Immunology, Host-Microbe Interactions, and Ecology of the Microbiome
Immune system architecture
Recognition, tolerance, and memory
The immune system balances detection of pathogens with tolerance to self and beneficial symbionts. Innate immunity provides rapid sensing, while adaptive immunity enables highly specific and durable responses through clonal selection and memory.
Paradigm
Immunity is a distributed sensing-and-memory network, not a single pathway.
Microbiome ecology
Community dynamics and host interaction
Microbial communities are shaped by nutrient competition, cross-feeding, spatial structure, phage predation, and host immunity. Perturbations can lead to dysbiosis, but causality is often difficult to establish.
Immune components
| Component | Primary role |
|---|---|
| Macrophage | Phagocytosis and cytokine signaling |
| B cell | Antibody production |
| T cell | Cell-mediated adaptive immunity |
| Complement | Opsonization and lysis |
Which immune cell type is primarily responsible for antibody secretion?
B cells differentiate into plasma cells that secrete antibodies.
Correct answer: B cell
What is one reason microbiome causality is hard to prove?
Microbiome composition correlates with many variables, so perturbation and longitudinal designs are often needed.
Correct answer: Host and environmental confounding
Frontier methods in immunology
Single-cell and spatial profiling
Single-cell RNA-seq, immune receptor sequencing, spatial transcriptomics, and perturbation screens are transforming immunology by resolving rare cell states, clonal expansion, and tissue context.
Which technology is especially useful for mapping immune cell states in tissue context?
Spatial transcriptomics preserves location while measuring molecular profiles.
Correct answer: Spatial transcriptomics
What does clonal selection explain?
Antigen-specific clones proliferate, generating adaptive immunity and memory.
Correct answer: The expansion of lymphocytes with receptors specific to an antigen