Host-commensal Interactions Research Articles

Sugar-rich foods exacerbate antibiotic-induced microbiome injury.

Intestinal microbiota composition is implicated in several diseases; understanding the factors that influence it are key to elucidating host-commensal interactions and to designing microbiome-targeted therapies. We quantified how diet influences microbiome dynamics in hospitalized patients. We recorded 9,419 meals consumed by 173 patients undergoing hematopoietic cell transplantation and profiled the microbiome in 1,009 longitudinally collected stool samples from 158 of them. Caloric intake was correlated with fecal microbiota diversity. Bayesian inference revealed associations between intake of sweets or sugars during antibiotic exposure with microbiome disruption, as assessed by low diversity or expansion of the pathobiont Enterococcus. We validated this observation experimentally, finding that sucrose exacerbated antibiotic-induced Enterococcus expansion in mice. Taken together, our results suggest that avoiding sugar-rich foods during antibiotic treatment may reduce microbiome injury.

Unveiling the immune dynamics of Neisseria persistent oral colonization.

Commensal bacteria are crucial in maintaining host physiological homeostasis, immune system development, and protection against pathogens. Despite their significance, the factors influencing persistent bacterial colonization and their impact on the host still need to be fully understood. Animal models have served as valuable tools to investigate these interactions, but most have limitations. The bacterial genus Neisseria, which includes both commensal and pathogenic species, has been studied from a pathogenicity to humans perspective but lacks models that study immune responses in the context of long-term persistence. Neisseria musculi, a recently described natural commensal of mice, offers a unique opportunity to study long-term host-commensal interactions. In this study, for the first time, we have used this model to study the transcriptional, phenotypic, and functional dynamics of immune cell signatures in the mucosal and systemic tissue of mice in response to N. musculi colonization. We found key genes and pathways vital for immune homeostasis in palate tissue, validated by flow cytometry of immune cells from the lung, blood, and spleen. This study offers a novel avenue for advancing our understanding of host-bacteria dynamics and may provide a platform for developing efficacious interventions against mucosal persistence by pathogenic Neisseria.

Age-related dysregulation of intestinal epithelium fucosylation is linked to an increased risk of colon cancer.

Colon cancer affects people of all ages. However, its frequency, as well as the related morbidity and mortality, are high among older adults. The complex physiological changes in the aging gut substantially limit the development of cancer therapies. Here, we identify a potentially unique intestinal microenvironment that is linked with an increased risk of colon cancer in older adults. Our findings show that aging markedly influenced persistent fucosylation of the apical surfaces of intestinal epithelial cells, which resulted in a favorable environment for tumor growth. Furthermore, our findings shed light on the importance of the host-commensal interaction, which facilitates the dysregulation of fucosylation and promotes tumor growth as people get older. We analyzed colonic microbial populations at the species level to find changes associated with aging that could contribute to the development of colon cancer. Analysis of single-cell RNA-sequencing data from previous publications identified distinct epithelial cell subtypes involved in dysregulated fucosylation in older adults. Overall, our study provides compelling evidence that excessive fucosylation is associated with the development of colon cancer, that age-related changes increase vulnerability to colon cancer, and that a dysbiosis in microbial diversity and metabolic changes in the homeostasis of older mice dysregulate fucosylation levels with age.

Implications of metabolism on multi-systems healthy aging across the lifespan.

Aging is increasingly thought to involve dysregulation of metabolism in multiple organ systems that culminate in decreased functional capacity and morbidity. Here, we seek to understand complex interactions among metabolism, aging, and systems-wide phenotypes across the lifespan. Among 2469 adults (mean age 74.7 years; 38% Black) in the Health, Aging and Body Composition study we identified metabolic cross-sectionally correlates across 20 multi-dimensional aging-related phenotypes spanning seven domains. We used LASSO-PCA and bioinformatic techniques to summarize metabolome-phenome relationships and derive metabolic scores, which were subsequently linked to healthy aging, mortality, and incident outcomes (cardiovascular disease, disability, dementia, and cancer) over 9 years. To clarify the relationship of metabolism in early adulthood to aging, we tested association of these metabolic scores with aging phenotypes/outcomes in 2320 participants (mean age 32.1, 44% Black) of the Coronary Artery Risk Development in Young Adults (CARDIA) study. We observed significant overlap in metabolic correlates across the seven aging domains, specifying pathways of mitochondrial/cellular energetics, host-commensal metabolism, inflammation, and oxidative stress. Across four metabolic scores (body composition, mental-physical performance, muscle strength, and physical activity), we found strong associations with healthy aging and incident outcomes, robust to adjustment for risk factors. Metabolic scores for participants four decades younger in CARDIA were related to incident cardiovascular, metabolic, and neurocognitive performance, as well as long-term cardiovascular disease and mortality over three decades. Conserved metabolic states are strongly related to domain-specific aging and outcomes over the life-course relevant to energetics, host-commensal interactions, and mechanisms of innate immunity.

272. Dissecting Host-Commensal Interactions During Early Life to Identify Mechanisms of Protection Against Autoimmune Diabetes

Abstract Background Major Histocompatibility Complex (MHC) and Human Leukocyte Antigen (HLA) loci have strong genetic linkage with type 1 diabetes (T1D) in mice and humans, respectively. The diabetes-prone non-obese diabetic (NOD) strain of mice have a unique MHC-II locus with a distinct MHC-II A molecule (Ag7) and lack expression of the MHC-II E molecule. Expression of this MHC-II A molecule is associated with development of T1D, whereas transgenic restoration of the MHC-II E molecule dominantly protects against T1D. The Silverman laboratory recently demonstrated that MHC-II E molecule expression selects for a diabetes-protective intestinal microbiota in early life though a key knowledge gap remains: how do these two factors — MHC-II molecules and commensal microbiota — work together during a critical early-life period of microbiome and immune system ontogeny to prevent T1D? To address this question, the Silverman laboratory developed a gnotobiotic mouse model by designing a microbial community consisting of 9 intestinal microbes cultured from these diabetes-protected (Ea16/NOD) mice – called “PedsCom”. This gnotobiotic model allows for mechanistic, well-controlled studies of interactions between commensal microbes and the developing immune system. Methods We used flow cytometry to sort commensal bacteria from PedsCom-colonized NOD and Ea16/NOD mice into IgA-coated and IgA-uncoated populations. We employed species-specific multiplex qPCR to quantify relative abundance of each PedsCom microbe in these sorted populations. Results Two microbes, K. cowanii and L. murinus, were preferentially IgA bound in both NOD and Ea16/NOD mice. L. johnsonii, A. caccae, and S. xylosus were preferentially IgA bound only in the presence of MHC-II E molecule expression. Many of the highly IgA coated microbes (K. cowanii, L. murinus, L, johnsonii, and A. caccae) translocate to the mesenteric lymph nodes. Conclusion: We propose that MHC-II expression facilitates specific mucosal IgA responses, that MHC-II E expression allows for additional epitope recognition amongst PedsCom members which may potentiate this effect, and that preferential IgA coating may promote contact with mucosa-associated lymphoid tissues as early steps in tolerogenic immune system ontogeny that protects against development of T1D. Disclosures All Authors: No reported disclosures

A physiologically relevant culture platform for long-term studies of in vitro gingival tissue

There is a clinical need to understand the etiologies of periodontitis, considering the growing socio-economic impact of the disease. Despite recent advances in oral tissue engineering, experimental approaches have failed to develop a physiologically relevant gingival model that combines tissue organization with salivary flow dynamics and stimulation of the shedding and non-shedding oral surfaces. Herein, we develop a dynamic gingival tissue model composed of a silk scaffold, replicating the cyto-architecture and oxygen profile of the human gingiva, along with a saliva-mimicking medium that reflected the ionic composition, viscosity, and non-Newtonian behavior of human saliva. The construct was cultured in a custom designed bioreactor, in which force profiles on the gingival epithelium were modulated through analysis of inlet position, velocity and vorticity to replicate the physiological shear stress of salivary flow. The gingival bioreactor supported the long-term in vivo features of the gingiva and improved the integrity of the epithelial barrier, critical against the invasion of pathogenic bacteria. Furthermore, the challenge of the gingival tissue with P. gingivalis lipopolysaccharide, as an in vitro surrogate for microbial interactions, indicated a greater stability of the dynamic model in maintaining tissue homeostasis and, thus, its applicability in long-term studies. The model will be integrated into future studies with the human subgingival microbiome to investigate host-pathogen and host-commensal interactions. Statement of significanceThe major societal impact of human microbiome had reverberated up to the establishment of the Common Fund's Human Microbiome Project, that has the intent of studying the role of microbial communities in human health and diseases, including periodontitis, atopic dermatitis, or asthma and inflammatory bowel disease. In addition, these chronic diseases are emergent drivers of global socioeconomic status. Not only common oral diseases have been shown to be directly correlated with several systemic conditions, but they are differentially impacting some racial/ethnic and socioeconomic groups. To address this growing social disparity, the development of in vitro gingival model would provide a time and cost-effective experimental platform, able to mimic the spectrum of periodontal disease presentation, for the identification of predictive biomarkers for early-stage diagnosis.

Host and microbe adaptation underlying true fungal commensalism

Abstract Fungi are found ubiquitously in the mammalian gut however the role of commensal fungi in the host is poorly understood. Laboratory mice are used to model host-fungi interactions however due to ultra-clean housing they do not harbor fungi. The human commensal fungus Candida albicans is widely studied to dissect host-commensal fungi interactions however prior dysbiosis of commensal bacteria is required to colonize laboratory mice. Insights from such forced host-fungal interactions are unsuitable for extrapolating mechanisms underlying fungal commensalism and its breakdown. To discover the natural fungal commensal of mice, we used pet-store “dirty” mice. We found that pet-store mice have a high fungal burden in their feces and their gut is predominantly colonized by single species of fungus, Kazachstania pintolopesii. Furthermore, we found that K. pintolopesii isolated from pet-store mice, stably colonized laboratory mice to high levels in the presence of an intact immune system and commensal bacteria. Laboratory mice colonized with K. pintolopesii exhibited increased neutrophil frequency in blood but did not show any pathological symptoms. Surprisingly, even a systemic K. pintolopesii challenge did not show any pathology in laboratory mice indicating unique adaptations of this fungus to the murine host. Remarkably, we found that laboratory mice stably colonized with K. pintolopesii are significantly protected from systemic C. albicans challenge suggesting that commensal fungi promote systemic antifungal responses in their host. In summary, our work established a novel unmanipulated murine model of fungal commensalism and provide unique insight into cellular and molecular mechanisms of mammalian host and fungal mutualism. This research was supported by grants from NIH (R01 DK113265), Searle Scholars program, and AAI Careers in Immunology Fellowship.

Bacteria require phase separation for fitness in the mammalian gut.

Therapeutic manipulation of the gut microbiota holds great potential for human health. The mechanisms bacteria use to colonize the gut therefore present valuable targets for clinical intervention. We now report that bacteria use phase separation to enhance fitness in the mammalian gut. We establish that the intrinsically disordered region (IDR) of the broadly and highly conserved transcription termination factor Rho is necessary and sufficient for phase separation in vivo and in vitro in the human commensal Bacteroides thetaiotaomicron. Phase separation increases transcription termination by Rho in an IDR-dependent manner. Moreover, the IDR is critical for gene regulation in the gut. Our findings expose phase separation as vital for host-commensal bacteria interactions and relevant for novel clinical applications.

Association of HLA-DPB1, NLRP10, OVOL1, and ABCC11 with the axillary microbiome in a Japanese population

BackgroundThe distinct diversity of the human skin microbiome depends not only on the body site but also the individual. Host-commensal interactions have been described for the gut microbiome, but little is known about the epidermal microbiome. ObjectiveThe present study investigated whether genetic variants associated with skin traits affect the axillary microbiome. MethodsEight skin trait-related single nucleotide polymorphisms and HLA-A, -B, -C, and –DPB1 were genotyped in 186 Japanese males. From axillary swabs, the intensity of a representative axillary odor, trans (E) isomer of 3-methyl-2-hexenoic acid (E3M2H), was quantified with gas chromatography-tandem mass spectrometry analysis, the diversity of the axillary microbiome was evaluated with a 16 s rRNA metagenomic approach, and the association of these characteristics was assessed statistically. ResultsA risk allele for atopic dermatitis of rs878860 in NLRP10 and the allele for wet earwax of rs17822931 in ABCC11 decreased the relative abundance of Corynebacterium. Conversely, these alleles increased the relative abundance of Staphylococcus. Metagenomic analysis revealed that β-diversity showed significant dissimilarity at the weighted Unifrac distance between minor allele carrier and non-carrier groups in HLA‐DPB1*05:01, rs17822931, and rs878860. HLA‐DPB1*04:01, HLA‐DPB1*05:01, and rs17822931 were associated with E3M2H. ConclusionsWe identified novel candidate loci associated with the axillary microbiome and malodor.

Fungal commensalism modulated by a dual-action phosphate transceptor.

Successful host colonization by fungi in fluctuating niches requires response and adaptation to multiple environmental stresses. However, our understanding about how fungal species thrive in the gastrointestinal (GI) ecosystem by combing multifaceted nutritional stress with respect to homeostatic host-commensal interactions is still in its infancy. Here, we discover that depletion of the phosphate transceptor Pho84 across multiple fungal species encountered a substantial cost in gastrointestinal colonization. Mechanistically, Pho84 enhances the gastrointestinal commensalism via a dual-action activity, coordinating both phosphate uptake and TOR activation by induction of the transcriptional regulator Try4 and downstream commensalism-related transcription. As such, Pho84 promotes Candida albicans commensalism, but this does not translate into enhanced pathogenicity. Thus, our study uncovers a specific nutrient-dependent dual-action regulatory pathway for Pho84 on fungal commensalism.

Intestinal Models for Personalized Medicine: from Conventional Models to Microfluidic Primary Intestine-on-a-chip.

Intestinal dysfunction is frequently driven by abnormalities of specific genes, microbiota, or microenvironmental factors, which usually differ across individuals, as do intestinal physiology and pathology. Therefore, it’s necessary to develop personalized therapeutic strategies, which are currently limited by the lack of a simulated intestine model. The mature human intestinal mucosa is covered by a single layer of columnar epithelial cells that are derived from intestinal stem cells (ISCs). The complexity of the organ dramatically increases the difficulty of faithfully mimicking in vivo microenvironments. However, a simulated intestine model will serve as an indispensable foundation for personalized drug screening. In this article, we review the advantages and disadvantages of conventional 2-dimensional models, intestinal organoid models, and current microfluidic intestine-on-a-chip (IOAC) models. The main technological strategies are summarized, and an advanced microfluidic primary IOAC model is proposed for personalized intestinal medicine. In this model, primary ISCs and the microbiome are isolated from individuals and co-cultured in a multi-channel microfluidic chip to establish a microengineered intestine device. The device can faithfully simulate in vivo fluidic flow, peristalsis-like motions, host-microbe crosstalk, and multi-cell type interactions. Moreover, the ISCs can be genetically edited before seeding, and monitoring sensors and post-analysis abilities can also be incorporated into the device to achieve high-throughput and rapid pharmaceutical studies. We also discuss the potential future applications and challenges of the microfluidic platform. The development of cell biology, biomaterials, and tissue engineering will drive the advancement of the simulated intestine, making a significant contribution to personalized medicine in the future. Graphical abstractThe intestine is a primary organ for digestion, absorption, and metabolism, as well as a major site for the host-commensal microbiota interaction and mucosal immunity. The complexity of the organ dramatically increases the difficulty of faithfully mimicking in vivo microenvironments, though physiological 3-dimensional of the native small intestinal epithelial tissue has been well documented. An intestinal stem cells-based microfluidic intestine-on-a-chip model that faithfully simulate in vivo fluidic flow, peristalsis-like motions, host-microbe crosstalk, and multi-cell type interactions will make a significant contribution.

Gut microbiota modulate susceptibility to bleomycin-induced lung injury.

Abstract Acute lung injury (ALI) resulting in acute respiratory distress syndrome (ARDS) affects almost 200,000 people in the US each year, leading to 75,000 deaths. Airway instillation of bleomycin (BLM) in mice is a widely used, yet challenging model for ALI due to high variability. We have observed that B6 mice from two SPF facilities at our University exhibit significantly different mortality and weight loss in response to BLM. To test whether the facility-dependent response to BLM can be transferred by the microbiome, we conventionalized germ-free (GF) B6 littermates in each facility and challenged with BLM. Conventionalized GF mice recapitulated the respective donors’ response to BLM. Further, fecal microbiota transfer from the facility where the mice had worse mortality into the mice in the facility with more survival rendered recipient mice more susceptible to BLM compared to controls, indicating that the differential gut microbiome between two facilities were sufficient to modulate BLM response. To identify microorganisms that drive the phenotype, we compared gut microbial community memberships by 16S rRNA and metagenomics sequencing. Interestingly, BLM highly susceptible mice had greater alpha diversity and harbored specific species of Bacteroides, Prevotella, and Helicobacter genera. Flow cytometry of the lung immune cell landscape at baseline revealed comparable composition and phenotype of adaptive immune cells regardless of facility. However, lung NK cells were significantly increased BLM highly susceptible mice. Thus, we demonstrate that distinct gut microbiota communities modulate death and weight loss in response to BLM-induced lung injury, implicating host-commensal interactions in regulating ALI outcomes.

Microbiota and Metabolites as Factors Influencing Blood Pressure Regulation.

The study of microbes has rapidly expanded in recent years due to a surge in our understanding that humans host a plethora of commensal microbes, which reside in their bodies and depending upon their composition, contribute to either normal physiology or pathophysiology. This article provides a general foundation for learning about host-commensal microbial interactions as an emerging area of research. The article is divided into two sections. The first section is dedicated to introducing commensal microbiota and its known effects on the host. The second section is on metabolites, which are biochemicals that the host and the microbes use for bi-directional communication with each other. Together, the sections review what is known about how microbes interact with the host to impact cardiovascular physiology, especially blood pressure regulation. © 2021 American Physiological Society. Compr Physiol 11:1731-1757, 2021.

Host-commensal interaction promotes health and lifespan in Caenorhabditis elegans through the activation of HLH-30/TFEB-mediated autophagy.

Gut homeostasis is maintained by the close interaction between commensal intestinal microbiota and the host, affecting the most complex physiological processes, such as aging. Some commensal bacteria with the potential to promote healthy aging arise as attractive candidates for the development of pro-longevity probiotics. Here, we showed that heat-inactivated human commensal Lactobacillus fermentum BGHV110 (BGHV110) extends the lifespan of Caenorhabditis elegans and improves age-related physiological features, including locomotor function and lipid metabolism. Mechanistically, we found that BGHV110 promotes HLH-30/TFEB-dependent autophagy to delay aging, as longevity assurance was completely abolished in the mutant lacking HLH-30, a major autophagy regulator in C. elegans. Moreover, we observed that BGHV110 partially decreased the content of lipid droplets in an HLH-30-dependent manner and, at the same time, slightly increased mitochondrial activity. In summary, this study demonstrates that specific factors from commensal bacteria can be used to exploit HLH-30/TFEB-mediated autophagy in order to promote longevity and fitness of the host.

A neu(ronal) player joins the T regulatory game

The enteric nervous system is surfacing as a key regulator of intestinal immunity and a liaison of host-commensal interactions. In this issue, Yan etal. identify neuronal interleukin-6 as a potent modulatorof regulatory T (Treg) cells in the intestine. This neuroimmune dialog is further refined by commensal microbiota, which impact the enteric nervous system and consequently the intestinal Treg cell pool.

How commensal microbes shape the physiology of Drosophila melanogaster.

The interactions between animals and their commensal microbes profoundly influence the host's physiology. In the last decade, Drosophila melanogaster has been extensively used as a model to study host-commensal microbes interactions. Here, we review the most recent advances in this field. We focus on studies that extend our understanding of the molecular mechanisms underlying the effects of commensal microbes on Drosophila's development and lifespan. We emphasize how commensal microbes influence nutrition and the intestinal epithelium homeostasis; how they elicit immune tolerance mechanisms and how these physiological processes are interconnected. Finally, we discuss the importance of diets and microbial strains and show how they can be confounding factors of microbe mediated host phenotypes.

Mānuka honey-derived methylglyoxal enhances microbial sensing by mucosal-associated invariant T cells.

Methylglyoxal (MGO) is the main antimicrobial determinant associated with using Mānuka Honey as a topical dressing. While direct mechanisms of Mānuka honey MGO's antimicrobial activity have been demonstrated, such as disruption of bacterial fimbria and flagella, no interaction of Mānuka honey-derived MGO with antimicrobial effector cells of the immune system, such as mucosal-associated invariant T cells (MAIT cells), has yet been reported. MAIT cells are an abundant subset of human T cells, critical for regulating a diverse range of immune functions, including antimicrobial defense mechanisms but also mucosal barrier integrity. MAIT cells become activated by recognition of an important microbial metabolite, 5-amino-6-d-ribitylaminouracil (5-A-RU), which is produced by a wide range of microbial pathogens and commensals. Recognition is afforded when 5-A-RU condenses with mammalian-cell derived MGO to form the potent MAIT cell activator, 5-(2-oxopropylideneamino)-6-d-ribitylaminouracil (5-OP-RU). Formation of 5-OP-RU and its subsequent presentation to MAIT cells by major histocompatibility (MHC)-related molecule 1 (MR1) facilitates host-pathogen and host-commensal interactions. While MGO is a metabolite naturally present in mammalian cells, it is unclear whether exogenous dietary MGO sources, such as those obtained from Mānuka honey intake, can contribute to 5-OP-RU formation and enhance MAIT cell activation. In this work, we report that endogenous MGO is the rate-limiting substrate for converting microbial 5-A-RU to 5-OP-RU and that Mānuka honey-derived MGO significantly enhances MAIT cell activation in vitro. Our findings posit a novel mechanism by which intake of a food item, such as Mānuka honey, can potentially support immune homeostasis by enhancing MAIT cell-specific microbial sensing.

Editorial: Understanding and Exploiting Host-Commensal Interactions to Combat Pathogens

Editorial: Understanding and Exploiting Host-Commensal Interactions to Combat Pathogens

Microbiota-dependent signals are required to sustain TLR-mediated immune responses

Host-commensal interactions are critical for the generation of robust inflammatory responses, yet the mechanisms leading to this effect remain poorly understood. Using a murine model of cytokine storm, we identified that host microbiota are required to sustain systemic TLR-driven immune responses. Mice treated with broad-spectrum antibiotics or raised in germ-free conditions responded normally to an initial TLR signal but failed to sustain production of proinflammatory cytokines following administration of repeated TLR signals in vivo. Mechanistically, host microbiota primed JAK signaling in myeloid progenitors to promote TLR-enhanced myelopoiesis, which is required for the accumulation of TLR-responsive monocytes. In the absence of TLR-enhanced monocytopoiesis, antibiotic-treated mice lost their ability to respond to repeated TLR stimuli and were protected from cytokine storm-induced immunopathology. These data reveal priming of TLR-enhanced myelopoiesis as a microbiota-dependent mechanism that regulates systemic inflammatory responses and highlight a role for host commensals in the pathogenesis of cytokine storm syndromes.

The microbiome in patients with atopic dermatitis

As an interface with the environment, the skin is a complex ecosystem colonized by many microorganisms that coexist in an established balance. The cutaneous microbiome inhibits colonization with pathogens, such as Staphylococcus aureus, and is a crucial component for function of the epidermal barrier. Moreover, crosstalk between commensals and the immune system is now recognized because microorganisms can modulate both innate and adaptive immune responses. Host-commensal interactions also have an effect on the developing immune system in infants and, subsequently, the occurrence of diseases, such as asthma and atopic dermatitis (AD). Later in life, the cutaneous microbiome contributes to the development and course of skin disease. Accordingly, in patients with AD, a decrease in microbiome diversity correlates with disease severity and increased colonization with pathogenic bacteria, such as S aureus. Early clinical studies suggest that topical application of commensal organisms (eg, Staphylococcus hominis or Roseomonas mucosa) reduces AD severity, which supports an important role for commensals in decreasing S aureus colonization in patients with AD. Advancing knowledge of the cutaneous microbiome and its function in modulating the course of skin disorders, such as AD, might result in novel therapeutic strategies.