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

Review by Terence Jagger

This is a truly fascinating book, about the complex ecosystem of microbes that lives inside us, all other animals, and sometimes each other – doing good, doing harm, and being neutral in surprising and dramatic ways. You are roughly half made up of species other than homo sapiens, but don’t think for a moment about getting rid of the other species, that way lies disaster and death. These microbes are known as the microbiome, and every animal has one – and they are enormously varied in themselves – my genes will be overwhelmingly similar to yours, but my microbiome may be very different, if for example I have a different diet, have travelled to different places, worked in different fields, use different soaps and cleaners to wash myself and my house, what medicines I may be taking. The microbes in my body vary dramatically from my guts to s skin, from the hot damp areas under my arms to the dry areas on my arms and hands, and they even vary from my left hand to my right.

Bacteria have had a bad press over the past couple of centuries or so, seen as dirty, the cause of disease – and indeed some are. But many of them are beneficent or even essential – their absence is linked with many physical and mental diseases, they are absolutely essential for herbivores like cows to digest grass, they stimulate the immune system and fight off dangerous pathogens. Some birds depend on them to paint their eggs with antibiotics and antifungals, the pufferfish uses them to create its famous poison, fish use then to create light, ants use them to stop their leaf cultures rotting. They are amazing, and they are everywhere.

Their numbers are so vast, and their intersections so complex, that we are only at the beginning of the journey of understanding them in humans and other animals, but Yong tells us how we got this far, and points out some future developments, vital in terms of medicine, environmental rehabilitation, and agriculture. Some of the things we have learned are immensely complex and surprising, and some are staggeringly simple.

I can’t cover everything in this very diverse, enthusiastic and accessible book, full of easy to understand science, great examples and stimulating ideas, and intriguing human stories, so let me pick a few themes that struck me particularly strongly, mainly around the human microbiome and its effect on our health (which sadly means I have to miss out a great deal of fascinating stuff about helping agriculture and the environment, rebuilding coral reefs, and fighting malaria, dengue and zika).

But to start at the beginning … you are born, and you are effectively sterile, with no bacteria on you or in you. This is not a good thing, and anyway it can’t last. But how you develop your own personal microbiome turns out to be really important. First of all, to accept all the bacteria you need, special immune cells suppress a lot of the defensive abilities of the immune system, so the bacteria can be accepted – which is one reason babies are so prone to infection in the early months. Mother’s milk, full of nutrition, also contains antibodies which help manage the microbial free for all which takes place in the new born baby. But human milk is really interesting from a microbial point of view – it is unusually complex, especially in terms of things called oligosaccarides, by the standards of other mammals, and is rich in lactose and fats. Lactose and fats are great nutrition – but the baby can’t digest the mass of oligosaccarides, so what are they there for? They are they to feed a microbe called Bifidobacteria infantis, which in turn provides nourishment for the baby, it stimulates the gut to seal itself to prevent leakage and intrusions, it is anti-inflammatory, and it may play an important role in creating siliac acid, key for brain development. Once weaned, we have a gut flora, and we feed it ourselves through diet and interaction with the rest of the world. I have just been travelling in Japan, so some of my bacteria which feed on wheat products have been having a hard time, while those that like rice, raw fish, soy and so on have been booming. “Getting used to the food” abroad is a real thing, and can be complex and can either happen within hours or can take weeks or longer. For example, Japanese people are much better than Westerners at digesting nori – the dark green seaweed common in Japanese cuisine – because they have long ago absorbed a microbe called Zobellia into their guts to help. Zobellia‘s original environment was the sea, where it lived on seaweed, but now it is helping humans digest, and is evolving itself to adapt to the changed conditions of the human gut. Hopefully I’ve picked some up while I’ve been travelling, but it won’t have been so easy, as modern processed nori will be Zobellia free, while modern Japanese inherit it from their mothers’ milk.

Over recent years the “bacteria are dirty and must be destroyed” mantra has been modified by various memes which stress the value of bacteria to, for example, human digestion, where “good bacteria” are deemed to have beneficial effects and are swallowed by millions of people in the form of probiotic yoghurts. The scientific evidence is that the bacteria in these drinks – millions, but still a tiny number compared with the population of your gut – are not well equipped to live in humans (they are often not natural human species, and have been extensively modified through breeding in labs) and don’t persist. It’s also notable that these yoghurts are all classed as foods, and not regulated as medicines, because there is almost no scientific evidence that they do any good (and the producers are careful not to claim that they do). But interest in the potential remains, and does seem to have some real basis. For example, people suffering continuous and extreme diahorrea as a result of clostridium difficile infection have been successfully treated with a faecal microbiota transplant – essentially swallowing (actually delivered through colonoscopy) blended faeces from a healthy person to set up a new gut flora. This has been very successful on a number of occasions, and is being increasingly used, including by people who are self administering! There are dangers, of course, and the way forward may be building communities of gut flora in the lab, screening them for pathogens and building customised mixtures for different people. We are unusual in finding coprophagy revolting, as many animals eat their own and others’ faeces, and this is one way a new microbe – perhaps allowing rabbits to eat a previously indigestible or toxic plant – can spread rapidly through the population and benefit the group as a whole.

There is growing evidence that the microbiome of human beings who live in modern urbanised societies have much less diverse microbiomes than those in less advanced societies, and the diversity seems to be declining. Some people have suggested that this is connected with the rise of the illnesses of the advanced societies, including coeliac disease, irritable bowel conditions, asthma, and even mental conditions like autism and schizophrenia, though the evidence is just not here yet. But there does seem to be a benefit, at both an individual level and species level, to nurturing our microbiomes; being breast-fed seems to be a good start, eating a varied diet is valuable, and living with other people – and even having a dog – all promote diversity (the dog promotes human-human interchange of microbes, and also contributes its own, allergy busting, bacteria).

Finally, a word on cleanliness. It’s clearly wrong, and impossible, to kill all the bacteria, but should we actually go in the other direction and say a little dirt may actually strengthen our microbiomes and our general health? Well, in a hospital, you clearly need to control certain pathogenic microbe populations, but actually you need a diverse population too – that may help keep the pathogens at bay. In one American hospital study, the outside air was full of harmless bacteria from the soil and plants, but the air trapped inside the hospital’s air-conditioning system was full of nasties from the patients, forever being recirculated. Luckily, there was a solution – opening the windows! And while we clearly need to keep out lavatories clean, toilet seats are actually most likely to be infected with faecal bacteria soon after cleaning – they are reinfected by normal use, then flushing the toilet sends the bacteria up into the air and so on, but thereafter the faecal and potentially dangerous bacteria are balanced as other species also return and outcompete them, only for the next disinfection to give the faecals another chance.

A truly fascinating and exciting book on a whole host of levels, in an area of science which is moving fast and will chance our lives and the environment dramatically over the coming decades. It may not be your normal reading matter, but its well worth putting it on the list.