microbiome

Defining Microbial and Host Pathways Driving Asymptomatic C. difficile Colonization Associated with Aging and High-Sugar Diets

SUMMARY Clostridioides difficile infection (CDI) is a leading cause of healthcare-associated diarrhea, with rising incidence in community settings and a growing burden of asymptomatic colonization. Asymptomatic car- riers, particularly among the elderly and individuals consuming high-sugar diets, represent a critical but underexplored reservoir for transmission and disease progression. This proposal introduces novel, anti- biotic-independent mouse models demonstrating that both dietary sugar and aging independently pro- mote asymptomatic C. difficile colonization. We hypothesize that these factors disrupt colonization re- sistance (CR) through distinct but overlapping microbial, metabolic, and immune pathways. In Aim 1, we will define how traditional and emerging dietary sugars alter the gut environment to permit C. difficile colonization using in vitro bioreactors and in vivo models. Aim 2 will identify age-associated changes in microbiota and mucosal immunity that impair CR, using longitudinal studies and fecal micro- biota transfer. Aim 3 will functionally validate C. difficile genes upregulated during asymptomatic carriage using CRISPR-Cas9 mutants in both sugar- and age-induced models. This integrative, multi-omics approach will uncover the mechanisms enabling asymptomatic colonization and identify microbial and host targets for intervention. The findings will inform microbiome-based strat- egies to prevent CDI in vulnerable populations and shift current paradigms in CDI risk assessment and prevention.

Pilot and Feasibility Program

PILOT AND FEASIBILITY PROGRAM: PROJECT SUMMARY The goal of the Cedars-Sinai Digestive Diseases Research Center (CSDDRC) Pilot and Feasibility (P&F) Program is to provide monetary support, expertise, and technical support to advance innovative basic, translational, and clinical research that matches the overall goal and themes of the Center. The central theme of the CSDDRC is mechanisms and measurements of the fibroinflammatory response in gastrointestinal (GI) tissues, which reflects Center members’ research in three subthemes: 1) Gut Microbiome, 2) Gastrointestinal (GI) and Liver Metabolism, and 3) GI and Liver Injury. The mission of CSDDRC P&F Program is to support new investigators, established investigators who are new to digestive and liver disease research, and established digestive and liver disease investigators who want to start new or collaborative research that promises to lead to a paradigm shift in the digestive diseases field. In partnership with the Enrichment Program, we will provide guidance for P&F awardees in the form of mentorship and collaboration opportunities. The CSDDRC Biomedical Research Cores will also support P&F awardees, facilitating rapid progress of their new and collaborative digestive and liver disease research. The P&F Program’s outcome measures will include the number of high-impact research publications, grant applications, and subsequent extramural funding for P&F awardees. We will accomplish our goals through the following three specific aims. Aim 1 will solicit research proposals from P&F candidates whose proposed research aligns with the central theme and the subthemes of the CSDDRC. We will advertise P&F support widely across campuses, in addition to contacting department/institute directors to solicit their recommendations for promising young and established investigators who are interested in working in digestive and liver diseases. Aim 2 will select pilot project applications that meet CSDDRC P&F Program goals using rigorous review criteria. Each year, the P&F Program will select four pilot projects to be funded by the P30 grant and matched by institutional support. Submitted applications will be peer- reviewed and preliminarily scored based on the NIH review format by three local expert reviewers. Subsequently, after oral presentations by the P&F applicants, the External Advisory Board (EAB) members will undertake a second round of review, scoring, and discussion at the P&F Program Review meeting following the CSDDRC Annual Symposium. Funding decisions will be made during the P&F Program Review meeting. Aim 3 will assist P&F project investigators with career development and obtaining extramural funding for digestive disease research. P&F awardees will benefit from the Enrichment Program’s well-organized mentoring structure, led by experienced members of the CSDDRC, which includes the Grants-in-Progress Mentoring Program, Gastrointestinal Research-in-Progress meetings, and grant application workshops. P&F awardees will also be mentored through direct interactions with P&F Program Directors, Core Directors, members of the Internal Advisory Board and EAB, and individual or collaborative mentor teams.

Investigating the nonlinear complex dynamics of the tuft cell-microbiome cross-talk: the impact of feedback loops on immune regulation, microbial modulation and response to tissue insults

Project Abstract Tuft cells (TCs) are specialized chemosensory epithelial cells that are emerging as critical regulators of intestinal homeostasis. Named over 70 years ago based on their distinct morphology, a defined function for TCs was only elucidated in the last decade. TCs in the small intestine sense succinate from helminths to initiate type 2 immune responses that mediate parasite expulsion. Recently, we discovered a novel physiologic function for TCs in the colon, where their role had been considered minimal. Succinate, a key microbial metabolite, is produced by colonic microbiota as both a precursor to other metabolites and a cross-feeding fuel source for pathogens. TCs respond to succinate by secreting interleukin-25 (IL-25), which activates type 2 cytokine- producing lymphocytes (T2Ls), amplifying TC expansion and reinforcing barrier function. We recently demonstrated that this SPB–TC–IL-25–T2L feedback loop is essential for protection against pathogen-induced colitis. Our preliminary data further suggest that TCs actively promote colonization by succinate-producing bacteria (SPBs), establishing positive feedback on TC-supporting microbes, while other epithelial cells such as goblet cells (GCs) and Paneth cells (PCs) may exert complementary or counterbalancing influences. Supported by new modeling insights, we hypothesize that these epithelial–immune–microbiome interactions form coordinated feedback loops that collectively optimize intestinal resilience. These loops may create a dynamic, multi-stable system that flexibly transitions between homeostatic and hyperplastic states, buffering against microbial fluctuations and pathogenic insults while preventing uncontrolled type 2 inflammation. Using a combination of mathematical modeling and experimental validation, we will develop a multi- layered systems framework to explore how epithelial–immune–microbial feedbacks shape resilience or breakdown in clinically relevant models of colonic infection and inflammation. Our three Aims will (1) develop, calibrate, and validate a mathematical model that integrates TCs, GCs, PCs, SPBs, and SCBs; (2) define the immunological circuits governing epithelial–microbiome equilibrium; and (3) determine how epithelial feedbacks regulate microbial community structure and resilience. In line with NIH’s new initiative to prioritize human-based research, our proposal combines computational modeling, human colonic organoids, and complementary mouse models. Organoid experiments will provide human-relevant data for model calibration, while in vivo studies validate systemic predictions, ensuring both rigor and translational relevance while minimizing reliance on animal models. This work will generate interoperable models that integrate epithelial, microbial, and immune networks, providing predictive insight into intestinal outcomes under homeostatic, infectious, and inflammatory conditions and informing therapeutic strategies for microbiome-targeted interventions.

Systems Biology of Early Atopy: Role of Human Milk (SunBEAm-Milk)

Surprisingly little is known about the effect of breastfeeding (BF) on infant immune system development besides an effect on the gut microbiome, but its impact on metabolites and Tregs could support protection against food allergy (FA). BF is currently recommended to prevent the development of allergic diseases, especially asthma/recurrent wheezing and AD in early childhood, but firm conclusions could not be drawn regarding FA due to high heterogeneity and low quality of studies. Reverse causation, recall bias and the poor accuracy of outcome assessment are significant limitations. Most are inadequately powered to specific FA; however, a recent study showed that exclusively BF infants had lower odds of egg, sesame, and peanut allergies. Importantly, immunomodulatory composition of HM varies between mothers, which has not been taken into consideration. For over two decades we have been developing methods to assess immunomodulatory factors in the complex matrix of HM and their association with infant FA. We have shown that high levels of HM total and specific IgA are associated with protection against cow’s milk allergy, but it is unclear whether HM IgA is responsible for or is a biomarker of the vertical transfer of protection. Infant fecal and systemic IgA levels during breastfeeding and after weaning are also elevated in infants at low risk for atopic disease raising the question of whether HM factors such as cytokines can promote IgA production in infants. Consistent with this, we showed that HM cytokines, such as APRIL, induce IgA production in naïve infant B cells, and infants receiving HM with higher levels of APRIL had lower incidence of allergic disease. Finally, lower levels of several HM fatty acids including short-chain fatty acids and DHA were associated with FA. While some these factors were are associated with maternal atopic disease, several of them are not and suggest a role for diet instead. The System Biology of Early Atopy (SunBEAm) population-based cohort of 2500 mother-infant pairs is >50% recruited and provides an unprecedented opportunity to assess association of HM feeding and immune factors in HM with development of infant immune system and FA/AD. The Common Sample comprises a subset of 100 dyads with FA, 100 with FA+AD, 100 with AD, 100 with no FA or AD and more extensively profiled biological data. Utilizing all 2-month HM samples available in the Common Sample, we will assess levels of immune factors in HM and their association with maternal/infant characteristics (Aim 1). Utilizing data from the whole cohort, we will assess the association between HM vs formula feeding on well-defined FA/AD further adjusted based on high vs low levels of HM immune components in the Common Sample (Aim 2b). Finally, we will examine the immune cell and epithelial effects of HM on infant immune markers and intestinal organoids (Aim 3). Key findings will be validated in an independent birth cohort. The ultimate goal is to uncover protective properties of BF and HM in FA and subsequent design of policies and prevention strategies to address the increasing rates of FA.

Host-pathogen-microbiome interactions in Mycoplasma genitalium pathology and treatment: experiments in a 3D organotypic cervical epithelium model to strengthen clinical guidelines

ABSTRACT Mycoplasma genitalium (MG) is an emerging sexually transmitted pathogen whose clinical outcomes in women are poorly understood. Unlike other bacterial sexually transmitted infections (STI), the CDC does not recommend MG screening for asymptomatic women because it is unclear how often asymptomatic MG leads to adverse reproductive outcomes like cervicitis, which can lead to further adverse outcomes, including pelvic inflammatory disease, infertility, and ectopic pregnancy. Epidemiologic data on MG and cervicitis are mixed, and mechanistic data primarily come from models that did not faithfully recapitulate in vivo cervical microphysiological conditions. Key elements they lacked are cervical mucus, which mediates host-pathogen interactions, and the cervicovaginal microbiota. The microbiota appears to contribute to MG outcomes, and our preliminary epidemiologic data indicate that MG and bacterial vaginosis (BV) may synergize to promote cervicitis. MG care is further complicated by its ongoing rise in antibiotic resistance. Resistance-guided therapy and novel antibiotics improve treatment outcomes, but these are not available in the US. Recent clinical and in vitro data indicate that metronidazole and tinidazole, two antibiotics that are available in the US and used to treat BV, may hold promise for improving MG treatment outcomes. The overall objective of this R21 is to generate robust experimental data to clarify MG pathology, evaluate potential therapies, and inform more thorough and actionable clinical recommendations. We developed an innovative in vitro 3D organotypic model of the cervical epithelium that is ideally suited for investigating MG pathology, host-MG-microbiota interactions, and potential therapies. The model uses primary human cervical cells and better recapitulates cervical epithelial structure and physiology (including cervical mucus production) than prior 2D models. It also allows for simultaneous STI infection and co- culture of live cervicovaginal microbiota. Using the 3D organotypic cervical epithelium model, we will determine if MG causes microbiota-dependent cervical epithelial damage, a hallmark of cervicitis (Aim 1), and we will test if metronidazole and tinidazole arrest MG infection (Aim 2). In both Aims, we will interrogate the potential mediating role of the microbiota by inoculating models with live representative cervicovaginal microbiota, and we will assess host-MG-microbiota interactions via transcriptomics. We hypothesize that a polymicrobial BV-like microbiota will exacerbate MG-induced cervical epithelial damage, and removal of a polymicrobial BV microbiota will partially mediate metronidazole’s and tinidazole’s anti-MG activity. The proposed Aims have high translational potential and will provide crucial pre-clinical evidence to inform more thorough and actionable MG testing and treatment guidelines and improve reproductive health outcomes. This R21 will generate some of the first experimental data on MG-host and MG-microbiota interactions, which we will use to support an R01 to validate these interactions during in vivo MG infection and identify novel therapeutic targets for MG.

From the guts to the brain through adaptive immunity in the prevention of Alzheimer’ disease

Dr. Pasinetti is the Saunders Family Chair and Professor of Neurology at Icahn School of medicine at Mount Sinai, New York. His studies allowed him to develop novel therapeutic approaches through investigation of preventable risk factors including mood disorders in the promotion of resilience against neurodegenerative disorder. In his presentation Dr. Pasinetti will discuss novel concepts about the gut-brain axis in mechanisms associated to peripheral adaptive immunity as therapeutic targets to mitigate the onset and the progression of Alzheimer’s disease and other form of dementia.

A microbiome-dependent gut-brain pathway regulates motivation for exercise

The person-to-person transmission landscape of the gut and oral microbiomes

Gut Feelings: The Microbiome as a Key Regulator of Brain & Behaviour Across the Lifespan

Western diet consumption and memory impairment: what, when, and how?

Habitual consumption of a “Western diet”, containing higher than recommended levels of simple sugars and saturated fatty acids, is associated with cognitive impairments in humans and in various experimental animal models. Emerging findings reveal that the specific mnemonic processes that are disrupted by Western diet consumption are those that rely on the hippocampus, a brain region classically linked with memory control and more recently with the higher-order control of food intake. Our laboratory has established rat models in which excessive consumption of different components of a Western diet during the juvenile and adolescent periods of development yields long-term impairments in hippocampal-dependent memory function without concomitant increases in total caloric intake, body weight, or adiposity. Our ongoing work is investigating alterations in the gut microbiome as a potential underlying neurobiological mechanism linking early life unhealthy dietary factors to adverse neurocognitive outcomes.

Gut-brain signaling as a driver of behavior and gene expression in a mouse model for autism spectrum disorder

In vitro bioelectronic models of the gut-brain axis

The human gut microbiome has emerged as a key player in the bidirectional communication of the gut-brain axis, affecting various aspects of homeostasis and pathophysiology. Until recently, the majority of studies that seek to explore the mechanisms underlying the microbiome-gut-brain axis cross-talk relied almost exclusively on animal models, and particularly gnotobiotic mice. Despite the great progress made with these models, various limitations, including ethical considerations and interspecies differences that limit the translatability of data to human systems, pushed researchers to seek for alternatives. Over the past decades, the field of in vitro modelling of tissues has experienced tremendous growth, thanks to advances in 3D cell biology, materials, science and bioengineering, pushing further the borders of our ability to more faithfully emulate the in vivo situation. Organ-on-chip technology and bioengineered tissues have emerged as highly promising alternatives to animal models for a wide range of applications. In this talk I’ll discuss our progress towards generating a complete platform of the human microbiota-gut-brain axis with integrated monitoring and sensing capabilities. Bringing together principles of materials science, tissue engineering, 3D cell biology and bioelectronics, we are building advanced models of the GI and the BBB /NVU, with real-time and label-free monitoring units adapted in the model architecture, towards a robust and more physiologically relevant human in vitro model, aiming to i) elucidate the role of microbiota in the gut-brain axis communication, ii) to study how diet and impaired microbiota profiles affect various (patho-)physiologies, and iii) to test personalised medicine approaches for disease modelling and drug testing.

Gestational exposure to environmental toxins, infections, and stressors are epidemiologically linked to neurodevelopmental disorders

Gestational exposure to environmental toxins, infections, and stressors are epidemiologically linked to neurodevelopmental disorders with strong male-bias, such as autism spectrum disorder. We modeled some of these prenatal risk factors in mice, by co-exposing pregnant dams to an environmental pollutant and limited-resource stress, which robustly dysregulated the maternal immune system. Male but not female offspring displayed long-lasting behavioral abnormalities and alterations in the activity of brain networks encoding social interactions, along with disruptions of gut structure and microbiome composition. Cellularly, prenatal stressors impaired microglial synaptic pruning in males during early postnatal development. Precise inhibition of microglial phagocytosis during the same critical period mimicked the impact of prenatal stressors on the male-specific social deficits. Conversely, modifying the gut microbiome rescued the social and cellular deficits, indicating that environmental stressors alter neural circuit formation in males via impairing microglia function during development, perhaps via a gut-brain disruption.

Microbiome and behaviour: Exploring underlying mechanisms

Environmental insults alter brain function and behaviour inboth rodents and people. One putative underlying mechanism that has receivedsubstantial attention recently is the gut microbiota, the ecosystem ofsymbiotic microorganisms that populate the intestinal tract, which is known toplay a role in brain health and function via the gut-brain axis. Two keyenvironmental insults known to affect both brain function and behaviour, andthe gut microbiome, are poor diet and psychological stress. While there isstrong evidence for interactions between the microbiome and host physiology inthe context of chronic stress, little is known about the role of the microbiomein the host response to acute stress. Determining the underlying mechanisms bywhich stress may provoke functional changes in the gut and brain is criticalfor developing therapeutics to alleviate adverse consequences of traumaticstress.

Gut Feelings: The Microbiota-Gut-Brain Axis Across the Lifespan

The microbiota-gut-brain axis is emerging as a research area of increasing interest for those investigating the biological and physiological basis of brain development and behaviour during early life, adolescence & ageing. The routes of communication between the gut and brain include the vagus nerve, the immune system, tryptophan metabolism, via the enteric nervous system or by way of microbial metabolites such as short chain fatty acids. Studies in animal models have shown that the development of an appropriate stress response is dependent on the microbiota. Developmentally, a variety of factors can impact the microbiota in early life including mode of birth delivery, antibiotic exposure, mode of nutritional provision, infection, stress as well as host genetics. Recently, the gut microbiota has been implicated in regulating the stress response, and social behaviour. Moreover, fundamental brain processes from adult hippocampal neurogenesis to myelination to microglia activation have been shown to be regulated by the microbiome. Further studies will focus on understanding the mechanisms underlying such brain effects and how they can be exploited by microbiota-targeted interventions including ‘psychobiotics’ and diet

New Strategies and Approaches to Tackle and Understand Neurological Disorder

Broadly, the Mauro Costa-Mattioli laboratory (The MCM Lab) encompasses two complementary lines of research. The first one, more traditional but very important, aims at unraveling the molecular mechanisms underlying memory formation (e.g., using state-of-the-art molecular and cell-specific genetic approaches). Learning and memory disorders can strike the brain during development (e.g., Autism Spectrum Disorders and Down Syndrome), as well as during adulthood (e.g., Alzheimer’s disease). We are interested in understanding the specific circuits and molecular pathways that are primarily targeted in these disorders and how they can be restored. To tackle these questions, we use a multidisciplinary, convergent and cross-species approach that combines mouse and fly genetics, molecular biology, electrophysiology, stem cell biology, optogenetics and behavioral techniques. The second line of research, more recent and relatively unexplored, is focused on understanding how gut microbes control CNS driven-behavior and brain function. Our recent discoveries, that microbes in the gut could modulate brain function and behavior in a very powerful way, have added a whole new dimension to the classic view of how complex behaviors are controlled. The unexpected findings have opened new avenues of study for us and are currently driving my lab to answer a host of new and very interesting questions: - What are the gut microbes (and metabolites) that regulate CNS-driven behaviors? Would it be possible to develop an unbiased screening method to identify specific microbes that regulate different behaviors? - If this is the case, can we identify how members of the gut microbiome (and their metabolites) mechanistically influence brain function? - What is the communication channel between the gut microbiota and the brain? Do different gut microbes use different ways to interact with the brain? - Could disruption of the gut microbial ecology cause neurodevelopmental dysfunction? If so, what is the impact of disruption in young and adult animals? - More importantly, could specific restoration of selected bacterial strains (new generation probiotics) represent a novel therapeutic approach for the targeted treatment of neurodevelopmental disorders? - Finally, can we develop microbiota-directed therapeutic foods to repair brain dysfunction in a variety of neurological disorders?

Interactions between the microbiome and nervous system during early development

The gut microbiota is emerging as an important modulator of brain function and behavior, as several recent discoveries reveal substantial effects of the microbiome on neurophysiology, neuroimmunity and animal behavior. Despite these findings supporting a “microbiome-gut-brain axis”, the molecular and cellular mechanisms that underlie interactions between the gut microbiota and brain remain poorly understood. To uncover these, the Hsiao laboratory is mining the human microbiota for microbial modulators of host neuroactive molecules, investigating the impact of microbiota-immune system interactions on neurodevelopment and examining the microbiome as an interface between gene-environment interactions in neurological diseases. In particular, our research on effects of the maternal microbiome on offspring development in utero are revealing novel interactions between microbiome-dependent metabolites and fetal thalamocortical axonogenesis. Overall, we aim to dissect biological pathways for communication between the gut microbiota and nervous system, toward understanding fundamental interactions between physiological systems that impact brain and behavior.

Modulation of C. elegans behavior by gut microbes

We are interested in understanding how microbes impact the behavior of host animals. Animal nervous systems likely evolved in environments richly surrounded by microbes, yet the impact of bacteria on nervous system function has been relatively under-studied. A challenge has been to identify systems in which both host and microbe are amenable to genetic manipulation, and which enable high-throughput behavioral screening in response to defined and naturalistic conditions. To accomplish these goals, we use an animal host — the roundworm C. elegans, which feeds on bacteria — in combination with its natural gut microbiome to identify inter-organismal signals driving host-microbe interactions and decision-making. C. elegans has some of the most extensive molecular, neurobiological and genetic tools of any multicellular eukaryote, and, coupled with the ease of gnotobiotic culture in these worms, represents a highly attractive system in which to study microbial influence on host behavior. Using this system, we discovered that commensal bacterial metabolites directly modulate nervous system function of their host. Beneficial gut microbes of the genus Providencia produce the neuromodulator tyramine in the C. elegans intestine. Using a combination of behavioral analysis, neurogenetics, metabolomics and bacterial genetics we established that bacterially produced tyramine is converted to octopamine in C. elegans, which acts directly in sensory neurons to reduce odor aversion and increase sensory preference for Providencia. We think that this type of sensory modulation may increase association of C. elegans with these microbes, increasing availability of this nutrient-rich food source for the worm and its progeny, while facilitating dispersal of the bacteria.

Depletion of Gut Microbiome and Exposure to Repeat Mild Traumatic Brain Injuries Modifies Social Behaviour and Neuropathological Changes Within the Adolescent Brain

Dissecting the contribution of host genetics and the microbiome in complex behaviors

A Gut-Brain Connection: Gut Microbiome Composition is Differentially Altered After Repetitive Mild Traumatic Brain Injury in Adolescent and Adult Rats

Gut microbiome depletion leads to altered neural dynamics and metabolism in the dorsal CA1 field of the hippocampus

Population-Level Links between Schizophrenia and the Gut Microbiome

Shotgun metagenomics reveals taxonomic and functional changes in the salivary microbiome in young adults with depression

Studies on Hippocampal Histoarchitecture and Neurochemistry in Psychologically Stressed Rats Given Gut Microbiome Supplementation

APOE genotype effects on the human gut microbiome

FENS Forum 2024

Entorhinal cortex as a hub in the gut microbiome–brain axis

FENS Forum 2024

Microbiome depletion alters spatial cognition and hippocampal place cell ensembles

FENS Forum 2024

Gut microbiome metabolites and Alzheimer’s disease

FENS Forum 2024

Navigating the challenges of investigating the influence of gestational gut microbiome disruption and perinatal asphyxia on neurodevelopmental reflexes in rat offspring

FENS Forum 2024

Understanding the influence of the gut microbiome on the mesolimbic system and its response to nicotine

FENS Forum 2024