The Second World War Codebreaker Who’s Helping Us Make Meaning of Our Microbes

And how a less diverse diet can lead to a less diverse microbiome.

Maybe it was just us, but perhaps you also took an interest in code-breaking as a kid?

If so, you may recall that a useful tool in cracking ciphers is a technique called frequency analysis.

When the encoding method is a simple substitution cipher (E becomes F, T becomes U, for example) you can make good headway in understanding a coded message by counting the number of times each letter is repeated, while also knowing that letters appear at differing frequencies.

In English, for example, the made-up words ETAOIN SHRDLU contain, in order, the 12 most frequent letters in a typical piece of text.

So if you have a lot of Fs, they’re likely to be Es, for example.

Of course, the codes, such as Enigma, that were famously used (and cracked) during the Second World War were ridiculously more complicated than mere substitution ciphers.

But imagine our delight when we recently learned that one of Britain’s 1940s Bletchley Park codebreakers was also responsible for developing a measure of diversity known as Simpson’s Diversity Index.

In fact, we currently use a version of it ourselves to rate the biodiversity of microbiome samples in our uBiome Explorer products.

Edward Simpson, born in 1922, became enamored with mathematical statistics when he joined the British Government Code and Cipher School, housed at Bletchley Park in Buckinghamshire.

(Cue James Bond music.)

While there, Simpson worked alongside computing pioneer Alan Turing, and he published his diversity index in 1942, slap bang in the middle of his other wartime work, as a young man of just twenty.

Substitution ciphers – as well as more complex codes – make use of probabilities, a concept that Simpson’s Diversity Index also adopts.

In broad terms, if applying Simpson’s idea to the diversity of your microbiome, his index is based on the probability that any two randomly selected microbes in your sample will come from the same species.

Of course, the very idea of the gut microbiome having diversity stems from the much longer-term study of the biological diversity of our planet.

And, sadly, humankind seems intent on wrecking this.

Just as we eradicated “unwanted” syllables from the words biological and diversity to create the presumably more efficient portmanteau term, “biodiversity,” a ballooning human population and conspicuous consumption has led to the eradication of entire species.

Not for nothing, some scientists label humans a global superpredator.

Go us, right?

Most biologists agree that healthy ecosystems depend on the richness of their species, so as diversity declines, so too does healthiness.

We’ll visit microbiome biodiversity in a moment (although, spoiler alert: higher microbial diversity is generally believed to be good for you), but let’s just focus on what high diversity actually means.

Statisticians and biologists say a diverse population needs two components: it requires plenty of different species, but it should also have abundant numbers of each.

In short, we need both richness and evenness.

Let’s think about two flowerbeds, which we’ll unimaginatively label A and B.

Each contains roses, begonias, and dahlias.

Flowerbed A has 10 roses, 9 begonias, and 11 dahlias.

Flowerbed B, on the other hand, contains 2 roses, 25 begonias, and 3 dahlias.

Both flowerbeds have the same richness (3 species) and the same overall number of plants (30), but Flowerbed A has more evenness than Flowerbed B, so it’s regarded as having the greater diversity.

From garden flora to the gastrointestinal kind, then.

We’ve already revealed that most scientists believe that greater microbial diversity is good for you.

In fact, food expert Michael Pollan summed up their views in a New York Times article, writing that a loss of diversity “may predispose us to obesity and a whole range of chronic diseases, as well as some infections.”

Sadly, just as we humans have brought about a steady decline in terrestrial biodiversity, many of us aren’t exactly playing the game in terms of maintaining good intestinal biodiversity, either.

But why might this be?

Well, there are almost certainly dozens of causes, including the fact that today, many of us lead more antiseptic lives, perhaps under the somewhat misguided impression that this is somehow more hygienic.

But a 2016 article in the scientific journal Molecular Metabolism also proposes that dietary diversity has been lost during the past 50 years, and as the paper explains, “the more diverse the diet, the more diverse the microbiome, and the more adaptable [it is] to perturbations.”

In 1942, nutritionist Victor Lindlahr published a book entitled “You Are What You Eat: how to win and keep health with diet,” which presumably made the “you are what you eat” phrase famous.

While he wasn’t thinking about the microbiome, we might do well to apply his thinking to that invaluable ecosystem of microorganisms, which, even as you read this, is gurgling away in your gut.

Same old food, same old microbiome, perhaps?

Maybe it’s time to ring the changes on your next food buying foray.

Or, even, on your next gppe cvzjoh gpsbz.

More reading

A healthy gastrointestinal microbiome is dependent on dietary diversity


Edward H. Simpson

Edward Simpson – Bayes at Bletchley Park

Holocene extinction

Lourens Baas Becking

Primary production

Say Hello to the 100 Trillion Bacteria That Make Up Your Microbiome

Simpson’s Diversity Index

Species Divergence and the Measurement of Microbial Diversity

Testing the Neutral Theory of Biodiversity with Human Microbiome

You are what you eat – the meaning and origin of this phrase