I Contain Multitudes: The Microbes Within Us and a Grander View of Life

by Ed Yong

The Earth is 4.54 billion years old. A span of time that big is too mind-boggling to comprehend, so let’s collapse the planet’s entire history into a single calendar year.1 Right now, as you’re reading this page, it is 31st December, just before the stroke of midnight. (Thankfully, fireworks were invented nine seconds ago.) Humans have only existed for the last 30 minutes or fewer. The dinosaurs ruled the world until the evening of 26th December, when an asteroid hit the planet and wiped them out (except for the birds). Flowers and mammals evolved earlier in December. In November, plants invaded the land and most of the major animal groups appeared in the seas. Plants and animals are all made up of many cells, and similar multicellular organisms had certainly evolved by the start of October. They may have appeared before that – the fossils are ambiguous and open to interpretation – but they would have been rare. Before October, almost every living thing on the planet consisted of single cells. They would have been invisible to the naked eye, had eyes existed. They had been that way ever since life first emerged, some time in March.

Even now, the photosynthetic bacteria in the oceans produce the oxygen in half the breaths you take, and they lock away an equal amount of carbon dioxide.

there are more bacteria in your gut than there are stars in our galaxy.

It’s commonly said that the average person contains ten microbial cells for every human one, making us rounding errors in our own bodies. But this 10-to-1 ratio, which shows up in books, magazines, TED talks, and virtually every scientific review on this topic, is a wild guess, based on a back-of-the-envelope calculation that became unfortunately enshrined as fact.7 The latest estimates suggest that we have around 30 trillion human cells and 39 trillion microbial ones – a roughly even split. Even these numbers are inexact, but that does not really matter: by any reckoning, we contain multitudes.

There are fewer than 100 species of bacteria that cause infectious diseases in humans;

If one partner benefited at the expense of the other, it was a parasite (or a pathogen if it caused disease). If it benefited without affecting its host, it was a commensal. If it benefited its host, it was a mutualist. All these styles of coexistence fell under the rubric of symbiosis.

Jeff Gordon, a pioneer we will meet in a later chapter, showed that our microbes control the storage of fat and the creation of new blood vessels, and that obese individuals have different gut microbes to lean ones.42

She found that the microbe activated a wide range of mouse genes that are involved in absorbing nutrients, building an impermeable barrier, breaking down toxins, creating blood vessels, and creating mature cells. In other words, the microbe told the mice how to use their own genes to make a healthy gut.8 Scott Gilbert, a developmental biologist, calls this idea co-development. It’s as far as you can get from the still-lingering idea that microbes are just threats. Instead, they actually help us become who we are.9

Next, the team showed that obese people (and mice) have different communities of microbes in their guts.10 The most obvious difference lay in the ratio of the two major groups of gut bacteria: obese people had more Firmicutes and fewer Bacteroidetes than their leaner counterparts. This raised an obvious question: does extra body fat tilt the Bacteroidetes/Firmicutes see-saw or, more tantalisingly, does the tilt make individuals fatter? The team couldn’t answer that question by relying on simple comparisons. They needed experiments.

Ridaura saw that the ‘lean’ microbes invaded guts that were already colonised by ‘obese’ communities, and stopped their new hosts from putting on weight. The opposite invasions never worked: the obese communities could never gain a foothold if the lean ones were around. It’s not that the lean communities were inherently superior. Instead, Ridaura had tipped the battles in their favour by feeding her mice with plant-heavy chow. The complex fibres in these meals created many opportunities for microbes with the right digestive enzymes – “job openings for them to fill”, in Gordon’s words. The obese communities had few species that could fill those positions but the lean communities were brimming with qualified candidates, including fibre-busting specialists like B-theta. So, when obese communities colonised lean guts, they found that every morsel of food was already being devoured and every niche had been filled. By contrast, when the lean communities entered obese guts, they found a glut of uneaten fibre – and flourished. Their success only evaporated when Ridaura fed the mice with fatty, low-fibre chow, designed to represent the worst extremes of the Western diet. Without fibre, the lean communities couldn’t establish themselves or stop the mice from putting on weight. They could only infiltrate the guts of mice that ate healthily. The old dietary advice still stands, overenthusiastic headlines be damned.

microbes matter but so do we, their hosts. Our guts, like all ecosystems, aren’t defined just by the species within them but also by the nutrients that flow through them. A

by monitoring the gut microbiomes of volunteers who ate twice-daily servings of Activia yoghurt for seven weeks. The bacteria in the yoghurt neither colonised the volunteers’ guts, nor changed the composition of their microbiomes. It’s the same problem that Herter and Kendall identified in the 1920s, and that Matthew Becker and others saw when working on probiotics for frogs. They’re like a breeze that blows through two open windows.16

The very word “probiotics” is an answer of sorts. The World Health Organization defines them as “live microorganisms which, when administered in adequate amounts, confer a health benefit on the host”. They are, by definition, healthy.

Substances that selectively nourish beneficial microbes are called prebiotics

He found that thoroughly scrubbed toilets are first colonised by faecal microbes, which are launched into the air by roiling, flushed water. Those species are eventually outcompeted by a diverse range of skin microbes, but once the toilet gets scrubbed again, the communities go back to square one. So, here’s the irony: toilets that are cleaned too often are more likely to be covered in faecal bacteria.

Outdoors, the air was full of harmless microbes from plants and soils. Indoors, it contained a disproportionate number of potential pathogens, which are normally rare or absent in the outside world, but had been launched from the mouths and skins of hospital residents. The patients were effectively stewing in their own microbial juices. And the best way of fixing that was remarkably simple: open a window.