Supplementing the body’s short chain fatty acids can improve stroke recovery, according to research in mice recently published in Journal of Neuroscience.
Short chain fatty acid supplementation may be a non-invasive addition to stroke rehabilitation therapies.
The gut microbiome influences brain health, including how the brain recovers from stroke.
Short chain fatty acids, a fermentation product from the bacteria in our guts, are a key component of gut health but their role in stroke recovery has not been explored.
Sadler et al. added short chain fatty acids to the drinking water of mice for four weeks before inducing a stroke.
The mice that drank the fatty acid water experienced a better stroke recovery compared to the control mice, including reduced motor impairment and increased spine growth on dendrites – a crucial memory structure.
Additionally, the fatty acid-supplemented mice expressed more genes related to microglia, the brain’s immune cells.
Post-stroke neuronal plasticity is altered by short-chain fatty acid treatment. Image is credited to Sadler et al., JNeurosci 2019.
Microglia activity could be responsible for increasing dendritic spines and improving stroke outcome.
This relationship indicates short chain fatty acids may serve as messengers in the gut-brain connection by influencing how the brain responds to injury.
Introduction to Gut Microbiota and Disease
The intestinal microbiome has recently been implicated in a host of chronic diseases ranging from inflammatory bowel disease (IBD), type 2 diabetes (T2D), and cardiovascular disease (CVD) to colorectal cancer [1,2,3]. The community of ~200 prevalent bacteria, virus, and fungi inhabiting the human gastrointestinal (GI) tract provide unique metabolic functions to the host and are fundamentally important in health and disease [4,5].
Microbiome refers to the collective genomes of all microorganisms inhabiting an environment. While isolating and culturing each individual species is an intractable task, a cutting-edge method of sequence analysis, metagenomics, has enabled the reconstruction of microbial species and their function from the collective nucleotide contents contained in a stool sample. Shotgun metagenomic sequencing analysis discovered 1952 unclassified bacteria species in the human gut microbiome in addition to the 553 bacteria previously cultured from the gut .
A central question in medicine concerns the nature of the relationship between human health and the gut microbiota, which refers to the community of microorganisms themselves, the relative abundance of individual species populations, and their function.
Metagenomics and analysis of twins data has revealed that environmental factors such as diet and household cohabitation greatly outweigh heritable genetic contributions to the composition and function of gut microbiota .
Analogous to the genetic heritability statistic, Rothschild et al. constructed a microbiome-association index. Significant associations are observed between the gut microbiome and host phenotypes for body mass index (BMI) (25%), waist-to-hip ratio (24%), fasting glucose levels (22%), glycemic status (25%), high-density lipoprotein (HDL) cholesterol levels (36%), and monthly lactose consumption (36%) .
Compared to BMI, waist-to-hip ratio is an anthropometric measurement of central obesity and stronger predictor of diastolic and systolic blood pressure, total cholesterol/HDL, and triglycerides  as well as death from CVD .
The Western diet has profound effects on the diversity and populations of microbial species that make up gut flora . The U.S. is home to the largest number of immigrants in the world, many of whom develop metabolic diseases post immigration.
Earlier epidemiological evidence revealed a fourfold increase in obesity risk is possible within 15 years of emigrating to the U.S. compared to populations remaining in their birth country . In a recent cross-sectional and longitudinal study of a multi-generational Asian American cohort, emigrating to the U.S. was shown to reduce gut microbial diversity and function . Alpha diversity was measured using the Shannon entropy, a quantitative index that accounts for the abundance and evenness of species residing in the host, as opposed to species richness, which is the number of species present.
Within the gram-negative Bacteroidetes phylum, bacterial strains from the genus Prevotella, whose enzymes degrade plant fiber, became displaced by dominant strains from the genus Bacteroides according to an individual’s time spent in the U.S. The ratio of Bacteroides to Prevotella increased by factors of 10, correlating with the time in decades spent in the U.S. Prior to this study, metagenomics had identified three clusters of variation in the human gut, referred to as enterotypes .
The first enterotype, high in Bacteroides and low in Prevotella, is found in individuals on a long-term Western diet high in animal protein, the nutrient choline, and saturated fat . The second enterotype is high in Prevotella, low in Bacteroides, and associated with a plant-based diet rich in fiber, simple sugars, and plant-derived compounds. While less distinct, a third potential enterotype was found with a slightly higher population of genus Ruminococcus within the phylum Firmicutes.
Enriched Ruminococcus is associated with irritable bowel syndrome (IBS) , and transient blooms of pro-inflammatory Ruminococcus have been associated with active flare-ups in IBD . R. gnavus, a prevalent gut microbe that proliferates in IBD, has been found to secrete a unique L-rhamnose oligosaccharide that induces tumor necrosis factor alpha (TNFα), a major pro-inflammatory cytokine .
Microbiota, the Immune Response, and Diet in IBD
IBD is a chronic GI disorder characterized by an overactive immune response to the gut microbiome. A serious, debilitating condition, IBD affects growth and development in children, increases the risk of colorectal cancer, and can lead to life-threatening complications . There are two forms of IBD, Crohn’s disease and ulcerative colitis, that differ in the inflamed areas of the intestine. Normally, anaerobic microbes in the gut derive their nutrients from fermentation of indigestible oligosaccharides and other carbohydrates escaping proximal digestion .
In IBD, respiratory electron acceptors generated as a byproduct of the inflammatory host response become environmental stressors that support bacterial growth . The disorder results in oxidative stress for the host and the microbiome, leading to gut dysbiosis in the form of decreased community richness and proliferation of facultative anaerobic Enterobacteriaceae and adherent invasive strains of Escherichia coli [16,20,21].
Drug therapies for IBD have traditionally included immunosuppressants in the form of corticosteroids, antimetabolite agents, or anti-TNF antibodies, often with ancillary administration of antibiotics . An alternative treatment, given predominantly to children, is a defined enteral nutrition formula. Dietary therapy has the advantage of obviating the need for immunosuppression and is thought to work by altering the composition of gut microbiota.
A longitudinal study involving metagenomic analysis was conducted of 90 children initiating treatment for Crohn’s disease . GI symptoms, mucosal inflammation, and microbial communities were compared for dietary and anti-TNF therapy and antibiotic use relative to healthy children. Microbial communities separated into two clusters based on composition.
The dysbiotic community associated with active disease was characterized by increased fungal representation, increased lactose-fermenting bacteria (Streptococcus, Lactobacillus, Klebsiella), and the presence of human DNA in the stool (from epithelial cells and white blood cells). Crohn’s patients also had reduced relative abundance of Prevotella and increased Escherichia compared to healthy children.
Treatment with antibiotics in the last six months was strongly associated with microbial dysbiosis , consistent with earlier findings that oral antibiotics for acne are a risk factor for new onset Crohn’s disease . Antibiotic-treatment was observed to enrich fungi such as Candida and Saccharomyces . Treatment with the enteral nutrition  or antibody therapies, on the other hand, reduced inflammation and markedly improved gut microbiota. The relative populations of fungi were reduced within one week of receiving the defined dietary formula, which lacked fiber .
Microbial Metabolites and Short-Chain Fatty Acids
SCFA Receptor Activation
Short-chain fatty acids (SCFAs) have attracted considerable attention for their role in human health . Obligate anaerobic bacteria (phyla Firmicutes and Bacteroidetes) encode a variety of enzymes for hydrolyzing complex carbohydrates (chains of sugar molecules) not digestible by the host such as resistant starch and fiber. Certain genera such as Lactobacillus and Bifidobacterium specialize in oligosaccharide fermentation, utilizing galactooligosaccharides (GOS), fructooligosaccharides (FOS), and polysaccharide inulin . Carbohydrate fermentation by anaerobes provides the host with important SCFAs such as acetate, propionate, and butyrate .
Several receptors have been identified for SCFAs such as free fatty acid receptor 3 (FFAR3 or GPR41) and niacin receptor 1 (GPR109A) . GPR41 and GPR109A are G-protein coupled receptors (GPCRs) found on intestinal epithelial cells, immune cells, and adipocytes. As endogenous agonists in GPCR signal transduction, SCFAs have a profound effect on physiological processes [32,33] independent of delivering calories to the host as carbon molecules . GPR41 is associated with increased energy expenditure, leptin hormone expression, and decreased food intake [31,35].
Analogous to the activity of niacin, butyrate activates GPR109A to suppress colonic inflammation and colon cancer development . Niacin is a known lipid-lowering agent: GPR109A inhibits triglyceride hydrolysis (lipolysis) in adipocytes, lowering blood levels of triglyceride and low-density lipoprotein (LDL) to reduce atherogenic activity. Acetate and propionate activate cell surface receptor GPR43 to induce neutrophil chemotaxis. GPR43 is anti-lipolysis and implicated in IBD, but contradictory results in mouse models leave doubt as to whether an agonist or antagonist will best treat colitis .
There is a growing interest in pursuing GPR41 and GPR43 as drug targets for the chronic inflammatory disorders asthma, arthritis, and obesity . Much work remains to be done to establish the appropriate disease models needed to study these conditions.
Colonic epithelial cells (colonocytes) are the control switch separating microbial homeostasis from gut dysbiosis . It is known that antibiotics deplete microbes that ferment essential SCFAs such as butyrate, which are normally responsible for maintaining microbial homeostasis [24,39]. The lack of butyrate silences metabolic signaling in the gut. Mitochondrial beta-oxidation in colonocytes becomes disabled, resulting in a transfer of oxygen, which freely diffuses across cell membranes from the blood to the GI lumen.
Oxygen in the colon then allows for pathogenic facultative anaerobes such as E. coli  to outcompete the benign obligate anaerobes that characterize a healthy gut [41,42]. Microbial homeostasis is normally maintained by peroxisome proliferator-activated receptor gamma (PPAR-γ). PPAR-γ is a nuclear receptor activated by butyrate and other ligands, is found in adipocytes and colonocytes, and is responsible for activating genes involved in glucose and lipid metabolism. Lack of butyrate signaling results in nitrate electron acceptors being released into the colon, which facultative anaerobes can also use for cell respiration, breaking down carbohydrates into carbon dioxide rather than fermenting them .
Facultative anaerobes, including Proteobacteria, could further affect nutrition by catabolizing SCFAs present in the lumen . The metabolic reprogramming of colonocytes is analogous to that of macrophages, which become polarized toward anaerobic glycolysis in response to proinflammatory signals. In ulcerative colitis, excessive epithelial repair results in lower PPAR-γ synthesis, which reduces beta-oxidation and increases oxygenation of colonocytes. Inflamed mucosae in colitis patients are increased in Proteobacteria, a major phylum of gram-negative bacteria, but decreased in gram-positive Firmicutes. Treatment with PPAR-γ agonist, however, can improve the microbial balance .
Fecal Biomarkers and IBS
Fecal biomarkers such as inflammatory proteins, antimicrobial peptides, and SCFA levels are emerging as a non-invasive screening tool for assessing and diagnosing various health conditions . Patients with IBD have lower fecal levels of acetate, propionate and butyrate, and higher levels of lactic and pyruvic acids than healthy individuals .
Given the relationship between bacterial fermentation products and atherosclerosis, ongoing research aims to characterize the fecal microbiota and SCFA signatures of individuals with high blood lipid levels . High levels of isobutyric acid could be one such biomarker for hypercholesterolemia.
Colonoscopy is an invasive exam relied on in the United States as a periodic screen for colorectal cancer , but annual screening is performed in many countries using a non-invasive fecal immunochemical test, which looks for microscopic blood in the stool . Current efforts are underway to identify novel microbial biomarkers for colorectal cancer given that it is associated with increased fecal levels of F. nucleatum, a promoter of tumorigenesis .
Unlike structural disorders such as IBD, IBS is a functional disorder and collection of GI symptoms observed in the absence of macroscopic signs of inflammation. Despite affecting 10–15% of the population and the potential for low quality of life, its etiology is unclear and current drug treatments are largely ineffective .
Diagnosis has traditionally relied on symptom criteria, stool characteristics, and questionnaires, once all other pathologies are ruled out . The Rome criteria sets classifications for four subtypes: IBS with predominant diarrhea (IBS-D), IBS with predominant constipation (IBS-C), and IBS with mixed or alternating-type bowel habits (IBS-M) depending on whether >25% of bowel movements belong to soft or hard type stool categories or both, respectively, followed by IBS unclassified (IBS-U) .
It has been known for some time that IBS patients have reduced microbial diversity compared to healthy subjects , see also References 6–9 in . Inflammatory proteins such as human β-defensin 2, a bactericide, have been identified as a useful fecal biomarker in IBS and IBD [48,51,52]. Lastly, the concentration difference in two SCFAs, propionic minus butyric acid, has been shown to be positive for all four IBS subtypes but negative in healthy subjects .
Elevated levels of interleukin 6, a pro-inflammatory peptide cytokine, and plasma levels of lipopolysaccharide (LPS) endotoxin, a marker of gram-negative bacterial translocation, were found to be elevated in a subpopulation of IBS-D patients with small intestinal permeability, analogous to that observed in celiac disease .
It is hypothesized that psychological stress can exacerbate the inflammatory condition by allowing translocation of harmful bacterial products across the intestinal epithelium. Known as “leaky gut”, a compromised epithelial barrier allows toxins and antigens in the GI lumen to enter the bloodstream. A healthy gut flora is important in maintaining the intestinal barrier.
By increasing the expression of tight cell junction proteins, beneficial probiotics such as Lactobacillus and Bifidobacterium can limit the development of autoimmune diseases in genetically susceptible individuals  and fatty liver disease in obese individuals . In alcoholic liver disease, alcohol consumption causes gut permeability by reducing the expression of REG3, a bactericidal protein normally responsible for restricting the mucosal colonization of luminal bacteria .
In the last decade, it has been discovered that the enteric and central nervous systems are linked via a bidirectional communication network termed the gut-brain axis. Gut-brain communication is disrupted in the cases of IBS and microbial dysbiosis , in the former leading to changes in intestinal motility and secretion and causing visceral hypersensitivity (hyperalgesia) .
Recurrent abdominal pain is a hallmark characteristic of IBS. Autism spectrum disorder, which is often associated with constipation, has been connected to gut dysbiosis in the form of an increased Firmicutes/Bacteroidetes ratio and high levels of facultative anaerobes Escherichia/Shigella and the fungal genus Candida [60,61]. It is suggested that leaky gut contributes to the pathogenesis of autism by increasing systemic metabolites that alter the neuroimmune and neuroendocrine systems, thus affecting the brain and neurodevelopment [61,62,63].
For the last century, the ketogenic diet (KD) has been used to treat refractory epilepsy in children’s hospitals , achieving a 50% reduction in seizure rates . KD restricts the proportion of carbohydrate intake to create a state of ketosis in which the body relies on ketone bodies for energy rather than glucose. Clinical studies are now investigating the use of KD for treating neurological conditions including autism, Alzheimer’s, and Parkinson’s disease, with promising results obtained for small cohorts .
The mechanism of action was initially thought to result from the normalization of aberrant energy metabolism associated with these disorders, but the role of the gut microbiota is now coming into focus. A recent comparison of KD-fed conventionally raised mice versus mice treated with antibiotics or reared germ-free revealed that alterations in the gut microbiota are required to reproduce the anti-seizure effects of KD . Following KD was observed to enrich the populations of the anaerobic genera Akkermansia and Parabacteroides. Moreover, increased levels of the inhibitory neurotransmitter γ-aminobutyric acid (GABA) were detected in metabolite profiles of the brain hippocampus of KD-fed mice and were observed to be microbiota-dependent. GABA is a principal means of reducing communication between brain cells, and neuronal excitability is enhanced in neurological conditions such as epilepsy, anxiety, and Alzheimer’s disease [66,68].
Besides dietary intervention, these and other observations suggest that supplementation with prebiotics or probiotics could be used to improve cognitive symptoms associated with neurological conditions ranging from autism to Alzheimer’s and Parkinson’s [69,70], giving rise to the notion of “psychobiotics” [71,72].
Fecal microbiota transplantation (FMT) is yet another therapeutic option, which involves the engraftment of microbes from a healthy donor . In a study of 18 autistic children, an eight-week course of FMT resulted in behavioral improvement and an 80% reduction in GI symptoms and abdominal pain associated with autism . Outcomes remained improved when assessed eight weeks after treatment had ended, lending support to the hypothesis that gut microbiota are at least partially responsible for autism symptoms.
Analysis of microbiota composition showed that FMT increased overall bacterial diversity and the abundance of fermentative Bifidobacterium and Prevotella in autistic individuals even after treatment cessation. In other clinical studies, FMT has demonstrated a 90% success rate for treating recurrent Clostridioides difficile infection, clinical remission rates of up to 78% in treating IBD, and symptom resolution or improvement in up to 70% of IBS patients . Interest is now growing for the application of FMT in other disorders ranging from Parkinson’s to metabolic syndrome [75,76]. In patients with metabolic syndrome, FMT was shown to improve insulin sensitivity for those with decreased baseline microbial diversity, but the effects did not persist in the long-term .
Other lines of clinical evidence on the gut-brain interaction show that gut microbiota influences the central nervous system by alterations in the release of neuroendocrine hormones and neurotransmitter activity. Dysfunctions in GABA receptor signaling are implicated in anxiety and depression, and beneficial bacteria Lactobacillus and Bifidobacterium convert the amino acid glutamate into GABA [78,79].
Metagenomic analysis of a 1054-person Flemish cohort revealed that butyrate-producing Faecalibacterium and Coprococcus associate with higher quality of life and improved mental health, while Dialister and Coprococcus are depleted in cases of depression . To improve cognitive symptoms associated with clinical depression and anxiety, beneficial probiotic strains of B. longum and L. helveticus have been administered clinically with promising results [72,80].
In a study comparing young and middle-aged mice, dietary supplementation with prebiotic inulin was observed to increase Bifidobacterium and Akkermansia, reduce neuroinflammation and anxiety, and improve cognition in middle-aged mice . The fact that alterations in gut microbiota can provide cognitive symptom relief could offer one basis for the relationship observed between quality of diet and one’s mental health status .
Calli McMurray – SfN
The image is credited to Sadler et al., JNeurosci 2019.
Original Research: Closed access
“Short-Chain Fatty Acids Improve Post-Stroke Recovery via Immunological Mechanisms”. Rebecca Sadler, Julia V. Cramer, Steffanie Heindl, Sarantos Kostidis, Dene Betz, Kielen R. Zuurbier, Bernd H. Northoff, Marieke Heijink, Mark P. Goldberg, Erik J. Plautz, Stefan Roth, Rainer Malik, Martin Dichgans, Lesca M. Holdt, Corinne Benakis, Martin Giera, Ann M. Stowe and Arthur Liesz.
Journal of Neuroscience doi:10.1523/JNEUROSCI.1359-19.2019.