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

by Ed Yong

Every mammal makes them but human mothers, for some reason, churn out an exceptional variety – scientists have identified over 200 human milk oligosaccharides, or HMOs, so far.32 They are the third-biggest part of human milk, after lactose and fats, and they should be a rich source of energy for growing babies. But babies cannot digest them.

these sugars pass through the stomach and the small intestine unharmed, and land in the large intestine where most of our bacteria live. So, what if they aren’t food for babies at all? What if they are food for microbes?

As it digests HMOs, B. infantis releases short-chain fatty acids (SCFAs) that feed an infant’s gut cells – so while mothers nourish this microbe, the microbe in turn nourishes the baby. Through direct contact, B. infantis also encourages gut cells to make adhesive proteins that seal the gaps between them, and anti-inflammatory molecules that calibrate the immune system. These changes only happen when B. infantis grows on HMOs; if it gets lactose instead, it survives but doesn’t engage in any repartee with the baby’s cells. It unlocks its full beneficial potential only when it feeds on breast milk.

Once we are weaned, it falls to us to nourish our own microbes. We do this partly through our diet, which provides a diverse flood of branching sugar molecules – glycans – to replace the lost HMOs.

if babies are born through a cut in their mother’s abdomen, their starter microbes come from her skin and the hospital environment, instead of her vagina.

C-section babies are more likely to develop allergies, asthma, coeliac disease, and obesity later in life.

Bottle-feeding might exacerbate these problems.

we have utterly failed to develop new drugs to replace the ones that are becoming obsolete. We are heading into a terrifying post-antibiotic era.

We have been tilting at microbes for too long, and created a world that’s hostile to the ones we need.

termites lose the lining of their guts, and all the microbes within, every time they moult their outer shells. So they regularly need to lick their sisters’ backsides to replenish their supply.

Many familiar animals, including cows, elephants, pandas, gorillas, rats, rabbits, dogs, iguanas, burying beetles, cockroaches, and flies, regularly eat each other’s faeces – a practice known as coprophagy.

even genetically identical mice that live in the same cage end up with slightly different microbiomes.

In his classic book The Extended Phenotype, Richard Dawkins introduces the idea that an animal’s genes (its genotype) do more than sculpt its body (its phenotype). They also indirectly shape the animal’s environment.

evolution by natural selection depends on just three things: individuals must vary; those variations must be heritable; and those variations must have the potential to affect their fitness – that is, their ability to survive and reproduce.

you don’t need to redefine evolutionary theory in order to appreciate that the fates of microbes can become deeply entangled with those of animals.

chemosynthesis: making your own food using chemical energy instead of light or solar energy.

Osedax mucofloris, the gutless bone-eating snot-flower worm,

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

All the animals that live at hydrothermal vents today, Riftia included, evolved from shallow-water species that became hosts for deep-sea microbes.

microbes shaped the evolution of the mammalian gut, and the shape of the mammalian gut influenced the evolution of microbes.

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.