L8 host symbiont 2 Flashcards
What is the focus of part 1 of the lecture framework?
Ecology of microbial communities, how they assemble on animal hosts, and what processes shape their composition and diversity.
What are the four fundamental ecological processes shaping the host microbiome?
Diversification, dispersal, selection, and drift.
What does diversification involve in host-associated microbial communities?
Generation of new genetic variation through mutation, leading to novel microbial forms with different ecological roles.
What is dispersal in the context of microbial ecology?
Movement of microbes from an external environment or other hosts to the host via vertical or horizontal transmission.
How do vertical and horizontal transmission differ?
Vertical transmission is parent-to-offspring; horizontal transmission is social or environmental transfer between hosts.
How does selection shape microbial communities on hosts?
The host’s internal environment (e.g., pH, oxygen, nutrient availability) acts as a selective filter determining which microbes can colonize.
What is genetic drift in microbial populations?
Random, stochastic changes in microbial abundances that can lead to the random loss or extinction of taxa.
What are eco-evolutionary feedbacks in host-microbe systems?
Evolutionary changes in microbes that alter their ecology and, in turn, feed back to influence host-microbe interactions.
Outline the full host-symbiont assembly framework using the four processes.
(1) Environmental microbe pool dispersal to host; (2) host selection via physiology, immunity, and microbial interactions; (3) stochastic drift; (4) microbial diversification mutations leading to eco-evolutionary feedback.
How can hosts be conceptualized in the metacommunity framework?
As discrete habitat patches in a landscape, where each host carries a local microbial community connected by dispersal.
What are within-host versus between-host interactions?
Within-host: selective filters, physiology, diet, immunity, microbial interactions. Between-host: vertical and horizontal transmission pathways.
How do we distinguish host ‘selection’ from host ‘control’?
Selection refers to general environmental traits filtering microbes; control refers to specific adaptive host traits evolved to influence which symbionts are retained or excluded.
What is an example of host control of microbial dispersal?
Stinkbug mothers smear eggs with symbiotic juice; koala mothers feed young a special secretion to ensure beneficial gut microbes.
What are priority effects in microbial assembly?
Early colonization by beneficial microbes that pre-empt later arrival of less favorable species.
How do hosts exert post-colonization control by environmental modification?
By altering tissue conditions (e.g., pH, nutrient supply, oxygen, moisture) to maintain niches favorable to beneficial microbes.
What is competition-based selection by the host?
Creating conditions that favor competitive dominance of preferred symbionts over others.
Give an example of competition-based selection in infants.
Human milk oligosaccharides selectively promote Bifidobacteria and Bacteroides growth in the infant gut.
What are the two facets of immune-mediated control?
Suppressive immunity (killing harmful microbes) and facilitatory immunity (supporting beneficial microbes).
How does IgA facilitate beneficial gut bacteria?
IgA binds and helps retain desirable bacteria, ensuring their persistence in the gut.
How do hosts use ecosystem-service feedback to regulate their microbiome?
By rewarding microbes that provide essential services and sanctioning non-beneficial ones (e.g., diarrhea flushes pathogens).
What is an example of a microbial sanction by the host?
Diarrhea expels pathogenic microbes from the gut.
What is an example of a microbial reward by the host?
Bobtail squid only develop their light organ when colonized by beneficial Vibrio symbionts.
List the key ecological processes in microbiome assembly.
Diversification, dispersal, selection, and drift.
Summarize the main mechanisms of host control in microbiome assembly.
Pre-colonization controls (egg-smearing, maternal secretions), post-colonization controls (environmental modulation, competition bias), immune-mediated control, and ecosystem-service feedback.
What are specialized compartments for microbial symbionts?
Host structures ranging from intracellular bacteriocytes to organ-level light organs and gut microstructures that house symbionts.
Why is physical containment of symbionts advantageous?
It prevents symbionts from invading sensitive tissues and guards against shifts along the parasitism–mutualism continuum.
What evidence shows many mutualists evolved from pathogens?
A study found 32 of 42 mutualistic bacteria have ancestral pathogenic states.
How do hosts regulate symbiont reproduction?
By controlling microbial population levels in compartments (e.g., aphid bacteriocytes regulate Buchnera).
Give an example of partner choice via compartmentalization.
Legumes selectively monitor rhizobia in nodules and can sanction non-fixing strains.
Describe the legume split-plant sanction experiment.
One root half received normal nitrogen/oxygen, the other argon replaced nitrogen; the argon side formed fewer nodules, showing oxygen limitation as a sanction.
What is the winnowing model in bobtail squid?
A multi-step colonization where cilia draw in microbes, mucus selects them, antimicrobials exclude unwanted bacteria, mucus breakdown attracts Vibrio, physical barriers filter, and light detection sanctions non-luminous cells.
What does the bobtail squid example illustrate?
Highly specific host control in a diverse seawater microbial environment.
What is cultivation symbiosis in beanbugs?
Hosts cultivate Burkholderia from soil each generation via a mucus-filled gut obstacle course that filters for the symbiont.
How was beanbug host-driven selection demonstrated experimentally?
In vitro Burkholderia didn’t outcompete others, but in vivo the natural strain dominated, showing active host selection.
Define host specificity in microbiome assembly.
When microbiome composition differs more between host species than within the same species.
How do ordination plots reveal host specificity?
Individual samples cluster by host species when community composition is more similar within species.
What does beta diversity analysis measure in this context?
Average dissimilarity within hosts vs. between hosts; lower within-species beta diversity indicates strong host selection.
What is phylo-symbiosis?
The pattern where microbiome similarity mirrors host phylogeny, correlating host divergence time with microbiome divergence.
Which vertebrates show strong phylo-symbiosis?
Primates and ungulates show positive correlation; birds and bats often do not due to greater dispersal.
What processes underlie phylo-symbiosis?
Divergence in host traits (selection), geographic variation (dispersal), stochastic drift, and co-diversification.
How can host trait divergence affect microbiomes?
Different immune or physiological adaptations filter microbes differently, generating host-specific communities.
How does geographic variation contribute?
Hosts in different regions encounter different environmental microbes, leading to distinct community assembly.
How does drift shape host microbiomes in allopatry?
Random extinction and stochastic changes cause divergence in symbiotic communities across isolated host populations.
What is co-diversification in host–microbe systems?
Parallel speciation where some microbes evolve alongside their host lineages, mirroring host phylogeny.
What central question guides investigations of microbiome variation between host species?
Whether differences in microbiome composition arise from intrinsic host factors or external environmental influences.
What are the two main approaches to dissect drivers of interspecific microbiome variation?
Laboratory (common garden experiments, microbiome transfers, host gene manipulation) and field studies (phylogeny/geography sampling, cophylogeny analyses).
What does a common garden experiment control for in microbiome studies?
It standardizes diet and environmental exposure across multiple host species to isolate host-intrinsic effects.
What did common garden studies of Nasonia wasps, mosquitoes, and Drosophila reveal?
Phylo-symbiosis persisted strongly in Nasonia and mosquitoes after removing environmental variation, but was weaker in Drosophila.
What is the purpose of microbiome swap (transplant) experiments?
To test how much the host environment versus microbial traits shape community composition by swapping microbiomes between hosts.
What were the outcomes of swapping fish and mouse microbiomes?
Fish microbiome in mice showed Proteobacteria enrichment; mouse microbiome in fish showed Firmicutes expansion, indicating host environments shape persistence but microbial traits remain.
How did manipulating Arminin antimicrobial peptide genes in Hydra demonstrate immune control?
Hydra with suppressed Arminin diverged more from their native microbiome when exposed to non-native microbes, showing these genes enforce species-specific communities.
What design do field comparative studies use to parse natural drivers of microbiome variation?
Cross-factorial sampling of multiple host species across different habitats, comparing within-species vs. between-species community similarity.
What key finding emerges from field studies of small mammals across habitats?
Host phylogeny outweighs environmental factors in shaping gut microbiomes, though co-occurring species can converge somewhat.
What is co-phylogeny (co-diversification) analysis in microbiome research?
Assessing congruence between host phylogenetic trees and microbial strain phylogenies to detect parallel evolution or partner fidelity.
How does the stinkbug system illustrate tight host–symbiont co-phylogeny?
Faithful vertical transmission via symbiont capsules produces strong congruence between stinkbug and bacterial phylogenies.
What do hominid microbiome studies using gyrB genes show?
Some bacterial clades co-diversify with their hosts (host-specific clustering), while others (e.g., Lachnospiraceae) frequently shift hosts with no phylogenetic congruence.
How can within-species microbiome variation be experimentally dissected?
By manipulating host genes (e.g., MyD88, Rag knockouts), diet, and dispersal opportunities in lab settings, alongside field sampling to contrast genetics vs. environment.
What effect does knocking out MyD88 have on mouse gut microbiomes?
It alters the relative abundance of taxa like segmented filamentous bacteria, highlighting the role of innate immune recognition in community assembly.
In diet vs. genetic strain experiments in mice, which factor dominated microbiome similarity?
Diet (e.g., chow vs. high-fat/high-sugar) was the primary driver, with host genotype having a secondary effect.
What do co-housing experiments in mice demonstrate about dispersal?
Co-housing leads to convergence of distinct microbiomes through social transmission, underscoring dispersal’s strong influence.
How does social network analysis reveal dispersal effects in the field?
By correlating tracked social association strength with microbiome similarity among individuals of the same species.
What did the wood mouse social association study find?
Social interaction strength, not host factors like sex, age, or kinship, best predicted gut microbiome similarity.
What does the “ecosystem on a leash” concept describe?
A model where microbial communities largely self-organize but are kept in check by host influences.
Why must microbial traits have a genetic basis for host-driven evolution?
Because only heritable traits can respond to host selection pressures and evolve over time.
What are the integrative take-homes on drivers of microbiome assembly?
Lab experiments isolate specific factors; field studies highlight dispersal’s dominance; co-phylogeny shows both co-diversification and host shifts, revealing complex, taxon-specific dynamics.
