Some of these bacteria would make us sick if they became too numerous — but they won’t unless something changes. Others are so unobtrusive you’d never know they’re there — but you might miss them when they’re gone. Besides looking out for their own tiny microbe-needs, these “good guys” also protect us by keeping the “bad guys” under control. It’s a symbiotic relationship — they depend upon us, we depend upon them.

What is this “microbiome” you may have seen referenced in news and health articles? Your personal microbiome is like a planet populated by 100 trillion microbes interacting with each other, and with your body’s own cells, to form a complex and constantly-changing system. Some of your microbiome is established early in life, largely passed on from your parents; some of it changes during your lifetime based on diet, lifestyle, and environment. We’re only beginning to understand how some of our modern advances — including widespread prescription antibiotics and anti-microbial cleansing products — may be impacting our health, via our microbiomes. Initial results suggest we’re crossing some dangerous lines. In the all-out war on germs, we’ve confused our allies with our enemies.

In the garden, permaculture teaches us that strengthening a diversity of native plants is the most effective method for shutting out invasive weeds. The same applies to our personal bacterial ecosystem. Instead of spraying chemical weed-killer at the first sign of a dandelion, let’s tend our internal garden with loving care. Here are some general principles — there are exceptions to every rule. Work with a health advisor you trust to develop a sustainable plan for tending your unique bacterial forest.

1. Avoid "bacteria killing" cleaning and hygiene products

After taking our germ-phobic culture by storm, hand-sanitizers have now proven themselves questionably effective, and probably harmful. The Center for Disease Control recognizes that many pathogens are more effectively removed by old-fashioned soap and water. Further, both chemical and alcohol-based sanitizers are causing some of these same pathogens to develop immunity to the very products designed to kill them: antibiotic resistance, happening on your skin. When you opt out of the antibacterial soaps, you get the added benefit of avoiding chemicals like the endocrine-disruptor triclosan, which has been shown to mimic thyroid hormones, cause weight gain or loss, and possibly contribute to auto-immune problems. Carry a travel-sized non-toxic liquid soap to avoid the chemical-laden dispensers in most offices, restaurants, and public buildings.

It’s easy to find safe and effective cleaning products that won’t result in a drug-resistant super-pathogen evolving on your countertop. And as far as your personal hygiene, don’t attempt to sterilize your body’s external surfaces. Your skin’s microscopic colonists form an important part of your immune defense, and if you wipe them out they will simply be replaced by opportunists, which may cause infection or inflammation. It’s a vicious cycle: we accidentally create an imbalance, causing a problem that requires treatment. The treatment (usually antibiotic in nature) turns into dependence on purchased products to maintain an increasingly fragile state of balance. Advertisers manipulate public fears to sell “maximum strength germ-fighting” products — let’s turn the tables by avoiding cleansers marketed as antibacterial.

2. Take only necessary antibiotics, and only as directed

Reserve antibiotic use for serious bacterial illness — never ask your doctor for antibiotics for a cold or flu (the pills won’t help a viral illness). When antibiotics are clearly indicated, ask your doctor to do a bacterial culture to determine the most effective drug for your infection, as you may be accidentally prescribed a drug to which your bacteria has already developed resistance.

Never take leftover antibiotics for a self-diagnosed infection — the wrong drug, wrong dosage, or wrong length of course can cause an incomplete treatment, resulting in a resistant infection. You will potentially end up sicker, with fewer options for effective treatment. By taking antibiotics irresponsibly, you may inadvertently contribute to the global health crisis of increasingly virulent resistant bacteria.

For infections that qualify as “annoying” rather than “dangerous”, consider trying a home remedy first, if your doctor agrees it’s safe. Many home remedies require more time and effort to be successful, but they can work — the payoff is skipping the course of antibiotics along with its consequences to your internal bacteria. Examples include a warm salt water soak for minor skin infections, garlic oil for mild ear infections, steam inhalation and diet modification for sinus infections, and boric acid or acidophilus for yeast infections. Especially if you find yourself in a cycle of chronic infection and antibiotic dependence, it may be worth your while to explore some alternatives in an attempt to break the cycle.

Ask questions before accepting “preventative” antibiotics. When a particular infection recurs too often, your doctor may offer a daily pill to ward off the possibility of a recurrence. There may be alternatives, including strengthening your defensive bacterial culture, or identifying and avoiding triggers to infection. Dermatologists routinely prescribe ongoing antibiotics for troubling but non-life-threatening conditions such as acne and rosacea, but the side effects and potential for resistance may negate the potential benefits of these drugs. New treatment such as light therapy show promise for skin healing without disrupting your bacterial ecology.

3. Avoid factory-farmed meat and dairy

he vast majority of supermarket meat comes from animals continually dosed with antibiotics under feedlot conditions. These drugs are administered not only to prevent the diseases rampant in such overcrowded, unsanitary conditions — there’s an even bigger motivator. Ranchers have found that adding antibiotics to animal feed stimulates fast weight gain. They can slaughter the animal at a younger age, sell more pounds of meat, and reap more profit. Just like many humans, these animals suffer from antibiotic-disrupted gut flora leading to obesity. Around 70% of antibiotics in the US are fed to healthy animals, not taken by humans.

The antibiotics — and the drug-resistant pathogens they breed — are passed on to the consumer in the packaged meat. Sounds delicious, doesn’t it? Find a local farmer you trust, ask questions about antibiotic use and buy your meat direct when you can. Fortunately, natural food stores now often carry meat labeled as “organic” or “naturally raised”. The organic label guarantees the absence of antibiotics (if an animal gets sick and is treated with antibiotics, the meat will no longer be labeled organic), but the “natural” claim is less specific — check with the manager or call the supplier directly to confirm what medications are administered to the animals.

4. Strengthen your own flora to resist infection

There’s no doubt: taking steps to get and stay healthy is your best chance to avoid both harmful infections and the antibiotics that fight them. Opt out by bolstering your systems with whole foods and exercise! Some studies even suggest that internal bacteria behave differently depending on how strong we are: if our microbes sense we are weak and sickly, even the “benign” ones might turn against us. Most of the wisdom on staying robust as a disease-prevention strategy is familiar and even grandmotherly. But for those of us already affected by modern microbiome imbalances caused by early or chronic antibiotic exposure, poor diet, or unknown environmental effects we might need a little extra help.

• Eat fermented foods. A growing wave of do-it-yourselfers are learning to make their own sauerkraut, kimchi, yogurt, kefir, and kombucha. All these traditional foods contain a host of live friendly cultures, which have been clinically shown to help some chronic digestive conditions. If you’re not inclined towards extra time in the kitchen, you can buy these foods at a local natural food store — just make sure you choose the “raw and unpasteurized” version in the refrigerated section, as any shelf-stable sauerkraut has no living microbes left.
• Get your hands dirty. Here’s yet another example of the healing powers of gardening! Some common soil microbes have historically been essential to our microbiome. In recent decades, hyper-hygiene and urban lifestyles mean many of us miss out on those dirt organisms. Bacteria in healthy soil may help everything from depression to immune regulation, and individuals have little to fear from being in contact with healthy garden soil. Help your kids get sufficient exposure to good clean dirt by finding more family gardening opportunities.
• Consume more prebiotics. Good bacteria need nourishment to thrive just like we do. Eating plenty of prebiotics — such as leeks, artichokes, garlic, beans, oats, onions and asparagus — keeps our flora happy and healthy. Prebiotics are full of non-digestible fiber. Though it may sound strange to consume food that can’t be digested, you’re feeding your helpful microbes without adding to your own calorie count. Prebiotic foods contain the short-chain fatty acids on which good bacteria thrive. As a simple rule, eat more whole fruits and vegetables! Don’t miss out on the fiber; eat the whole thing. Consuming only the juice, or the tender parts of the vegetable, defeats the purpose. Those asparagus tips might be sweet and succulent, but your gut needs the fibrous stalk too.
• Consider probiotic supplements. Questions surround the use of probiotics in pill form. Are they effective? Is there any reliable way to measure their effect? Which product is more or less effective than another? These questions remain largely unanswered. Most health advisers agree that changing your diet and eating pro- and pre-biotic foods will have a more lasting effect on your health. But many also say that taking a probiotic capsule probably can’t hurt, and might help, especially if your gut is under added stress from taking a course of antibiotics. The organisms in the probiotic supplement may not be able to take up residence in your intestine and permanently improve your flora, but they may do a little good for your digestion on their way through.

5. Let your child's microbiome flourish without disruption

Much evidence points toward the crucial window of development that begins in the womb and spans the first few years of life. Our adult microbiomes may be robust enough to handle the disruption of an occasional course of antibiotics and recover their previous diversity, but in the beginning of life, such treatment may have a more lasting impact. Current research is probing the life-long effects of early antibiotic treatment, theorized to include many autoimmune conditions, allergic and inflammatory disorders such as Crohn’s Disease, and metabolic disturbances such as obesity and diabetes.

What helps children to establish a solid foundation of “good bacteria” which will protect them in later years? Their first protection comes from their mother, during birth: children born vaginally are inoculated with many helpful microbes that C-section babies don’t receive. Sometimes, of course, a C-section is unavoidable — but there are several reasons to avoid choosing surgical birth for convenience or comfort (it often turns out to be neither convenient nor comfortable, after the fact).

Breastfeeding continues the transmission of protective bacteria, as does avoiding optional antibiotics for minor infections that are likely to run their course in either mother or child, such as mild mastitis, ear infections, and sinus infections. Talk to your pediatrician about whether the antibiotics are truly necessary, or if there might be alternative comfort measures to care for your child until her body naturally defeats the intruders. Learn the warning signs that mean antibiotic treatment is more urgent. And don’t forget, as babies grow into explorers: forests, organic vegetable plots, and other healthy natural areas contain a variety of wholesome microorganisms which are not only safe to touch, but may contribute healthfully to the essential biodiversity of your child’s microbial landscape. Let them snack from the garden and don’t fret if they haven’t scrubbed that carrot first.

Modern antibiotic drugs were introduced around 1909, with the discovery of a new treatment for syphilis, previously almost incurable. The antibiotic revolution was furthered with the development and mass-production of penicillin in the 1940s. We can imagine the joy and gratitude of the world toward the scientists who introduced these miracle drugs. Untold thousands of lives were saved each year, and human life changed. It must have seemed that we had won the war against infectious disease forever — unfortunately, it turns out these pathogens are more determined and adaptable than we could imagine.

But there’s more to the antibiotic story — bacteria-killing substances occur naturally in many plants and minerals, and these compounds may have played a role in ancient human history as well. Interestingly, research has discovered traces of antibiotic substances (like tetracycline) in 2000 year old Sudanese bones, suggesting our ancestors may have ingested antibiotic containing substances in food, which noticeably affected their health. Traditional Chinese Medicine has used antimicrobial treatments for millennia, and the long-standing use of some of these herbs could actually have contributed to the development of drug-resistant microbes.

But when these treatments were concentrated and refined in pill form and readily available to all, the medical landscape was transformed. If there’s one thing we can say about our modern era, it has been defined by the incredible speeding up of change. The gradual, almost imperceptible changes in bacterial cultures and evolutionary characteristics of plants and animals have been replaced by mind-boggling transformations in the course of a single season.

Antibiotic resistance is nothing mysterious — it’s simply an evolutionary process, sped-up by modern conditions. Just like “survival of the fittest” on the plains of Africa, it’s the strongest bacteria that get to breed and pass on their traits. When most bacteria are wiped out by a drug, a hardy few might survive. Bacteria mutate and adapt at dizzying speed. The surviving few now have no competition for space or resources, and reproduce like crazy. Soon, we’ve replaced a multitude of relatively weak and susceptible bacteria with an army of robust and indestructible ones. Those that manage to survive the next drug as well are even tougher. Fortunately, research shows that the process of creating these super-bacteria on farms can be reversed: when a feedlot operation converted to organic practices, the resistant bacteria were almost immediately subdued, and the ordinary non-resistant bacteria regenerated, since under normal conditions they were the best adapted to survive. The European Union has already banned the routine use of antibiotics on livestock, but here in North America, consumers need to spread the word and exercise choice (and sometimes spend a bit more) to help influence farming practices.

Strengthening our microbial health requires changing our thinking. As long as we believe what advertisers have been telling us for decades, we will continue to do as we’re told. Though dangerous pathogens do exist, our best defense may already be teeming upon all of our surfaces. Let’s keep washing our hands before dinner and taking advantage of the many lifesaving advances in medical and sanitation technology. Powerful tools such as antibiotics will help us most when we use them sparingly. Everyday, we can return to the ancient practice of acceptance and welcome — a productive collaboration with the host of creatures both around us, upon us, and within us.