Community Restoration – In Your Nose

I’ve previously posted about using probiotics/bioaugmentation as a way to reduce or prevent infection.  At EEID 2013, many talks and posters considered this role of the microbiome.  I’m going to quickly give you an example, and then talk about a really cool discussion topic: using perturbations to cultivate bacterial communities associated with healthy organisms.

Katherine Lemon studies the bacterial communities in the human nose.  (Swag points go to her for a talk entitled “Nose picking for progress: mining for bacterial strains with therapeutic potential.”)  Specifically, she’s interested in Staphylococcus aureus, a bacteria that she calls a “pathobiont.”  S. aureus hangs out in the noses of ~30% of adults, typically not causing any problems, but sometimes it goes rogue and becomes a serious pathogen.  Interestingly, it looks like other bacteria species in the respiratory tract can inhibit S. aureus growth, just like some bacteria inhibit Bd on amphibians.

Your guess about what is going on here is as good as mine. I never said my cartoons make sense.

During her talk, Katherine talked about diseases of “dysbiosis.”  These are diseases that result from something being off in the symbiotic bacterial community.  How can we treat such diseases?  Well, this is a good place for community ecologists to step in, because the question really is: how do we go from our current community (the community associated with a diseased state) to a different community (the community associated with a healthy state)?  The field of restoration ecology may be a particularly good place to start.

First, there’s the interesting example of the fecal transplant.  This has been in the news recently, so you’ve probably heard of it.  In short, people with dysbiosis resulting in diarrhea are treated by having feces from someone with a healthy bacterial community “transplanted” into their intestine.  Katherine mentioned something that I hadn’t known about these fecal transplants.  That is, first, the patient is given a laxative, which pretty much totally flushes out the old bacteria community.  I find that really interesting, because in restoration ecology, you don’t typically wipe out the old community and just try to stick the target community in it’s place.

How is treating a disease of dysbiosis like restoring a plant/animal community?  How is it different?  Isn’t this awesome?!

Parasite(ish)-Host Coevolution

Continuing on my not-parasite-but-kinda-similar trend, let’s talk about bacteria and phages.  This post was stimulated by a really cool talk by Britt Koskella, from the University of Exeter.  She has a wordpress site and has been tweeting about the EEID conference, so head that way for more cool stuff.  (Maybe she’ll also come correct places where I butcher her work.)

A bacteriophage is a virus that infects bacteria.  In Britt’s case, the bacteria of interest are parasites of the horse chestnut tree.  She studies the co-evolution of these three groups: the trees, the bacteria, and the phages.  Importantly, because these organisms/phages have very different life spans, we expect phages to evolve faster than bacteria, which should in turn evolve faster than trees.

Question 1:  Do we see local adaptation of phages to the bacteria of a given tree?  Answer:  Yep!  If you take leaves from multiple trees and culture the bacteria from those leaves, and then test all the phages on all of those bacteria cultures, you find that phages do best on bacteria from the tree that they were collected on.  Also, phages did better on bacteria from the interior of the leaves, which makes sense because the exterior is likely highly controlled by abiotic processes (e.g., UV radiation).

My cartoon of Britt’s graph. Phages are more successful at infecting bacteria from the tree they were collected on (sympatric tree) than other trees (allopatric trees).

Question 2:  Given that we see local adaptation of phages to bacteria, does that adaptation vary with time?  Answer:  Yep!  In this part, Britt calculated “local adaptation” as an index comparing phage success on bacteria from sympatric vs. allopatric trees.  She cultured bacteria from trees from each month in the season, and tried the phages from the last month on all of those cultures.  Does that make sense?  So, September phages on September bacteria, September phages on August bacteria, September phages on July bacteria, etc.  Here’s what she found: phages were most adapted to the bacteria from the previous month (=August), and then adaptation declined as you went further back in time.  She suggested that this is demonstrative of fluctuating selection, rather than an arms race between bacteria and phages.  That is, in an arms race, you should never see a decline in phage success as you go backwards in time.

Phages are most adapted to the bacteria of the prior month, and then adaptation declines as you continue backwards in time.

So, that was a lot about the phage evolution, but what about the bacteria?  Question 3: Do bacteria evolve resistance to phages?  Answer: Yep!  Since she had all of those monthly bacteria  and phage samples, she tested bacterial resistance to phages that were from the past time step, the present time step, and the future time step.  Bacteria were most resistant to past phages, indicating that bacteria evolve to resist their phage.  They were least resistant to phages from the future, which indicates that phages also evolve to better infect bacteria.  Neat!

(Edit: Check out Britt’s comment below about whether this pattern is the result of pairwise coevolution or species sorting.  More coolness to come!)


All of the parasite-host co-evolution stuff is super cool.  Britt also looks at co-evolution in other disease systems, and you can check out some of that work here.

Don’t you really, really want to do experiments where you’re looking “into the future?”  Futuristic snails must be awesome.  I’m sensing an upcoming cartoon…


Britt Koskella. 2013. Bacteria-phage interactions within a long-lived host.  EEID.

Koskella, B., Thompson, J.N., Preston, G.M. & Buckling, A. 2011. Local biotic environment shapes the spatial scale of bacteriophage adaptation to bacteria. The American Naturalist177(4):440-51.

More coming soon!