitated by transcription factors like AP-1 (Ikeguchi et al., 2018).

Trimethylamine N-oxide (TMAO) is a metabolite produced by the gut microbiota from specific dietary nutrients and is linked to cardiovascular and neurological disorders. Imbalances in the gut microbiota can result in elevated levels of circulating TMAO (Meng et al., 2019).

According to clinical research, individuals with MCI and AD exhibit elevated levels of TMAO in their cerebrospinal fluid (CSF) compared to those without cognitive impairment. Elevated CSF TMAO has also been linked to Aβ42, a biomarker of AD pathology, and neurofilament light chain protein, which indicates neuronal degeneration (Vogt et al., 2018). Another study conducted on mid-aged male C57BL/6 mice, 24 and 72 h after a sham operation, observed that a choline-enriched diet significantly elevated serum TMAO levels. This diet also increased the activation of microglia and astrocytes surrounding the hematoma compared to a regular diet. However, TMAO did not impact the expression of p38 mapk, myd88, hmgb1, or il-1β, and the precise mechanism of its activation remains unknown (Li et al., 2022). In animal experiments, conducted by Meng et al. (2019), elevated circulating TMAO levels were found to contribute to cognitive decline. This was associated with increased microglia activity, neural inflammation, and the generation of reactive oxygen species (ROS) in the hippocampus of surgically treated rats. Furthermore, elevated TMAO levels were shown to down-regulate the hippocampal antioxidant enzyme, methionine sulfoxide reductase (MsrA), potentially increasing vulnerability to surgically induced oxidative stress, ultimately leading to heightened neural inflammation and post-operative cognitive decline in aged rats.

Nicotinamide nitrogen oxide (NAMO), an oxidized derivative of nicotinamide, is primarily synthesized by certain intestinal bacteria, including Lactobacillus gasseri and Lactobacillus reuteri. NAMO plays a crucial role in regulating microglia activation. Research by Li et al. (2023) has shown that NAMO, as an intestinal metabolite, promotes the production of nicotinamide adenine dinucleotide (NAD +) and facilitates mitophagy, a process that clears damaged mitochondria. This in turn inhibits microglia activation and the subsequent inflammatory responses. Nicotinamide riboside (NR), a precursor to nicotinamide adenine dinucleotide (NAD +), a form of vitamin B3, has demonstrated promising effects. In a separate investigation, NR was discovered to decrease the activation of microglia in mice exhibiting depression-like symptoms induced by alcohol consumption. Furthermore, NR lowered the levels of both pro-inflammatory (IL-1β, IL-6, and TNF-α) and anti-inflammatory (IL-10 and TGF-β) cytokines in the brains of these mice. NR also notably up-regulated the expression of brain-derived neurotrophic factor (BDNF) and alleviated the inhibition of the AKT/GSK3/β-catenin signaling pathway in the hippocampus. These findings demonstrate the efficacy of NR treatment in preventing excessive microglia activation (Jiang et al., 2020).

Extensive studies have been carried out on urolithin, the gut metabolite of red raspberry polyphenols. Numerous studies have consistently highlighted its potential to reduce both inflammation and oxidative stress (Espín et al., 2013; Kujawska et al., 2019). Nevertheless, the exact mechanism behind these effects is yet to be completely understood. In a study by Toney et al. (2020), urolithin A (UroA), derived from the gut metabolism of red raspberry polyphenols (RRW), was found to not only decrease the induction of iNOS gene expression but also promote the polarization of M2 microglia. This dual action is achieved by suppressing exposure to pro-inflammatory cytokines and modulating the JNK/c-Jun signaling pathway. Another in vitro study revealed that Urolithins effectively reduced the levels of NO, IL-6, prostaglandin E2, and TNF-α in the media of LPS-stimulated BV-2 microglial cells. Moreover, Urolithins demonstrated a capacity to mitigate apoptosis and the release of caspases 3/7 and caspases 9 in H₂O₂-induced oxidative stress of BV-2 microglial and SH-SY5Y neuron cells. In summary, these discoveries propose that urolithin could potentially provide protection to the nervous system by blocking caspase activation when cells undergo apoptosis due to oxidative stress (DaSilva et al., 2019).

Proteus mirabilis, a gram-negative rod-shaped bacterium commonly found in the intestinal microbiota, synthesizes a urea-inducible urease (PMU), known as a factor contributing to its virulence (Armbruster et al., 2018). Investigation of PMU’s non-enzymatic activities in human and mouse cell models revealed its potential to induce platelet aggregation, elevate intracellular calcium ions, and generate ROS. In vitro experiments with microglia BV-2 cells indicated that PMU could stimulate the release of pro-inflammatory cytokines IL-1β and TNF-α, suggesting its neurotoxic and neuroinflammatory effects on microglia. These results indicated that PMU, in addition to its primary enzymatic function of catalyzing urea breakdown to produce ammonia, possesses non-enzymatic activities associated with pathogenicity, including pro-inflammatory and neurotoxic effects (Grahl et al., 2021).

Helicobacter pylori’s urease (HPU), a cellular protein, was studied in vitro by Uberti et al. (2022). Their research showed that HPU reduced the viability of SH-SY5Y neuroblastoma cells and BV-2 microglia, triggered the generation of ROS, elevated intracellular calcium ion levels, and induced the release of the inflammatory factors IL-1β and TNF-α. In animal experiments, rats subjected to daily intraperitoneal injection of HPU (5 micrograms) for 7 days displayed hyperphosphorylated tau protein in hippocampal tissue and an overexpression of Iba1, a marker of microglial activation. Behavioral assessments demonstrated cognitive impairments in object recognition and elevated cross-maze tests among HPU-treated rats. These findings suggest the possibility that Helicobacter pylori infection could exacerbate AD pathology through its urease-mediated tau protein pathology (Hanger et al., 2009).

Numerous studies consistently demonstrate that bacterial-derived LPS activates microglia, prompting the production of inflammatory mediators and cytokines, including NO, IL-6, TNF-α, and PGE2 (Z. Chen et al., 2012; Zhao et al., 2022). These inflammatory biomarkers is crucial in the development of AD by instigating the production of aberrant proteins, including tau protein, Aβ, and α-synuclein (Ju Hwang et al., 2019; Kim et al., 2021). This cascade ultimately activates the apoptotic pathway (caspase activation), leading to a proinflammatory environment and microglial proliferation (DaSilva et al., 2019). Clinical investigations have revealed the presence of Gram-negative bacterial LPS, E. coli K99 hair protein, and DNA in the brains of both control and AD groups. However, the AD group exhibited elevated levels of K99 and LPS compared to the control group. Furthermore, it was observed that LPS co-localized with Aβ1-40/42 within Aβ plaques and the perivascular region of the AD brain. These findings imply the relevance of Gram-negative bacteria to the pathology of AD (Zhan et al., 2016). In another investigation, it was discovered that long-term systemic exposure to Porphyromonas gingivalis (PgLPS) led to cognitive deterioration in mice of middle age. This effect was attributed to the actions of IL-6 and IL-17, which are common risk factors. Additionally, PgLPS was found to be involved in the accumulation of Aβ in neurons via NF-κB translocation. Moreover, there was an increased expression of IL-17 in microglial cells (Gu et al., 2020). Furthermore, Lactobacillus reuteri NK33 and Bifidobacterium adolescentis NK98 were found to inhibit microglia activation by modulating the entry of LPS into the brain and suppressing the activation of NF-κB and the expression of IL-6 in LPS-treated BV-2 cells (Jang et al., 2019).