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Kindle Notes & Highlights
by
Ed Yong
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January 18, 2019 - November 7, 2022
Walt Whitman: “I am large, I contain multitudes.”
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.
There are fewer than 100 species of bacteria that cause infectious diseases in humans;
Your cells carry between 20,000 and 25,000 genes, but it is estimated that the microbes inside you wield around 500 times more.
almost three-quarters of a newborn’s strains can be traced directly back to its mother.
It takes anywhere from one to three years for a baby’s microbiome to reach an adult state.
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.
In people, cases of inflammatory bowel disease are usually accompanied by an overabundance of bacteria that provoke the immune system and a lack of those that restrain it.
Epulopiscium fishelsoni, a bacterium that lives only in the guts of the brown surgeonfish, is about the size of this full stop.
If zebrafish or mice grow up in the absence of bacteria their guts don’t develop fully, their pillars are shorter, their walls leakier, their blood vessels look more like sparse country lanes than a dense urban grid, and their cycle of regeneration pedals in a lower gear.
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.
He showed that a single sugar molecule in its coat, polysaccharide A (PSA), could boost the numbers of helper T cells on its own.
If he colonised germ-free versions of the bolder strain with microbes from the timid strain, they became more timid themselves. The opposite was also true: germ-free versions of the timid mice were emboldened by the microbes of their more intrepid cousins.
After the mice ingested this strain, known as JB-1, they were better able to overcome anxiety: they spent more time in the exposed parts of a maze, or the centre of an open field.
They saw that JB-1 changed how different parts of the brain – those involved in learning, memory, and emotional control – responded to GABA, a pacifying chemical that quiets the buzz of excitable neurons.
Richard Stouthamer discovered a group of asexual, all-female wasps, which only reproduced by cloning themselves. This trait was the work of a bacterium, Wolbachia: when Stouthamer treated the wasps with antibiotics, the males suddenly reappeared and both sexes started mating again.
Where Wolbachia does allow males to survive, it still manipulates them. It often changes their sperm so that they cannot successfully fertilise eggs unless the eggs are infected with the same strain of Wolbachia.
One recent study estimated that it infects at least four in every ten species of arthropods – the animal group that includes insects, spiders, scorpions, mites, woodlice, and more.
If the injury is severe, and enough mitochondria are released, the resulting body-wide inflammation can build into a lethal condition called systemic inflammatory response syndrome (SIRS).
“Every symbiosis is, in its degree, underlain with hostility, and only by proper regulation and often elaborate adjustment can the state of mutual benefit be maintained. Even in human affairs, the partnerships for mutual benefit are not so easily kept up, in spite of me being endowed with intelligence and so being able to grasp the meaning of such a relation. But in lower organisms, there is no such comprehension to help keep the relationship going. Mutual partnerships are adaptations as blindly entered into and as unconsciously brought about as any others.”
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.
Bacteriocytes have repeatedly evolved in different lineages. Some insects slot them between other cells; others bundle them together into organs called bacteriomes, which branch off from the gut like clusters of grapes.
When the insect first makes that shell in adulthood, it relaxes its control of the bacteria, which quadruple in number. But once the shell is set, the weevil no longer needs its microbial companions – and kills them.
Nearly all animals use mucus to cover tissues that are exposed to the outside world. For us, that means guts, lungs, noses, and genitals.
A few years ago, Rohwer’s team member Jeremy Barr noticed that phages love mucus. In a typical environment, there will be 10 phages for every bacterial cell.23 In mucus, there will be 40.
Rohwer suspects that phages were the original immune system
a dense inner one that sits directly on top of the epithelial cells, and a loose outer one beyond that. The outer layer is full of phages, but it’s also a place where microbes can anchor themselves and build thriving communities. They abound here. By comparison, very few of them exist in the dense inner layer. That’s because the epithelial cells liberally spray this zone with antimicrobial peptides (AMPs) – small molecular bullets that take out any encroaching microbes.
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.
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.
In one camp, paediatricians found that microbes called Bifidobacteria (or Bifs to their friends) were more common in the stools of breast-fed infants than bottle-fed ones. They argued that human milk must contain some substance that nourishes these bacteria – something that later scientists would call the ‘bifidus factor’. Meanwhile, chemists had discovered that human milk contains carbohydrates that cow milk does not, and were gradually whittling this enigmatic mixture down to its individual components – including several oligosaccharides.
they confirmed that the mysterious bifidus factor and the milk oligosaccharides were one and the same – and that they nourished gut microbes.
Human milk has evolved to nourish this microbe and it, in turn, has evolved into a consummate HMOvore. Unsurprisingly, it is often the dominant microbe in the guts of breast-fed infants. 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
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In most reefs, fleshy algae are kept in check by grazers like surgeonfish and parrotfish, which nibble them down to well-trimmed lawns. But humans kill the grazers with spears, hooks, and nets. We also kill top predators like sharks, leading to population explosions of medium-sized predators, which then take out the grazers. Either way, we give the algae an advantage. The well-trimmed lawns become overgrown fields, and the neighbouring corals start to die.
That something turned out to be dissolved organic carbon (DOC); essentially, sugars and carbohydrates in the water. When algae get too numerous on a reef they make huge amounts of DOC and create a banquet for coral microbes.
Those that got microbes from lean donors put on 27 per cent more fat, while those with obese donors packed on 47 per cent more fat.
Akkermansia muciniphila, one of the more common species of gut bacteria, is over 3,000 times more common in normal mice than in those genetically predisposed to obesity. If obese mice eat it, they lose weight and show fewer signs of type 2 diabetes.
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.
Such is the case with inflammatory bowel disease, or IBD.
Both major types of IBD – ulcerative colitis and Crohn’s disease – have been around for centuries, but rates have soared since World War II, especially in developed countries.
Scientists have identified over 160 genetic variants that are tied to the disease, but since these variants are common in the general population and relatively stable in their prevalence, they cannot possibly explain the disease’s precipitous rise. They do, however, point to a different culprit. Most of them are involved in producing mucus, solidifying the lining of the gut, or regulating the immune system – all things that keep microbes in line. And although human genes don’t change fast enough to account for the sudden rise of IBD, microbes do.
The IBD microbiome tends to be less diverse and less stable than its healthier counterparts. It lacks anti-inflammatory microbes, including fibre-fermenters like Faecalibacterium prausnitzii and B. fragilis. In their place are blooms of inflammatory species like Fusobacterium nucleatum and invasive strains of E. coli.
The best that anyone has been able to do is to show that microbes are already dysbiotic in people who have only recently been diagnosed.17
These principles apply to other inflammatory diseases too, including type 1 diabetes, multiple sclerosis, allergies, asthma, rheumatoid arthritis and more.
But pets are not our most important sources of old microbial friends. That honour goes to our mothers. When babies emerge from the womb they are colonised by mum’s vaginal microbes – an endowment that creates chains of transmission which cascade through generations.
Maria Gloria Dominguez-Bello found that 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.24
This might explain why C-section babies are more likely to develop allergies, asthma, coeliac disease, and obesity later in life.
Saturated fats can nourish inflammatory microbes. So can two common food additives, CMC and P80, used to lengthen the shelf life of ice cream, frozen desserts, and other processed foods; they also suppress anti-inflammatory bugs.
when fibre is absent, our starving bacteria react by devouring whatever else they can find – including the mucus layer that covers the gut.
