Brain-Gut Axis: Microglia under focus

Image Courtesy  GerryShaw

Image Courtesy GerryShaw

Author: Isabelle Arnoux Edited by: Vanessa Hübner

The brain-gut axis represents the reciprocal communication between the enteric and the central nervous systems. The gut microbiota – a complex repertoire of microorganisms – influences multiple processes to maintain the host’s health such as food metabolism, immune responses and social interactions. Recently, it has been highlighted that the microbiota influences brain functions and microglia properties. Microglial cells are the resident macrophages of the central nervous system and, besides their well-known immune functions in pathological conditions, they shape the brain circuitry during the development and participate in the homeostasis of the adult brain. A control of microglia by microbiota could either prevent or initiate cerebral events.

Microbiota controls microglia maturation during brain development

During brain development, microglial cells are involved in neuronal survival and apoptosis, synaptogenesis, elimination of supernumerary synapses, wiring of brain circuits and synapse maturation. Disrupting microglia function at these early stages leads to neurodevelopmental disorders such as autism and schizophrenia. Interestingly, a microbial imbalance (dysbiosis) of the gut microbiota is also found in these disorders, pointing toward a possible link between microbiota and microglia.

Recently, Erny and co-workers showed that commensal microbes drive microglia maturation (1). They observed that adult germ-free mice, who were never exposed to bacteria or viruses and consequently, do not possess a microbiota, expressed underdeveloped microglia. The microglial cells were unreactive and failed to induce an immune response in the presence of bacteria or viruses. A transcriptomic analysis revealed that genes expressed by microglia are severely impacted by the lack of microbiota in both prenatal and adult stages, suggesting that maternal microbiota prime microglia for their future (2, 3). Microglia also showed sex-specific impacts on germ-free mice: males are more affected at prenatal stage and females are more altered in adult. This sexual difference could explain the sex prevalence found in some disorders involving microglia dysfunctions. For example, neurodevelopmental disorders such as autism spectrum disorders and schizophrenia have a higher incidence in men, but Alzheimer’s disease, a neurodegenerative disorder afflicting adults, burdens more women.

Acute microbiota depletion by antibiotics treatment modulates microglia functions

Antibiotics treatments are commonly used to treat bacterial infection, and their properties enable them to kill microorganisms living in the gastro-intestinal tract. The acute depletion of the gut microbiota can affect microglia and brain functions.

Minocycline – a tetracycline-based antibiotic – leads to controversial effects on microglia,either suppressing or supporting toxic microglia activation, depending on the pathophysiological context. Administered at key stages of the development, minocycline activates microglia and compromises neuronal survival by annihilating the critical release of trophic factors (4, 5). Conversely, minocycline treatment exerts a neuroprotective effect under disease conditions by inhibiting microglia immune response in Parkinson’s disease, Huntington’s disease, multiple sclerosis etc. In addition, doxycycline, another tetracycline antibiotic, reduces microglia number in adults, which may lead to an increased neurogenesis (6). Although in vitro studies demonstrated a direct inhibition of microglia activation, minocycline and doxycycline might have a dual action and could also act on microglia activity by depleting the gut microbiota. Further studies are required to investigate how tetracycline affects microglia in vivo and to test whether acute microbiota disruption is beneficial in neurological disorders.

To maximize the impoverishment of gut microbiota, some research teams have tested the effects of a mix of antibiotics on microglia. They found that a cocktail of four antibiotics (cefoxitin, gentamycin, metronidazole and vancomycin) modified the morphology of microglia towards an immature phenotype without affecting their cell numbers (1). Another cocktail of antibiotics (ampicillin, streptomycin, colistin and amphotericin) altered the expression of genes associated with signal transduction and immune response, making them less responsive to environmental challenges (3).

Collectively, a gut microbiota composed of diverse microbes is required to constantly maintain microglia properties and reactivity. A perturbation of microbiota composition by antibiotics compromised microglia functions, which can affect neuronal activity.

Microbiota drives microglia activation in neurological disorders

“All disease begins in the gut” said Hippocrates. Centuries later, compelling evidence indicated that the gut microbiota differs in patients suffering from neurological disorders. Scheperjans and colleagues found a reduction of Prevotellaceae bacteria and a greater abundance of Enterobacteriaceae bacteria in Parkinson’s disease patients compared to healthy controls (7). Parkinson’s disease is a common neurodegenerative disorder characterized by a toxic accumulation of α-synuclein particularly in the dopaminergic neurons of the striatum, which leads to motor deficits. In a mouse model of the disease, microglial cells showed an activated phenotype characterized by a morphological change and the secretion of immune factors. But, the absence of microbiota prevents microglia activation in a germ-free mouse model of Parkinson’s disease (8). Furthermore, the colonisation of germ-free mice by the microbiota of Parkinson’s disease mice induces microglia activation and motor dysfunctions. This suggests that the altered microbiota composition participates in Parkinson’s disease progression by modulating the inflammatory response of microglia.

The microbiota also impacts the progression of Alzheimer’s disease, another neurodegenerative disorder caused by aggregation of amyloid-ᵦ peptides into extracellular amyloid plaques. The microbiota composition varies between mouse models of the disease and healthy controls (reduction of Firmicutes, Verrucomicrobia, Proteobacteria and Actinobacteria with an increase in Bacteriodetes and Tenericutes) (9). In addition, mice developing Alzheimer’s disease and devoid of microbiota show a reduction of amyloid load and inflammatory factors. It has already been pointed out that microglia are involved in the pathogenesis of Alzheimer’s disease, but their role is still to be elucidated. On the one hand, the actions of microglia could be protective; because they are rapidly recruited at amyloid plaques, it has been hypothesized that they could eliminate the plaques via their phagocytic activities. On the other hand, they display an activated phenotype, which could be harmful as they release inflammatory and toxic factors. Therefore, finding a way to control microglia activity via the microbiota is critical to better control Alzheimer’s disease progression and perhaps to reverse symptoms.

Also, the microbiota influences other neurological disorders, such as multiple sclerosis (10) in which microglia participates in the chronic neuroinflammation and demyelination/remyelination processes. In a Nature paper published in 2018, Rothhammer et al. showed that microbial metabolites of tryptophan dietary regulate the inflammatory reaction in a mouse model of multiple sclerosis (11). Notably, microglial and astrocytic pathogenicities were reduced through a mechanism mediated by the activation of the aryl hydrocarbon receptor in microglia. This study highlighted a direct link between microglia and microbiota in the context of multiple sclerosis.

The microbiota composition is often altered in neurological disorders and impacts microglia functions. Therefore, the manipulation of microbiota could be highly beneficial to counterbalance detrimental microglial responses.

Manipulations of the microbiota as therapeutic solutions in neurological disorders

As previously mentioned, antibiotics treatment leads to an acute depletion of gut microbiota, which, in turn, affects microglia properties in physiological conditions. But, what are the consequences of antibiotics on microglia in disease conditions?

In a mouse model of Alzheimer’s disease, long-term treatment with broad spectrum antibiotics reduces the variety of gut microbes. At brain level, this treatment decreases amyloid plaques by two-fold (12). Furthermore, Minter and collaborators observed other improvements: a reduction of inflammatory factors, a modification of microglia morphology and less microglia surrounding the plaques. Antibiotics administration is also beneficial in the mouse model of Parkinson’s disease. This treatment improves motor deficits associated to the disease and restores microglia morphology (8). Although the complete mechanism is not yet known, these studies open a new therapeutic avenue for treating Alzheimer’s and Parkinson’s disease hallmarks and microglia response.

Furthermore, metabolites released by gut microbes can influence the activity of brain cells. The short-chain fatty acids – a bacterial fermentation product – have received particular attention. In a germ-free mouse model of Parkinson’s disease, the addition of these metabolites to the drinking water impaired motor performance, activated microglia and triggered the aggregation of α-synuclein (8). Since the short-chain fatty acids are sufficient to induce the Parkinson’s disease symptoms, it is suggested that they have a pivotal role in the pathology onset and progression. The receptors of short-chain fatty acid (FFAR2) are not expressed by brain cells, but they are strongly expressed by splenic myeloid cells (1). Researchers suggest that interaction of the receptor with short-chain fatty acids at the periphery produces brain-permissive metabolites that act on microglia.

The composition of the microbiota can be manipulated by fecal transplantation. The microbiota-targeted technique is based on the infusion of feces from a donor delivered to the gastrointestinal tract of a receiver. In a mouse model of Parkinson’s disease, the administration of fecal matter from normal control mice improves motor function, survival of dopaminergic neurons and level of striatal neurotransmitters (dopamine and serotonin) (13). In addition, the pathological activation of astrocytes and microglia was reduced, leading to a decrease of the neuroinflammation. On the contrary, a fecal transplantation of feces from Parkinson’s disease to healthy mice triggers motor deficits, striatal neurotransmitter loss and neuroinflammation (8,13). Consequently, the rebalance of gut microbiota by fecal transplantation from healthy donors has a neuroprotective effect and offers a potential strategy to treat neurological disorders. 

Lastly, the gut microbiota composition can be modified by the use of prebiotics, probiotics or synbiotics. Prebiotics are food ingredients, stimulating the growth of some bacteria, probiotics are live microorganisms and synbiotics are the association of prebiotics and probiotics. In a clinical trial, probiotics supplementation improves cognitive functions in Alzheimer’s patients (14). Interestingly, prebiotics and probiotics decrease microglia activation and restore cognitive function by improving hippocampal plasticity in obese insulin-resistant rats (15). The manipulation of gut microbiota has advantageous effects and alleviates some disease symptoms. But, further studies are required to determine if the use of prebiotics and/or probiotics positively modulate disease aspects and by which mechanisms.



1. Host microbiota constantly control maturation and function of microglia in the CNS. Erny D, Hrabě de Angelis AL, Jaitin D, Wieghofer P, Staszewski O, David E, Keren-Shaul H, Mahlakoiv T, Jakobshagen K, Buch T, Schwierzeck V, Utermöhlen O, Chun E, Garrett WS, McCoy KD, Diefenbach A, Staeheli P, Stecher B, Amit I, Prinz M. 2015, Nat Neurosci.

2. Microglia development follows a stepwise program to regulate brain homeostasis. Matcovitch-Natan O, Winter DR, Giladi A, Vargas Aguilar S, Spinrad A, Sarrazin S, Ben-Yehuda H, David E, Zelada González F, Perrin P, Keren-Shaul H, Gury M, Lara-Astaiso D, Thaiss CA, Cohen M, Bahar Halpern K, Baruch K, Deczkowska A, Lorenzo-Vivas E, Itzk. 2016, Science.

3. Microbiome Influences Prenatal and Adult Microglia in a Sex-Specific Manner. Thion MS, Low D, Silvin A, Chen J, Grisel P, Schulte-Schrepping J, Blecher R, Ulas T, Squarzoni P, Hoeffel G, Coulpier F, Siopi E, David FS, Scholz C, Shihui F, Lum J, Amoyo AA, Larbi A, Poidinger M, Buttgereit A, Lledo PM, Greter M, Chan JKY, Amit I, Bey. 2018, Cell.

4. Paradoxical effects of minocycline in the developing mouse somatosensory cortex. Arnoux I, Hoshiko M, Sanz Diez A, Audinat E. 2014, Glia.

5. Layer V cortical neurons require microglial support for survival during postnatal development. Ueno M, Fujita Y, Tanaka T, Nakamura Y, Kikuta J, Ishii M, Yamashita T. 2013, Nat Neurosci.

6. Doxycycline increases neurogenesis and reduces microglia in the adult hippocampus. Sultan S, Gebara E, Toni N. 2013, Front Neurosci.

7. Gut microbiota are related to Parkinson's disease and clinical phenotype. Scheperjans F, Aho V, Pereira PA, Koskinen K, Paulin L, Pekkonen E, Haapaniemi E, Kaakkola S, Eerola-Rautio J, Pohja M, Kinnunen E, Murros K, Auvinen P. 2015, Mov Disord.

8. Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease. Sampson TR, Debelius JW, Thron T, Janssen S, Shastri GG, Ilhan ZE, Challis C, Schretter CE, Rocha S, Gradinaru V, Chesselet MF, Keshavarzian A, Shannon KM, Krajmalnik-Brown R, Wittung-Stafshede P, Knight R, Mazmanian SK. 2016, Cell.

9. Reduction of Abeta amyloid pathology in APPPS1 transgenic mice in the absence of gut microbiota. Harach T, Marungruang N, Duthilleul N, Cheatham V, Mc Coy KD, Frisoni G, Neher JJ, Fåk F, Jucker M, Lasser T, Bolmont T. 2017, Sci Rep.

10. Commensal microbiota and myelin autoantigen cooperate to trigger autoimmune demyelination. Berer K, Mues M, Koutrolos M, Rasbi ZA, Boziki M, Johner C, Wekerle H, Krishnamoorthy G. 2011, Nature.

11. Microglial control of astrocytes in response to microbial metabolites. Rothhammer V, Borucki DM, Tjon EC, Takenaka MC, Chao CC, Ardura-Fabregat A, de Lima KA, Gutiérrez-Vázquez C, Hewson P, Staszewski O, Blain M, Healy L, Neziraj T, Borio M, Wheeler M, Dragin LL, Laplaud DA, Antel J, Alvarez JI, Prinz M.  Nature. 2018.

12. Antibiotic-induced perturbations in gut microbial diversity influences neuro-inflammation and amyloidosis in a murine model of Alzheimer's disease. Minter MR, Zhang C, Leone V, Ringus DL, Zhang X, Oyler-Castrillo P, Musch MW, Liao F, Ward JF, Holtzman DM, Chang EB, Tanzi RE, Sisodia SS. 2016, Sci Rep.

13. Neuroprotective effects of fecal microbiota transplantation on MPTP-induced Parkinson's disease mice: Gut microbiota, glial reaction and TLR4/TNF-α signaling pathway. Sun MF, Zhu YL, Zhou ZL, Jia XB, Xu YD, Yang Q, Cui C, Shen YQ. 2018, Brain Behav Immun.

14. Effect of Probiotic Supplementation on Cognitive Function and Metabolic Status in Alzheimer's Disease: A Randomized, Double-Blind and Controlled Trial. Akbari E, Asemi Z, Daneshvar Kakhaki R, Bahmani F, Kouchaki E, Tamtaji OR, Hamidi GA, Salami M. 2016, Front Aging Neurosci.

15. Decreased microglial activation through gut-brain axis by prebiotics, probiotics, or synbiotics effectively restored cognitive function in obese-insulin resistant rats. Chunchai T, Thunapong W, Yasom S, Wanchai K, Eaimworawuthikul S, Metzler G, Lungkaphin A, Pongchaidecha A, Sirilun S, Chaiyasut C, Pratchayasakul W, Thiennimitr P, Chattipakorn N, Chattipakorn SC. 2018, J Neuroinflammation.