Sex-dependent interactions between prodromal intestinal inflammation and LRRK2 G2019S in mice promote endophenotypes of Parkinson's disease.

Gastrointestinal (GI) disruptions and inflammatory bowel disease (IBD) are commonly associated with Parkinson's disease (PD), but how they may impact risk for PD remains poorly understood. Herein, we provide evidence that prodromal intestinal inflammation expedites and exacerbates PD endophenotypes in rodent carriers of the human PD risk allele LRRK2 G2019S in a sex-dependent manner. Chronic intestinal damage in genetically predisposed male mice promotes α-synuclein aggregation in the substantia nigra, loss of dopaminergic neurons and motor impairment. This male bias is preserved in gonadectomized males, and similarly conferred by sex chromosomal complement in gonadal females expressing human LRRK2 G2019S. The early onset and heightened severity of neuropathological and behavioral outcomes in male LRRK2 G2019S mice is preceded by increases in α-synuclein in the colon, α-synuclein-positive macrophages in the colonic lamina propria, and loads of phosphorylated α-synuclein within microglia in the substantia nigra. Taken together, these data reveal that prodromal intestinal inflammation promotes the pathogenesis of PD endophenotypes in male carriers of LRRK2 G2019S, through mechanisms that depend on genotypic sex and involve early accumulation of α-synuclein in myeloid cells within the gut.

Complex carbohydrate utilization by gut bacteria modulates host food preference.

The gut microbiota interacts directly with dietary nutrients and has the ability to modify host feeding behavior, but the underlying mechanisms remain poorly understood. Select gut bacteria digest complex carbohydrates that are non-digestible by the host and liberate metabolites that serve as additional energy sources and pleiotropic signaling molecules. Here we use a gnotobiotic mouse model to examine how differential fructose polysaccharide metabolism by commensal gut bacteria influences host preference for diets containing these carbohydrates. Bacteroides thetaiotaomicron and Bacteroides ovatus selectively ferment fructans with different glycosidic linkages: B. thetaiotaomicron ferments levan with ß2-6 linkages, whereas B. ovatus ferments inulin with ß2-1 linkages. Since inulin and levan are both fructose polymers, inulin and levan diet have similar perceptual salience to mice. We find that mice colonized with B. thetaiotaomicron prefer the non-fermentable inulin diet, while mice colonized with B. ovatus prefer the non-fermentable levan diet. Knockout of bacterial fructan utilization genes abrogates this preference, whereas swapping the fermentation ability of B. thetaiotaomicron to inulin confers host preference for the levan diet. Bacterial fructan fermentation and host behavioral preference for the non-fermentable fructan are associated with increased neuronal activation in the arcuate nucleus of the hypothalamus, a key brain region for appetite regulation. These results reveal that selective nutrient metabolism by gut bacteria contributes to host associative learning of dietary preference, and further informs fundamental understanding of the biological determinants of food choice.

Ketogenic diet therapy for pediatric epilepsy is associated with alterations in the human gut microbiome that confer seizure resistance in mice.

The gut microbiome modulates seizure susceptibility and the anti-seizure effects of the ketogenic diet (KD) in animal models, but whether these relationships translate to KD therapies for human epilepsy is unclear. We find that the clinical KD alters gut microbial function in children with refractory epilepsy. Colonizing mice with KD-associated microbes promotes seizure resistance relative to matched pre-treatment controls. Select metagenomic and metabolomic features, including those related to anaplerosis, fatty acid ß-oxidation, and amino acid metabolism, are seen with human KD therapy and preserved upon microbiome transfer to mice. Mice colonized with KD-associated gut microbes exhibit altered hippocampal transcriptomes, including pathways related to ATP synthesis, glutathione metabolism, and oxidative phosphorylation, and are linked to susceptibility genes identified in human epilepsy. Our findings reveal key microbial functions that are altered by KD therapies for pediatric epilepsy and linked to microbiome-induced alterations in brain gene expression and seizure protection in mice.

The maternal microbiome promotes placental development in mice.

The maternal microbiome is an important regulator of gestational health, but how it affects the placenta as the interface between mother and fetus remains unexplored. Here, we show that the maternal gut microbiota supports placental development in mice. Depletion of the maternal gut microbiota restricts placental growth and impairs feto-placental vascularization. The maternal gut microbiota modulates metabolites in the maternal and fetal circulation. Short-chain fatty acids (SCFAs) stimulate cultured endothelial cell tube formation and prevent abnormalities in placental vascularization in microbiota-deficient mice. Furthermore, in a model of maternal malnutrition, gestational supplementation with SCFAs prevents placental growth restriction and vascular insufficiency. These findings highlight the importance of host-microbial symbioses during pregnancy and reveal that the maternal gut microbiome promotes placental growth and vascularization in mice.

Gut microbiota Turicibacter strains differentially modify bile acids and host lipids.

Bacteria from the Turicibacter genus are prominent members of the mammalian gut microbiota and correlate with alterations in dietary fat and body weight, but the specific connections between these symbionts and host physiology are poorly understood. To address this knowledge gap, we characterize a diverse set of mouse- and human-derived Turicibacter isolates, and find they group into clades that differ in their transformations of specific bile acids. We identify Turicibacter bile salt hydrolases that confer strain-specific differences in bile deconjugation. Using male and female gnotobiotic mice, we find colonization with individual Turicibacter strains leads to changes in host bile acid profiles, generally aligning with those produced in vitro. Further, colonizing mice with another bacterium exogenously expressing bile-modifying genes from Turicibacter strains decreases serum cholesterol, triglycerides, and adipose tissue mass. This identifies genes that enable Turicibacter strains to modify host bile acids and lipid metabolism, and positions Turicibacter bacteria as modulators of host fat biology.

Toward understanding links between the microbiome and neurotransmitters.

The gut microbiota modulates neurobiological activity in various animal lineages. This is often proposed to occur through interactions with neurotransmitters and other neuromodulatory molecules in the host. Our commentary will discuss recent research that establishes microbiota-neurotransmitter connections, gaps in current understanding, and outstanding questions that may guide future advances in the field of microbiota-nervous system interactions.

Extending genetic risk for Alzheimer's disease from host to holobiont.

The gut microbiota is implicated in risk for Alzheimer's disease (AD). A study in Science reports that depleting gut bacteria in mice with genetic risk for AD reduces neuropathology in a sex-dependent manner. This is reversed by administering short-chain fatty acids, suggesting that specific bacterial metabolites increase susceptibility to AD.

The maternal microbiome promotes placental development in mice.

The maternal microbiome is an important regulator of gestational health, but how it impacts the placenta as the interface between mother and fetus remains unexplored. Here we show that the maternal gut microbiota supports placental development in mice. Depletion of the maternal gut microbiota restricts placental growth and impairs feto-placental vascularization. The maternal gut microbiota modulates metabolites in the maternal and fetal circulation. Short-chain fatty acids (SCFAs) stimulate angiogenesis-related tube formation by endothelial cells and prevent abnormalities in placental vascularization in microbiota-deficient mice. Furthermore, in a model of maternal malnutrition, gestational supplementation with SCFAs prevents placental growth restriction and vascular insufficiency. These findings highlight the importance of host-microbial symbioses during pregnancy and reveal that the maternal gut microbiome promotes placental growth and vascularization in mice.

Gut microbiota: A sweet tale of mice and microbes.

The gut microbiota regulates host metabolism and feeding behavior. A new study shows that microbiota depletion leads to sucrose overconsumption and increases motivation to obtain sucrose in mice, suggesting that the gut microbiota suppresses overconsumption of palatable foods.

Vagal interoception of microbial metabolites from the small intestinal lumen.

The vagus nerve is proposed to enable communication between the gut microbiome and brain, but activity-based evidence is lacking. Herein, we assess the extent of gut microbial influences on afferent vagal activity and metabolite signaling mechanisms involved. We find that mice reared without microbiota (germ-free, GF) exhibit decreased vagal afferent tone relative to conventionally colonized mice (specific pathogen-free, SPF), which is reversed by colonization with SPF microbiota. Perfusing non-absorbable antibiotics (ABX) into the small intestine of SPF mice, but not GF mice, acutely decreases vagal activity, which is restored upon re-perfusion with bulk lumenal contents or sterile filtrates from the small intestine and cecum of SPF, but not GF, mice. Of several candidates identified by metabolomic profiling, microbiome-dependent short-chain fatty acids, bile acids, and 3-indoxyl sulfate stimulate vagal activity with varied response kinetics, which is blocked by co-perfusion of pharmacological antagonists of FFAR2, TGR5, and TRPA1, respectively, into the small intestine. At the single-unit level, serial perfusion of each metabolite class elicits more singly responsive neurons than dually responsive neurons, suggesting distinct neuronal detection of different microbiome- and macronutrient-dependent metabolites. Finally, microbial metabolite-induced increases in vagal activity correspond with activation of neurons in the nucleus of the solitary tract, which is also blocked by co-administration of their respective receptor antagonists. Results from this study reveal that the gut microbiome regulates select metabolites in the intestinal lumen that differentially activate chemosensory vagal afferent neurons, thereby enabling microbial modulation of interoceptive signals for gut-brain communication. HIGHLIGHTS: Microbiota colonization status modulates afferent vagal nerve activityGut microbes differentially regulate metabolites in the small intestine and cecumSelect microbial metabolites stimulate vagal afferents with varied response kineticsSelect microbial metabolites activate vagal afferent neurons and brainstem neurons via receptor-dependent signaling.

Interactions between the gut microbiome and ketogenic diet in refractory epilepsy.

Epilepsy is one of the most common neurological diseases globally, afflicting approximately 50 million people worldwide. While many antiepileptic drugs exist, an estimated one-third of individuals do not respond to available medications. The high fat, low carbohydrate ketogenic diet (KD) has been used to treat refractory epilepsy in cases when existing antiepileptic drugs fail. However, there are many variations of the KD, each of which varies greatly in its efficacy and side effects. Increasing evidence suggests that interactions between the KD and gut microbiome may modulate the effects of the diet on host physiology. Herein, we review existing evidence of microbiome differences in epileptic individuals compared to healthy controls. We highlight in particular both clinical and animal studies revealing effects of the KD on the composition and function of the microbiome, as well as proof-of-concept animal studies that implicate the microbiome in the antiseizure effects of the KD. We further synthesize findings suggesting that variations in clinical KD formulations may differentially influence host physiology and discuss the gut microbial interactions with specific dietary factors that may play a role. Overall, understanding interactions between the gut microbiota and specific nutritional components of clinical KDs could reveal foundational mechanisms that underlie the effectiveness, variability, and side effects of different KDs, with the potential to lead to precision nutritional and microbiome-based approaches to treat refractory epilepsy.

STENSL: Microbial Source Tracking with ENvironment SeLection.

Microbial source tracking analysis has emerged as a widespread technique for characterizing the properties of complex microbial communities. However, this analysis is currently limited to source environments sampled in a specific study. In order to expand the scope beyond one single study and allow the exploration of source environments using large databases and repositories, such as the Earth Microbiome Project, a source selection procedure is required. Such a procedure will allow differentiating between contributing environments and nuisance ones when the number of potential sources considered is high. Here, we introduce STENSL (microbial Source Tracking with ENvironment SeLection), a machine learning method that extends common microbial source tracking analysis by performing an unsupervised source selection and enabling sparse identification of latent source environments. By incorporating sparsity into the estimation of potential source environments, STENSL improves the accuracy of true source contribution, while significantly reducing the noise introduced by noncontributing ones. We therefore anticipate that source selection will augment microbial source tracking analyses, enabling exploration of multiple source environments from publicly available repositories while maintaining high accuracy of the statistical inference. IMPORTANCE Microbial source tracking is a powerful tool to characterize the properties of complex microbial communities. However, this analysis is currently limited to source environments sampled in a specific study. In many applications there is a clear need to consider source selection over a large array of microbial environments, external to the study. To this end, we developed STENSL (microbial Source Tracking with ENvironment SeLection), an expectation-maximization algorithm with sparsity that enables the identification of contributing sources among a large set of potential microbial environments. With the unprecedented expansion of microbiome data repositories such as the Earth Microbiome Project, recording over 200,000 samples from more than 50 types of categorized environments, STENSL takes the first steps in performing automated source exploration and selection. STENSL is significantly more accurate in identifying the contributing sources as well as the unknown source, even when considering hundreds of potential source environments, settings in which state-of-the-art microbial source tracking methods add considerable error.

Are changes in the gut microbiome a contributor or consequence of autism-why not both?

Alterations in the gut microbiome have been associated with autism spectrum disorder (ASD), but whether they are a cause, effect, or confounder remains unclear. In a recent issue of Cell, Yap and colleagues report that ASD-associated microbiota changes are likely a consequence of low diet diversity.1.

The Gut Microbiome as a Regulator of the Neuroimmune Landscape.

The gut microbiome influences many host physiologies, spanning gastrointestinal function, metabolism, immune homeostasis, neuroactivity, and behavior. Many microbial effects on the host are orchestrated by bidirectional interactions between the microbiome and immune system. Imbalances in this dialogue can lead to immune dysfunction and immune-mediated conditions in distal organs including the brain. Dysbiosis of the gut microbiome and dysregulated neuroimmune responses are common comorbidities of neurodevelopmental, neuropsychiatric, and neurological disorders, highlighting the importance of the gut microbiome-neuroimmune axis as a regulator of central nervous system homeostasis. In this review, we discuss recent evidence supporting a role for the gut microbiome in regulating the neuroimmune landscape in health and disease.

Signaling inflammation across the gut-brain axis.

The brain and gastrointestinal tract are critical sensory organs responsible for detecting, relaying, integrating, and responding to signals derived from the internal and external environment. At the interface of this sensory function, immune cells in the intestines and brain consistently survey environmental factors, eliciting responses that inform on the physiological state of the body. Recent research reveals that cross-talk along the gut-brain axis regulates inflammatory nociception, inflammatory responses, and immune homeostasis. Here, we discuss molecular and cellular mechanisms involved in the signaling of inflammation across the gut-brain axis. We further highlight interactions between the gut and the brain in inflammation-associated diseases.

Alterations in the gut microbiota contribute to cognitive impairment induced by the ketogenic diet and hypoxia.

Many genetic and environmental factors increase susceptibility to cognitive impairment (CI), and the gut microbiome is increasingly implicated. However, the identity of gut microbes associated with CI risk, their effects on CI, and their mechanisms remain unclear. Here, we show that a carbohydrate-restricted (ketogenic) diet potentiates CI induced by intermittent hypoxia in mice and alters the gut microbiota. Depleting the microbiome reduces CI, whereas transplantation of the risk-associated microbiome or monocolonization with Bilophila wadsworthia confers CI in mice fed a standard diet. B. wadsworthia and the risk-associated microbiome disrupt hippocampal synaptic plasticity, neurogenesis, and gene expression. The CI is associated with microbiome-dependent increases in intestinal interferon-gamma (IFNg)-producing Th1 cells. Inhibiting Th1 cell development abrogates the adverse effects of both B. wadsworthia and environmental risk factors on CI. Together, these findings identify select gut bacteria that contribute to environmental risk for CI in mice by promoting inflammation and hippocampal dysfunction.

Malnutrition and the microbiome as modifiers of early neurodevelopment.

Malnutrition refers to a dearth, excess, or altered differential ratios of calories, macronutrients, or micronutrients. Malnutrition, particularly during early life, is a pressing global health and socioeconomic burden that is increasingly associated with neurodevelopmental impairments. Understanding how perinatal malnutrition influences brain development is crucial to uncovering fundamental mechanisms for establishing behavioral neurocircuits, with the potential to inform public policy and clinical interventions for neurodevelopmental conditions. Recent studies reveal that the gut microbiome can mediate dietary effects on host physiology and that the microbiome modulates the development and function of the nervous system. This review discusses evidence that perinatal malnutrition alters brain development and examines the maternal and neonatal microbiome as a potential contributing factor.