Your Microbiome’s Composition: Nature, Nurture, or Plain Randomness?

Guess what type of creature represented you in this research?

In 1995, the European Journal of Physics published a paper apparently proving that when a slice of buttered toast falls from table height, it will land butter-side down 62% of the time.

We humans love good, solid, logical explanations, and in this case the researchers explained that when toast falls from a table, it only has time to perform half a somersault during its fall to the floor.

And since it starts butter-side up, it’s more likely to end up the other way round at the conclusion of this brief journey.

See? A logical explanation.

Another conundrum – closer to home for us at uBiome – is why individuals’ microbiomes vary so much from person to person.

According to scientists at the University of Colorado, Boulder, although your human genome is around 99.9% identical to the person waiting in front of you in the supermarket checkout line, your microbiomes could be 80% to 90% different.

Is there a logical explanation?

Perhaps it’s something genetic or environmental?

Or maybe it’s to do with the contents of your carts, meaning you and your neighbor eat completely different diets?

Well, while such factors undoubtedly play some part in the composition of your microbiome, researchers at MIT have just published a fascinating paper strongly suggesting that another important contributing factor is… chance.

We’ll explain more in a minute, but the headline finding of this intriguing study was that when identical living organisms were kept in an identical environment, and fed an identical diet of two strains of bacteria, their guts were colonized by either one strain or the other, rather than a mix of the two.

And there was a roughly 50/50 chance which strain would predominate.

The study was conducted at MIT’s Gore Lab, which is an ecological systems biology facility.

The lab’s Principal Investigator, Jeff Gore, an Associate Professor of Physics at MIT, explained why an experiment such as this needed the help of creatures other than humans: “What you would like to do is take a bunch of identical individuals, place them in identical environments, and then look to see whether the microbial communities are the same or different. That’s a very difficult experiment to do with people, but with model organisms it’s feasible.”

A model organism, by the way, is a non-human species that can be extensively studied, with the expectation that findings from experiments with this organism will also cast light on the workings of another species.

So who, or what, was your stand-in for this study?

Well, it was a species of worm, named Caenorhabditis elegans.

Yup, you were represented by a worm.

C. elegans is a transparent roundworm, about 1 mm in length, which has some of the same organ systems as large animals, although no circulatory or respiratory systems.

This makes it an ideal, if perhaps unwitting, participant in laboratory studies, of which there have been many.

For example, back in 1998, this unassuming little worm was the first multicellular organism to have its whole genome sequenced.

Rather strangely, the gut of C. elegans ordinarily contains granules that emit a brilliant blue fluorescence when observed under ultraviolet light, and the worm’s transparency means this glow can be seen from the outside.

It was this combination of fluorescence and transparency that laid the groundwork for the MIT study.

The ingenious researchers engineered two strains of E. coli, one of which produced a green fluorescent protein, the other producing a red fluorescent protein.

Worms were cultivated to be germ-free, with no bacteria in their guts, and also sterilized so they were unable to reproduce during the experiment.

So, what’s a worm to do when it can’t get up to any funny business?

Well, there’s always eating, and C. elegans is fortunately particularly partial to bacteria.

The scientists placed the tiny critters in a liquid culture for a week, ensuring they all experienced a uniform environment.

This culture contained evenly distributed, equal amounts of the red and green E. coli.

What happened after seven days, then?

Well, when the worms were observed under a microscope using ultraviolet light, individuals glowed either completely red or completely green.

It meant that each worm’s gut had been colonized entirely by one strain or the other, rather than a combination of the two.

Jeff Gore observed: “Whichever color bacteria is lucky and happens to survive getting eaten and sticks to the gut, this bacterium starts growing, and it can grow to dominate the gut community.”

What a fascinating finding.

As we’ve seen, microbiomes vary extensively between individuals, even those living in the same environment, and the composition of someone’s microbiome can have important health consequences.

The prospect that sheer chance can play some part in bacterial composition is really most intriguing.

Researchers went on to obtain similar results using two different species of bacteria – Enterobacter aerogenes and Serratia marcescens.

Once again, the guts of worms kept in a liquid culture containing equal proportions of the two species ended up being dominated by one species or the other.

So, while there’s apparently a logical explanation for your toast falling butter-side down (meaning that Murphy’s Law has perhaps been scientifically validated), when it comes to the composition of your microbiome, it could be that a certain amount of randomness is involved.

A case of microbial “first come, first served,” perhaps.

More reading

A Short History of C. elegans Research

Breakfast at Murphy’s (or why the toast lands butter-side down)

Caenorhabditis elegans

Defining the Human Microbiome

Gore Lab

Microbiome diversity is influenced by chance encounters

Stochastic assembly produces heterogeneous communities in the Caenorhabditis elegans intestine

Tumbling toast, Murphy’s Law and the fundamental constants