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

by Ed Yong

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

Animals belong to a group of organisms called eukaryotes, which also includes every plant, fungus and alga.

All eukaryotes share these traits because we all evolved from a single ancestor, around two billion years ago.

Before that point, life on Earth could be divided into two camps or domains: the bacteria, which we already know about, and the archaea, which are less familiar and have a fondness for colonising inhospitable and extreme environments. These two groups both consisted of single cells that lack the sophistication of eukaryotes.

a bacterium somehow merged with an archaeon,

It’s our creation story: two great domains of life merging to create a third,

The archaeon provided the chassis of the eukaryotic cell while the bacterium eventually transformed into the mitochondria.5

the merger that created it – the one between an archaeon and a bacterium – was so breathtakingly improbable that it has never been duplicated,

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

The human skin microbiome is the domain of Propionibacterium, Corynebacterium, and Staphylococcus, while Bacteroides lords over the gut, Lactobacillus dominates the vagina, and Streptococcus rules the mouth.

Many conditions, including obesity, asthma, colon cancer, diabetes, and autism, are accompanied by changes in the microbiome, suggesting that these microbes are at the very least a sign of illness, and at most a cause of it.

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.

The easiest way of checking if an animal needs microbes to develop properly is to deprive it of them.

Why have animals effectively outsourced parts of their development to other species?

They were the rulers of the planet long before we arrived. And when we did arrive, of course we evolved ways of interacting with the microbes around us.

choanoflagellates.

choanos are the closest living relatives of all animals.

All modern animals are multicellular creatures that begin life as a hollow ball of cells and eat other things for sustenance, so it’s reasonable to think that our common ancestor shared the same traits.

It’s not a stretch to think that some molecules produced by bacteria may have influenced the development of the first animals.”

Navy folks call it “the squiggly worm”. Michael Hadfield, a marine biologist at the University of Hawaii, knows it as Hydroides elegans.

They follow clues like chemical trails, temperature gradients, and even sounds, to find the best spots for metamorphosis.

H. elegans was drawn to bacteria and specifically to biofilms

After a few minutes, it anchors itself by extruding a thread of mucus from its tail, and secretes a transparent sock around its body.

This transformation utterly depends upon bacteria.

only a few could induce metamorphosis, and only one did so strongly. Its gargled mouthful of a name is Pseudoalteromonas luteoviolacea. Mercifully, Hadfield just calls it P-luteo.

The oceans are swarming with baby animals that only complete their life cycles upon contact with bacteria – and often P-luteo in particular.

The presence of a biofilm provides a larval animal with important information. It means that: (a) there’s a solid surface, (b) which has been around for a while, (c) isn’t too toxic, and (d) has enough nutrients to sustain microbes. Those reasons are as good as any to settle down. The better question would be: Why wouldn’t you rely on bacterial cues? Or better still: what choice do you have?

flatworm Paracatenula

Pretty much everything behind the brain is either microbe or living quarters for microbes.

Paracatenula is a master of regeneration. Cut it in two, and both ends become fully functional animals. The back half will even re-grow a head and brain.

the only bit of the flatworm that can’t regenerate is the bacteria-free head. The tail will re-grow a brain but the brain alone will not produce a tail.

our bodies are continuously built and reshaped by the bacteria inside us.

an animal’s genome doesn’t provide everything it needs to create a mature immune system. It also needs input from a microbiome.

the immune system isn’t innately hard-wired to tell the difference between a harmless symbiont and a threatening pathogen. In this case, it’s the microbe that makes that distinction clear.

The immune system isn’t just a means of controlling microbes. It is at least partly controlled by microbes.

if you list all the chemicals the microbes produce – their metabolites – you can tell what those species are actually doing.

changing a mouse’s microbiome can change its behaviour, the chemicals in its brain, and its susceptibility to the mouse versions of anxiety and depression.

In the last few years, I’ve seen the viewpoint that “all bacteria must be killed” slowly give ground to “bacteria are our friends and want to help us”, even though the latter is just as wrong as the former.

evolution doesn’t work that way. It doesn’t necessarily favour cooperation, even if that’s in everyone’s interests.

The microbiome is incredibly important but it doesn’t mean that it’s harmonious,” says evolutionary biologist Toby Kiers.

The gut is a dark world, so microbes that depend on sunlight to make their food cannot thrive. It lacks oxygen, which explains why the overwhelming majority of gut microbes are anaerobes – organisms that ferment their food, and grow without this supposedly essential gas.

The skin is different:

Sunlight is abundant, but is also a problem because of the ultraviolet radiation it contains. Oxygen matters here too, and since most of the skin is exposed to fresh air, aerobes thrive.

Mucus is made from giant molecules called mucins, each consisting of a central protein backbone with thousands of sugar molecules branching off it. These sugars allow individual mucins to become entangled, forming a dense, nearly impenetrable thicket – a Great Wall of Mucus that stops wayward microbes from penetrating deeper into the body. And if that wasn’t deterrent enough, the wall is manned by viruses.

you probably think of Ebola, HIV, or influenza: well-known villains that make us sick. But most viruses infect and kill microbes instead. These are called bacteriophages – literally, “eaters of bacteria” – or phages,

The immune system’s main function is to manage our relationships with our resident microbes. It’s more about balance and good management than defence and destruction.

Rather than limiting microbes, our immune system evolved to support even more of them.29

To allow our first microbes to colonise our newborn bodies, a special class of immune cells suppresses the rest of the body’s defensive ensemble, which is why babies are vulnerable to infections for their first six months of life.30 It’s not because their immune system is immature, as is commonly believed: it’s because it is deliberately stifled to give microbes a free-for-all window during which they can establish themselves.

Mother’s milk is full of antibodies which control the microbial populations of adults – and babies take up these antibodies during breastfeeding.

Every mammal mother, whether platypus or pangolin, human or hippo, feeds her baby by literally dissolving her own body to make a white fluid that she secretes through her nipples.