L8 host symbiont 2

Question 1

What is the focus of part 1 of the lecture framework?

Answer 1

Ecology of microbial communities, how they assemble on animal hosts, and what processes shape their composition and diversity.

Question 2

What are the four fundamental ecological processes shaping the host microbiome?

Answer 2

Diversification, dispersal, selection, and drift.

Question 3

What does diversification involve in host-associated microbial communities?

Answer 3

Generation of new genetic variation through mutation, leading to novel microbial forms with different ecological roles.

Question 4

What is dispersal in the context of microbial ecology?

Answer 4

Movement of microbes from an external environment or other hosts to the host via vertical or horizontal transmission.

Question 5

How do vertical and horizontal transmission differ?

Answer 5

Vertical transmission is parent-to-offspring; horizontal transmission is social or environmental transfer between hosts.

Question 6

How does selection shape microbial communities on hosts?

Answer 6

The host’s internal environment (e.g., pH, oxygen, nutrient availability) acts as a selective filter determining which microbes can colonize.

Question 7

What is genetic drift in microbial populations?

Answer 7

Random, stochastic changes in microbial abundances that can lead to the random loss or extinction of taxa.

Question 8

What are eco-evolutionary feedbacks in host-microbe systems?

Answer 8

Evolutionary changes in microbes that alter their ecology and, in turn, feed back to influence host-microbe interactions.

Question 9

Outline the full host-symbiont assembly framework using the four processes.

Answer 9

(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.

Question 10

How can hosts be conceptualized in the metacommunity framework?

Answer 10

As discrete habitat patches in a landscape, where each host carries a local microbial community connected by dispersal.

Question 11

What are within-host versus between-host interactions?

Answer 11

Within-host: selective filters, physiology, diet, immunity, microbial interactions. Between-host: vertical and horizontal transmission pathways.

Question 12

How do we distinguish host ‘selection’ from host ‘control’?

Answer 12

Selection refers to general environmental traits filtering microbes; control refers to specific adaptive host traits evolved to influence which symbionts are retained or excluded.

Question 13

What is an example of host control of microbial dispersal?

Answer 13

Stinkbug mothers smear eggs with symbiotic juice; koala mothers feed young a special secretion to ensure beneficial gut microbes.

Question 14

What are priority effects in microbial assembly?

Answer 14

Early colonization by beneficial microbes that pre-empt later arrival of less favorable species.

Question 15

How do hosts exert post-colonization control by environmental modification?

Answer 15

By altering tissue conditions (e.g., pH, nutrient supply, oxygen, moisture) to maintain niches favorable to beneficial microbes.

Question 16

What is competition-based selection by the host?

Answer 16

Creating conditions that favor competitive dominance of preferred symbionts over others.

Question 17

Give an example of competition-based selection in infants.

Answer 17

Human milk oligosaccharides selectively promote Bifidobacteria and Bacteroides growth in the infant gut.

Question 18

What are the two facets of immune-mediated control?

Answer 18

Suppressive immunity (killing harmful microbes) and facilitatory immunity (supporting beneficial microbes).

Question 19

How does IgA facilitate beneficial gut bacteria?

Answer 19

IgA binds and helps retain desirable bacteria, ensuring their persistence in the gut.

Question 20

How do hosts use ecosystem-service feedback to regulate their microbiome?

Answer 20

By rewarding microbes that provide essential services and sanctioning non-beneficial ones (e.g., diarrhea flushes pathogens).

Question 21

What is an example of a microbial sanction by the host?

Answer 21

Diarrhea expels pathogenic microbes from the gut.

Question 22

What is an example of a microbial reward by the host?

Answer 22

Bobtail squid only develop their light organ when colonized by beneficial Vibrio symbionts.

Question 23

List the key ecological processes in microbiome assembly.

Answer 23

Diversification, dispersal, selection, and drift.

Question 24

Summarize the main mechanisms of host control in microbiome assembly.

Answer 24

Pre-colonization controls (egg-smearing, maternal secretions), post-colonization controls (environmental modulation, competition bias), immune-mediated control, and ecosystem-service feedback.

Question 25

What are specialized compartments for microbial symbionts?

Answer 25

Host structures ranging from intracellular bacteriocytes to organ-level light organs and gut microstructures that house symbionts.

Question 26

Why is physical containment of symbionts advantageous?

Answer 26

It prevents symbionts from invading sensitive tissues and guards against shifts along the parasitism–mutualism continuum.

Question 27

What evidence shows many mutualists evolved from pathogens?

Answer 27

A study found 32 of 42 mutualistic bacteria have ancestral pathogenic states.

Question 28

How do hosts regulate symbiont reproduction?

Answer 28

By controlling microbial population levels in compartments (e.g., aphid bacteriocytes regulate Buchnera).

Question 29

Give an example of partner choice via compartmentalization.

Answer 29

Legumes selectively monitor rhizobia in nodules and can sanction non-fixing strains.

Question 30

Describe the legume split-plant sanction experiment.

Answer 30

One root half received normal nitrogen/oxygen, the other argon replaced nitrogen; the argon side formed fewer nodules, showing oxygen limitation as a sanction.

Question 31

What is the winnowing model in bobtail squid?

Answer 31

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.

Question 32

What does the bobtail squid example illustrate?

Answer 32

Highly specific host control in a diverse seawater microbial environment.

Question 33

What is cultivation symbiosis in beanbugs?

Answer 33

Hosts cultivate Burkholderia from soil each generation via a mucus-filled gut obstacle course that filters for the symbiont.

Question 34

How was beanbug host-driven selection demonstrated experimentally?

Answer 34

In vitro Burkholderia didn’t outcompete others, but in vivo the natural strain dominated, showing active host selection.

Question 35

Define host specificity in microbiome assembly.

Answer 35

When microbiome composition differs more between host species than within the same species.

Question 36

How do ordination plots reveal host specificity?

Answer 36

Individual samples cluster by host species when community composition is more similar within species.

Question 37

What does beta diversity analysis measure in this context?

Answer 37

Average dissimilarity within hosts vs. between hosts; lower within-species beta diversity indicates strong host selection.

Question 38

What is phylo-symbiosis?

Answer 38

The pattern where microbiome similarity mirrors host phylogeny, correlating host divergence time with microbiome divergence.

Question 39

Which vertebrates show strong phylo-symbiosis?

Answer 39

Primates and ungulates show positive correlation; birds and bats often do not due to greater dispersal.

Question 40

What processes underlie phylo-symbiosis?

Answer 40

Divergence in host traits (selection), geographic variation (dispersal), stochastic drift, and co-diversification.

Question 41

How can host trait divergence affect microbiomes?

Answer 41

Different immune or physiological adaptations filter microbes differently, generating host-specific communities.

Question 42

How does geographic variation contribute?

Answer 42

Hosts in different regions encounter different environmental microbes, leading to distinct community assembly.

Question 43

How does drift shape host microbiomes in allopatry?

Answer 43

Random extinction and stochastic changes cause divergence in symbiotic communities across isolated host populations.

Question 44

What is co-diversification in host–microbe systems?

Answer 44

Parallel speciation where some microbes evolve alongside their host lineages, mirroring host phylogeny.

Question 45

What central question guides investigations of microbiome variation between host species?

Answer 45

Whether differences in microbiome composition arise from intrinsic host factors or external environmental influences.

Question 46

What are the two main approaches to dissect drivers of interspecific microbiome variation?

Answer 46

Laboratory (common garden experiments, microbiome transfers, host gene manipulation) and field studies (phylogeny/geography sampling, cophylogeny analyses).

Question 47

What does a common garden experiment control for in microbiome studies?

Answer 47

It standardizes diet and environmental exposure across multiple host species to isolate host-intrinsic effects.

Question 48

What did common garden studies of Nasonia wasps, mosquitoes, and Drosophila reveal?

Answer 48

Phylo-symbiosis persisted strongly in Nasonia and mosquitoes after removing environmental variation, but was weaker in Drosophila.

Question 49

What is the purpose of microbiome swap (transplant) experiments?

Answer 49

To test how much the host environment versus microbial traits shape community composition by swapping microbiomes between hosts.

Question 50

What were the outcomes of swapping fish and mouse microbiomes?

Answer 50

Fish microbiome in mice showed Proteobacteria enrichment; mouse microbiome in fish showed Firmicutes expansion, indicating host environments shape persistence but microbial traits remain.

Question 51

How did manipulating Arminin antimicrobial peptide genes in Hydra demonstrate immune control?

Answer 51

Hydra with suppressed Arminin diverged more from their native microbiome when exposed to non-native microbes, showing these genes enforce species-specific communities.

Question 52

What design do field comparative studies use to parse natural drivers of microbiome variation?

Answer 52

Cross-factorial sampling of multiple host species across different habitats, comparing within-species vs. between-species community similarity.

Question 53

What key finding emerges from field studies of small mammals across habitats?

Answer 53

Host phylogeny outweighs environmental factors in shaping gut microbiomes, though co-occurring species can converge somewhat.

Question 54

What is co-phylogeny (co-diversification) analysis in microbiome research?

Answer 54

Assessing congruence between host phylogenetic trees and microbial strain phylogenies to detect parallel evolution or partner fidelity.

Question 55

How does the stinkbug system illustrate tight host–symbiont co-phylogeny?

Answer 55

Faithful vertical transmission via symbiont capsules produces strong congruence between stinkbug and bacterial phylogenies.

Question 56

What do hominid microbiome studies using gyrB genes show?

Answer 56

Some bacterial clades co-diversify with their hosts (host-specific clustering), while others (e.g., Lachnospiraceae) frequently shift hosts with no phylogenetic congruence.

Question 57

How can within-species microbiome variation be experimentally dissected?

Answer 57

By manipulating host genes (e.g., MyD88, Rag knockouts), diet, and dispersal opportunities in lab settings, alongside field sampling to contrast genetics vs. environment.

Question 58

What effect does knocking out MyD88 have on mouse gut microbiomes?

Answer 58

It alters the relative abundance of taxa like segmented filamentous bacteria, highlighting the role of innate immune recognition in community assembly.

Question 59

In diet vs. genetic strain experiments in mice, which factor dominated microbiome similarity?

Answer 59

Diet (e.g., chow vs. high-fat/high-sugar) was the primary driver, with host genotype having a secondary effect.

Question 60

What do co-housing experiments in mice demonstrate about dispersal?

Answer 60

Co-housing leads to convergence of distinct microbiomes through social transmission, underscoring dispersal’s strong influence.

Question 61

How does social network analysis reveal dispersal effects in the field?

Answer 61

By correlating tracked social association strength with microbiome similarity among individuals of the same species.

Question 62

What did the wood mouse social association study find?

Answer 62

Social interaction strength, not host factors like sex, age, or kinship, best predicted gut microbiome similarity.

Question 63

What does the “ecosystem on a leash” concept describe?

Answer 63

A model where microbial communities largely self-organize but are kept in check by host influences.

Question 64

Why must microbial traits have a genetic basis for host-driven evolution?

Answer 64

Because only heritable traits can respond to host selection pressures and evolve over time.

Question 65

What are the integrative take-homes on drivers of microbiome assembly?

Answer 65

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.