Immunogenetics: The Human Microbiota Study Guide

Fundamental Definitions and Core Concepts

• Microbiota: This is a collective term describing the total array of microscopic organisms that reside on or within the human body. Humans and other mammals serve as hosts to these diverse microbial communities.

• The Microbiota Composition: The microbiota includes several distinct groups of organisms:

  • Prokaryotes: Specifically bacteria and archaea.

  • Viruses: This includes bacteriophages (viruses that infect bacteria) as well as eukaryotic viruses.

  • Eukarya: Primarily consisting of fungi and protozoa.

• Microbiome: This term refers specifically to the combined genomes of all organisms that constitute the microbiota.

• Mycobiota: A specific subset of the microbiota consisting solely of fungi.

• Virome: The total collection of all viruses found in or on humans, including those that have been integrated into the human genome.

• Dysbiosis: A condition defined by a state of disequilibrium or imbalance in the microbial communities residing at a specific body site.

• Colonization Sites: Specialized subcommunities of these microbes colonize the barrier surfaces of the human body, including the digestive, respiratory, and urogenital tracts, as well as the skin.

The Symbiotic Relationship and Mutualism

• Evolutionary Purpose: The human immune system is believed to have evolved to facilitate a peaceful coexistence with these microorganisms. This relationship supports three primary functions:

  • Immune Homeostasis: Maintaining a balanced immune state.

  • Pathogen Resistance: Preventing the colonization of harmful microbes.

  • Digestion: Assisting in the breakdown of food materials in exchange for a nutrient-rich habitat provided by the host.

• Cross-Talk: There is a continuous and perpetual communication (cross-talk) between the microbiota and the immune system throughout the entirety of an individual’s life.

• Mutualism in the Gut: The relationship is characterized by mutualism, where both host and microbe perform unique, necessary functions for one another.

• Metabolic example (SCFAs): Certain bacteria reside in the anaerobic environment of the cecum and proximal colon. They utilize insoluble carbohydrates that the host's own digestive enzymes cannot process.

  • Anaerobic Fermentation: The bacteria break down these carbohydrates through fermentation.

  • Byproducts: This process generates Short-Chain Fatty Acids (SCFAs), specifically butyrate.

  • Function of Butyrate: Butyrate is used preferentially as a fuel source by colonocytes (cells of the colon) and also exerts influence over host metabolism and immunity.

Developmental Immunogenetics: Prenatal and Postnatal Maturation

• Fetal Development: In the distal ileum of the fetus, the formation of the mesenteric lymph node and Peyer patches is critical for:

  • Initiating immune responses to commensal microbiota, pathogenic invaders, and self-antigens.

  • Establishing a mucosal firewall that prevents gut bacteria from systemic dissemination (spreading through the whole body).

• Prenatal vs. Postnatal Structures:

  • Prenatal: Characterized by the presence of LTi cells (Lymphoid Tissue inducer cells) and cryptopatches.

  • Postnatal: Involved in the maturation of isolated lymphoid follicles and the presence of M cells, Dendritic cells, Goblet cells, and Paneth cells.

• Antigens and Signaling: The system detects MAMPS (Microbe-Associated Molecular Patterns). Paneth cells secrete antimicrobial peptides, and Goblet cells produce mucus.

• Passive Immunity Acquisition:

  • Acquisition Timing: Exposure to the microbiota begins in utero and accelerates rapidly during and after the birth process.

  • Maternal Mucosal Memory: The neonate acquires microbiota from the mother. During transvaginal delivery, the neonate is seeded with the mother’s native microbiota.

  • Immunoglobulin Transmission: Immunoglobulin A ($IgA$) is the primary antibody isotype generated by mammary glands and passed to the infant via breast milk.

  • Function of IgA: It inhibits bacterial translocation across the neonatal intestinal epithelium, limiting inflammatory damage and providing passive immunity against pathogens.

  • Immunosuppressive Factors: Breast milk contains $TGF-\beta$ and $IL-10$, which promote tolerogenic (peaceful) immune responses to the newly acquired microbiota.

Intestinal Immune System Architecture and "Checks and Balances"

• The Intestinal Epithelium: Acts as an essential component in a network of checks and balances that prevent pathogen invasion while limiting collateral damage from commensals.

• Key Immune Cell Subsets:

  • invariant NK T cells (iNKT): These are thymus-derived cells expressing an invariant TCR (T-cell receptor) that recognizes lipid antigens presented by the nonclassic MHC class I molecule, CD1d.

  • Tregs (Regulatory T cells): $FOXP3+$ Tregs are exported from the thymus in the first few days of life to seed lymphoid and non-lymphoid tissues.

  • CD4s: Includes $IFN-\gamma$-producing $Th1$ cells and $IL-17$-producing $Th17$ cells, positioned for adaptive responses.

  • Dendritic Cells (DCs): These cells sample luminal bacteria by extending their dendrites between epithelial cells and into the lumen. Once loaded with antigens, they migrate to the mesenteric lymph nodes.

  • B-Cell Interaction: Antigen-loaded DCs interact with B and T cells to stimulate the production of anti-commensal $IgA$. These plasma cells then migrate back to the lamina propria to secrete $IgA$ and limit translocation.

• Epithelial Components:

  • Intestinal Epithelial Cells (IECs): A single layer of polarized columnar cells sealed by tight junctions.

  • Goblet Cells: Secrete mucins to form a bilayered mucus sheath (inner and outer layers), separating bacteria from the epithelium.

  • Paneth Cells: Contain abundant AMPs (antimicrobial peptides) and immunomodulating proteins.

  • pIgR (Polymeric Immunoglobulin Receptor): Facilitates the transcytosis of soluble polymeric isoforms of $IgA$ into the lumen.

Innate Lymphoid Cells (ILCs)

• General Characteristics: ILCs are a line of early defense at mucosal surfaces. Unlike T helper cells, they do not express antigen receptors; they are activated by cytokine signals. This allow for a rapid response to microbial challenges and aids in developing an adaptive response.

• Functional Subsets of ILCs:

  • ILC1:

    • Transcriptional Regulator: $T-bet$.

    • Cytokines Produced: $IFN-\gamma$ and $TNF-\alpha$.

    • Significance: Intracellular bacteria response; cancer immunosurveillance.

  • ILC2:

    • Transcriptional Regulator: $GATA-3$.

    • Cytokines Produced: $IL-4$, $IL-5$, and $IL-13$.

    • Significance: Helminth (parasitic worm) immunity; wound healing; potentially involved in atopic disorders.

  • ILC3:

    • Transcriptional Regulator: $ROR\gamma t$.

    • Cytokines Produced: $IL-17$ and $IL-22$. Additionally, $TNF-\alpha$, $GM-CSF$, and $LIF$.

    • Significance: Populate intestinal lymphoid follicles; mucosal immunity; potentially involved in psoriasis.

The Microbial Phyla and Virome

• GI Bacterial Phyla: The majority of colonizing bacteria in humans belong to three phyla:

  • Bacteroidetes

  • Firmicutes

  • Proteobacteria

• The Virome Details:

  • Bacteriophages: These infect prokaryotic cells and can exist in a quantity $10$-fold greater than prokaryotes. They influence the intestinal community through viral gene transfer of virulence factors and antibiotic-resistant genes.

  • Eukaryotic Viruses: These can permanently infect the host (asymptomatic for decades), persisting locally or systemically and impacting tissue-specific immunity.

• The Mycobiota Details: Commensal fungi (e.g., Candida, Cladosporium, and Aspergillus) are found in the mouth, lungs, intestines, vagina, and skin, though they represent a smaller total proportion of the microbiota.

Dysbiosis and Extraintestinal Manifestations

• Influencing Factors: Microbiota composition is affected by birth delivery method, diet, antibiotic treatment, and environmental exposures.

• Obesity and Metabolic Syndrome: Conditioned by increased gut permeability and aberrant bacterial translocation.

  • Fecal Transplant Evidence: In studies with mouse cotwins, mice transplanted with human "obese" microbiota showed increased weight and adipose tissue compared to those with "lean" microbiota.

  • LPS (Lipopolysaccharides): Found at low levels in healthy individuals but significantly high in obese and Type $2$ diabetic patients.

  • Mechanism: LPS activates macrophages via TLR4, leading to the secretion of $IL-6$ and $TNF-\alpha$. This chronic inflammation contributes to defective insulin signaling (insulin resistance), leading to Type $2$ DM, hepatic steatosis, and Cardiovascular Disease (CVD).

• Early Life Influences: Low-dose antibiotics in early life increase obesity risk. Conversely, being raised around livestock or with limited sanitary amenities reduces the risk of childhood inflammatory bowel disease (IBD).

The Microbiota-Immunity-Cancer Triad

• Oncogenic Bacteria: Strains like Enterococcus faecalis produce Reactive Oxygen Species (ROS) that cause DNA damage.

• Pathogenic Infection and Cancer: Approximately $1$ in $6$ cancers develop from infections:

  • Helicobacter pylori: Gastric carcinoma.

  • Human papillomavirus (HPV): Cervical cancer.

  • Hepatitis B and C: Hepatocellular carcinoma.

• Triad Mechanism: Dysbiosis (infection/environment) disrupts homeostasis, leading to persistent inflammation. This promotes cancer progression. Antitumor immune responses to novel tumor antigens utilize the same pathways as antipathogen responses and are therefore subject to similar immune suppression mechanisms.

Skin and Respiratory Microbiota

• Skin Microbiota:

  • Resident Bacteria: Propionibacterium, Corynebacterium, Staphylococcus.

  • Resident Fungi: Malassezia.

  • Defenses: Skin microbes trigger innate responses via AMPs (cathelicidins and $\beta$-defensins), complement systems, and $IL-1$.

  • Acne Vulgaris: Follicular clogging leads to an outgrowth of Propionibacterium acnes. Breach of the follicular wall causes a neutrophil influx (pustules). Staphylococcus epidermidis also plays a role in dysregulated TLR expression.

  • Atopic Dermatitis (AD): Characterized by xerosis (dry skin) and pH changes. Over $90\%$ of patients have skin lesions colonized by Staphylococcus aureus. High levels of psoriasin, human $\beta$ defensin-2, and RNase 7 are found.

• Respiratory Microbiota:

  • Portal for airborne microbes.

  • Primary Bacteria: Prevotella, Veillonella, and Streptococcus.

  • Pulmonary Failure: Impairment of defenses leads to chronic diseases like asthma, COPD, cystic fibrosis, and bronchiectasis.

Clinical Advances

• Microbiota Restoration: Transplantation of donor microbiota is a successful therapeutic approach.

• Fecal Microbiota Therapy (FMT): Fecal transplantation is utilized as a safe and effective treatment for chronic Clostridium difficile infection.

Questions & Discussion

• Question posed in lecture: "Which Ig isotype is being acquired in utero?"

• Discussion contextualized: While the lecture emphasizes $IgA$ transmission via breast milk (passive immunity postnatal), the specific prompt regarding in utero acquisition typically refers to maternal IgG crossing the placenta, though the subsequent slides focus heavily on the mucosal memory of $IgA$ and its role in protecting the neonate after delivery.

Fundamental Definitions and Core Concepts

• Microbiota: Represents the total collection of microorganisms residing on or within the human body. These include bacteria, archaea, fungi, and viruses that form complex communities and are crucial for various physiological processes.

• The Microbiota Composition: Comprises several distinct groups:

  • Prokaryotes: Includes both bacteria and archaea, which play critical roles in metabolism and immune modulation.

  • Viruses: Encompasses bacteriophages that target bacteria and eukaryotic viruses that infect human cells.

  • Eukarya: Primarily involves fungi and protozoa that can interact with human hosts and influence health.

• Microbiome: This term specifically refers to the genetic material of all the microorganisms within the microbiota, which can significantly affect an individual’s physiology and health susceptibility.

• Mycobiota: Subset of the microbiota, solely comprising fungal organisms, which can impact immune responses and gut function.

• Virome: The full collection of viruses that inhabit the human body, including those integrated into the host’s genome, influencing health and disease.

• Dysbiosis: Refers to the imbalance in microbial communities due to various factors such as diet, antibiotic use, or disease, potentially leading to adverse health effects.

• Colonization Sites: Microbial communities inhabit various barrier surfaces, including the gastrointestinal tract, respiratory system, urogenital tracts, and skin, each with unique functions and compositions.