The Home Guide To Antibiotics

Have you ever had Lyme Disease? If you live in the northeast and go for long walks without checking for ticks afterward, there’s a distinct possibility that a few days later you’ll develop the bullseye rash signifying an infected tick bite. This happened to me once, and I knew it meant I would have to take a course of antibiotics.

If left unchecked, Lyme disease bacteria, most commonly B. burgdorferi, use their corkscrew shape to twist their way into tissues where they don’t belong, including the skin, heart, lungs, and nervous system. As the disease progresses, it can cause an array of awful symptoms like arthritis, severe headaches, memory fog, fatigue, heart palpitations, and more. No, thank you! Fortunately, if diagnosed early, there are effective antibiotic treatments that can help your immune system fight off these invaders and get you fast-tracked toward recovery.

A century ago, bacterial pathogens like Lyme Disease were a very serious problem for everyone. Despite our understanding of germ theory, even infections from a small cut or stomach bug could be fatal. The discovery of antibiotics completely shifted the ‘battle’ in our favor. For better or worse, that is now changing.

I hope that this guide sheds some light on antibiotics and allows you to make informed decisions regarding their use and your subsequent recovery. I would like to note that this topic is too complex to break down properly in a single blog post. To help address this, I’ve included a variety of links throughout this article to videos and scientific papers for you to check out if you want to explore deeper.

What Are Antibiotics?

Put simply, antibiotics are poisons created by plants, animals, fungi, and other microbes that exclusively harm bacteria. These compounds have developed in nature over billions of years of evolution to help organisms defend themselves against bacterial infection. 

With the aid of antibiotics (in conjunction with vaccines), humans have been able to eradicate some of the world’s most virulent bacterial diseases and save hundreds of millions of lives. For almost a century, antibiotics have been our silver bullet against bacteria.

It is important to note that there are a wide variety of antibiotics, and they cannot be used interchangeably. What worked for one bacterial infection will not necessarily work for another, so consult a doctor if you’re worried about an infection. DO NOT just pop a couple of pills you’ve stashed in the closet. 

The Critical Mistake People Make When Taking Antibiotics

When I had Lyme Disease, the doctor did prescribe a course of antibiotics. When I received my medication, it was accompanied by a long lecture and a pamphlet, explaining that I really must finish my full prescription of antibiotics, even if the symptoms disappear.

At the time, it didn’t really make sense to me. Why would I want to keep taking antibiotics even after I feel better? The side effects of antibiotic treatments can often be unpleasant. Your skin may feel sensitive, you’re constantly tired, and you sometimes get stomachaches (or worse). I would prefer as short an experience with them as possible. As inconvenient as it might seem, there is a critical reason for completing your antibiotic treatment as prescribed. Let me explain.

It is generally true that most of the target bacteria will die toward the beginning of antibiotic treatment. The only ones that are left will be the fiercest, most resistant, most problematic germs. At low numbers, they won’t be able to put up much of a fight and may go into hiding. Hence, your symptoms will improve, and you will think you’re all better.

Great. Except you’re not all better. If you stop your antibiotic treatment early, you’re giving those pathogens the opportunity to peek out from their hiding places, share antibiotic-resistant genes, and start replicating again. But instead of a regular infection like before, these new germs will be the product of only the strongest, most highly resistant bacteria – the survivors.

In a couple of days you’ll feel sick again, but this time your antibiotic won’t be effective.

Next thing you know, you’ll be back at the doctor’s office getting a new type of antibiotic treatment that attacks your disease differently. If you were to repeat the same mistake and stop taking your antibiotics early again, you would find yourself full of a double-drug resistant pathogen (and the cycle can repeat indefinitely).

Basically, you’d be doing a science experiment proving the Theory of Evolution via ‘survival of the fittest’ inside your own body.

The length of antibiotic treatment, prescribed by your doctor, is based on how long on average it takes that specific drug to kill enough pathogens for your immune system to take over and safely finish the job on its own. It might seem that by stopping your treatment early and trying to cut corners, all you’ve done is take a gamble and potentially prolong your healing process. But that is just the tip of the iceberg.

The Antibiotic Crisis

Since the discovery of penicillin in 1928, humanity has been in a race to uncover new antibiotics faster than bacteria can evolve drug resistance from their excessive misuse. Today, these fears remain very real, and many doctors are now encountering bacterial strains that are immune to every antibiotic we have. As you can imagine, these superbugs are a serious problem.

Without novel antibiotics or alternative treatments, we could once again find ourselves back in a world where we have no surefire protection against bacterial infections. Scientists are looking for other solutions but in the meantime, we need more ammunition, which means new antibiotics. The problem is that the rate of antibiotic development is not keeping up with the rate at which bacteria are developing resistance and spreading.

So why am I telling you this? Yes, I want to convince you to take your antibiotic treatments seriously, but there’s another important takeaway here. We have become completely dependent on antibiotics to solve all our health problems while showing no consideration for how their overuse impacts our lives.

The Human Microbiome

The average human body is home to around 100 trillion bacteria. Although clustered together they would only be about the size of your fist, they make up approximately 90% of all the cells in your body. The vast majority of these bacteria are really good for you.

They help your body do crucial things like make essential vitamins and hormones, digest your food, strengthen your immune system, improve your mood, break down toxic compounds, and provide competition against any bad bacteria that might try to invade. Removing all those good bacteria from your body would be equivalent to removing an organ, and studies show healthy people tend to have a large and diverse bacterial community.

These good bacteria have evolved alongside us for millions of years, passing from one human generation to the next via the birth canal and home environment, and are an integral part of you being you. Guess what our antibiotic and disinfectant-crazed modern society has done to our bacterial communities?

Missing Microbes

Many antibiotics kill bacteria indiscriminately (especially, as the name suggests, “broad-spectrum antibiotics”). To use a blunt metaphor, taking antibiotics to kill a pathogen is like dropping a nuke on a city to kill some terrorists. Will it work? Probably! Will there be casualties? MILLIONS.

In the case of your body, the casualties are billions of bacterial natives residing in your body that are doing nothing to harm you. If you have a serious bacterial infection, you should absolutely take antibiotics! None of those good bacteria will have a home anyway if you’re dead or overrun with the disease.

But that doesn’t mean you should carpet-bomb your microbes because you have a minor sore throat.

Many recent studies suggest that the overuse of antibiotics and our low bacterial diversity are contributing to the surge of many modern plagues including but not limited to obesity, celiac disease, type 1 and type 2 diabetes, depression, and excessive allergies, as well as increased rates of certain cancers (including breast, prostate, and stomach cancer).

Until recently, a common mantra among doctors was “the only good bacterium is a dead bacterium”, and as such antibiotics are traditionally seen as doing no harm. To this day, doctors in a hurry will often prescribe them ‘just in case’. This not only comes from the doctors but from parents, who are more concerned with their child’s immediate comfort than the drug’s enduring health impacts or that antibiotic misuse reduces a medication’s effects for everyone in the long term.

Very often, antibiotics are even prescribed for prevention rather than treatment. “Seventy percent of kids coming in with what is considered an upper respiratory infection walk out with an antibiotic” (Martin Blaser, Missing Microbes). I haven’t even mentioned the abuse of antibiotics in the global food industry, where they’re used to grow animals quickly in intolerable living conditions. These antibiotics even end up dumped into our water supply.

Recovering From Antibiotic Treatment

So, what do we do about all this? We have a dependency on a set of drugs that are quickly becoming ineffective, and in the meantime, we are only beginning to grasp that they have been causing all sorts of long-term health problems. The solution is, whether you are currently taking antibiotics or not, to cultivate a healthy and diverse community of bacteria inside your body.

So how can you do that? I wish it were as easy as taking a magic pill. Despite what some marketing campaigns might tell you, taking yet another medication is not necessarily the solution.

The key is to think of your body’s bacteria the same way you’d think about a garden. If you sprayed poison on your plants and they all died, what would grow back first? The weeds. Without intervention, something similar occurs in your gut after an antibiotic dose. The fastest-growing, generally less beneficial bacteria will take over once their competition is gone.

If you don’t want weeds to take over an empty patch of soil, you need to use the right fertilizer and plant your crops quickly and intentionally. So, while you are taking antibiotics, and for several weeks/months afterward, you need to be extra vigilant about growing good bacteria in your gut to stop the weeds from taking over.

Here's the Part Where I Tell You to Eat Your Vegetables

This is not a revolutionary recommendation, but let me explain. Scientists have been studying the bacteria in our guts extensively for the past few decades. They’ve looked at which bacteria grow in different human populations, from Amazonian tribes to New Yorkers, and have studied the impact of different diets, exercise regimens, sleep schedules, and much more.

The general conclusion: most of the bacteria responsible for doing all those beneficial things for our health eat fiber. The ‘weeds’ that don’t help you and contribute to health problems? They usually eat processed foods and sugar. Shocking, I know.

If you want more good bacteria to grow in your body, you need to consistently give them a source of food. Similarly, if you don’t want your body to be overrun with ‘weed’ bacteria, you need to avoid processed sugars, especially if you’re taking antibiotics. The simplest way to control what is growing in your ‘garden’ is to control what you’re feeding your microbes.

I had a microbiology professor who would recommend including 10-20 different sources of fiber in your diet every day. That might seem like an impossible number, but I can tell you from personal experience that it’s not as difficult as you’d think. If you’re smart about it, you can do most of it with a smoothie and a good salad.

My rule of thumb is that if by the end of most days, you’ve eaten plants that are green, orange, red, yellow, and purple, you’re doing it right. I’m also a big proponent of seeds and grains (flaxseeds, barley, oats, etc.) because they’re an easy way to get rich sources of fiber that taste good. Scientists call sources of fiber that bacteria love ‘prebiotics’.

I recommend you do some research yourself and find out which prebiotics you could include in your diet that would make both you and your microbes happy.

Probiotics to the Rescue?

At this point, you might be thinking, “Great, so I need to eat more vegetables and fiber to feed my microbes. But what if I don’t have enough ‘good’ bacteria to begin with?” Maybe you aren’t a big fan of fiber yet or maybe you’ve been sick and suspect that your good gut bacteria population is a small minority. There are many ways to increase their numbers!

Yes, I’m talking about probiotics. Probiotics refer to what’s called a ‘functional food’ that contains living bacteria that have been found to improve your health. Usually sold as powders or capsules, they contain billions of specific bacterial species which probiotic companies believe are beneficial for some aspect of your health.

We’re currently in the ‘wild-west’ stage of probiotic development. There are thousands of companies out there making probiotic products, but very few of them have been ‘FDA approved’ or generally greenlighted by the scientific community.

To oversimplify a complex issue, I’ll just say that yogurt bacteria are not here to save your life. You’re not a dairy product. You can’t just swallow a strain of Lactobacillus and expect your whole bacterial gut community to be rejuvenated (although they may help). The key is diversity. A healthy ecosystem is made up of many different coexisting organisms.

If you’re serious about including a probiotic supplement in your diet, I strongly recommend doing some research and looking at reviews, keeping in mind the power of placebos. My concern is that many of these pills fail to actually deliver living communities of the promised bacteria into your gut. Fortunately, while we wait for companies and scientists to figure these supplements out properly, there are still other effective probiotic options that have proven efficacy for thousands of years.

Ferments Are Your Friends

Let’s talk about ferments! Ferments are foods that consist of both prebiotics and probiotics. Basically, they’re made up of microbial communities already living in the foods that they love. They are also the perfect beneficial bacteria delivery system.

They provide more diverse communities of good microbes and also enter your body riding on their favorite foods, which gives them a head start when they’re colonizing your gut compared to the starving freeze-dried yogurt bacteria in many probiotic pills. Humans have been making fermented foods for thousands of years, and so not surprisingly there are thousands of different types of ferments. As such, I guarantee that you can find at least a few ferments that you’ll be able to add to your regular diet without much effort.

Some common examples of ferments that I love include miso, yogurts, kefir, some cheeses, sauerkraut, kimchi, some hot sauces, kombucha, and pickles (and keep in mind you can pickle most vegetables). While most probiotic pills are still very much “under development”, fermentation has been practiced since the beginning of human civilization, and for good reason.

Ferments are a great way to preserve foods, and they have a variety of health benefits. If you aren’t used to including ferments in your diet they might seem a little weird at first. Just keep in mind that most of your pre-industrial ancestors, regardless of where they are from, survived thanks to ferments and so can you!

Heal, Grow, Thrive

Besides what you eat, there are a variety of other complex factors that help control which bacteria live inside you. For example, how much you exercise, how long you sleep, the sensitivity of your immune system, your mental health, what medicines or drugs you’re taking, your genetics, where you live, your age, your proximity to animals, and your daily habits all contribute to the composition of your bacterial community.

It is for these reasons that there does not exist a ‘one size fits all’ approach to building the best microbial ecosystem. However, I don’t think anyone should be surprised to learn that living a healthy lifestyle, like the C. Twain Method, generally correlates with having a healthier microbial gut community.

Unfortunately, unhealthy habits tend to reinforce themselves and can be difficult to break free from. Studies suggest that sugar-craving bacteria can send signals to your brain that make you happier when you think about eating sugary foods. The more sugar you eat, the more you feed those microbes, the stronger their signals are in your brain. But if you can starve those bacteria by cutting off their favorite food sources, you might find that it is much easier to cut sugar cravings, which aren’t really yours in the first place.

Or Take a Poop Pill

Whether you are taking a course of antibiotics or not, cultivating a diverse microbial community is one of the best things you can do for your health. If you believe that your body is in ‘dysbiosis’, meaning completely out of balance and overrun with bacteria that are making it impossible for you to be healthy, the road to recovery can be very challenging.

Feeding your good bacteria and starving the bad ones will be essential in the long term.

If that feels impossible right now, it may be worth consulting a doctor. There are a variety of excellent tests that can determine the current composition of your bacterial community and help you decide on the best course of action.

Transplants of bacterial communities from a healthy donor have already been used to save many individuals suffering from overrun gut ecosystems, for treating superbug infections, promoting a healthy body weight, or boosting mental health. Fecal transplants are highly effective, but you may find it easier to stomach eating ferments, which is an important part of the C. Twain Method.

The C. Twain Method is my mom’s answer to the dis-ease created by her years of antibiotic use. She healed herself by healing her microbiome, and this entire website is dedicated to sharing the holistic approach that she knows worked for her and many others. Continue to visit the site for tips and tools so that you too can thrive.

Be a good host for the microbes that help you the most. They, in turn, will take excellent care of you.