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

It’s time we became friends with microbes. And not just with them but with their very idea, because it’s likely going to be crucial to our lives on this planet and beyond. For a long time most humans have regarded bacteria as a nuisance. This is because we become aware of them only when something goes wrong, only when they cause diseases like tuberculosis and diarrhea. But as Ed Yong reveals in this sweeping, exciting tour of biology, ecology and medicine which is pregnant with possibility, the vast majority of microbes help us in ways which we cannot possibly fathom, which permeate not just our existence but that of every single other life form on our planet. The knowledge that this microbial universe is uncovering holds tantalizing clues to treating diseases, changing how we eat and live and potentially effecting a philosophical upheaval in our view of our relationship with each other and with the rest of life.

Yong’s book shines in three ways. Firstly it’s not just a book about the much heralded ‘microbiome’ – the densely populated and ubiquitous universe of bacteria which lives on and within us and which rivals our cells in terms of numbers – but it’s about the much larger universe of microbes in all its guises. Yong dispels many misconceptions, such as the blanket statements that bacteria are good or bad for us, or that antibiotics are always good or bad for us. His narrative sweeps over vast landscape, from the role of bacteria in the origins of life to their key functions in helping animals bond on the savannah, to new therapies that could emerge from understanding their roles in diseases like allergies and IBD. One fascinating subject which I think Yong could have touched on is the potential role of microbes in seeding extraterrestrial life.

The universal theme threading through the book is symbiosis: how bacteria and all other life forms function together, mostly peacefully but sometimes in a hostile manner. The first complex cell likely evolved when a primitive life form swallowed an ancient bacterium, and since this seminal event life on earth has never been the same. They are involved in literally every imaginable life process: gut bacteria break down food in mammals’ stomachs, nitrogen fixing bacteria construct the basic building blocks of life, others play critical roles in the water, carbon and oxygen cycle. Some enable insects, aphids and a variety of other animals to wage chemical warfare, yet others keep coral reefs fresh and stable. There’s even a species that can cause a sex change in wasps. Perhaps the most important ones are those which break down environmental chemicals as well as food into myriad interesting and far-ranging molecules affecting everything, from mate-finding to distinguishing friends from foes to nurturing babies’ immune systems through their ability to break down sugars in mother’s milk. This critical role that bacterial symbiosis plays in human disease, health and even behavior is probably the most fascinating aspect of human-bacteria co-existence, and one which is only now being gradually teased out. Yong’s central message is that the reason bacteria are so fully integrated into living beings is simple: we evolved in a sweltering, ubiquitous pool of them that was present and evolving billions of years before we arrived on the scene. Our relationship with them is thus complex and multifaceted, and as Yong demonstrates, has been forged through billions of years of messy and haphazard evolution. For one thing, this therefore makes any kind of simple generalization about them almost certainly false. And it makes us realize how humanity would rapidly become extinct in a world suddenly devoid of microbes.

Secondly, Yong is adept at painting vivid portraits of the men and women who are unraveling the secrets of the microbial universe. Old pioneers like Pasteur, Leeuwenhoek and Koch come alive in crisp portraits (for longer ones, I would recommend Paul DeKruif's captivating classic, "Microbe Hunters"). At the same time, new pioneers herald new visions. Yong crisscrosses the globe, from the San Diego Zoo to the coral reefs of Australia to the savannah, talking to adventurous researchers about wasps, aphids, hyenas, squid, pangolins, spiders, human infants and all the microbes that are intimately sharing their genes with these life forms. He is also a sure guide to the latest technology including gene sequencing that has revolutionized our understanding of these fascinating creatures (although I would have appreciated a longer discussion on the so-called CRISPR genetic technology that has recently taken the world by storm). Yong’s narrative makes it clear that innovative ideas come from the best researchers combining their acumen with the best technology. At the same time his sometimes-wondrous narrative is tempered with caution, and he makes it clear that the true implications of the findings emerging from the microbiome will take years and perhaps decades to unravel. The good news is that we're just getting started.

Thirdly, Yong delves deeply into the fascinating functions of bacteria in health and disease, and this involves diseases which go way beyond the familiar pandemics that have bedeviled humanity throughout its history. Antibiotics, antibiotic resistance and the marvelous process of horizontal gene transfer that allows bacteria to rapidly share genes and evolve all get a nod. Yong also leads us through the reasonable but still debated 'hygiene hypothesis' which lays blame for an increased prevalence of allergies and autoimmune disorders at the feet of overly and deliberately clean environments and suburban living. He discusses the novel practice of fecal transplants that promises to cure serious intestinal inflammation and ailments like IBD and Crohn’s disease, but is also wary about its unpredictable and unknown consequences. He also talks about the fascinating role that bacteria in newborn infants’ bodies play when they digest crucial sugars in mother’s milk and affect multiple functions of the developing baby’s body and brain. Unlike proteins and nucleic acids, sugars have been the poor cousins of biochemistry for a long time, and their key role in microbial symbiosis only highlights their importance for life. Finally and most tantalizingly, the book describes potential impacts that the body’s microbiome and its outside guests might have on animal and human behavior itself, leading to potential breakthrough treatments in psychiatry. The real implications of these roles will have to be unraveled through the patient, thoroughgoing process that is the mainstay of science, but there is little doubt that the arrows seem to be pointing in very promising directions.

“There is grandeur in this view of life”, Darwin said in his magnum opus “The Origin of Species”. And just how much grandeur there exactly is becomes apparent with the realization that Darwin was dimly aware at best of microbes and their seminal role in the origin and propagation of life. Darwin saw life as an 'entangled bank' full of wondrous species: I can only imagine that he would have been enthralled and stupefied by the vision of this entangled bank presented in Ed Yong's book.

This is an amazingly good and a very important book. Anyone, from doctor to vet to a sufferer with ibs or weird gut issues should have it as the base line for understanding where the science is at and where it is going..

While praising this book as one of the greats in current science, there are some things to be aware of. At first, I had some struggles with it. It seemed a bit too fuzzy, scientifically speaking. It seemed to be a bit anecdotal. It wasn’t a tight science book. I thought about this a lot. What was I missing? And then i finally worked through it. This IS a book of anecdotes. It IS a book without mathematics and proven scientific theories. And then i worked through it some more. This is a fuzzy narrative about a field that is not yet to the level of proven and mathematical science. Yong has written an incredible preview of science that is in the process of becoming. Once I understood this view, I no longer had any struggles with it.

There are so many stories here. There are so many details so that i now have to go back and read it again and underline things this time. It will probably take three readings to get even a grasp of the breadth of what Yong is writing about. Every re-reading, i expect, will make it even better.

Part of the problem in hard science is that there are so many things to know. Atmospherics, physics, geology and botany are very complex . I’m suspecting that the world that Yong is describing is going to be even one step beyond that.

Great start as an intro into new medicine and new science.

This book was my substrate for Sandor Katz's "The Art of Fermentation." This is the book I cannot loan without having a backup copy. This is the book that gave me more intimacy with Wikipedia than any other. This is the book that makes my unsophisticated mind able to comprehend scientific principles. This is the book that you can't just take out of the library, you have to have a copy so you can quote from it immediately. This book has yet to enter my bathroom, because it's unhealthy to be sitting down as long as the shortest time I've spent reading this book. Also, this book debunks both sides of many microbe/fungus/algae myths. Most importantly, this book engages, and changes your mind, early and often. Ed Yong wrestles microbial science from the fingers of geeks and nerds (they still have a grip, but have to share now) and presents it with a raconteur's skill. It is with this skill that he takes on ham-handed misconceptions and throws them effortlessly around the room like a smiling aikido master. Perhaps his most important public service is his assiduous debunking of the simplistic and fevered biome-panacea hysteria that seems to be sweeping the social media these days. Any time you can get people to temper their visceral reactions with well-reasoned logic, you've achieved a milestone.

Welp...just got the book. I liked Yong's TED talk which is why I bought his book. I'm only a few pages in and have already found a few errors. Most notably, endosymbiosis has occurred at least twice, not once (chloroplasts, ahem...) and possibly more than that (plastids, peroxisomes, all those other organelles, not to mention those pesky plasmids...golly gosh! I guess I better not mention horizontal gene transfer, should I?). At this point I would describe this work as light reading, or even, dare I say...popsci.

“I Contain Multitudes” by Ed Yong explains in 355 pages the amazing benefit that microbes have on earth and in us. This 2016 non-fiction novel informs his readers about the world of microbes and the symbiotic relations they have with their host through a variety of examples as the author dives into the world of microbes. Ed Yong is an award winning science writer that breaks down this new small world in easy to digest layman examples to educate readers the importance of these small organisms with their host. He has traveled to many institutions and spoke the experts of various fields in the world of microbiology to understand the tremendous impact that microbes have. He mainly goes into the world of animals and their relationship with microbes, but he wonderfully connects these examples to help us understand the future of probiotics and disease in humans.

As Yong goes into his examples, it is clear that the microbial world is in a delicate balance with our reality. Although he does focuses on animal, mainly humans and their relationship with microbes, he does points out that Jack Gilbert and Josh Neufeld stated if plants were don’t have any microbes, they surely will fail and can lead to societal collapse because there food chain would fail. Plants depends on microbes to fix nitrogen or give it key nutrients to help the plants flourish. This example he uses early on in the book really set the tone for the rest of the examples and how far a single microbe influence can have a snowball effect on us.

Ed starts the reader’s journey with Baba, a pangolin at the San Diego Zoo with Baba’s keeper swabbing the Baba’s body to understand his microbiome. Ed lays out the foundation to the rest of the book by explaining basic key terms and concepts of the diversity of microbes on the body. As the book progress, Ed goes into the importance of microbes to humans. He states that if animals were sterile, free of any microbes, they would die. For example, if sap-sucking bugs lack their bacteria in their gut, they would parish because they wouldn’t be able to get all the nutrients they need without those important bacteria.

Like Baba, humans have their own unique microbiome throughout their body, like the how the skin microflora differs from the gut microflora. This diversity on the human body is so interesting, that even the microflora of the right hand would be different than the microflora of the left hand. This diversity is also unique from person to person.

The journey of a human obtaining their own unique microbiome starts at birth. In the womb, the fetus is completely sterile, but during birth, the baby obtains its first microbes can be traced back to their mom. He does goes into how the differences of birthing method, vaginal and cesarean section affects a child’s first microbes. These microbes can affect the child’s immune responses in the future. Even having a pet or an older sibling in the development of a child can may reduce the possibility of allergies of the child as a result of constant exposure at a young age to a variety of microbes from diverse locations. This trains the immune system at an early age to help fight infections later in life.
It is emphasized that a mother is the biggest player in shaping the child’s microbiome. Not just from the birthing method, but also the role of breast milk. Yong divulges in the amazing properties of break milk for babies on how it plays a huge role on a babies gut microbiota. Breast milk is one of humans first prebiotic for a baby, since it not only nourishes and protect the immune system of the baby, but provides nutrients to the child’s first set of bacteria, L. infantilis in their gut.

Yong even states that the gut microbiome can also affect behavior. He starts his example with lab mice, and if pregnant mother with infection during pregnancy, it can have healthy offspring that can have behavioral abnormalities in adulthood such as repetitive behaviors and social aversion, which is similar to the humans conditions of autism and schizophrenia. When looking at the gut microbiota diversity of a mice with such quirks to a normal mouse, there is a difference in the variety, even when everything is the same, such as environment and nutrition.

This behavior in mice is relates to behavior in autistic individuals, although it is stated that mice don’t have autism since autism, according to Emily Willingham, is shaped by society and what seems to be normal. When gut microbes from autistic children were transplanted into the gut of healthy mice, the mice’s behavior did change by repetitive burying of a marble and low frequency of squeaks, which could be related to autistic behaviors of children. Yong mentions that that the gut microbe are partially responsible for such behaviors in autistic children, but it cannot be the sole reason.
Fascinatingly, germ free mice that lacked a gut microbiome had behavior differences of their normal microbiota counterpart, these mice were more timid. When introduced to the bacteria commonly found in yoghurt and dairy products, Lactobacillus rhamnosus, specifically the strain JB-1 to their gut, the mice were able to overcome anxiety through the same tests that were made to test psychiatric drugs. Apparently, the strain JB-1 acted like a low dose of anti-anxiety and antidepressants, according to Cyan from the University of Cork. The researched looked into the brains of the mice of JB-1 and showed that brains response to GABA changed with the strain. The suspected that the nerve that that carries signal from the brain to gut aided JB-1 in the influence of the improved behavior in the mice. Yong informs reader of current research that correlated the behavior to the gut microbiota, demonstrated that there is more than meets the eye of the microflora animals.

Not only does the book go into detail of the symbiosis humans and their microbes, it proved examples of how microorganisms help with survival of the host, like the illuminating Vibrio fischeri and the Hawaiian bobtail squid. When the Hawaiian bobtail squid hatches from their egg, it is born without V. fischeri. Interestingly enough, the bobtail squid has immature crypts which houses these bacteria. When V. fischeri goes to colonize the squid. Once these bacteria colonize the squid, it start to mature the remaining organs to help it survive in their environment. It take more than just a few of the V. fischeri to help the Hawaiian bobtail squid survive. Once the bacteria reached a certain threshold of one turn on their bioluminescent to hide the bobtail squid’s shadow in the water and also produce antimicrobial properties to it can reduce competition by making it impossible for other microbes to occupy the bobtail. In exchange for helping the bobtail squid V. fischeri gains protection and a constant supply of nutrients.
The symbiosis of a microorganism and its host can be an indicator of the health of the host and environment, such as dying coral reefs on Christmas Island. The dying reefs are a prime example of a delicate balance of the symbiosis of microbes, because a reason for these reefs to dye is algae. The rise of algae is a result of the disruption of the food chain, such as the decrease of sharks. Sharks host an abundance of algae, if they are gone, the algae population stays in the water as wells are the production of dissolved organic carbon. This dissolved organic carbon will allow the microbe populations toe exponentially increase; therefore, consuming all the surrounding oxygen, essentially chocking the corals.

Usually there are 10 percent of the local microbe species in coral are pathogenic and cause disease because the normal coral microflora keeps the population of microbes in check. Around Christmas Island it is around 50 percent because of the abundance of nutrients from the algae. As coral die, it makes room for more of this algae to grow, which leads to a never ending cycle of dying coral and flourishing microbial community and algae.

As Yong enlightens readers of the benefit of microbes in the world, he leads us to microbes place in medical field. Like his previous example of the how microbes can affect behavior, he leads us to thinking about the potential uses of microbes in treating diseases or maximizing the effect of medicine. For example, digoxin has been used to treat patients with hearts that are failing, but it the patients has Eggerthella lenta in their gut microbiome, digoxin will not work because the bacteria converts the drug into an inactive form. This isn’t the only drug and microbe pair that affect treatment. Yong brings up fecal transplant or a more refined and cleaner version to be the future of treatments, not just in behavior but in all sorts of treatments to help reduce symptoms or treat disease. Even brings up that inside the hospital is riddling with a high concentrations pathogenic microbes, but if a window is just opened to allow the outside microbes to come in and occupy space in the hospital. These outside microbes in the environment will push out and decrease the pathogenic microbial population.
Readers do not need to come from a science background to read and thoroughly understand this book, because Ed Yong wonderfully explains the purpose of each example and how it correlated back the balance of a delicate symbiosis of the microbe and its host. This book is amazing to for readers of all backgrounds, but I would recommend this book to mothers, physicians and health fanatics since Ed Yong displays the importance of microbes to the positive health of the human body and the environment. A disruption of microbes can cause huge impact on the host or environment, which can allow us to pinpoint the cause of the disruption. Microbes and their effects are great indicator of the health of where it is occupying. Essentially, microbes are not as evil as we have been taught to think.

The issue with Ed Yong’s book is the fact he didn’t mention quorum sensing one in the book, because that would help the reader understand how microbes effect their own population or the community they live with. Also, Ed Yong jumped around a lot in examples, I felt like he could have separated examples by relevance. Personally, I would have started his examples with the symbiosis of the bugs then to talk about the corals the impact of environments. Then use antibiotic resistance as a transition from animals to humans, then go into behaviors affected by microbes. He could have concluded with fecal matter transplant and using microbes as treatments and then ended with the research of tracking a building’s, new or old microbiome.
It took until the end to understand the purpose of this book, because Yong starts out with going on this adventure to understand the world of microbes without giving a reason. It later chapters, everything comes together on why this subject is important. The future of medicine and treatments could possibly lie in the hands of the microscopic organisms. Even understanding the environmental health can be indicated by the concentration or shift in diversity of microbes. He mentions that probiotics would be uniquely prescribed to patients with a nutrient regime to either enhance to effectiveness of medicine or to be the medicine itself to help with certain symptoms or diseases. Over all, Ed Yong did an amazing job on informing readers on the world of microbes in a way that a variety of backgrounds could understand.

This book is well-written at the sentence and paragraph level, but could use some serious organizational help. The book is a long ramble from one microbiome anecdote to another, without any serious effort regarding structure. It's just "here is an interesting thing I have learned about microbes, oh and here is another, and another..." Related to that is a lack of any central thesis or point of view, other than the basic idea that microbes are an important thing we need to know about, and they don't all make you sick. That's all fine, and the book is enjoyable enough, but the author missed an opportunity to create some coherence out of this.

On a more technical note, there were some pretty serious omissions as well. I'm not sure how one writes a book about the importance of microbes as part of multi-cellular organisms, especially humans, without mentioning the theory that the human appendix has evolved as a haven for beneficial gut flora. Or the complex interaction between microbes in the vagina. Or talk about human babies being born, but then just don't mention that they are covered in vernix caseosa which, may have evolved in part to help develop gut flora. Or not mention the idea that toxoplasmosis infections might influence human behavior. These are all mainstream topics in human microbiology that would be interesting to a broad set of readers, so their omission is particularly strange.

Put all of these problems together, and the book seems to be pretty much a summary of whatever conversations the author happened to have with the particular researchers he happened to meet with. Which is ok, I guess, but also kind of lame. It's a great subject, and the author does have writing talent, but this book is just ok.

ScienceThrillers review:

For once, the publisher’s summary does not overstate. I Contain Multitudes, written by one of my favorite science communicators, Ed Yong, IS astonishing and it DOES change the reader’s view of nature. Heck, I have taught microbiology at the college level and it STILL changed my way of seeing life on Earth.

The surprise, for me, was how this book covers not only the science of the human microbiome, but spreads its net more widely across all forms of life. This is a good thing, because Yong has a gift for choosing, organizing, and telling stories about microbiome science. I loved his stories about desert woodrats and creosote poison (microbes to the rescue!), about human breast milk as a fertilizer for “good” gut bacteria, and about the profound importance of the microbiome for insects. His collected tales range far and wide but weave together in a tribute to microbes and their underappreciated importance–nay, necessity–for life. He also brings in just enough description of the scientific method to make experiments comprehensible. And he avoids hype, telling a nuanced tale that includes wonder for what microbiome science might yield in the future with caution against overselling what we actually know now.

I Contain Multitudes is a splendid work of popular science. Accessible, entertaining, literate, and important, I highly recommend this book.

If you enjoy this book, you might enjoy [[ASIN:0199941319 The Amoeba in the Room: Lives of the Microbes]]

If you are going to have a baby, or if you are consuming probiotic pills, or if you are consuming the new fad probiotic yogurts, or even if you consume yogurt for the sake of microbes, then read up on this book since it will save you a lot of unwanted calories and more importantly it will save you a lot of money.

Yong's book is written 10 years too soon. The microbiome is a hot topic these days and lots of research is in progress, but what scientists know about the microbiome and, especially, its connection to human health is quite modest. In fact an early chapter in the book makes this point and scientists quoted there warn against the exaggerated claims made for the medical manipulation of the microbiome. Nevertheless, by the end of the book Yong is spinning fantasies about individualized probiotic cocktails that cure significant medical problems. I'm afraid that he falls for his own hype.

Unfortunately, the writing is pedestrian and formulaic. For example, one chapter started with an anecdote about a man cutting down a "dead tree" that was "growing" in his yard. How a dead tree grows would be a really interesting scientific question! In general, each chapter starts with conversations with one or more interesting scientists. This introduces topic X, which is then discussed in the majority of the chapter. The chapter then finishes with another personal conversation with a scientist that links to topic Y, which will be discussed in the very next chapter.

This was a fairly good read. It was really more about the animal kingdom than it was about human health, so it was a bit disappointing in that respect. The data was accurate, for the most part, but dismissive when it came to the human microbiome.