At the virtual AAT-AD/PD meeting, held April 2 to 5 online, researchers substantiated some prior hints on potential causal connections between the throngs of bacteria inhabiting the gut, how microglia function in the brain, and deposition of Aβ plaques. Using antibiotics, caloric restriction, stool transplants, or probiotics to shift the gut microbiome, scientists reported that they were able to modulate microglial phenotypes and Aβ burden. They zeroed in on specific bacterial strains that either helped or hindered the brain’s immune cells, and uncovered profound differences between male and female mice in this regard. As they begin to drill down into details of the elusive gut-brain connection, some researchers envision microbiome-based therapies for neurodegenerative disease.

  • In male mice, antibiotic treatment calmed microglia, cleared plaques.
  • Bacteriodes activated microglia and boosted plaques; Faecalibaculum did the opposite.
  • It’s not just Aβ: Probiotics blocked α-synuclein aggregates in worms.

Sangram Sisodia of the University of Chicago reported striking sex-specific effects of the microbiome on the brain. Previously, Sisodia’s group had found that treating APP/PS1 mice with broad-spectrum antibiotics did not destroy the microbiota in their gut, but altered their composition. This remodeling differed in males and females. Males had an increase in certain Bacteriodes species and a drop in a strain of E. coli; females saw more Akkermansia, E. coli, and Proteobacteria, while Bifidobacterium species plummeted.

Notably, these microbiome changes appeared to affect the brain in sex-specific ways (Dodiya et al., 2019). In antibiotic-treated APP/PS1 males, microglia took on a homeostatic gene expression signature, whereas untreated APP/PS1 microglia have the neurodegenerative disease phenotype (MGnD). Treated male mice also had a lower amyloid plaque burden. In contrast, antibiotic-mediated microbiome remodeling had no such effect on the brain in female mice.

At AD/PD, Sisodia showed some detail on causal connections between the microbiome, microglia, and amyloid plaques. He noticed that the benefits of antibiotic treatment in the male APP/PS1 mouse brain were wiped away when the animals subsequently received regular doses—via gastric gavage—of fecal matter from untreated mice. Their microglia rounded up, retracted their processes, and re-expressed the neurodegenerative gene signature, which included higher levels of TREM2 and ApoE4. And plaques roared back. Essentially, the fecal transplant reverted animals back to their pre-antibiotic disease state, establishing that the gut microbiota indeed modulated microglial phenotypes and Aβ burden. To confirm that microglia caused the changes to Aβ burden, Sisodia’s group wiped out the mice’s microglia using a CSF-1R antagonist, which deprives these cells of survival signals (Sep 2019 news). In these mice-sans-microglia, fecal transplants did not affect Aβ plaque burden.

In all, Sisodia’s data suggested that the composition of microbes in the male gut influences form and function of microglia in the brain, which, in turn, affects Aβ deposition.

The reason behind this sex difference in microglial response is unclear, Sisodia said. It may lie beyond microbiome remodeling. Other studies have described sex-specific microglial phenotypes, as well as differences in the way the microbiome shapes microglial development in the two sexes (Thion et al., 2018Jun 2018 news; Jul 2019 conference news). 

What exactly are the gut microbes that hold sway over microglia and Aβ plaque deposition in a mouse’s brain? At AD/PD, Howard Weiner of Brigham and Women’s Hospital in Boston had some tentative answers. Previously, this group had reported that Tg2576 mice on a calorie-restricted diet had fewer Aβ plaques. The meager chow reduced numbers of Bacteriodes species, while boosting Faecalibaculum (Cox et al., 2019). 

The researchers reported that feeding APP/PS1 mice on normal chow with Bacteriodes fragilis upped amyloid plaque load. Bacteriodes have been independently reported to rise in the human gut with age and AD (Odamaki et al., 2016; Vogt et al., 2017). 

At AD/PD, Weiner reported that supplementing the chow of mice with a strain of Faecalibaculum had the opposite effect on microglia. Feeding this bacteria to mice converted their microglia from an MGnD phenotype to a homeostatic state, and lessened expression of inflammatory cytokines in their brains. Interestingly, Weiner reported that in the cortices of mice fed Bacteriodes fragilis, expression of three genes known to promote amyloidogenic processing of APP—Cdk5, Gga1, and Prkcb—shot up. Together, the data suggested that specific bacterial species in the gut could modulate Aβ deposition not only by influencing microglia, but also by tweaking Aβ42 production.

Finally, Weiner reported that treating APP/PS1 mice with metronidazole, an antibiotic that targets anaerobic bacteria including Bacteroides, lessened Aβ plaque load. The effect was stronger in female mice, which started out with a higher plaque load than males. On the face of it, this result contrasted with Sisodia’s. The cocktail of five antibiotics Sisodia’s group used included metronidazole and benefited males more than females. Sisodia told Alzforum that, according to data in an upcoming paper from his lab, treatment with metronidazole, or any other lone antibiotic, did not affect plaque load.

Maria Doitsidou of the University of Edinburgh used a reductionist approach to identify a bacterial strain that assuaged a different neurodegenerative proteopathy, that is, α-synuclein aggregation. Doitsidou reviewed recent data from a C. elegans model of synucleinopathy (Goya et al., 2020). In a nutshell, the researchers screened 40 bacterial strains for their ability to prevent α-synuclein aggregation in worms broadly overexpressing a fluorescently tagged version of the human protein in muscle. The probiotic B. subtilis strain PXN21 did the trick. While untreated worms were full of fluorescent synuclein aggregates, those that noshed on B. subtilis had none. What’s more, switching the worms from their normal diet of E. coli to the probiotic strain later in life dissipated aggregates that had already formed.

The findings independently confirm previous C. elegans studies led by Roberto Grau at Rosario National University, Argentina. He had found that B. subtilis blocked α-synuclein aggregation and delayed neurodegeneration (Apr 2018 conference news). Grau’s study appeared in the February issue of Journal of Alzheimer’s disease (Cogliati et al., 2020). 

For her part, Doitsidou took stock of gene-expression changes in C. elegans in response to eating B. subtilis versus E. coli. Among the genes expressed differently were those involved in lipid metabolism, specifically of sphingolipids. Several genes pegged as PD risk factors are involved in sphingolipid processing, including GBA1. Other groups have linked microbial short-chain lipids to microglia and Parkinson’s (Dec 2016 news). 

Doitsidou said that her lab is testing B. subtilis extracts on PD patient-derived dopaminergic neurons, and feeding the probiotic strains to mouse models of synucleinopathy. She hopes to identify the specific bacterial metabolites that quash α-synuclein aggregation. In addition, the researchers are working with Edinburgh neurologists to start a clinical trial that will evaluate B. subtilis probiotics in people with PD.

Giovanni Frisoni of the University of Geneva presented a nugget of human data on this topic. People with AD, PD, and other neurological disorders have altered gut microbiomes, and mouse fecal transplant studies suggest that these shifted microbiomes could cause or exacerbate disease (Cattaneo et al., 2017; Dec 2016 news; Feb 2017 news). Frisoni wondered whether, on the flip side, fecal transplants from people without AD, especially people at lowest risk for the disease, might protect against it.

To test this idea, researchers dosed 1-year-old 3xTg mice with fecal matter from one of four people at varying risk for Alzheimer’s. One 76-year-old donor with an ApoE3/4 genotype already had the disease. The three other donors were cognitively normal: a 65-year-old with one ApoE4 allele, a 72-year-old ApoE2 carrier, and a 24-year-old ApoE3 homozygote. Frisoni reported that 3xTg mice that received stool via a feeding tube from the person with AD displayed more AD-like behavior, including more anxiety and less movement, than those who received stool from other 3xTg mice, or saline. Mice gavaged with stool from the young donor or from the ApoE2 carrier performed better on a novel object recognition test of memory than did mice treated with stools from any of the other donors, or saline. Stool from the young donor or the ApoE2 carrier also appeared to reduce plaque load in the 3xTg mice. Frisoni stressed that the experiments were preliminary, and part of ongoing analyses.

The mechanism underlying these effects is unclear. Still, they imply that medications processed from feces of healthy people might, in theory, somehow stave off disease in those who are at risk.—Jessica Shugart


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News Citations

  1. Are Microglia Plaque Factories?
  2. Girl Power? In Mice, Female Microglia Protect Against Ischemic Injury
  3. Down to Sex? Boy and Girl Microglia Respond Differently
  4. Do Immune Responses Promote, or Prevent, Parkinson’s Disease?
  5. Do Microbes in the Gut Trigger Parkinson’s Disease?
  6. Microbes in the Gut Egg on Aβ Pathology in Mice

Research Models Citations

  1. 3xTg

Paper Citations

  1. . Sex-specific effects of microbiome perturbations on cerebral Aβ amyloidosis and microglia phenotypes. J Exp Med. 2019 Jul 1;216(7):1542-1560. Epub 2019 May 16 PubMed.
  2. . Microbiome Influences Prenatal and Adult Microglia in a Sex-Specific Manner. Cell. 2018 Jan 25;172(3):500-516.e16. Epub 2017 Dec 21 PubMed.
  3. . Calorie restriction slows age-related microbiota changes in an Alzheimer's disease model in female mice. Sci Rep. 2019 Nov 29;9(1):17904. PubMed.
  4. . Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study. BMC Microbiol. 2016 May 25;16:90. PubMed.
  5. . Gut microbiome alterations in Alzheimer's disease. Sci Rep. 2017 Oct 19;7(1):13537. PubMed.
  6. . Probiotic Bacillus subtilis Protects against α-Synuclein Aggregation in C. elegans. Cell Rep. 2020 Jan 14;30(2):367-380.e7. PubMed.
  7. . Bacillus Subtilis Delays Neurodegeneration and Behavioral Impairment in the Alzheimer's Disease Model Caenorhabditis Elegans. J Alzheimers Dis. 2020;73(3):1035-1052. PubMed.
  8. . Association of brain amyloidosis with pro-inflammatory gut bacterial taxa and peripheral inflammation markers in cognitively impaired elderly. Neurobiol Aging. 2017 Jan;49:60-68. Epub 2016 Aug 31 PubMed.

Further Reading


  1. . Transcriptional and Translational Differences of Microglia from Male and Female Brains. Cell Rep. 2018 Sep 4;24(10):2773-2783.e6. PubMed.
  2. . Gut microbiota are related to Parkinson's disease and clinical phenotype. Mov Disord. 2015 Mar;30(3):350-8. Epub 2014 Dec 5 PubMed.