Microbes 2.0 – A Tiny Manifesto

I have struggled with the prospect of sterilization. Not sterilization of myself, as in vasectomy; but sterilization of other things, as in antibiotics and antiseptics. The whole idea of sterilizing feels like a bad idea to me. It’s apparent to me that not everyone agrees with me on this, to say the least. As a society, we’re hip-deep in antibiotics, antibacterials, antiseptics, antimicrobials… Why is everybody so mad at the microbes?

In my own life, it seems like the more deeply involved in self-sufficiency I get, the more I need to know about sterilization. When I wanted to brew beer, when I wanted to brew compost tea, when my tomatoes got some awful sudden-death virus, when I canned the surviving tomatoes… It seems like everything I want to do these days requires that you sterilize one thing or another.

My wife and I have had an ongoing conversation about the different ways to sterilize things, which methods are the best for different things, and when it is really required that you sterilize something. The whole thing came to a head recently, as we have been forced to confront the issue of sterilization again and again during her pregnancy. Some of the advice you get when you’re expecting a child is, paradoxically, very sterile. It’s all about cutting out any unnecessary risks. No unpasteurized dairy, no unpasteurized juice, no deli meats, no unwashed produce, no sushi, no soft eggs… No sprouts! I get it. I understand the concern. You’re worried about getting germs on your baby. But if you travel far enough down this sterile rabbit hole, you’ll be wearing a hazmat suit for 9 months.

So far, we have been able to reach a healthy compromise at our house. We’re cutting down on unnecessary risks without trying to create a laboratory environment for the baby. Our normal approach is ‘all things in moderation.’ Our pregnant approach is more like ‘most things in moderation, except sushi.’ Maybe we’d feel differently if we lived in Seattle, but in Austin sushi’s off the menu, for now. We agree that the compromise will end as soon as the baby’s immune system is up and running. Then he or she can drink all of the unpasteurized juice they want.

I half-way joked with my wife that, in a world where we’re surrounded with sterilization, I want her to eat some fast food hamburgers while she’s pregnant to inoculate the baby against fast food ingredients.

Nature Abhors a Vacuum

The whole idea of sterilization is counterintuitive to me. In nature, things don’t come in ones, all alone. All other natural life occurs in groups. Here’s why sterilization seems like a bad idea to me: You kill everything to get rid of one specific bad thing, or a few bad things. The idea that you should exterminate all life in order to remove one problem species is horrible. We would never do this in the macro world, that is, in our yards and gardens. Would you burn your lawn to get rid of the dandelions? We would never do this on a global level. Why would we do this on a micro level, within our bodies?

All life occurs in groups, guilds, and communities. You don’t just have a grove of cedar trees. You have a grove of cedar trees with hollies, sage, sedge grass, and some violets. Blue jays, waxwings, and sparrows; squirrels and rabbits; mice and moths; roaches, beetles, and ants; moss, lichens, and mushrooms. The idea that you would destroy all of this because one of the plants is unwanted seems rash and short-sighted. So it is in the forest. So it is in the soil. So it is in your gut.

When this type of wholesale eradication actually happens in nature, unintended consequences are a common result. As evidence, I submit the shoulders of the most recently constructed highway near you, where everything from canopy to soil has been destroyed. If you live in the fancy part of town, the roadside might be covered in some rolled out sod grass sheets, painted green like Astroturf. If you live in the hood, it’s probably more like smoothed-over dirt. It doesn’t matter either way. When that rolled out sod grass dies, it’s going to be replaced by the same annual “weeds” that are growing down the street where they never bothered with the sod in the first place. I write the word “weeds” with a wince; these are hopefully native annuals known as pioneer plants. More likely, though, they are invasive foreign annuals that outcompete the native plants for the nutrients left in the disturbed soil. When you eradicate an ecosystem, there are unintended consequences. You can’t be sure what will move in, in the old ecosystem’s place.

There is at least one example in modern medicine that illustrates the same scenario playing out in our internal microbiome. Have you heard of fecal transplants? They’ve generated quite a buzz, because they’re gross. Here’s the scenario: A person takes antibiotic medicine to treat an infection. As an unintended consequence of the medication, the person kills off the healthy bacteria in their gut. In the absence of the normal healthy bacteria, a new species begins to dominate. This “weed” of the gut is Clostridium difficile, a bacterium whose infection symptoms are constant severe abdominal pain and watery diarrhea up to 15 times a day. Scientists struggled to find a remedy and traditional treatments weren’t helping. Patients found themselves in an ongoing cycle of treatment and relapse. In 2011 doctors at the Mayo Clinic performed the first fecal transplant to treat C. difficile, during which they took healthy stool from a patient’s brother, and injected it into the patient’s own colon. The brother’s gut had not been subjected to the original antibiotic medicine, and still had its normal healthy bacteria culture. When you eradicate a microbial ecosystem, there are unintended consequences. You can’t be sure what will move in, in the old microbes’ place.

Healing is not a quick or easy process for ecosystems in the macro world. Remember those weeds along the highway? Those weeds are the first response of the scarred ecosystem to begin healing itself. The annual weeds will come and go for several years, fostering life in the soil. Slowly, larger perennials will begin to show up. Over many years the little leafy plants will give way to small shrubby trees that retain water, shade the ground, and drop leaves to foster more life in the soil. When the ground is ready, it will accept the seeds from larger trees nearby, dropped by the birds that live in the protection of the young forest. The process of a forest restoring itself might take hundreds or thousands of years. Why should we assume that the healing of our own internal micro-ecosystem is not a proportionately complex process?

The Microbial World within Us

Several years ago I read an article in Scientific American that summarized the role of microbial life, including bacteria, in the human body. I was amazed to learn that the average adult human contains up to 10 times more microbial cells than actual human cells, and that all the microscopic bacteria in my body could fill up a half gallon jug. At the time that I read the article, I was already aware of the idea that antibiotics might be a bad idea because of their tendency to produce antibiotic-resistant bacteria. But this article was really my first exposure to the reality that human life is dependent upon microbial life, and that attempts to kill off bacteria could actually kill off people.

As humans, we experience an onslaught of bacteria during birth and during our first interactions with our mothers, especially during breastfeeding. As we grow and begin to explore the world, we constantly enrich and diversify the microbial cultures within us. Bacteria thrive in the human body, where they play key roles in our digestive processes, immune system processes, and even our genetics. While there are a few bad microbes that can cause sickness in your body, there are over 10,000 distinct species of microbes in and on your body that are important for your bodily health. These include bacteria, protozoa, worms, yeasts, and more. All told, there are over 100 trillion microbes living inside you as you read this right now.

The War on Microbes

Modern science has a pretty crappy track record when it comes to microbes. Scientists became vaguely aware of microbes when Antonie van Leeuwenhoek reported the existence of “animalcules” in the 1670s. Then for almost 300 years, science ignored van Leeuwenhoek’s findings, focusing instead on “spontaneous generation,” which was the idea that life randomly and unpredictably springs up in beef broth. Aside from a few notable exceptions like the work of Louis Pasteur, there were very few practical applications for microbiology until the development of penicillin in the 1940s. Three guys shared the 1945 Nobel Prize in Medicine for developing penicillin, and from there scientists went on an epic Rambo-style microbe-killing spree. They developed a slew of chemicals that could kill off microbes of all kinds. Fast forward to 2010, when the powerful antibiotic azithromycin (Zithromax, Zmax, Z-Pak, and Sumamed) has become perfectly common-place, with 258 million prescriptions in the US annually according to the New England Journal of Medicine. Scientists and doctors haven’t been the only guilty parties. We the people swallowed the pills. And the advent of antimicrobial products like Purell hand sanitizer and antibacterial dish soaps allowed all of us to take part in the “War on Microbes,” without the need for a Ph. D.

Microbes are very resilient little buggers. If you follow the news today, you are probably aware that microbes are definitely winning the “War on Microbes.” They are adapting to resist the chemicals we design to kill them, and they appear to be adapting much more quickly than the scientists who are scrambling to invent new chemicals. In 2001, the Union of Concerned Scientists began calling attention to the potential threat posed by widespread antibiotic use in farm animals. Their warnings were largely ignored by industrial agriculture and veterinary medicine. A little over a decade later, in 2013, the CDC issued a report detailing antimicrobial resistant threats to the US population, and the World Health Organization followed with its own report in 2014. Drug-resistant bacterial strains are no longer the stuff of science fiction, there are hundreds of thousands of cases reported annually world-wide.

But there is a good guy in this story; and if you’re reading this, the good guy is probably you! While scientists spent the last 50-plus years finding ways to kill off the microbes in our bodies with chemicals for profit, gardeners have been finding ways to nurture the microbes in their gardens and develop them into thriving colonies of microscopic life. The work of Rudolph Steiner, Eve Balfour, and others spread throughout the world of gardening and organic farming, and by the 1960s aerobic composting had become standard practice for growing organic produce. Gardeners composted on good faith for decades, observing the benefits of active cultures in their gardens without a deep understanding of the science involved.

It has long been a belief in the organic gardening community that eating a small handful of healthy, sweet garden soil is beneficial for gardeners of all ages. There is actually an ancient practice of eating kaolin clay from the ground that was brought across the Atlantic by slaves and thrives even today in the southern US. Somehow, many among us knew by intuition that the microbes around us were an asset, more than they were a threat. Then in 1999 the USDA commissioned Elaine Ingham’s Oregon State research team to publish the Soil Biology Primer, and the microscopic world of the soil food web was revealed in detail to gardeners and environmentalists around the world. The 2010 book Teaming with Microbes brought knowledge of the soil food web to even more gardeners, earning the Silver and Gold Awards from the Garden Writers Association.

Today we seem to be approaching a milestone, as more and more people begin to understand the nature of the microbial world around us, and within us. We all have our very own microbiome, a tiny ecosystem like a biological fingerprint. The Human Genome Project helped to fan the flames of awareness about microbes. As an unexpected consequence of that project, researchers discovered that our genetic map includes no fewer than 40 genes that have been borrowed from the microbes within our bodies during our evolution as a species. Even if we remain sexually loyal to our own species, our genes do not. The HGP discovered that in order to understand ourselves as functioning beings, we need to consider the genetics of each of the 10,000 microbial species that exist within us, in addition to the 24,000 genes that make up our human genome. These findings led to the creation of the Human Microbiome Project in 2008, as a direct offshoot of the Human Genome Project.

Microbes in the Media

All of these developments point to a new understanding of microbes and microbiomes in ourselves and our environment. Practical applications for this understanding are beginning to crop up in the media increasingly often. Here are a few of the stories I’ve noticed:

In 2013, researchers at Washington University in St. Louis and UCLA were studying Propionibacterium acnes, the bacteria that was believed to cause acne in some people. They were surprised to find several strains of the species, most of which were present on both people with and people without acne. Further research found that one strain of the bacteria was specifically beneficial against acne, and was found only on people who did not exhibit signs of acne. For years, dermatologists had been prescribing chemicals in an attempt to kill off the bacteria. But the problem was not that simple, and the bacteria itself was the cure they were seeking.

A study published by the journal Science in August 2014 found that the microbiomes of our indoor living spaces react surprisingly quickly to changes in their inhabitants. When a new person, or pet, enters or leaves a home, the microbiome of that home reflects the change within a few days. So if you take in a new roommate, you also take in their microbes. This same study found that when a couple left their home and moved into a hotel room, the microbiome of the hotel room was completely colonized by the couple’s microbes within 24 hours. This should be comforting if you’re someone who fears the germs that others leave behind in hotel rooms. Not to worry, your germs actually eat their germs. The study’s authors found that by examining a person’s microbes, they could identify many things about the person including their pets, their personal relationships, and sometimes even their profession and hobbies.

A February 2015 study published in the journal Pediatrics found that children who are exposed to microbes in the kitchen have a significantly decreased chance of developing allergies and asthma later in life. The study specifically looked at dish washing techniques, and found a lower instance of allergy and asthma in homes where the dishes are hand washed, as opposed to using a mechanical dishwasher with chemical detergent. The study confirms that exposure to microbes builds tolerance in the immune systems of children. Interestingly, the study also found increased tolerance in children whose families regularly ate fermented food, and in children whose families purchased food directly from farmers.

Also in February 2015, the journal Cell Systems published a fascinating study in which scientists profiled the microbes living in the New York City subway system. They identified almost 1700 different species of microbe, including some pretty scary ones whose names we all know, like anthrax, and even the bubonic plague. The study’s authors concluded that the concentrations of these pathogens posed no risk to public health, but rather that these bacteria in very small numbers are normal inhabitants of a very complex urban environment. They didn’t find massive amounts of germs, or massive proportions of the same bugs. They found an accurate profile of the population of New York. The profile they produced can actually be extrapolated to mirror the makeup of current US Census data for the city. As a testament to the strength of the microbes, one station which flooded during hurricane Katrina in 2005 still held many marine microbes that would normally be found in the Atlantic Ocean, not on the subway, when it was tested 10 years later.

Scientists and the public are still a long way off from truly understanding our microbial environment. As Dr. Robert Orenstein from the Mayo Clinic puts it, “The microbiome of the gut is not inactive; it’s diverse and plays many roles in health and well-being that are just now being explored. With molecular biology and the sequencing of these species, this can only get bigger. It’s like the beginning of the space program.” Probably the most interesting find from the NYC subway study was that of all the microbial DNA collected, almost half of it originated from microbes that have yet to be identified. Hopefully, with a little encouragement, our leading scientists will continue to work on understanding the microbial world around us, rather than trying to find new ways to kill it.

At my house, we will continue to ‘kinda sorta’ sanitize ourselves for a few more months. Then, we’ll be back to our normal unpasteurized lives with an extra set of hands in the dirt.