🪱Microbiomes Unit 5 – Microbiome Interactions and Immunity

Key Concepts and Definitions

• Microbiome refers to the collective genomes of all microorganisms in a particular environment, including bacteria, archaea, viruses, and fungi
• Microbiota consists of the actual microorganisms themselves that inhabit a specific niche or environment within a host organism
• Symbiosis describes close and long-term interactions between different biological species, which can be mutualistic (beneficial to both), commensal (beneficial to one while not affecting the other), or parasitic (beneficial to one while harming the other)
• Dysbiosis occurs when there is an imbalance in the composition of the microbiome, often associated with disease states or disruptions to normal host functions
• Pathobionts are typically harmless microbes that can become pathogenic under certain conditions (dysbiosis, immunodeficiency)
• Gnotobiotic animals are raised in sterile conditions and intentionally colonized with known microbes to study host-microbe interactions in a controlled setting
• Metagenomics involves sequencing and analysis of genetic material from environmental samples, allowing for the study of microbial communities without the need for cultivation

Microbiome Composition and Diversity

• Human microbiome is composed of trillions of microorganisms, with the gut being the most densely populated site
• Bacterial phyla Firmicutes and Bacteroidetes dominate the gut microbiome, with smaller proportions of Actinobacteria, Proteobacteria, and Verrucomicrobia
• Microbial composition varies across different body sites (skin, oral cavity, vagina) due to unique environmental conditions and host factors
• Microbiome diversity can be assessed at various taxonomic levels (species, genus, phylum) and through measures of alpha diversity (within-sample) and beta diversity (between-samples)
• Factors influencing microbiome composition include diet, age, geography, antibiotic use, and host genetics
• Establishment of the microbiome begins at birth, with mode of delivery (vaginal vs. cesarean) and feeding method (breastfeeding vs. formula) having significant impacts on early microbial colonization
• Microbiome composition stabilizes in adulthood but can still be influenced by long-term dietary patterns and other environmental exposures

Microbiome-Host Interactions

• Microbiome engages in complex cross-talk with the host through various signaling pathways and metabolic interactions
• Microbial metabolites (short-chain fatty acids, secondary bile acids) can modulate host immune responses, metabolism, and brain function
• Microbes compete with pathogens for nutrients and attachment sites, providing colonization resistance against infection
• Microbiome influences host gene expression through epigenetic modifications and regulation of transcription factors
• Disruptions to microbiome-host interactions can contribute to the development of inflammatory bowel disease, obesity, and neurological disorders
• Germ-free animal models demonstrate the critical role of the microbiome in normal host development and function
  • Germ-free mice exhibit impaired immune development, altered metabolic profiles, and behavioral abnormalities compared to conventionally-raised mice

Immune System Basics

• Innate immunity provides rapid, non-specific defense against pathogens through physical barriers (skin, mucus), antimicrobial peptides, and immune cells (neutrophils, macrophages, dendritic cells)
• Adaptive immunity involves antigen-specific responses mediated by T lymphocytes and B lymphocytes, which can provide long-lasting protection through immunological memory
• T cells differentiate into various subsets (CD4+ helper T cells, CD8+ cytotoxic T cells, regulatory T cells) with distinct functions in coordinating immune responses and maintaining tolerance
• B cells produce antibodies that neutralize pathogens and mark them for destruction by other immune cells
• Innate and adaptive immune systems work together to maintain homeostasis and protect against infection
• Mucosal immune system (gut-associated lymphoid tissue, Peyer's patches) plays a critical role in maintaining tolerance to commensal microbes while mounting responses against pathogens

Microbiome's Role in Immune Development

• Microbiome is essential for the proper development and maturation of the immune system
• Germ-free animals exhibit underdeveloped lymphoid tissues, reduced antibody production, and altered T cell populations compared to conventionally-raised animals
• Specific bacterial species (Bacteroides fragilis, Clostridium clusters IV and XIVa) have been shown to promote the development of regulatory T cells, which maintain immune tolerance
• Microbial colonization in early life shapes the balance between T helper cell subsets (Th1, Th2, Th17) and influences susceptibility to allergic and autoimmune disorders
• Microbiome-derived short-chain fatty acids (butyrate, propionate) regulate the differentiation and function of various immune cell populations
• Disruptions to the microbiome during critical developmental windows (birth, infancy) can have long-lasting impacts on immune function and disease risk

Immune Responses to Microbiome

• Host immune system must maintain a delicate balance between tolerance to commensal microbes and responsiveness to pathogens
• Innate immune cells (dendritic cells, macrophages) sense microbes through pattern recognition receptors (Toll-like receptors, NOD-like receptors) and modulate their responses based on microbial signals
• Secretory IgA antibodies coat commensal bacteria and prevent their adherence to the intestinal epithelium, maintaining spatial segregation between microbes and host tissues
• Regulatory T cells and anti-inflammatory cytokines (IL-10, TGF-β) suppress excessive immune responses against commensal microbes
• Disruptions to immune-microbiome cross-talk can lead to chronic inflammation and tissue damage, as observed in inflammatory bowel disease and other disorders
• Certain microbes (segmented filamentous bacteria) can induce the development of Th17 cells, which play a role in mucosal immunity but can also contribute to autoimmune pathology when dysregulated

Dysbiosis and Disease

• Dysbiosis, or imbalances in the composition and function of the microbiome, has been associated with various disease states
• Inflammatory bowel diseases (Crohn's disease, ulcerative colitis) are characterized by reduced microbial diversity, increased abundance of pathobionts (adherent-invasive E. coli), and decreased levels of beneficial bacteria (Faecalibacterium prausnitzii)
• Obesity and metabolic disorders are associated with alterations in the ratio of Firmicutes to Bacteroidetes, as well as reduced microbial gene richness
• Allergic disorders (asthma, atopic dermatitis) have been linked to reduced microbial diversity in early life and altered immune development
• Neurological conditions (autism spectrum disorder, Parkinson's disease) have shown associations with gut microbiome alterations, suggesting a role for the gut-brain axis in these disorders
• Antibiotic use can disrupt the microbiome and increase the risk of Clostridioides difficile infection, which is characterized by severe intestinal inflammation and diarrhea
• Fecal microbiota transplantation has emerged as a promising therapy for recurrent C. difficile infection, aiming to restore a healthy microbiome

Research Methods and Technologies

• 16S rRNA gene sequencing allows for the identification and relative quantification of bacterial taxa within a microbiome sample
• Shotgun metagenomics involves sequencing all DNA in a sample, providing information on microbial community composition, functional potential, and strain-level variations
• Metatranscriptomics and metaproteomics enable the study of microbial gene expression and protein production in situ
• Metabolomics techniques (NMR spectroscopy, mass spectrometry) allow for the identification and quantification of microbial metabolites that mediate host-microbe interactions
• Gnotobiotic animal models, including germ-free and humanized mice, provide controlled systems for studying the effects of specific microbes or microbial communities on host physiology
• Organoid cultures, derived from stem cells, offer a way to model host-microbe interactions in a simplified and tractable in vitro setting
• Imaging technologies (FISH, SEM) enable the visualization of microbes and their spatial relationships within host tissues
• Computational tools (machine learning, network analysis) are increasingly being applied to integrate and interpret large-scale microbiome datasets