Summary
I Contain Multitudes: The Microbes within Us and a Grander View of Life is about the surprisingly large amount of interactions animal and plant biology have with microbes, including mostly bacteria, but also viruses and protists, to the point that it is very difficult to say where one organism ends and another begins. With humans, this is most strongly emphasized in our gut microbiome, which is now conceived by some to be an organ of the human body.
There are a lot of re-emerging themes throughout the book that sort of build on each other, so it was sort of hard for me to pick out exact themes for the chapters, so I'll just briefly discuss those ideas and then summarize some bigger themes.
The first chapter, "living islands," reminds us that humans, and in fact, all animals, and in fact, all plants as well, are kind of new on the scene of Earth, which has been dominated by single-celled organisms like bacteria for a much longer time. The two main themes of this chapter is that 1) all the big plants and animals that we think of in biology evolved in the context of a world of bacteria, and so we might expect that a lot of our biology interacts with this ecosystem, and 2) that we are, in fact, homes to vast numbers of bacteria. He also introduces a major theme that bacteria are not necessarily "good" or "bad," but that there are deep and complex connections and interactions that can have positive or negative impacts depending on our current environments and needs.
Chapter 2 is about "the people who thought to look" and goes into a bit of the history of people who have looked at microbes over the centuries. He begins with Anton van Leeuwenhoek who was a Dutch lens maker who first discovered animalcules. In the 1800s, the ability for microbes to causes diseases was proved by Pasteur and Koch, and "germ theory" became the dominant way of thinking about bacteria, and then in the late 1800s, Martinus Beijerinck found that bacteria could fix nitrogen from the air into ammonia for plants, which ushered in the idea that hey, maybe good bacteria exist, too.
Then there was another mini-revolution in the mid-1900s with the discovery of archaebacteria and bacteria that could live in crazy environments that led to an even broader interest in microbial life and the influence of microbes in biology. This revolution was mainly led by Carl Woese, who pioneered using ribosomal RNA to establish phylogenetic taxonomies, and he was at the University of Illinois at Urbana-Champaign, where Payel and I went to school, so I have to do a shout out. (woot woot).
Chapter 3, "Body builders," is fundamentally about the idea that many functions that are vital to the body in many species of animal have been outsourced to microbes. There were lots of examples of this including the requirement of the presence of certain microbe-produced molecules to induce maturation and glowing in squids, mosquitos that can't survive into adulthood without their microbes, or, in mammals, proper functioning of the gut and immune systems, and as signaling systems.
Chapter 4, "Terms and Conditions Apply," builds on the previous chapter and really tries to dismantle the idea that microbes are either good or bad. Whether their presence is beneficial or deleterious depends on where they are and in what context. He also builds on the idea of symbiosis to talk about how the microbial hosts' immune system is almost always in constant battle with the microbe, even if the microbe benefits the host. This theme also reappears a lot throughout the book. Wholbachia is a great example of this as a bacteria that infects like 4 out of 10 arthropods, and in some cases is extremely parasitic, while in other cases, like in some nematodes, is completely essential to the worm's survival. There is always a tension, and the immune system in general may have evolved mainly as a way to manage the complex ecology of a system of microbial symbiotes.
Chapter 5, "In sickness and in health," talks about evidence that dysbiosis of our microbiome plays a role in disease. He starts by talking about the necessity of microbes in coral reef health, but moves to talking about gut health. He introduces the idea that fecal transplants can affect obesity and malnourishment. He also has a section in this chapter talking about the hygiene hypothesis, which is that our immune systems don't properly develop due to modern hygiene and the overuse of antibiotics which contributes to allergies and auto-immune disease.
Chapter 6, "The Long Waltz," hones in on the idea that animals and their microbes co-evolved, and in fact can trade genes. The chapter opens with the story of man whose hand was pierced by a piece of a tree branch as he was cutting it down. His hand eventually became infected, and when scientists sequenced the DNA in a cyst they found unusual bacterial DNA among the sequences that only existed in insects before. This chapter introduces the idea that the reason for symbiosis to evolve so commonly is that it can act as a sort of cheat code around gradualism. He also introduces an important concept called holobiont, which is a term that encompasses the unity around many organisms whose fates are highly intertwined.
Chapter 7, "Mutually Assured Success" builds on that idea and shows how microbes coming together allow organisms to expand into new niches quickly and easily. This might be because they can metabolize a certain food, or make a nutrient that is absent in the animal, or break down toxins in the case of the desert woodrat that can only eat creosote if it has a certain bacteria.
Chapter 8, "Allegro in E Major," focuses on horizontal gene transfer, again building on the themes earlier in the book. This is the ability for bacteria to share genes with their peers. For example, the chapter talks about the bacteria Zobellia that transferred some genes to human gut bacteria to allow them to eat Nori, which I thought was really cool.
The final chapters talk about the future and the possibility of engineering our own microbes and microbial environments.
Chapter 9 , "Microbes A'la Carte," talks about how medicine is changing with the newer more nuanced microbial view. Fecal transplants work incredibly well for certain conditions, like C. diff infections, but not for others. Pro-biotics also have limited efficacy. But targeting symbioses in certain animals is a promising strategy. At the same time, our use of antibiotics, and our fast travel around the world is spreading microbial diseases very quickly, such as fungal infections in amphibians.
Chapter 10, "Tomorrow the World," thinks about how we may restructure our environments in this new microbial world view. For instance, should we always clean surfaces so thoroughly? He cites some evidence that hospitals or toilet seats can have worse bacterial profiles by being cleaned too frequently because the more dominant bacteria cannot be present to push out more dangerous ones.
Discussion Questions:
Ed Yong calls for a more nuanced view of our relationship with microbes in health care. This is particularly relevant in terms of hygiene. I had heard about the hygiene hypothesis in allergies before, but I had never heard things like toilets were actually cleaner before you disinfected the seat. Where should we draw the line for optimal health and disease prevention in terms of our cleanliness?
What do you think about the idea of symbiosis being a mechanisms for accelerated evolution, but also as a mechanisms for introducing genetic risk, such as the slow motion extinction event in cicadas because of speciating into 7 distinct species that were completely co-dependent. Is there some threshold of optimal average symbiosis that biology is evolving towards?
What do you think about the idea of symbiosis driving speciation? Is this just due to developing unique niches, that separate animals into clusters, or is there something else going on?
What do you think about the view that all symbioses have the potential to be both beneficial and destructive due to underlying competition? Can you think of examples of how we might be able to take advantage of this competition in healthcare?