Antimicrobials

One of the consequences of understanding disease as being caused by germs is a widespread perception that all germs are bad.

This finds its ultimate expression, perhaps, in certain varieties of obsessive-compulsive disorder, but the idea that "all germs are bad" is a now generalized one. It has recently expanded to include the idea that "all fungi and molds are bad;" basically, if you can't see it, it is bad and therefore, in one way or another, dangerous.

While germ paranoia of the hand-wringing variety may be amusing when regarded from a clinical distance, it becomes a truly dangerous thing in the minds of the ignorant. People are trained to believe not only that all germs are bad, but that if they are sick in any way they ought to at once take drugs designed to kill germs (antibiotics.)

Drug companies have found it most expedient to encourage such ideas in the interests of boosting sales; and, recently, personal care product companies who manufacture soaps decided that it would be a teriffic idea to market antibacterial soap—even though soap is, by its very nature, already antibacterial. Triclosan, the common antibiotic ingredient touted (and used) as an additive to soaps, toothpastes, and other products, has been put, so it seems, in every soap dispenser in America.

Lo and behold. Bacteria are developing resistance to triclosan.

In the same way, doctors began, back in the late 1980's, to prescribe antibiotics to children every time they had an ear infection—in spite of the fact that statistics showed that antibiotics didn't really help ear infections clear up that much faster. Well, mothers wanted the doctors to do something against all those bad germs... what were they paying them for, anyway? It turned out to be more expedient to write the child a prescription than to have to listen to the mother complain. And the next thing you know, bacteria that cause ear infections were not only on the rise... they were drug-resistant.

The phenomenon of MDR (Multi Drug Resistant) bacteria is so well known by now that it's hit the mainstream. Everyone has read at least one horror story about a patient who got this, that or the other bug which just couldn't be killed. What isn't well known is that our over-use of antibiotics—which has drawn little or no real legislative attention from the health authorities in any nation—is causing these problems on a greater and greater scale. The "superbugs" that cause these disease problems are not, furthermore, living in isolation. They have spread otu into the egenral population and are passing their resistance genes on to foreign strains of bacteria—other bacteria which, in many cases, we don't even know about.

This deeply disturbing trend, another issue that has been underreported in the media and under-studied in labs, comes about because of the ability of bacteria to share genetic material between species via plasmids, gene packages that can engage in what amounts to interspecies sex. This proclivity was greeted with astonishment and delight when biologists first discovered it in the 1950's—it seemed miraculous—but as drug resistance spreads deeper and deeper into bacterial populations, it's looking decidedly more hellish than heavenly. The problems we've created by dosing our children with antibiotics for ear infections have moved well past their original targets.

The issue is even more widespread, because humans are not, actually, the prime users of antibiotics in society today. That dubious privilege belongs to farm animals... of which more in the next post.

Adjusting the Earth

Today we're going to examine a subject a little more down to earth.

We truly don't appreciate just how much creatures adjust the environment around them to suit the microbes they need.

Trees are an excellent example of this. All plants, for that matter. Every plant has a community of fungi and microbes it needs around its roots in order to help take up the nutrients it requires for survival and growth.

Disruptions to this community can spell the death of the plant; and in plant monocultures, such as those propagated by modern agriculture—where we actually encourage a complete lack of species diversity— we are creating a situation wide-open to problems.

But let's get back to the trees, which are the subject of today's post. Every tree has a very specific microbial need around its roots; and the nutrients that the tree's leaves deliver when they fall are exactly the right blend of chemicals and are at exactly the right acidity for that particular tree.  (This may seem like a minor matter, but small changes in pH can lead to large changes in microbiology.) This means that the leaves, when they fall, are creating the best possible conditions to nurture their tree's future growth. They're also finely tuned to create conditions that do not favor the growth of hostile species; so trees and other plants condition the soils around them to lower the chances of competition. This is equally true in forests, prairies, and even marshlands. 

You might think that if you take those leaves away and put other leaves from a different tree (or some other composting material)  in their place, it will have the same effect, but that's not exactly the case. When you take the leaves away from the tree, over the long term, you're depriving it of the specific micro-environment it needs, a finely tuned set of relationships which evolved over millions of years, and substituting another, much less beneficial one.

It may not seem this way when you rake leaves up and move them, but the habit of moving litter away from its natural environment is contributing to long-term degradation of soil microbial communities all over the world, wherever it's practiced. While it doesn't kill plant and tree populations right away, it places them under constant low grade, long-term stress, and it steadily degrades the soils in which the trees are growing. 

Soils build far more slowly than we deplete them; and the majority of human activity is soil-destroying and soil-depleting activity. Real estate development creates so much soil disruption in a single year worldwide that nature would require thousands of years to create new soils to repair the damage. We can get away with such nonsense for only just so long before it catches up with us. Many of the areas being developed are the ones with the best soils; which means that agriculture is gradually being pushed out to the margins of habitable landscapes, where it is more tenuous and requires a much greater investment in energy, time, and resources to cultivate. These marginal landscapes are, furthermore, microbially impoverished, compounding the problem.

While one can counteract the various soil deficits we create by artificially boosting plant yields using fertilizers, this practice is something like using cocaine to stimulate yourself and stay awake. It works really well, but for only just so long; eventually, a dependency arises, and the results are, in the long-term, disastrous. The tremendous proliferation of corporations who sell chemical products -fertilizers, herbicides and insecticides- to dump on lawns by the millions of tons per year are not helping any; the general public, poorly educated on soil conservation at best, is aggressively marketed with disinformation which tells them to amend their homeowner soils using clumsy, unsustainable, but—for the corporations—very "profitable" methods.

Like the overuse of antibiotics, which is breeding whole new generations of disease-causing but drug-resistant bacteria, the widespread effects of poor agricultural practices are causing long-term, hidden changes to the way that the microbes around us are supporting what grows in our soil. We can't see it, so we don't worry about it; but we should.

The artificially created environments in which most cultivated and suburban plants are growing is inherently unsustainable without the support of artificial means; and it's likely that it will take centuries for the long-term implications of the impoverishment of our microbial environment to become apparent. It's quite possible that in many places, we will discover soils have been rendered essentially sterile because of the lack of the correct long term microbalance.

Even worse, because we have so few people interested in studying this right now, we are unlikely to identify and analyze the microbial communities around plants to any degree of the depth necessary in order to know how to preserve them.

By the time the things we need to know are evident, they may well be gone.

Trees die slowly

There's nothing random about microbes. Each one has, like larger organisms, a specific niche and set of tools to exploit it.

That extends past life into death. When creatures die each one has their own specialized set of organisms designed to feed on its remains. That's true of plants as well as animals.

Let's take the above photograph of leaves as an example. The microbes digesting the two species are feeding on different chemistries; each leaf has its own peculiar mix of nutrients, proteins, and insecticides (natural pesticides) in the form of aromatics. Hence the different patterns of decay on the leaves: the microbes involved may well be different (though perhaps related) strains, even though the leaves fell in close proximity to one another. Each leaf has a particular set of microbes that breaks it down most efficiently; and here, efficiency is everything. The faster a leaf is broken down, the sooner its nutrients become available to the plants that are still growing in the immediate vicinity; and this applies especially to the tree the leaves fell from. So there is an evolutionary dialogue taking place between the tree, its fallen leaves, and its microbes. Microbes that digest its leaves better thrive; leaves with a chemical balance (acidity and nutrient mix) suited to the microbes feed them better; and the faster the leaf nutrients are freed up and leach into the soil (creating new soil in the process) the faster the tree can use them.

There's a principle to be learned here. Efficiency, in an ecosystem, is everything. Ecosystems rely on processing nutrients both before and after the death of organisms in order to thrive. Species that process nutrients faster, in symbiosis with their microbial partners, add efficiency to the system and enhance the ability of those organisms to thrive, reproduce, and hold their own against other species.

When efficiencies are lost— or new efficiencies arise, for example, the arrival of a new flood of nutrients better suited to the efficient growth of alternate species—the dominant species in any ecosystem, microscopic or macroscopic, begin to change.  This is because ecosystems are dynamic entities that respond to changes in efficiency by favoring the organisms, or mix of organisms, best able to use them efficiently. If kudzu, for example, uses an available niche more efficiently than native plants, it grows faster.

This holds true of microbes and fungi as well as larger animals. What it means that an alteration of microbial communities leads to new arrangements in the soil, water, and even air. Residents of North Carolina found this out to their increasing dismay in the 1990's when pfisteria, a dinoflagellate protist you really don't want in your waterways, underwent explosive growth in the tidal areas of North Carolina because of a flood of nutrients entering the watershed from the explosive growth of huge, factory-type hog farming upstream. The microorganisms cause debilitating disease and massive fish kills.

Let's be clear: from the point of view of the microbes, this is not a bad thing. The overall efficiencies of the tidal ecosystems in the Albermarle, Croatan, and other NC sounds haven't deteriorated as a result of this pollution. Odds are the systems are still equally efficient; but they are no longer the same systems.

And this is the lesson: changes in microbial populations can lead to fundamental long term changes in ecosystem efficiency, resulting in drastic changes to the animal and plant communities that depend on them. This phenomenon is still poorly understood, but if the fish kills in North Carolina (and, unfortunately, many other parts of the world)  have taught us one thing, it's that these changes are often unfavorable for man.

Spectacular fish kills are more obvious than slower, long term changes in soil-based microbial populations, but the changes we can't see up front are far more insidious and will, in the long run, be much more difficult to manage. Trees under stress caused by microbial changes may die much more slowly; and the causes may not be identified until well after it's too late.

Environment and Community

 Sandpiper, foraging for larval mole crabs and other zooplankton

Kitty Hawk, North Carolina

 photograph by the author

We are used to the idea of mankind altering his environment to make it more suitable for him. We not only build houses; we landscape areas, dig ditches, build highways, and so on. But it may come as a surprise to readers to hear that microorganisms routinely alter their own environment to make it suitable for themselves. The creatures that depend on them — ourselves, for example — also alter their own environments, believe it or not, to make them more suitable for the microorganisms that they need.

We're going to take one of the most striking examples of that today, although there will be more to look at later on. We've already explained that human beings require a healthy, and wide variety, of microorganisms in their gut in order to digest foods properly. Without them, we die.

Where do we get those microorganisms? Well, of course, we swallow some from our environment. But more importantly, we inherit some of them — quite literally inherit them, since we acquire them from our mother during the process of natural birth.

As peculiar as it may seem, the birth canal — the vagina — is a rich environment for bacterial growth, and in the days just before birth, it turns out, this environment is heavily populated with bacteria from the mother's own gut bacteria community. She has, in other words, a range of all the microbes that the child will need for its digestive system waiting for it in her birth canal. When the child finally leaves the sterile environment of the amniotic fluid — when the water breaks and birth begins — the infant moves through the vagina, opening and closing its mouth, and inevitably swallows billions — perhaps even trillions — of the bacteria that it will need to populate its gut with. So the first organisms it needs other than its mother are, logically enough, bacteria. And the very first act of its life, before it even leaves the birth canal, is to set up housekeeping with them.

Obviously, children that are born by cesarean section don't get this benefit. The rising tide of children born in this matter in modern Western societies is leading to a large number of children who don't start life out with the correct gut bacteria populations. This has long-term implications, since the developmental well-being of the child depends in large part on making sure it has the right gut bacteria from the moment it begins to ingest foods. Otherwise, it's digestive processes don't work properly, and, in addition, the immune system doesn't develop properly. This can lead to all kinds of overreactive immune system situations in later life, and may well lead to diseases such as autism, diabetes, and other maladies such as bipolar disorder and other psychological deficits.

Oddly enough, this could all be corrected by taking children born by cesarean, swabbing the mother's vagina, and making sure that some of that liquid was put in the child's mouth. But no one seems to think of things this obvious.

It gets a little more complicated than that. Breast milk, it turns out, has essential proteins in it which, although they don't do much for the child — it can't digest them — are in fact perfect for the gut bacteria developing the child's intestines. And it furthermore carries an additional wide population of bacteria that are absolutely necessary for the well-being of the child. Follow the links for some fascinating insights into this.

The point is that there is nothing passive about the way that bacteria are delivered to an infant so that it's gut bacteria populations develop properly. Nature is arranging things specifically so that the bacteria are not only present, but have exactly the right environment to support the growth of the organism. So you human beings don't just have bacteria; nature makes certain that they have bacteria, and it makes certain they have the right bacteria. It creates conditions ideal for those bacteria, delivers them, and then nurtures them. This is an example of bioengineering that goes to the root of what community means. Nature, and life, is a community, not a collection of individuals who act independently of one another. The perception of independent action is largely illusory, yet we endorse it as one of the foundations of our social contract.

Nature teaches us otherwise.

 Of course, human beings are far from the only organisms that do this. Think about this: every single organism with a gut has bacteria in it, and every single one of them undoubtedly has similar mechanisms to ensure that it has the right bacteria in it. The entire animal world is engaged in this activity — unseen, and underappreciated. Unfortunately, the action of chemicals in the environment and the accelerating spread of foreign bacteria into new environments is guaranteeing greater and greater disruption of this system, which leads to all kinds of diseases. Because we don't understand how the  system is constructed, many of these diseases don't, at least at first, appear to be linked to the microbial population, but most of them are, in one way or another. The situation becomes more serious every decade, with disturbing diseases such as psychological and immune system disorders becoming more and more prevalent.

We keep looking for the causes of these diseases in our genes; but it may well be that the causes of them lie in our microbial populations, a place we have only just recently started to look at more seriously.

 These arrangements do not stop with animals, which we will discuss in the next post.

The microbial atmosphere

Empire State Building, New York, Sept. 2013

Photograph by the author

You can't see them, but you are currently surrounded by a sea of microbes. Not just trillions of them; googols of googols of them (googol being the number one followed by one hundred zeros.) There are so many bacteria and microbes on the surface of the planet, in fact, that they form what is more or less an atmosphere, a living medium through which all life "swims." This medium is breathed in constantly by all breathing creatures; it is swallowed. It lives on, in, and around every living creature. The presence of microbes is 100% constant from the day an animal is born until the day it dies.

If we were deprived of this microbial medium, we'd all die. Everything would die. These are the fundamental and essential conditions that life exists under and is supported by: a sea of life through which we constantly swim.

Any impoverishment of the environment can lead to issues. Killing off microbes protects us, to some extent, from disease; but the negative consequences can be disastrous. Polio, for example, was rarely a problem before the twentieth century. Poor water quality very nearly guaranteed that infants were exposed to it; for reasons yet to be fully understood, the virus has little effect on infants, so the virus-rich water supply conferred immunity on the majority of the population. It was only when water supplies were cleaned up that children began to reach young adulthood without immunity; the results were disastrous. Although cleaning up the water supply has bee a good thing in many ways, it is definitely possible to have too much of a good thing; and the steady pace of extermination of microbes in the child-rearing environment is leading both to a host of old diseases on the rise and new, emergent diseases.

The bottom line is that we need the microbial communities we inhabit. Cleaning them up too much, sterilizing the environment, turns out to directly affect the development and responses of our immune system, with sometimes disastrous results.

Although I'm sure it sounds like a reach, it's useful to think of the microbial environment we inhabit as an atmosphere. Like air, it invisibly surrounds us, and like air it's a medium that we absolutely require for daily life. We literally and figuratively breathe it in and out.

Interestingly, science has readily identified and embraced the chemical atmosphere of air and water as essential to the support of life, but the microbial atmosphere has been largely ignored, even though it comprises a living atmospheric medium for all larger life forms. Found in the air, soil, and water, one might argue that bacteria and fungi bridge the gap between the these chemical media and macrobiotic life forms. They are, seen from a slightly different but analogous perspective, a tissue that holds the macrobiota of the planet together by translating chemical constituents into usable forms.

So we live in an atmosphere of microbiota; and we depend on them so much that it becomes apparent symbiosis is, on the whole, a more prevalent lifestyle than competition.

This is so much the case that larger organisms don't juts host microbes; they go out of their way to create situations that favor the microbes they need for their own survival. More, quite literally, than meets the eye goes on in this regard; and we'll discuss that in the next post.

Man and microbe

Here we are at the tangled, integrated end of a process that began about three billion years ago with bacteria and other microbes, evolved from them, and carried them along through billions of years of evolution... only to discover each one of us is the unwitting repository for trillions of microbes, without whom we could not survive.

To cast an even more interesting light on it, one of the possible—and credible—origin-of-life theories is that life came from outer space. Yes... life may be alien. The theory is more accepted than the idea that God created life out of thin air, at least in standard scientific circles.

One of the reasons this theory is considered credible is that DNA is an incredibly sophisticated, highly evolved and optimized molecule. It's so good at what it does that it just doesn't seem as though there was enough time after the molten fireball of earth cooled off enough to support life for it to have evolved to the state we find it in in the earliest fossil records... about 3.4 billion years ago.  The question of how life evolved at all in the hostile environment of early earth is still actively puzzling scientists.

The earliest fossils are recognizably similar to organisms still around today, which just about guarantees they shared a version of the same DNA we find in ourselves. DNA, it turns out, is so very, very good at what it does that many of the structures it uses to create specific proteins, molecules, and body structures are preserved as analogs to one another in creatures that diverged five hundred million years ago or more.

Bodies change... niches change... but although in some ways DNA changes a lot, in other ways, it's actually a very, very conservative molecule. It rarely, if ever, re-invents if what it already has can be reconfigured to work in a new way. Organisms (we can think of DNA, in a broad sense, as an evolving organism) this highly developed, consistent, and durable probably took hundreds of millions of years to reach that level of sophistication; and this is, to be sure, rather unlikely to have taken place at an accelerated pace under the hostile conditions provided on the early earth.

In a certain sense, man himself is a collection of microbes, since each cell—fully integrated and cooperative though they may be—functions as an individual organism. We're reminded of this in unpleasant ways when we get cancer—this, after all, is the ultimate example of just how independent and, in fact, malevolently autonomous cells can still be under the right circumstances. White blood cells (macrophages)  wander around acting on behalf of our defensive systems; cancerous cells act something like that, only when they crawl between tissues, they are looking for places to metastasize—settle down, set up house, and... eventually... kill us, if we're unlucky.

So we're communities of microbes, hosting larger communities of biota. It's estimated there may be as many as 100 trillion "foreign" microbes in the average human being. Multiply that by a planet of 6 billion people... we're up to six billion trillion microbes, and that's just the ones resident in us humans. In contrast, consider that there are probably about ten trillion of our own cells in a human body. The microbes we carry outnumber us by about 10 to 1... or 100 trillion to one, if you want to count our conscious self as one, and our microbes as being on the other side of that fence.

We live, furthermore, in a sea of microbes, one so dense as to give people with OCD the willies.

The point of this excursion is to explain that we depend on our microbial population for survival. We don't just have the microbes; we need them, and the vast majority of them have been evolving in conjunction with animals... first arthropods, then amphibians and fish, then reptiles, and mammals, until finally they ended up here with us. Each microbe we host is exquisitely tuned to living on or in our body.

It isn't just this way for humans. All of life on earth is ultimately arranged this way; everything depends on microbes to function.

We'll take that up in the next post.

Why microbes?

In order to gain a deeper understanding of why microscopic lifeforms are so important to the existence of life in general, we need to begin with the fact that these were the very first life forms.

Not only did all other forms of life develop from them, because they formed the initial communities from which all further developments in life evolved, all these developments in life ultimately built their livelihood directly on the foundations laid by this community of organisms.

Growth depends on the acquisition of nutrients, and in any given environment—especially, perhaps, the most primitive ones on early earth— the total amount of nutrients is quite limited. It furthermore always costs something in terms of energy to acquire nutrients and concentrate them. This is what microscopic life — the first cells — did. In doing so, they created richer, far more concentrated repositories of nutrients.

It turns out that one of the best ways to acquire richer sources of nutrients is to exploit pre-concentrated ones that already exist—that is, steal them, which usually takes less energy than doing the work of concentrating them. And indeed, very early on, lifeforms began not only to compete with each other for the available raw nutrient resources; they learned how to take them from one another. In other cases, they learned to cooperate with one another and share resources; but in either strategy, it became expedient to lock the nutrient resources up in one way or another so that they couldn't be easily shared or stolen. The idea was to make the cost of acquiring these richer sources of nutrients – that is, the bacteria themselves – high enough that it wasn't worth it to others, unless they were willing to give something in return. That could include anything from a mutually beneficial exchange of valuable substances up to the taking of the other party's life in order to get what they had. Cooperation and competition.

Locking these nutrients up took two obvious directions. One of them was to develop body shapes and forms that had strong defensive capabilities. Groups of cells cooperating were better able to defend themselves than single cells; and so one of the first steps in life was the advent of cellular communities, which developed into what we now call organisms. The organism is the microbiological equivalent of individuals and societies banding together to form an army. Communities of cells were better able to defend their resources; they were also, it turns out, better able, in many instances, to acquire them. It wasn't long, in fact, before they began actively altering the environment around them to favor their survival. This took a number of forms—still with us today—which we'll talk about later.

The second line of defense for nutrient resources was to lock them up in chemical forms that couldn't be used by adversaries. One of the best examples of this chemical defense mechanism is cellulose, which is incredibly effective at taking nutrients and locking them up in an unavailable form. It works so well that almost every plant on earth now builds its life around the production of cellulose. This has forced the many larger organisms that want to feed on it—after all, it is incredibly abundant!— to develop mechanisms that can defeat the chemical "locks" on cellulose by digesting it.

The mechanisms that allow animals to digest cellulose are all primarily microbiological. Because it's difficult to attack cellulose in any other than a chemical way, digestive juices of various kinds must process it, all the way from the macrobiotic (gut) level to the microbiotic (fermentation) one.

Despite several billion years of evolution since the advent of the first single cell organisms, everything on the planet is still arranged in exactly this way. Cells lock nutrients up to make them unavailable; and animals and plants which choose to acquire them have to use chemical tools to unlock those nutrients. Even the largest creatures with the biggest teeth and the most powerful muscles can only do the initial job of acquiring the foods; microbiotic forces have to unlock them and make them available. And in the vast majority of cases, in fact, probably all cases, larger organisms have recruited their own colonies of microorganisms to help them do this. (The whole process of decay is deeply tied to this activity.)

This means that when you get a meal for yourself, the meal isn't just for you. It's for the microbes in you as well; you need to feed them, or they can't feed you. Eating the wrong things for them will ultimately lead to bad results for you as well, because it will favor the development of microorganisms that aren't beneficial to your digestive process.

Although forms and sizes have changed over billions of years, the fundamental underpinnings of the food chain have never changed. Given the strong persistence of DNA throughout life as we know it, it's very likely that not only DNA, but also the nutrient-storing molecular forms it encodes for, are much the same as they were billions of years ago. We know, for example, that there were plants of one kind or another using chlorophyll that long ago. They are still doing it today — and so we exist in an unbroken chain that relies on chlorophyll and its molecular productions for energy. Without it, sunlight couldn't be converted; and without the sugars that it converts molecules into, pretty much nothing on the surface of the planet could live. (There is, of course, another chapter to this story—creatures under the surface.)

In a certain sense, then, microbes are running the show; all of us are just vehicles for their action and dispersal. The more efficiently an organism interacts with the microbial community it supports, the more effectively it competes in the acquisition of nutrients. So the microbiological community actually fuels the process of evolution in ways that are still not well understood.

Because of our general ignorance in these matters—and the impression that we can do little or nothing to intelligently manage such things—we have, on the one hand, blithely ignored our relationship with microbes and, on the other, attempted to exterminate the ones that we know cause disease. Both approaches have turned out to have their drawbacks; the one, because we cause harm we don't know about, and the other, because our short-term management of infectious disease in both livestock and humans has led to unforeseen problems in microbe evolution.

Microbe evolution is taking place all around us, all the time, and at a much more rapid pace than our own. 

We'll take that up next.