Panama meeting day #4

Raquel presenting the summary of the “what is a healthy microbiome?” discussion.

Discussion day!   After I took a nice jungle hike this morning we had another good breakfast and then convened in the classroom for some really amazing discussions.   We split into two big groups today.   The first group was supposed to discuss  “What is a healthy microbiome? Does microbial diversity matter for the host? Are more microbes better? Or fewer beneficial symbionts?”.  We had a great discussion about these topics, our group contained a nice mix of microbiome folks and community ecologists.   We started off saying that it was basically impossible to define a healthy microbiome, but in the end we did come up with some possible parameters to consider (e.g. stability, resilience to pathogens, correlated with host/ecosystem health).   A large part of the discussion was about diversity (is it always good?, what does it even mean?, how do we define it?) and how to actually measure “health” of either an ecosystem, a host, or a microbiome.

Jungle trail on station

The second group was tasked with “How to identify the tipping point from symbiosis to dysbiosis in host-associated microbiomes?“.  They started with the same conclusions that health is difficult to define and subjective.   They described a continuum from “stable/similar/symbiosis” via “in flux” to “dissimilar/variable/dysbiosis”.  Emphasized the need to draw on existing ecological theory to explore and quantify this concept of tipping points.   Key points here would be community assembly, resilience, hysteresis, and feedback loops.

After another delicious lunch, we came back to the classroom for the next set of discussions.   This time there were three groups, tasked with the following topics:

  • 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)?

I got to hang out with the “deciphering drivers” group.  We spend the first third of the discussion trying to come up with general principles to describe drivers of community structure (e.g. biotic factors, host traits, abiotic factors, chance).   The rest of the time was spent listing the various specific drivers that we thought, at a minimum, should be described or at least considered in a marine microbiome study.   Examples of host traits to consider were genotype, age, life history, lifestyle, population/demography, transmission mode, compartmentalization, and diet.  Example of environmental traits included temperature, salinity, electron donors/acceptors, niche-specific co-variants (very broad!), stoichiometry, community structure/ecology, sampling context, light, natural history of the site, and location.

Coconuts to palms

The second group talked about null models.  This is a tough one for me to summarize since I have no ecology or stats in my background.  They talked about how we use null models without knowing it when we do statistical tests, but they might not be the right model for the hypotheses we want to test.   They went through the idea of building a model and what do you need for that (adding terms to the null model).   They then slid into a list of considerations before starting an experiment (replicates, physical environment, sampling potential for broader community etc.).   Last was tossing ideas around about other cool things we could do in this system.  Discussed artificial systems, pooling all the neighbors for microbiome context, enrichment protocols, and bottom-up versus top-down controls on the microbiome.

Anemones (by Jonathan Eisen)

The last group talked about monitoring approaches for the microbiome and potential model systems.  Defined monitoring as observational studies, across either space or time.  Model systems would contain well-defined taxa with known relationships between the host and the microbiome.  Emphasized that model systems require the ability to manipulate experimentally.  Asked about what the impact of the microbiome on the host effect on ecosystem services might be.  Spend the second half of their time trying to figure out what is the low-hanging fruit in the marine microbiome world.   Included bioblitzes, doing work in places where environmentally rich context exists, unique systems (e.g. powerplants), reciprocal transplants, herbivorous fishes, and coral restoration.

Dinner! (some kind of jack)

Had a nice long break, during which I was able to take a cab to the end of the road, walk out on a reef, catch a few fish, clean one for dinner, then take a cab back.  In 70 minutes!  Once we got rolling we did lightning talks (<5 minutes) by various participants.

-Matt LeRay talked about marine symbioses and showed a cool video of examples.

-Tiago Pereira talked about his work on various systems including his current work on marine nematodes.  Particularly interested in spatial-temporal variation in natural systems.   Focused at the moment on marine and terrestrial nematode microbiomes.

-Bob Thacker talked about his work on sponge microbiomes here at Bocas del Toro.  Every species has a very distinct microbiome.

-Jarrod Scott talked about some of the IstmoBiome work at Bocas del Toro and Isla Coiba.  Described a summary of the metagenomic data generated from their water samples at both locations over time.   Have ~140 MAGs (metagenome assembled genomes).

-Lizzy Wilbanks talked about her research interests… having come to microbiome research from a chemistry background.  Interested in ecophyisology, bacterial metabolism, biogeochemical cycles, interactions between species, how do ecological/evolutionary interactions shape microbial symbioses.

-Doug Rasher talked about his work on apparently disparate systems, but which operate on similar fundamental operating principles.  Went into more detail about herbivory on coral reefs and the effect that has on interactions between corals and algae.  Presented some results from a collaboration with Jarrod on fish gut microbiomes.

-Maggie Sogin works on gutless worms found seagrass beds and nearby sediments on Elba Island.  As the name implies, they have no guts… and have symbionts below the cuticle.  They hypothesize that the worms actually digest the symbionts directly which is pretty awesome.  She is working on the flow of sugar through the system via metagenomics and metabolomics.

I missed the next two talks (Ben Yuen and Becky Vega-Thurber) after an unscheduled change in the plan.  Sorry Becky and Ben!

-Then Koty Sharp talked about her work on Astrangia poculata (a hard coral).  She studies the microbiome and how it changes over time (seasonality is a major driver).

And evening off!  Some discussion about hitting the bars in town but we’ll see… I’ll post this now just in case.

Here’s the tweets from the day:

About David Coil

David Coil is a Project Scientist in the lab of Jonathan Eisen at UC Davis. David works at the intersection between research, education, and outreach in the areas of the microbiology of the built environment, microbial ecology, and bacterial genomics. Twitter

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