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

Thoughts: Decent. Before beginning to read it, I had heard I Contain Multitudes recommended in a bunch of different places. There were some new facts and examples, and I found the book to be well-written, but I was already aware of almost all of the concepts Yong discusses. I’d recommend the book to anyone used to thinking of microbes mostly as germs and pathogens.

(The notes below are not a summary of the book, but rather raw notes - whatever I thought, at the time, might be worth remembering.)

Yong, Ed. 2016. I Contain Multitudes: The Microbes Within Us and a Grander View of Life. Ecco.

Prologue: A Trip to the Zoo

1. Living Islands

2. The People Who Thought to Look

• 35: The term symbiosis is “a neutral one, implying any form of coexistence. If one partner benefitted at the expense of the other, it was a parasite (or a pathogen if it caused disease). If it benefitted without affecting its host, it was a commensal. If it benefitted its host, it was a mutualist. All these styles of coexistence fell under the rubric of symbiosis.”

3. Bodybuilders

• 72: “since the 1970s, a trickle of studies have shown that any kind of stress—starvation, sleeplessness, being separated from one’s mother, the sun arrival of an aggressive individual, uncomfortable temperatures, overcrowding, even loud noises—can change a mouse’s gut microbiome. The opposite is also true: the microbiome can affect a host’s behavior, including its social attitudes at its ability to deal with stress.”
• 75-76: outlines the hypothesis that one’s gut microbes can influence what a person eats, in order to better feed that microbe - i.e. microbes that digest fiber, for example, cause dopamine to be released in their host’s brain when they consume food that contains fiber.

4. Terms and Conditions Apply

• 78: How Wolbachia is able to spread through a population of insects: Wolbachia “often changes [the sperm of male insects infected by it] so that they cannot successfully fertilize eggs unless the eggs are infected with the same strain of Wolbachia. From the females’ perspective this incompatibility means that infected females (which can mate with whomever they like) gain a competitive advantage over uninfected females (which can only mate with uninfected males). With every passing generation, the infected females become more common, as do the Wolbachia they carry.”
• 81: “even symbionts as essential and long-standing as mitochondria… 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 underway and mounts a strong defense.” Can lead to a condition called systemic inflammatory response syndrome (SIRS) if enough mitochondria are released this way.
• 85: evolutionary biologist Toby Kiers: “we need to separate important from harmonious. The microbiome is incredibly important but it doesn’t mean that it’s harmonious.”
  • Yong: “A well-functioning partnership could easily be seen as a case of reciprocal exploitation.”
• 93-94: human milk oligosaccharides (OMHs) - complex sugars in human milk that cannot be digested by babies - over 200 kinds identified so far. They seem to preferentially nourish beneficial bacteria, and thus shape the gut microbiomes of babies.

5. In Sickness and In Health

• 122: factors affecting urban dwellers that with limit the number of microbes we are exposed to, and are associated with increased risk of allergic and inflammatory diseases: “smaller families; a move from muddy countryside to concrete cities, a preference for chlorinated water and sanitized food, and a growing distance from livestock, pets and other animals.”

6. The Long Waltz

• 155: book mentioned: Richard Dawkin’s The Extended Phenotype: “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. Beaver genes build beaver bodies, but since those bodies go on to make dams, the genes are also redirecting the flow of rivers.”
• 157: Holobiont: “a collection of organisms that spends a significant parts of their lives together” Coined by Lynn Margulis, recognizing that “every creature lives in communities with many others.”
• 158: “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.”
  • Eugene Rosenberg and Ilana Zilbert-Rosenberg, inspired by the holobiont, coined the term hologenome, suggesting that natural selection can act on the whole of the DNA of a holobiont.
  • 159: Even as natural selection acts on a hologenome as a whole, it also acts on all the individual components - individual organisms, and individual stretches of DNA within those organisms.
• 162: several scientists, including Ivan Wallin and Lynn Margulis, have speculated that symbiotic relationships are one of the main drivers of speciation. Yong gives an example from the work of Seth Bordenstein and Jack Werren, where two closely-related wasp species, each harboring a different strain of Wolbachia, cannot reproduce with each other, but when the Wolbachia is killed off via antibiotics, hybrids can survive.

7. Mutually Assured Success

• 171: Book mentioned: Robert Kunzig’s Mapping the Deep, about the unexpected discovery of thriving ecosystems in the deep ocean.
• 182: We can reshape our gut microbiomes very quickly (within days) by changing what we eat, selecting for species that are good at digesting the nutrients present in those foods.

8. Allegro in E Major

• 194: horizontal gene transfer is important in the function of gut microbiomes, as evidenced by the discovery by Jan-Hendrick Hehemann of a gene from Zobellia galactanivorans, a marine, seaweed-digesting organism (which couldn’t survive life in the gut) in the genome of a gut bacterium, Bacteroides plebeius - B. plebius had picked up the gene from the Zobellia and incorporated it into its own genome.
• 199: Braconid wasps have integrated the genes of viruses into their own genomes - when they lay eggs in caterpillars, they inject the hosts with immune-system-suppressing viral particles which their cells secrete.

9. Microbes à la Carte

• 223: According to research by the Cochrane Collaboration, there is sufficient evidence for the effectiveness of probiotics in only two conditions (only infectious diarrhea, and necrotising enterocolitis)
  • 222-223: In many cases, microbes (e.g. those in yogurt) are not actually able to get established in the guts of organisms that eat probiotic foods, and most studies of the effectiveness of probiotics have used sample sizes too small for robust conclusions to be drawn from them.

10. Tomorrow the World