I Contain Multitudes - The Microbes Within Us And A Grander View Of Life, by Ed Yong

This is the best book I’ve read about symbiosis in the animal kingdom, and presumably the best book there is on this topic.

“All zoology is really ecology. We cannot fully understand the lives of animals without understanding our microbes and our symbioses with them.” From this thesis, Ed Yong, award-winning science writer published in Wired, the New York Times, the Guardian, Nature, New Scientist, Scientific American and more, broadens our understanding of the many roles bacteria play in the lives of many animals.

Leafcutter ants carry antibiotic-producing microbes on their body and use them to disinfect the fungi they cultivate underground. The spiky pufferfish uses bacteria to make tetrodotoxin, a lethal substance to poison predators. The colorado potato beetle uses bacteria in its saliva to suppress the defenses in the plants it eats, much like the ant lion does thanks to bacteria in its saliva to paralyze its victims. Buchnera supplements aphids with aminoacids they couldn’t get from sap. The desert woodrat can eat the toxic creosote bush thanks to toxin-degrading bacteria they carry. A dynasty of over 20 000 species of Braconid wasps inject their eggs in living caterpillars, along with viruses (called bracoviruses) to suppress the caterpillar’s immune system. Moranella is a small bacterium living in Tremblaya which is a bigger bacterium that itself lives inside the citrus mealybug. The three symbionts cooperate to make nutrients like phenylalanine, one having the genes for some of the enzymes of the reaction, the other bacterium for others and the host doing the last part.

After a quick history of beneficial microbes on-lookers starting with 17th century Antony van Leuuwenhoeak, the first man to ever see bacteria thanks to his exceptional home-made microscopes, and finishing in the 20th century with the birth of metagenomics, Ed Yong demonstrates that many animals need bacteria not only to live, but also to form themselves. The microbes are indispensable in their body development. The mosquito Aedes aegypti can’t develop after larval stage without bacteria. The worm Hydractinia reaches adulthood only upon contact with bacteria living on the shells of hermit crabs, while H. elegans metamorphoses to its adult form only when it anchors to a biofilm. When animals were born to the world, he reminds, it was already full of bacteria, so it would be surprising if their lives didn’t depend on bacterial cues. Indeed, a bacterial film means to the worm that the present surface is solid and stable enough, isn’t too toxic and that there are enough nutrients around to sustain microbes.

However, “the world of symbiosis is one in which our allies can disappoint us and our enemies rally to our side. It’s a world where mutualisms shatter for the matter of a few millimeters.” Symbionts help their hosts but can create vulnerabilities. They need to be fed, housed and transmitted, which costs energy. This is apparent in the case of the Human Milk Oligosaccharides in breastmilk, an energy investment from the mother that is not destined to feeding the baby but to feeding the right Bifidobacteria to allow the development of a healthy microbiome. Similarly, Wolbachia protects flies and mosquitoes from viruses and other pathogens, it allows some wasps to lay eggs and produces B vitamins for bed bugs, but it gives an advantage to females (sperms are too small to transmit Wolbachia so males are a dead-end to the bacteria), decreasing sexual reproduction and therefore genetic diversity in the species. “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” (H.G. Wells, 1930). This is true between insects and Wolbachia as it is between humans and their microbes, which are beneficial when in balance and contained. Contained in numbers, in functions, in locus, contained by the immune system – which should not be seen as an army fighting bacteria, but as a manager supporting them; contained by antibodies, phages and the right foods. But a combination of excessive sanitation, antibiotics and modern diets have disrupted such containment systems in our contemporary developed world, causing a loss in some microbes such as the ones bearing anti-inflammatory functions, and leading to a soar in Inflammatory Bowel Diseases. “We are starving our microbial selves”, as Sonnenburg puts it. Smaller families, C-section and infant formula also disrupt the transmission of beneficial microbes, which could explain why B. infantis is present in 60-90% of infants from developing countries like Bangladesh or Gambia and only 30-40% of infants in developed countries like USA, Italy or Sweden.

Yong’s opinion on probiotics is the only part I find limiting. He relies on a Cochrane review that concluded on the beneficial effects of probiotics in infectious diarrhea, antibiotic associated diarrhea and necrotizing enterocolitis, while the data on allergies, asthma, eczema, obesity, diabetes, IBD, autism and other disorders associated with the microbiome are deemed as not so clear. In my point of view, beyond the studies on animal models and association studies, even if clinical trials with a relatively small number of volunteers are more prone to bias and statistical flukes, their multiplicity and the combined information given by human data, correlation studies, animal data, and in vitro evidence showing the mechanisms behind, all in all give great prospects for probiotics in a wide number of indications. Yes, the regulators should control for claims, but the governments should also help drive and reward more probiotics research – which is more complicated than research on drugs because of the immense variability between strains and individual microbiomes, in addition to the dynamism inherent to these ecosystems, but also more rewarding for public health since probiotics show benefits without side effects. Yes, the concept of probiotics is still sound, and not only for the second generation ones like Akkermansia muciniphila or Faecalibacterium prausnitzii – it’s not because they have better chances at colonizing the colon that they will have better chances at improving health, and before wishing for a long term colonization, there is much work to be done to ensure the safety of a definitive microbiome modification in this highly personal environment.

If you are looking to find out how our microbes can support our health, this is not the main focus of this book. But if you want to understand how microbes, in general, interact with living organisms, here you will find enough examples and explanations to broaden your understanding of life as a whole, as an interacting community, as an ecosystem and no longer as seperated individuals. The potential behind this “grander view of life” is huge. The study of Janthinobacterium lividum (J-liv) could save amphibians from the worst infectious disease ever recorded among vertebrates, protecting frogs and salamanders from the destructive Batrachochytrium dendrobatis (Bd) deadly fungus. Research on Wolbachia could kill filarial nematodes, the parasites responsible for lymphatic filariasis, improving 150 million lives, as well as clear Aedes aegypti mosquitoes from the dengue virus, preventing the infection of 400 million people a year.

The author is particularly knowledgeable and mostly relates science from talking directly with the researchers. When he explains a mechanism behind a mutualistic relationship, he usually details the story of how it was discovered and demonstrated, making every example and argument convincingly backed by evidence. He is also using the latest science, for instance not reporting the good old figure of 10 bacteria to 1 eucaryote cell in the human body, but using the latest estimates of 30 trillion human cells and 39 trillion microbial ones in our body – more or less a 1 to 1 ratio.

In conclusion this is an excellent read for whom wants to expand the understanding of symbiosis, and in this way, embrace a grander view of life.