The Bacterial Microbiome, and Fish Tacos

Mostly when I think about what I want to be when I grow up, I wish I were a scientist.  Some days, it’s an CIA code breaker.  Some days it’s a musician in the New York Philharmonic.  But more often than not, I want to be a scientist.  Admittedly, I’m not sure what kind because almost everything in science interests me.  For the most part though, I waver between an astrophysicist (black holes! utter coolness) and a biologist.

Today, I want to be a biologist because this morning, I read about Fish Taco.[i]

Why would a recipe inspire me to pine for a career change, you ask?  “Fish Taco” – as in “Functional Shifts Taxonomic Contributors,” not a Mexican pescatarian delight.  Fish Taco is a computational method whereby scientists at the University of Washington are attempting to figure out what functional imbalances of the bacterial microbiome lead to disease.[ii]

“The method allows us to pinpoint which microbial species in our microbiome are responsible for each functional imbalance so they can be targeted for therapy,” says the senior author of the paper, Elhanan Borenstein.  Basically, Fish Taco analyzes not just what is in a given bacterial microbiome but also, what are the various bacteria doing.  (I refer you back to my last couple of posts on the metabolome.)

In this published study, the researchers used Fish Taco to analyze the microbiomes of people with type 2 diabetes and inflammatory bowel disease, in an attempt to figure out what imbalance contributed to the diseases.  Not surprisingly to me, they found that the functional shift can be driven by diverse combinations of species.

While I think this is a brilliant first step, it really does highlight the difficulty of studying parts of the biome in isolation.  That is, one person may have X shift in bacteria lead to a particular disease while another person may have Y shift lead to the same disease.  What are the differentiating factors?  And do all people with X or Y shift develop that disease or do some remain healthy?  If not, why not? Do some people with that exact shift develop a different disease?

And remember too – these researchers are only studying the bacterial microbiome at this point.  They haven’t yet even begun to look at the virome, the mycobiome, the macrobiome…and how each of these affects the other, not just our state of health or disease.  What if it turns out that someone with X shift does not develop the disease because they have a particular type of virome?  Or a particular yeast in their mycobiome?

The complexity is mind blowing.

Every time I read something like this, it strikes me yet again how early we are in this research, and yet… how amazing it would be to actually be involved in sorting this all out.  When you think of the number of diseases we already know stem from alterations in the human biome (and how many more are suspect), you realize we are on the path – someday, a long time from now – to discovering how to prevent and cure so many, many things.


[i] University of Washington Health Sciences/UW Medicine. “‘FishTaco’ sorts out who is doing what in your microbiome: A new method reveals roles different bacteria play in microbiome imbalances linked to disease.” ScienceDaily. ScienceDaily, 19 January 2017. <>.

[ii] Ohad Manor, Elhanan Borenstein. Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome. Cell Host & Microbe, 2017; DOI: 10.1016/j.chom.2016.12.014

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