coming chapters. Interactions between the immune system and microbes begin at birth,shaping one another throughout your life.It makes sense.One essential property of your resident organisms is that they resist invaders.In essence,your friendly bugs are happy where they live and with the living they make.They do not want outsiders coming in.For example,when invaders try to gain a foothold in the intestines,they must first pass the gauntlet of your stomach acid,which is designed to kill most bacteria;the acid comes from the host,but its production is stimulated by resident bacteria,like H.pylori.If an outsider does reach your gut,it must find a source of food,a place to settle.But it's crowded down there.Your resident bacteria don't want to give up their hard-earned spots clinging to your intestinal walls.They certainly don't want to share their meal.so they secrete substances.including their own antibiotics,which are poisonous to other bacteria. Some invading microbes may gain a toehold for a few days and then be gone,a scenario that happens much more often than not.The fact is,your microbes keep things pretty stable.When you kiss someone,lots of organisms pass between you. But after a while-minutes,hours,days at most-you and your partner will look like you did,in terms of your microbes,before the kiss.There are exceptions (you can acquire harmful pathogens from your lover),and I will get to them.But your ability to resist invaders,even from someone attractive enough to kiss,normally is profound.The same goes for sexual intercourse.There is an exchange not just of fluids but of microbes,and there are changes in both hosts.But after a while,you and your lover are back to how you were before,like nothing (microbially speaking)ever happened.It is possible that some microbes may migrate between partners with regularity,but so far we don't have any candidates,with the exception of pathogens,which often have evolved techniques for spreading among individual hosts. Even changes in diet may not change your microbes all that much.Over time, months and years,the composition of a person's gut microbiome is relatively stable,but yours and mine are different.In one small study,people ate a Mediterranean diet for two weeks:high fiber,whole grains,dry beans/lentils,olive oil,and five servings of fruits and vegetables each day.This diet is strongly associated with a reduced risk of cardiovascular disease.The subjects gave blood samples for the analysis of lipids that have been correlated with heart disease and stool samples to determine which microbes were present before and after dieting The researchers found a decrease in total cholesterol and a lowering of so-called bad cholesterol,or LDL-a good thing indeed.But the dieters'microbes did not change.Instead each person appeared to have a unique microbial signature,like a fingerprint.The signature remained true,even after manipulation of his or her diet 3
coming chapters. Interactions between the immune system and microbes begin at birth, shaping one another throughout your life. It makes sense. One essential property of your resident organisms is that they resist invaders. In essence, your friendly bugs are happy where they live and with the living they make. They do not want outsiders coming in. For example, when invaders try to gain a foothold in the intestines, they must first pass the gauntlet of your stomach acid, which is designed to kill most bacteria; the acid comes from the host, but its production is stimulated by resident bacteria, like H. pylori. If an outsider does reach your gut, it must find a source of food, a place to settle. But it’s crowded down there. Your resident bacteria don’t want to give up their hard-earned spots clinging to your intestinal walls. They certainly don’t want to share their meal. So they secrete substances, including their own antibiotics, which are poisonous to other bacteria. Some invading microbes may gain a toehold for a few days and then be gone, a scenario that happens much more often than not. The fact is, your microbes keep things pretty stable. When you kiss someone, lots of organisms pass between you. But after a while—minutes, hours, days at most—you and your partner will look like you did, in terms of your microbes, before the kiss. There are exceptions (you can acquire harmful pathogens from your lover), and I will get to them. But your ability to resist invaders, even from someone attractive enough to kiss, normally is profound. The same goes for sexual intercourse. There is an exchange not just of fluids but of microbes, and there are changes in both hosts. But after a while, you and your lover are back to how you were before, like nothing (microbially speaking) ever happened. It is possible that some microbes may migrate between partners with regularity, but so far we don’t have any candidates, with the exception of pathogens, which often have evolved techniques for spreading among individual hosts. * * * Even changes in diet may not change your microbes all that much. Over time, months and years, the composition of a person’s gut microbiome is relatively stable, but yours and mine are different. In one small study, people ate a Mediterranean diet for two weeks: high fiber, whole grains, dry beans/lentils, olive oil, and five servings of fruits and vegetables each day. This diet is strongly associated with a reduced risk of cardiovascular disease. The subjects gave blood samples for the analysis of lipids that have been correlated with heart disease and stool samples to determine which microbes were present before and after dieting. The researchers found a decrease in total cholesterol and a lowering of so-called bad cholesterol, or LDL—a good thing indeed. But the dieters’ microbes did not change. Instead each person appeared to have a unique microbial signature, like a fingerprint. The signature remained true, even after manipulation of his or her diet. 32
Yet in other studies of diet,the changes in microbial populations were more significant.In a recent study,changing diet to exclusively plant origin or animal source led to extensive changes,but these lasted only as long as the person was consuming the special diet.We do not know if the diet were to be continued for a year whether the changes would become permanent.We will have to carry out many more studies to better understand the effects of diet on gut microbes.But for now it seems as if relative proportions of the various bacteria in your gut go up and down within discrete boundaries.Research is now aimed at understanding those borders and the extent to which yours and mine are the same and the degree to which they change over a lifetime. If you are host to 100 trillion microbes and each microbe is a tiny genetic machine,how many genes are cranking away within your resident microbes and what are those genes doing? -2.000.000 What are they doing? 00 23.000 As discussed above,among the goals of NIH's Human Microbiome Project was to sequence the genetic material of microbes taken from healthy young adults.Not only was a census conducted that defined which microbes were present("who is there")but also the genes that they carried and their functions ("what is there").The main findings suggest that your microbes and mine have millions of unique genes, and a more current estimate is 2 million.Your human genome,by comparison,has about 23,000 genes.In other words,99 percent of the unique genes in your body are bacterial,and only about 1 percent are human.Our microbes are not mere passengers;they are metabolically active.Their genes are encoding products that benefit them.Their enzymes can produce ammonia or vinegar,carbon dioxide methane,or hydrogen that other microbes use as sources of food and,in ways we are still working out,they also make many more complex products that benefit us A recent survey conducted by a large group of scientists in Europe (begun as the MetaHit consortium)showed something else.A census of nearly three hundred Europeans showed that the number of unique bacterial genes in subjects'guts varied dramatically.The distribution of individuals wasn't normal;it was not a bell 33
Yet in other studies of diet, the changes in microbial populations were more significant. In a recent study, changing diet to exclusively plant origin or animal source led to extensive changes, but these lasted only as long as the person was consuming the special diet. We do not know if the diet were to be continued for a year whether the changes would become permanent. We will have to carry out many more studies to better understand the effects of diet on gut microbes. But for now it seems as if relative proportions of the various bacteria in your gut go up and down within discrete boundaries. Research is now aimed at understanding those borders and the extent to which yours and mine are the same and the degree to which they change over a lifetime. If you are host to 100 trillion microbes and each microbe is a tiny genetic machine, how many genes are cranking away within your resident microbes and what are those genes doing? As discussed above, among the goals of NIH’s Human Microbiome Project was to sequence the genetic material of microbes taken from healthy young adults. Not only was a census conducted that defined which microbes were present (“who is there”) but also the genes that they carried and their functions (“what is there”). The main findings suggest that your microbes and mine have millions of unique genes, and a more current estimate is 2 million. Your human genome, by comparison, has about 23,000 genes. In other words, 99 percent of the unique genes in your body are bacterial, and only about 1 percent are human. Our microbes are not mere passengers; they are metabolically active. Their genes are encoding products that benefit them. Their enzymes can produce ammonia or vinegar, carbon dioxide, methane, or hydrogen that other microbes use as sources of food and, in ways we are still working out, they also make many more complex products that benefit us. A recent survey conducted by a large group of scientists in Europe (begun as the MetaHit consortium) showed something else. A census of nearly three hundred Europeans showed that the number of unique bacterial genes in subjects’ guts varied dramatically. The distribution of individuals wasn’t normal; it was not a bell 33
curve.Instead,researchers found two major groups.The larger group of 77 percent of the people had an average of about eight hundred thousand genes.The smaller RR2socrteoteioigoeamam the people who had the low gene counts were more likely to be obese.This was a striking result,which we will discuss in more depth later. Understanding the ecological structure of our resident microbes presents a tricky puzzle.In a large ecosystem,say a forest,ecologists can directly observe numerous individuals and species behaving and interacting in real time,on daily,seasonal and annual scales.But we can't yet study microbial ecosystems in anywhere near the same way.As mentioned above,one of our best current methods is to count and identify all the genes in a given community.As a task,that is a bit like scooping up an acre of forest,putting it through a gigantic blender,and then counting the leftover fragments of leaf,wood,bone,roots,feather,and claw,and deducing from the detritus what we can about the woodland's species and their interactions. We can figure out some functions of our bacterial genes by comparing them with other known genes.Initial findings from the Human Microbiome Project and from the European MetaHit program account largely for what we call "housekeeping genes,because they are both routine and necessary for life.For example,genes for cell-wall manufacture and maintenance abound since all bacteria have to build cell walls.Similarly,all bacteria must have genes that allow them to replicate their own DNA so they can reproduce.Genes that code for a crucial enzyme,DNA polymerase,needed for making new strands,have been identified.Humans have several varieties of this gene,whereas your resident microbes may have thousands, each one slightly different,depending on which bacterium it comes from. There also are less subtle differences in the genes of microbes found in different areas of the body.While genes for housekeeping tasks remain consistent, skin bacteria have more genes related to oils than do bacteria living in the colon. Vaginal bacteria have genes to help them create and deal with acidic conditions.At this point in our knowledge,we can safely predict that bacteria will carry out specialized functions in each of the body's habitable niches and that the differences involved are much greater than those seen in the human genome.For example,the difference in height between the tallest and the shortest adult on Earth is perhaps two-or threefold.Organisms in a typical microbiome may range,in their individual representation,by a staggering ten million-fold.Bacterial specialization is a thrilling and largely unexplored realm in uncovering what makes each of us distinct in terms of our health,metabolism,immunity,and even cognition. While we have yet to identify the function of some 30 to 40 percent of bacterial genes identified by the large projects,we do know that some species are rare and 34
curve. Instead, researchers found two major groups. The larger group of 77 percent of the people had an average of about eight hundred thousand genes. The smaller group (23 percent of the subjects) had only about four hundred thousand genes. Two distinct groups; this was not expected. But the most interesting observation is that the people who had the low gene counts were more likely to be obese. This was a striking result, which we will discuss in more depth later. * * * Understanding the ecological structure of our resident microbes presents a tricky puzzle. In a large ecosystem, say a forest, ecologists can directly observe numerous individuals and species behaving and interacting in real time, on daily, seasonal, and annual scales. But we can’t yet study microbial ecosystems in anywhere near the same way. As mentioned above, one of our best current methods is to count and identify all the genes in a given community. As a task, that is a bit like scooping up an acre of forest, putting it through a gigantic blender, and then counting the leftover fragments of leaf, wood, bone, roots, feather, and claw, and deducing from the detritus what we can about the woodland’s species and their interactions. We can figure out some functions of our bacterial genes by comparing them with other known genes. Initial findings from the Human Microbiome Project and from the European MetaHit program account largely for what we call “housekeeping” genes, because they are both routine and necessary for life. For example, genes for cell-wall manufacture and maintenance abound since all bacteria have to build cell walls. Similarly, all bacteria must have genes that allow them to replicate their own DNA so they can reproduce. Genes that code for a crucial enzyme, DNA polymerase, needed for making new strands, have been identified. Humans have several varieties of this gene, whereas your resident microbes may have thousands, each one slightly different, depending on which bacterium it comes from. There also are less subtle differences in the genes of microbes found in different areas of the body. While genes for housekeeping tasks remain consistent, skin bacteria have more genes related to oils than do bacteria living in the colon. Vaginal bacteria have genes to help them create and deal with acidic conditions. At this point in our knowledge, we can safely predict that bacteria will carry out specialized functions in each of the body’s habitable niches and that the differences involved are much greater than those seen in the human genome. For example, the difference in height between the tallest and the shortest adult on Earth is perhaps two- or threefold. Organisms in a typical microbiome may range, in their individual representation, by a staggering ten million–fold. Bacterial specialization is a thrilling and largely unexplored realm in uncovering what makes each of us distinct in terms of our health, metabolism, immunity, and even cognition. While we have yet to identify the function of some 30 to 40 percent of bacterial genes identified by the large projects, we do know that some species are rare and 34
vulnerable to extinction.As with vaginal microbes,bacterial populations can be extremely dynamic.The number of cells representing a particular species can vary from,say,one cell to a trillion.Let's assume an animal is exposed to a new food that contains a chemical never before encountered.The bacterial species that is today represented by one hundred cells could,given a triggering change in the intestinal environment such as the new food,become billions of cells within a few days.If faced with loss of a prized food or with competition by its hungry fellow bacteria,the numerically dominant species could then drop in numbers several thousand fold or more.It is this dynamism and flexibility that are at the heart of the microbiome and contribute to its staying power.But the species represented by a hundred cells in normal times doesn't have a big margin for error.It could also encounter an antibiotic that wipes it out permanently. I call these rare species contingency microbes.Not only can they exploit an unusual food chemical (which more common bacteria cannot),but they may provide genetic protection against threats,such as a plague that humans have not before encountered.To me,this is a flashing red light.Diversity is essential.What if we lose critical rare species?What if human keystone species disappear?Would there be cascading effects leading to secondary extinctions? The fact that we can coexist with bacteria raises a profound set of questions.Why don't they wipe us out?Why do we tolerate them?In the dog-eat-dog world of Darwinian competition how have we achieved a stable relationship with our microbes? Public-goods theory provides clues.A public good is something that everyone shares,such as the clean air you breathe at the seacoast,a bright sunny day,a local street built with your tax dollars,or your favorite public radio station.But nothing is ever really free.Public radio must be supported;someone has to pay.Even if clean air is public,your car might emit pollution that affects my clean air.My breathing and your driving occur in the same space. In a smoothly functioning social world,each individual is expected to contribute to the public interest.You can listen to public radio and not pony up but, if everyone did that,public radio would go bankrupt.If everyone had a car out of tune,our common air and sunlight would be degraded.In this sense,people who use a public good but don't give sufficiently,or who add to the common expense may be considered "cheaters";they benefit but do not pay their fair share of the enterprise. However,out in the jungle,where "survival of the fittest"rules supreme, "cheating"seems like a pretty good strategy.The cheater might be able to lay more eggs or find better nesting sites and,over generations,be more successful (have more offspring)since its ratio of benefit per cost is more favorable.The cheater 35
vulnerable to extinction. As with vaginal microbes, bacterial populations can be extremely dynamic. The number of cells representing a particular species can vary from, say, one cell to a trillion. Let’s assume an animal is exposed to a new food that contains a chemical never before encountered. The bacterial species that is today represented by one hundred cells could, given a triggering change in the intestinal environment such as the new food, become billions of cells within a few days. If faced with loss of a prized food or with competition by its hungry fellow bacteria, the numerically dominant species could then drop in numbers several thousand fold or more. It is this dynamism and flexibility that are at the heart of the microbiome and contribute to its staying power. But the species represented by a hundred cells in normal times doesn’t have a big margin for error. It could also encounter an antibiotic that wipes it out permanently. I call these rare species contingency microbes. Not only can they exploit an unusual food chemical (which more common bacteria cannot), but they may provide genetic protection against threats, such as a plague that humans have not before encountered. To me, this is a flashing red light. Diversity is essential. What if we lose critical rare species? What if human keystone species disappear? Would there be cascading effects leading to secondary extinctions? * * * The fact that we can coexist with bacteria raises a profound set of questions. Why don’t they wipe us out? Why do we tolerate them? In the dog-eat-dog world of Darwinian competition, how have we achieved a stable relationship with our microbes? Public-goods theory provides clues. A public good is something that everyone shares, such as the clean air you breathe at the seacoast, a bright sunny day, a local street built with your tax dollars, or your favorite public radio station. But nothing is ever really free. Public radio must be supported; someone has to pay. Even if clean air is public, your car might emit pollution that affects my clean air. My breathing and your driving occur in the same space. In a smoothly functioning social world, each individual is expected to contribute to the public interest. You can listen to public radio and not pony up but, if everyone did that, public radio would go bankrupt. If everyone had a car out of tune, our common air and sunlight would be degraded. In this sense, people who use a public good but don’t give sufficiently, or who add to the common expense, may be considered “cheaters”; they benefit but do not pay their fair share of the enterprise. However, out in the jungle, where “survival of the fittest” rules supreme, “cheating” seems like a pretty good strategy. The cheater might be able to lay more eggs or find better nesting sites and, over generations, be more successful (have more offspring) since its ratio of benefit per cost is more favorable. The cheater 35
has a selective advantage.However,if"cheaters"always won,cooperation would fall apart.Why wouldn't everyone cheat and not pay for public radio?How can different life-forms live together if there is a built-in selective advantage for breaking the rules?Cheating has the power to make the whole system break down. Yet clearly cooperation occurs everywhere we look:bees and flowers;sharks and pilot fish;cows and their rumen bacteria allowing them to create energy from grass,termites,aphids.As far as we know,ruminants have existed for millions of years and insects like termites and aphids even longer.This tells us that cheaters don't always win.Simply put,the penalty for cheating must be sufficiently high that cheating is disadvantageous,so that cheaters don't triumph.If there were no consequences,more people would speed when they drive.Penalties work The same holds true for you and your microbes.Natural selection favors hosts that have a system of penalties in place that cannot be evaded:the more the cheating,the higher the penalty.Such penalties can deflect the spoils of"ill-gotten" gains.Thus a bacterium in the termite gut that oversteps its bounds can trigger a very strong immune response,putting it back in its place.This works,but it can be expensive for the host to have such a system.Some might die fighting off cheaters with an overly aggressive immune response.When the host dies,so do all of its inhabitants.When this happens,all of the genes,from both the host and its residents are lost for all of posterity.Other termites that did not have a cheater arise and take up the niche vacated by their newly deceased sibling. The tension between competition and cooperation plays out on a thousand stages. Game theory,inspired by the great economist and mathematician John Nash (whose story has been told in the book and movie A Beautiful Mind),sheds light on the phenomenon of cooperation,on why coevolved systems appear to select for individuals who largely play by the rules.It is a way of understanding behavior in social settings-how people make decisions to optimize outcomes and how markets operate.Nash envisioned a situation that has since been called the "Nash equilibrium."It can be summarized as a strategy in a game with two or more players in which the outcome is optimized by playing within the rules,if you cheat, your outcome is worse than if you played fair and square. Ecosystems that have been around a long time,like our bodies,have solved this fundamental tension between conflict and cooperation.We have persevered.But this theory has relevance as we consider our changing world.What that means is that cooperation is tenuous:don't mess with it,because then all bets will be off.I worry that with the overuse of antibiotics as well as some other now-common practices,such as Cesarian sections,we have entered a danger zone,a no-man's- land between the world of our ancient microbiome and an uncharted modern world 36
has a selective advantage. However, if “cheaters” always won, cooperation would fall apart. Why wouldn’t everyone cheat and not pay for public radio? How can different life-forms live together if there is a built-in selective advantage for breaking the rules? Cheating has the power to make the whole system break down. Yet clearly cooperation occurs everywhere we look: bees and flowers; sharks and pilot fish; cows and their rumen bacteria allowing them to create energy from grass, termites, aphids. As far as we know, ruminants have existed for millions of years and insects like termites and aphids even longer. This tells us that cheaters don’t always win. Simply put, the penalty for cheating must be sufficiently high that cheating is disadvantageous, so that cheaters don’t triumph. If there were no consequences, more people would speed when they drive. Penalties work. The same holds true for you and your microbes. Natural selection favors hosts that have a system of penalties in place that cannot be evaded: the more the cheating, the higher the penalty. Such penalties can deflect the spoils of “ill-gotten” gains. Thus a bacterium in the termite gut that oversteps its bounds can trigger a very strong immune response, putting it back in its place. This works, but it can be expensive for the host to have such a system. Some might die fighting off cheaters with an overly aggressive immune response. When the host dies, so do all of its inhabitants. When this happens, all of the genes, from both the host and its residents, are lost for all of posterity. Other termites that did not have a cheater arise and take up the niche vacated by their newly deceased sibling. The tension between competition and cooperation plays out on a thousand stages. Game theory, inspired by the great economist and mathematician John Nash (whose story has been told in the book and movie A Beautiful Mind), sheds light on the phenomenon of cooperation, on why coevolved systems appear to select for individuals who largely play by the rules. It is a way of understanding behavior in social settings—how people make decisions to optimize outcomes and how markets operate. Nash envisioned a situation that has since been called the “Nash equilibrium.” It can be summarized as a strategy in a game with two or more players in which the outcome is optimized by playing within the rules; if you cheat, your outcome is worse than if you played fair and square. Ecosystems that have been around a long time, like our bodies, have solved this fundamental tension between conflict and cooperation. We have persevered. But this theory has relevance as we consider our changing world. What that means is that cooperation is tenuous: don’t mess with it, because then all bets will be off. I worry that with the overuse of antibiotics as well as some other now-common practices, such as Cesarian sections, we have entered a danger zone, a no-man’sland between the world of our ancient microbiome and an uncharted modern world. 36