Dysbiosis, Infection, and Protection
“I grew up on antibiotics. Every ailment—sore throats, earaches, flus—warranted a trip to the doctor and in most cases some kind of prescription.”
—Carré Otis, model and actress
Your microbiome contains bugs that protect and benefit you, and it contains bugs that can harm you. Remember that by “bugs,” I mean the bacteria, fungi, and viruses that make up your microbiota. Less than 1 percent of microorganisms can harm you. The other 99 percent do no harm and may even improve your health.15
Microbiology and medicine have historically concentrated on the bugs that harm us, also called pathogens. These are the big, bad bugs that can create disease and make us miserable. However, amidst all of the fanfare about the bad bugs, everyone overlooked the good bugs. You’ve heard the saying “One bad apple spoils the bunch”? Well, the bad bugs have given all of the bugs in our microbiome a bad rap. Even the bugs that are beneficial or harmless to us have been swept up with the bad opinion we have of bacteria.
I want you to learn in this book that bad bugs are the minority. They can’t do any damage if you have strong, healthy levels of good bugs. And the strategy for the future, in this great age of understanding the microbiome, is to promote and nourish your good bugs instead of trying to kill the bad ones.
Your beneficial microbiota protect you from pathogens, make vitamins, regulate your immune response, and can even help you lose weight. But most importantly, they form a living resistance against infection by bad bugs. I like to imagine an endless line of little bacterial soldiers, standing shoulder to shoulder, physically preventing enemy bacteria from penetrating their lines. In Chapter 5, we will dive into more detail about the microbes that call our mouths home. But first, let’s talk about the relationship between good bugs and bad ones.
We are exposed to many bad bugs all day, every day. But when our good bugs are healthy and forming a strong defensive line, the bad bugs cannot wiggle their way through our defenses and create infection. When a pathogen is in high numbers, or if good bugs are weak and provide an opportunity, it can cause an infection.16 In an infection, a microorganism invades the body’s tissues and multiplies, and the body reacts to the infection or to the toxins it makes. Many pathogens make toxins that are harmful to us. Certain disease-causing bacteria, fungi, and parasites can lead to infections. In a healthy person, these infections are short-lived but in a weak or sick person, they can be deadly. However, the other 99 percent of normal bacteria that live in your mouth and your gut do not count as infections, since they are your commensal, or normal, microbiota. Let’s look at some of the bad bugs that you probably get exposed to every day, without realizing it.
Salmonella is a pathogenic bacterium that has a bad reputation because even a few cells of it can cause food poisoning and symptoms of diarrhea, vomiting, and fever. It is common in raw meat, poultry, eggs, and washed, ready-to-eat foods like berries, tomatoes, and leafy greens.
Escherichia coli O157 is another common cause of infection or food poisoning we hear about in the news. It’s brought on by eating contaminated, undercooked foods such as hamburger meat, lettuce, or spinach. Many, many kinds of E. coli are harmless and they naturally live in our bodies as well as those of livestock. However, E. coli O157 can cause bloody diarrhea.
Here’s the amazing thing: You get exposed to Salmonella and E. coli O157 in your daily life via contaminated food, undercooked food, restaurants, contaminated water, sick people handling your food, door handles, bathrooms, etc. These are all sources. Even though you don’t have bloody diarrhea or vomiting, you do get exposed to these bacteria on a regular basis. But, your good bugs are doing their jobs. They are preventing E. coli O157 and Salmonella and the other bacteria, fungi, and parasites like them from setting up shop and creating infection in your body. Thank you, good bugs!
Of course, on the off chance that you do get food poisoning, it likely means that your defenses are compromised. Either your immune system is down or your microbiome is weakened. In these instances, the bug could easily invade, replicate, and harm you. It can also just be bad luck—a particularly toxic form of a bacteria in high amounts.
Now that we understand what an infection is, let’s talk about dysbiosis. Dysbiosis is a major concept in gut health, oral health, and the human microbiome. Our good bugs are stable and live in harmony with us unless they are disturbed by medicine, disease, low pH (acidity), or major dietary changes.17 When these bugs are thrown out of balance, it causes dysbiosis.
Just like a tropical rainforest, the microbial community in the mouth (and in the gut) is rich and complex. Millions and billions of bacteria live together in harmony with some competition for resources. Some are growing, some are dying, and most are eating, making waste, and making energy and other by-products. When all your bacteria, fungi, and viruses are living together in balance, without making you sick, but protecting you from outside invaders, your microbiome is in good health.
Dysbiosis is when microbes don’t grow enough or when they overgrow from their normal balance, causing you symptoms. Simply, dysbiosis is imbalance in your microbiome. It’s not an infection per se, because it is an unhealthy shift in your microbial communities that can give you symptoms, rather than a single, well-known pathogenic microbe causing infection, like Salmonella or E. coli O157.
In dysbiosis, certain bacteria in the community can grow and take over, causing imbalance in the system. When growing out of control, these bugs can produce toxins that harm us, they can irritate the adjacent tissues, and they can activate the immune system. When the wrong bugs start to take over, they can crowd out beneficial bacteria, which opens you up to infections by pathogens. For example, gut dysbiosis can cause gas, bloating, loose stools, or maldigestion, and it can make a person more likely to pick up Clostridium difficile, a pathogenic bacterium that causes diarrhea. Oral dysbiosis can cause cavities, gingivitis, root canal infections, or bad breath (Chapter 6). Just like we now understand the power and magnificence of our healthy microbiome, we also need to understand that dysbiosis weakens it and leaves us wide open to disease and infection.
There are a few different types of dysbiosis:18
• Insufficient growth of normal microbiota is a type of microbial imbalance that results from not having enough good bacteria. This leaves the host open to infection and bacterial overgrowth.
• Loss of microbial diversity is a type of dysbiosis that occurs when you don’t have a rich, healthy variety of microorganisms.
• Overgrowth of normal microbiota occurs when normal microbes grow excessively. This can cause mild symptoms or no symptoms at all.
• Overgrowth of potentially harmful organisms does not usually cause a problem, but if given the opportunity, they will rise to power and take over. These microbes can cause symptoms and they can crowd out good bugs. They also may cause no symptoms.
Once you have dysbiosis, it may or may not be easy to fix. In a healthy person who is eating a healthy diet, taking probiotics alone might be enough to tip the scales back to a healthy microbiome. Someone with chronic symptoms may need to consult with a healthcare practitioner to treat their microbial dysbiosis. Even in a healthy person, a single infection could cause dysbiosis and their microbiome may never fully get back to normal. In this situation, a health professional can really help. Clinicians often try to boost beneficial bacteria, wipe out the problem-causing microbes, and then continue rebuilding the good bacteria and strengthening the immune system. We discuss these treatments and how to find a provider in Chapter 9.
If your microbiome is made up of all of the normal bugs that inhabit your body, then the make-up of those bugs is your microbial balance. Interestingly, each person’s microbiome has its own “setpoint,” or homeostasis, and it doesn’t match to anyone else’s (except maybe to family members living in the same house). So, the composition of your microbiome is unique to you. While you and I may carry many of the same kinds of microbes, it’s pretty much certain that there will be a lot of differences and we will carry our bugs in different proportions from each other. This has led some researchers to identify groups of bacteria that are common to most of us (called “enterotypes” or a “core microbiome”), which we will discuss more in Chapter 5.
If there is no “optimum” bacterial balance for all of us, it makes it pretty hard to tell someone that their microbiome is healthy or that it’s not healthy enough. It also makes it impossible to know what bacterial imbalance, or dysbiosis, looks like for a given individual. But the answer to this riddle is to test your microbiome over time so that you can learn what is normal, or not normal, for you. Testing the microbiome helps us figure out normal bacterial balance, dysbiosis, and infection, although it is still an imperfect science. I will tell you more about how to test your microbial compadres in Chapter 9.
Antibiotics are one of the biggest dangers to our microbiomes. These medications transformed medicine 100 years ago, allowing us to live longer lives and to defeat deadly infections.19 Yay! However, antibiotics have a serious side effect. They wipe out all of our bacteria, not just infection-causing bacteria. And while our microbiomes grow back rapidly after we finish antibiotics, they never return to their original stable state.20 Antibiotics shift bacterial communities and deplete diversity within three or four days of beginning treatment.21 As you might imagine, cutting down your microbes is a serious crime. These bugs help you make nutrients, prime your immune system, fight and defend against foreign invaders, and tune your metabolism.
Antibiotics should be used with caution, but unfortunately, doctors haven’t always been so wise. I grew up in the ’80s and ’90s. My sister, brother, and I had regular ear infections growing up, so there was usually a bottle of bubble gum–flavored antibiotics—amoxicillin—in the refrigerator (Yummy! Not.)Antibiotics were prescribed when there were ear infections, colds, and sore throats. We now know that these were not good reasons to take antibiotics, because these ailments are not always caused by a bacterial infection. Research shows that 50 percent of antibiotics prescribed at doctors’ offices are unnecessary.22 And 30 to 60 percent of antibiotics prescribed in the intensive care unit of the hospital are unnecessary or inappropriate.
In 2010, there were enough antibiotic prescriptions written in the United States to give every single American one dose.
On a bigger scale, something much graver and more dangerous than pathogenic bacteria has emerged from overuse of antibiotics: antibiotic-resistant bacteria. These are superbugs that cannot be destroyed with antibiotics. Take the pathogens we talked about earlier as an example: These are bugs that can cause infections in people and have unwanted effects like diarrhea, vomiting, and fever. Now, give those bugs antibiotics for a short time. The medication will kill most of the pathogenic bacteria, but not all. Any bacterial survivors are likely resistant to the antibiotic. It’s Darwinian natural selection.
Bacteria are very adaptable. They grow and multiply lightning-fast. They also can easily share their DNA with each other to help their survival. If you try to kill a bacterial infection a few times unsuccessfully, you are slowly cultivating a pathogen that can resist the antibiotic. This is why the doctor will now tell you to take all of your antibiotics for the full duration of the prescription, even after your symptoms have gone away. If you stop early, then you are just training certain bacteria how to withstand antibiotics. If you apply this strategy of prescribing lots of unnecessary antibiotics to large human populations (like in hospital settings) over decades, you have essentially bred a highly dangerous superbug that can’t be destroyed with antibiotics.
“When antibiotics first came out, nobody could have imagined we’d have the resistance problem we face today. We didn’t give bacteria credit for being able to change and adapt so fast.”
—Bonnie Bassler, molecular biology professor and chair, Princeton University
See Chapter 9 for treatments to help your microbiome bounce back when you have no other choice but to take antibiotics. “Herbal antibiotics” can help remove infections and don’t have the same tendency of creating antibiotic-resistant superbugs.
Takeaways
• Infections are caused by microbes that invade the body, multiply, and cause a reaction, including illness.
• Dysbiosis is a state of microbial imbalance: either too few or too many bugs. It can also cause illness.
• Good bugs are your number one defense against infection and dysbiosis.
• Antibiotics kill infections but also kill good bugs.
• Antibiotic overuse has created drug-resistant superbugs.