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Kindle Notes & Highlights
by
Ed Yong
Read between
February 29 - March 7, 2024
am large, I contain multitudes.’
There are fewer than 100 species of bacteria that cause infectious diseases in humans;
Fewer than 100 opens opportunities
They help to digest our food, releasing otherwise inaccessible nutrients. They produce vitamins and minerals that are missing from our diet. They break down toxins and hazardous chemicals. They protect us from disease by crowding out more dangerous microbes or killing them directly with antimicrobial chemicals.
How they help
substances that affect the way we smell.
Smell...
Leafcutter ants also carry antibiotic-producing microbes on their bodies, and use these to disinfect the fungi that they cultivate in underground gardens.
The spiky, expandable pufferfish uses bacteria to make tetrodotoxin – an exceptionally lethal substance which poisons any predator that tries to eat it.
Pufferfish
Some nematode worms kill insects by vomiting toxic glowing bacteria into their bodies;
They can glow?
Grazing mammals, like cows, sheep, antelope, and deer would starve since they are utterly dependent on their gut microbes to break down the tough fibres in the plants they eat.
Utter dependency
Aphids, cicadas, and other sap-sucking bugs would perish without bacteria to supplement the nutrients that are missing from their diets.
He realised that as he sailed east from Bali to Lombok
East of bali has very different fauna
No man is an island?
Not so: we’re all islands from a bacterium’s point of view.17
All men are islands. Compare with Ben Howard singing "No man is an island"
When microbiologists first started cataloguing the human microbiome in its entirety they hoped to discover a ‘core’ microbiome: a group of species that everyone shares. It’s now debatable if that core exists.18
Microbiome species vary wildly between individuals
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.
Bacterial species across the body
Those in dental plaque vary above and below the gum-line. On the skin, microbes in the oily lakes of the face and chest differ from those in the hot and humid jungles of the groin and armpit, or those colonising the dry deserts of the forearms and palms.
Put simply, the bacteria on your forearm are more similar to those on my forearm than to those in your mouth.
When each baby is born, it leaves the sterile world of its mother’s womb and is immediately colonised by her vaginal microbes; 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. Then,
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.
For now, let us note that these questions can be answered only by collecting small pieces of data, just as Darwin and Wallace did on their seminal voyages. The stamp collecting is important.
Collecting data and noting these down are important
Knight recently tried surveying the metabolites of human faces, but found that beauty products, like sunscreens and face creams, drowned out the natural microbial metabolites.23
How cosmetics might be affecting health
ant-eating mammals, including pangolins, armadillos, anteaters, aardvarks, and aardwolves (a type of hyena), all have similar gut microbes, even though they have been evolving independently for around 100 million years.
How environment not habits affect microbiomes
There’s good reason to think that their microbes are involved. 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.
Why can organisms as disparate as humans and bacteria live together and cooperate? Because we share a common ancestor. We store information in DNA using the same coding scheme. We use a molecule called ATP as a currency of energy.
San Diego Zoo
Pilgrimage
At the main entrance, vessels full of microbes part with money so that they
The cells of animals such as many sea anemones and flatworms also turned out to contain algae, while those of carpenter ants harboured living bacteria.
Inside cells?
No other scientists saw the value of this work and Woese had no competitors: ‘It was a one-horse race,’ he would later say.
Further reading
Methanobacterium thermoautotrophicum
Important fella
Micropia – the world’s first museum devoted entirely to microbes.
To visit in netherlands
The human armpit is not unlike a hyena’s scent gland – warm, moist, and rich in bacteria.
Armpit vibes
Even symbionts as essential and long-standing as mitochondria, the energy-providing power plants that exist in all animals’ cells, can wreak havoc if they end up in the wrong place. A cut or a bruise can split some of your cells apart and spill fragments of mitochondria into your blood – fragments that still keep some of their ancient bacterial character. When your immune system spots them, it mistakenly assumes that an infection is under way and mounts a strong defence. If the injury is severe, and enough mitochondria are released, the resulting body-wide inflammation can build into a lethal
...more
How mitochodria can kill
Ever wonder why two people can walk through a midge-filled forest and one emerge with dozens of welts while the other just has a smile? Your microbes are part of the answer.
How they affect smell
acacia trees rely on ants to defend them from weeds, pests, and grazers. In return, they give their bodyguards sugary snacks to eat and hollow thorns to live in. It looks like an equitable relationship, until you realise that the tree laces its food with an enzyme that stops the ants from digesting other sources of sugar. The ants are indentured servants.
Tree defence
However, concealed niches, like sweat glands, can support the growth of oxygen-hating anaerobes like Propionibacterium acnes, the microbe that causes acne.
Acne
‘microbialisation score’,
Data score
Recall that every individual animal, whether human or coral, is an ecosystem in itself.
Note similarity to the theme - humans are systems
Such is the case with inflammatory bowel disease, or IBD.
Further reading
A single dog can have a huge effect. When Susan Lynch hoovered up the dust of 16 homes, she found that those without furry pets were ‘microbial deserts’. Those with cats were far richer in microbes, and those with dogs were richer still.23 It turned out that man’s best friend is a chauffeur for man’s old friends.
In case we needed mkore reasons for another dog
CMC and P80, used to lengthen the shelf life of ice cream, frozen desserts, and other processed foods;
Check these
antibiotics provide, and those foundations are now crumbling. We have used these drugs so indiscriminately that many bacteria have evolved to resist them, and some nigh-invincible strains can now shrug off every medicine we throw at them.
Further reading
Blaser now speaks about H. pylori with affection. It is one of the oldest of our old friends, having infected humans for at least 58,000 years.
Ancient relationship
Until recently, most microbiome research had focused on people from WEIRD countries – that is, Western, Educated, Industralised, Rich, and Democratic.
in germ-free mice, they strongly hint at a causal effect. Still, they
Streptomyces are microbes that excel at killing other microbes; this one group is the source of two-thirds of our own antibiotics.
Natural source for antibiotics
An animal’s diet affects its microbiome; the microbes affect its smell; and its smell affects its attractiveness. It all made sense, and it fitted nicely with the hologenome concept.
Diet seems to affect sexual attraction in flies. Possible in other creatures
And if the insects swallowed a dose of antibiotics and lost their microbes, they also lost their sexual biases.
Cavanaugh’s epiphany was both right and revolutionary.
Further Read
He eventually homed in on a strain of Lactobacillus casei, grew it in fermented milk, and, in 1935, created the first bottle of the dairy drink called Yakult.
Yakult origins
But many of these were done using isolated cells or laboratory animals, and their relevance to people isn’t clear.
Studies confirming claims
