Overview
The magnitude and frequency of environmental stressors are impacting the dynamics of host microbe interactions. The breakdown of mutualistic relationships can cascade through entire ecosystems with devastating effects on biodiversity and ecological services. Emerging evidence suggests that a set of environmental conditions must be met to initiate the switch from beneficial to detrimental interactions. For example, temperature anomalies beyond some number of days lead to the exclusion of zooxanthellae by host corals. In the case of corals, a well-studied system, symbionts consume too much sugar and get expelled from the host when temperature rises. There is a fine line between mutualism and parasitism.
Existing studies of microbial communities on marine hosts highlight in most cases: 1) a great diversity of microbial partners (i.e., one host - one microbe such as interactions highlight the squid-vibio model are not the norm); 2) some hosts have much more diverse microbiomes than others (e.g., within sponges and corals). The significant of these large differences in diversity is not well understood but microbial diversity (both alpha and beta) might have an import role in host fitness and stability in changing environmental conditions.
General Discussion
Is a higher richness of microbes beneficial to a host? Do diverse associations promote host fitness and stable holobionts in changing environmental conditions?
How to identify the tipping point from symbiosis to dysbiosis in host-associated microbiomes (beyond corals-zooxanthellae)? How to differentiate microbial imbalance from natural variations in microbiomes (e.g., driven by seasonality, changes in diet and life history events)? What is a healthy microbiome?
Discussion Questions
2A: What is a healthy microbiome? Does microbial diversity matter for the host? Is more microbes better? Or fewer beneficial symbionts?
Group members, moderator, note taker/presenter
2B: How to identify the tipping point from symbiosis to dysbiosis in host-associated microbiomes?
Group members, moderator, note taker/presenter
2C: Modelling of host-microbe interactions. How do we go from describing the variation to deciphering what is driving it.
Group members, moderator, note taker/presenter
2D: A null model for microbial communities
Group members, moderator, note taker/presenter
2E: Monitoring host-microbe interactions: can we identify model systems or hosts to monitor (e.g., host-microbiomes with cosmopolitan distribution)?
Group members, moderator, note taker/presenter
Outcomes
Tipping points (from healthy to unhealthy microbiomes)
Stability, similarity in the microbiome in time and space, that is, the community structure. Does healthy microbiome mean stable? Different timing points might show different community structure (e.g. uniqueness, complete distinctness).
Disruption of the community structure might increase diversity which in turn can also lead to an unstable/unhealthy system, that is, high diversity does not always mean healthier microbiome
How can we evaluate these tipping points? Dispersion analysis, estimating variance?
Should we consider host and microbial regulations, trade-offs in the system? How to measure the impacts on the host (e.g. host growth, metabolism, density in the environment)
Dysbiosis not always lead unhealthy/mortality
Importance of associating host/microbiome changes with environment variables, so we can predict tipping points between healthy to unhealthy microbiome
Can we define a set of conditions in the environment to predict tipping points (e.g. nutrients, temperature, etc.)?
Resilience/Succession in microbiome (prior, during, and post disturbance, e.g. antibiotic usage). If the system is prone to tipping, often the system cannot recover, how can we test that?
Can/should we quantify tipping points in the microbiome? Soil microbiome literature seems to be rich in this aspect
Multi stressors should be evaluated when evaluating healthy microbiomes and tipping points
To what degree microbiomes assemble because the host is controlling the system and to what the degree the microbiomes are the controllers (assembly and disassembly of microbiomes)
What is the outcome of tipping points? Does it always lead to dysbiosis?
Example of dysbiosis in bats seem to show how unbalance their microbial community was and how affected the host health.
Adaptable communities to couple with potential changes
Key functional traits need to be maintained
Diversity is not always good, since it can make the system unstable
Relative abundance is not always a good metric (not always functionally active)
Different ways to measure diversity, species richness, beta and alpha diversity, functional diversity
Healthy microbiomes are not always ease to be determined, but relative. Should we move away from it?
There is also short term and long term issues related to microbiome and what is a healthy microbiome. Ecological and evolutionary time scales should be considered.
Total metrics, without teasing a part the potential subgroups can mask some important patterns
Stable as predictable/predictability
Complete dysbiosis can also occur (quiescence can be an alternative as well).
Schedule
0700-0830 Breakfast
0900–1200 Topic 2
0900–0915
Introduction to Topic 2 (Laetitia/Matt)
0915–1015
Break-out groups
- 2A: **What is a healthy microbiome? ** Does microbial diversity matter for the host? Are more microbes better? Or fewer beneficial symbionts?
- 2B: How to identify the tipping point from symbiosis to dysbiosis in host-associated microbiomes?
10:15–1045
Report and discuss ideas
1045–1115 Break
1115–1200
Summary and discussion of morning sessions
1200–1300 Lunch
1300–1500
Break-out groups: Modelling of host-microbe interactions.
Introduction by Jonathan Eisen
2C: How do we go from describing the variation to deciphering what is driving it.
2D: A null model for microbial communities
2E: Monitoring host-microbe interactions: can we identify model systems or hosts to monitor (e.g., host-microbiomes with cosmopolitan distribution)?
1500–1545
Report and discuss ideas
1545–1700 Break
1700–1830
General discussion How do we progress from surveying the microbiome to modeling it? How do we move from defining variation to understanding what is driving it?
1830–1930 Dinner
After dinner social mixing, relaxing, resting, individual time.
19:30–
For those interested Laetitia will organize a voluntary session on modeling the null model of microbial colonization of a host that night.
We need a theoretical framework that simulates how a Null hypothesis would look like. In the case of microbiomes this is a distribution of microorganisms (in a simple case just 16S reads) on hosts that does not follow any form of coevolution with the host. Just random assemblages that follow rules of colonization, migration, drift and mutation.