Ed Yong

I Contain Multitudes

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tarjei lovebothas quoted7 months ago
The variations that exist between body parts dwarf those that exist between people. Put simply, the bacteria on your forearm are more similar to those on my forearm than to those in your mouth.
tarjei lovebothas quoted7 months ago
There are fewer than 100 species of bacteria that cause infectious diseases in humans;8 by contrast, the thousands of species in our guts are mostly harmless. At worst, they are passengers or hitchhikers. At best, they are invaluable parts of our bodies: not takers of life but its guardians.
Soliloquios Literarioshas quotedlast year
When animals get sick, we frequently lose our appetite – a sensible tactic that diverts energy from foraging and towards getting better. It also means that our gut microbes experience a temporary famine. Sick mice deal with this problem by releasing emergency rations: a simple sugar called fucose. Gut microbes can snip off this sugar and feed on it, staying alive while they wait for their hosts to resume normal service.40
Soliloquios Literarioshas quotedlast year
These interactions matter, because they foster stability. If a single bacterium was too efficient at harvesting glycans, it might eat away the mucus barrier itself, creating openings through which other microbes could enter. But if there are hundreds of competing species, they can all keep each other from gluttonously monopolising the food supply. By offering a wide array of nutrients we feed a wide range of microbes and stabilise our enormous, diverse communities. And those communities, in turn, make it harder for pathogens to invade. By setting the table correctly, we ensure that the right guests turn up to dinner, while gatecrashers are locked out
Soliloquios Literarioshas quotedlast year
They have already found something weird: phages are great at sticking to mucus, but they do so ten times more efficiently if there’s breast milk around. Something in the milk helps them anchor in place. The culprits seem to be little spheres of fat, encased in proteins that resemble those in mucus. If you let a glass of milk sit in the open, the layer of fat that forms on the surface is full of these globules. They provide nutrition to a baby, but they might also give baby’s first viruses a foothold in the gut
Soliloquios Literarioshas quotedlast year
German was right: it’s far more than a bag of chemicals. It nourishes baby and bacteria, infant and infantisalike. It’s a preliminary immune system that thwarts more malevolent microbes. It is the means by which a mother ensures that her children have the right companions, from their first days of life.39 And it prepares the baby for life ahead.
Soliloquios Literarioshas quotedlast year
Human breast milk stands out among that of other mammals: it has five times as many types of HMO as cow’s milk, and several hundred times the quantity. Even chimp milk is impoverished compared to ours. No one knows why this difference exists, but Mills offers a couple of good guesses. One involves our brains, which are famously large for a primate of our size, and which grow incredibly quickly in our first year of life. This fast growth partly depends on a nutrient called sialic acid, which also happens to be one of the chemicals thatB. infantisreleases while it eats HMOs. It is possible that by keeping this bacterium well fed, mothers can raise brainier babies. This might explain why, among monkeys and apes, social species have more milk oligosaccharides than solitary ones, and a greater range of them to boot. Larger groups mean more social ties to remember, more friendships to manage, and more rivals to manipulate. Many scientists believe that these demands drove the evolution of primate intelligence; perhaps they also fuelled the diversity of HMOs.

An alternative idea involves diseases. Pathogens can easily bounce from one host to another, so group-living animals need ways of protecting themselves against rampant infections. HMOs provide one such defence. When pathogens infect our guts, they almost always begin by latching onto glycans – sugar molecules – on the surface of our intestinal cells. But HMOs bear a striking resemblance to these intestinal glycans, so pathogens sometimes stick to them instead. They act as decoys to draw fire away from a baby’s own cells. They can block a roll call of gut villains including Salmonella; Listeria; Vibrio cholerae, the culprit behind cholera; Campylobacter jejuni, the most common cause of bacterial diarrhoea; Entamoeba histolytica, a voracious amoeba that causes dysentery and kills 100,000 people every year; and many virulent strains of E. coli.They may even be able to obstruct HIV, which might explain why most infants who suckle from infected mothers don’t get infected despite drinking virus-loaded milk for months. Every time scientists have pitted a pathogen against cultured cells in the presence of HMOs, the cells have come out smiling. This helps to explain both why breast-fed babies have fewer gut infections than bottle-fed ones and why there are so many HMOs. “It makes sense that they would need to be diverse enough to handle a range of pathogens, from viruses to bacteria,” says Mills. “I think it’s the amazing diversity that provides a constellation of protections.
Soliloquios Literarioshas quotedlast year
These parallel tracks met in 1954, thanks to a partnership between Richard Kuhn (chemist, Austrian, Nobel laureate) and Paul Gyorgy (paediatrician, Hungarian-born American, breast-milk advocate). Together, they confirmed that the mysterious bifidus factor and the milk oligosaccharides were one and the same – and that they nourished gut microbes. (It often takes partnerships between different branches of science to understand the partnerships between different kingdoms of life.)
Soliloquios Literarioshas quotedlast year
It earns its keep. 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. Likewise, for a child to reap the full benefits that milk can provide, B. infantis must be present.36 For that reason, David Mills, a microbiologist who works with German, actually sees B. infantisas part of milk, albeit a part that is not made in the breast
Soliloquios Literarioshas quotedlast year
The rangers only get time off at the very start of our lives, when in microbiological terms we are blank slates. 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. But without the immune system’s full selective powers, how can a mammalian baby ensure that it gets the right communities?

Its mother helps. Mother’s milk is full of antibodies which control the microbial populations of adults – and babies take up these antibodies during breastfeeding. When immunologist Charlotte Kaetzel engineered mutant mice that could not produce one of these antibodies in their milk, she found that their pups grew up with bizarre gut microbes.31 They were full of species that are typically found in people with inflammatory bowel diseases, and many of these bacteria wormed their way through the gut walls to inflame the lymph nodes lying underneath. As we saw earlier, many harmless bacteria are harmless only by virtue of where they are. Milk keeps them restrained. And it does much more than that. Milk is one of the most astounding ways in which mammals control their microbes.
Soliloquios Literarioshas quotedlast year
Milk is a mammalian innovation. 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. The ingredients of that fluid have been tweaked and perfected through 200 million years of evolution to provide all the nutrition that infants need. Those ingredients include complex sugars called oligosaccharides. 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.

When German first learned about HMOs, he was gobsmacked. Why would a mother spend so much energy manufacturing these complicated chemicals if they were indigestible and therefore useless to her child? Why hasn’t natural selection put its foot down on such a wasteful practice? Here’s a clue: 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?
Soliloquios Literarioshas quotedlast year
These measures – the mucus, the AMPs, and the antibodies – also determine the species that get to stay in the gut.27 We know this because scientists have bred many lines of mutant mice that lack one or more of these components. They all end up with irregular collections of microbes, and usually some kind of inflammatory disease. So the gut’s immune system isn’t an undiscriminating barrier; it isn’t haphazardly mowing down any microbe that gets close. It is selective in its control. It’s reactive, too. For example, many bacterial molecules stimulate gut cells to produce more mucus; the more bacteria there are, the more heavily fortified the gut becomes. Likewise, gut cells release certain AMPs upon receiving bacterial signals; they aren’t constantly shooting into the demilitarised zone, but firing when their targets get too close
Soliloquios Literarioshas quotedlast year
As I write this, Wikipedia still defines the immune system as “a system of biological structures and processes within an organism that protects against disease”. If the system activates, it is because it has sensed a pathogen – a threat that it then wipes out. To many scientists, however, warding off pathogens is just a bonus trick. 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
Soliloquios Literarioshas quotedlast year
But we also need more specific ways of fine-tuning our microbial communities, and firmer blockades for keeping them in place. Remember that location is important: microbes can easily switch from beneficial allies to fatal threats depending on where they are. So, many animals set up actual barriers for walling off their microbial gardens.
Soliloquios Literarioshas quotedlast year
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.
Soliloquios Literarioshas quotedlast year
This concept has profound implications. It suggests that phages – which, remember, are viruses – have a mutually beneficial relationship with animals, including us. They keep our microbes in check and we, in return, help them to reproduce by offering them a world full of bacterial hosts: Phages are 15 times more likely to find a victim if they stick to mucus. And since mucus is universal in animals, and phages are universal in mucus, this partnership probably started at the dawn of the animal kingdom. In fact, Rohwer suspects that phages were the original immune system – the means through which the simplest animals controlled the microbes at their door.24 These viruses were already plentiful in the environment. It was a simple matter of concentrating them by giving them a layer of mucus in which to anchor themselves. From this basic beginning, more complex means of control emerged
Soliloquios Literarioshas quotedlast year
Like all the best relationships, these ones take work. Every major transition in the history of life – from single-celled to multi-celled, from individuals to symbiotic collectives – has had to solve the same problem: how can the selfish interests of individuals be overcome to form cooperative groups?
Soliloquios Literarioshas quotedlast year
The skin is different: it varies from cool, dry deserts like the forearm to warm, humid jungles like the groin or armpits. 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. However, concealed niches, like sweat glands, can support the growth of oxygen-hating anaerobes like Propionibacterium acnes, the microbe that causes acne. All over our bodies, the laws of physics and chemistry sculpt bundles of biology
Soliloquios Literarioshas quotedlast year
The human gut might seem like nirvana for microbes, with its regular baths of food and fluid. But it is a challenging environment, too. That food supply comes in a fast-flowing torrent, so microbes need to grow quickly or carry molecular anchors to maintain a foothold. 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. Some of them are so reliant on the absence of oxygen that they die in its presence
Soliloquios Literarioshas quotedlast year
The very term symbiosis has been twisted so that its original neutral meaning – “living together” – has been infused with positive spin, and almost flaky connotations of cooperation and harmony. But evolution doesn’t work that way. It doesn’t necessarily favour cooperation, even if that’s in everyone’s interests. And it saddles even the most harmonious relationships with conflict.
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