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

by Ed Yong

But in the deepest oceans, sunlight isn’t an option. You could filter the meagre snow of organic matter raining down from above but to really thrive, you need a different source of energy. For Riftia’s bacteria, that’s sulphur, or rather the sulphides that spew out of the vents. The bacteria oxidise these chemicals and use the liberated energy to fix carbon. This is chemosynthesis: making your own food using chemical energy instead of light or solar energy. And rather than producing oxygen as a waste product, as photosynthetic plants do, these chemosynthesising bacteria churn out pure sulphur. Hence the yellow crystals in Riftia’s trophosome.

Life on Earth originated at deep-sea vents, and first took the form of chemosynthetic microbes.

By sundering plant carbohydrates with their broad toolkits, B-theta and other microbes release substances that directly nourish our own cells. Collectively, they provide 10 per cent of our energy intake, and a whopping 70 per cent of a cow’s or sheep’s.

To eat a diet of plants, animals need microbes in both great diversity and great abundance.

So, mammalian success was founded on vegetarianism, and that vegetarianism was founded on microbes.

Maybe this readiness to pick up new microbes from one another explains why these rodents are so versatile and successful.

In this world, genes aren’t just heirlooms to be passed on vertically from one generation to the next, but commodities to be traded horizontally, from one individual to another. This is exactly the world that bacteria live in.

DNA flows so freely between them that the genome of a typical bacterium is marbled with genes that arrived from its peers.

Sixty years on, we know that HGT is one of the most profound aspects of bacterial life. It allows bacteria to evolve at blistering speeds. When they face new challenges, they don’t have to wait for the right mutations to slowly amass within their existing DNA. They can just borrow adaptations wholesale, by picking up genes from bystanders that have already adapted to the challenges at hand.

The spread of these antibiotic-resistant bacteria is undoubtedly one of the greatest public health threats of the twenty-first century, and it is testament to the unbridled power of HGT.

Over time, useful mutations become more common, while harmful ones fade away. This is classic natural selection – a slow and steady process that affects populations, not individuals.

The Japanese have been eating nori for so long that their gut microbes are peppered with digestive genes from oceanic species.

Dunning-Hotopp published her results with a clear statement: genes move from bacteria to animals.

The mere presence of a guitar in someone’s bedroom doesn’t make them Slash.

parasitoids – body-snatchers that implant their young inside other insects.

They are metabolic wizards that can digest everything from uranium to crude oil.

If you want to defend yourself from another creature or eat a new source of food, there’s almost certainly a microbe that already has the right tools for the job. And if there isn’t, there soon will be: these things reproduce rapidly and swap genes readily. In the great evolutionary race, they sprint, while we crawl.

These simple equations still drive much of modern medical thought. By contrast, the maths of the microbiome are more complicated, because they involve large, changing networks of connected, interacting parts.

They are easy to grow, they are already found in fermented foods, and they can survive the trip through both a commercial packaging plant and a consumer’s stomach. “But most of them never arose in the human gut, and they don’t have the factors that allow them to dwell for a long time there,” says Jeff Gordon.

There’s no such thing as alternative medicine; if it works, it’s just called medicine.

What we need, then, are personalised infusions. We cannot expect the same probiotic strains, or the same donor stools, to treat a variety of diseases.

I contain multitudes, yes, but only some of them; the rest, I extend into the world like a living aura.

In both settings, sterility is a curse not a goal, and a diverse ecosystem is better than an impoverished one. These principles are the same whether we’re talking about a human intestine or an aquarium tank – or even a hospital room.

This makes perfect sense to an ecologist: fresh air brings in harmless environmental microbes that take up space and exclude pathogens.

Almost every architectural design choice affects the microbial ecology of buildings, which could then affect the microbial ecology of us. Or, as Winston Churchill said, “We shape our buildings, and afterwards our buildings shape us.”

“bioinformed design”.

Gilbert is here to talk to Leung and Weigert about implementing his ideas on a much larger scale. He wants to use the principles that he is learning through the home, aquarium, and hospital projects to shape the microbiomes of entire cities, starting with Chicago.