Germs that make you healthy


Over the past few years, I’ve mentioned in passing the importance of your gut microbiome in controlling your weight and keeping you healthy, but this article will explain in detail why it’s important and just how you can do that.

We’ve all heard of the concept of good bacteria in our intestines that aid in digestion, but most people don’t really understand that digestion is just a tiny part of what these microorganisms do for us. People have heard that eating yogurt provides good intestinal bacteria (which is true), but most people still cling to the harmful belief that all other germs will make you sick and you need to stay as clean as possible to stay healthy. Sanitation and vaccines truly are two of the things that have improved our health and extended our lifespans tremendously, but we’ve swung the pendulum too far the other way. Trying to live in a completely sterile world has begun causing different kinds of disfunction such as autoimmune diseases like type 1 diabetes, muscular dystrophy, rheumatoid arthritis, multiple sclerosis, irritable bowel syndrome, Crohn’s disease, food allergies, and celiac disease. An imbalanced microbiome (called dysbiosis) has also been shown to contribute to certain types of cancer, obesity, autism, depression, anxiety, bipolar disorder, and eating disorders. A balanced microbiome keeps your body functioning optimally while an imbalanced one can cause your body to turn on itself, causing chronic inflammation, damage to your own tissues, improper regulation of neurotransmitters, unintended gene expression, and a host of other problems that we’re only now beginning to understand.

You’re not an organism, you’re a super organism

We’ve all been raised with the concept that all bacteria and viruses are parasites that invade our bodies, inflict harm to our cells so that they can multiply, and then eventually get killed off by our immune systems. While that is certainly true with many microorganisms, there are far more beneficial ones than the dozens of types that you get from yogurt. It’s estimated that there are actually over a 1000 unique species of bacteria living in our bodies. These tiny little organisms outnumber our own cells by about 10 to 1 which means there are over 100 trillion beneficial bacteria in our bodies at any time. There are beneficial viruses as well, and they in turn outnumber the bacteria by about 10 to 1, meaning you also have quadrillions of good viruses in your body. They all add up to a roughly 2 to 4 pound “secret organ” that works with your digestive and immune systems to keep other invaders out and help process the foods you eat to extract nutrients that your body cannot metabolize on its own. By comparison, the large intestines (where a good majority of them live) weighs about 4 pounds.

Environmental vs. genetic factors

How do we know these diseases are caused because of imbalances with the microbiome? Genetic predisposition plays a role, but scientists were surprised during the Human Genome Project to find just how little genetics played in various diseases. They were hoping our genes would be the key to identifying and ultimately stopping all kinds of ailments, but it turned out that 90 percent of the cause for most diseases was environmental rather than genetic. As they tried to map these environmental triggers, scientists noticed that patients with these diseases had larger concentrations of some bacteria species and not others. They also noticed that a less diverse range of intestinal bacteria typically resulted in disfunction. In other words, a smaller variety of bacteria species in the microbiome meant that the patient was more likely to have or eventually develop some sort of disease. What they weren’t sure of yet was whether the changes to the microbiome were the cause of the disease or simply a symptom.

Transplanting health (or disfunction)

To test it, they tried to see if they could transfer these healthy or diseased states into other recipients by transplanting their microbiomes. They started in rats, of course, using both rats with normal microbiomes as well as those raised in a completely sterile environment (so they were completely microbe-free). They were able to transfer disorders from one rat to another plus they found they could transfer disease-resistance into rats that were actually genetically predisposed to those diseases. It was an exciting discovery, and fecal microbial transplants have subsequently been used in humans to transfer healthy microbes from donors to sick patients to cure them of intestinal diseases like recurrent Clostridium difficile. In treating patients with this disease, they also noticed the transplants could help with neurological diseases like multiple sclerosis and Parkinson’s disease.

The concept of fecal transplants highlights the importance of the microbiome in our health, but the story of one transplant (as well as confirmation in many rat and human studies) shows the importance of the microbiome in obesity. One woman received a fecal transplant from her overweight daughter to cure her recurrent Clostridium difficile. It worked, but she then gained 34 pounds over the next 16 months, going from 136 pounds to 170 pounds (which eventually classified her as obese) despite eating a restricted diet and exercising.

Certain bacteria will make you more efficient at harvesting calories from the foods you eat, and others will even slow your metabolic rate so you burn less calories when at rest. It’s why people in colder climates tend to be heavier than people in warmer climates. In the past, that efficiency helped Northerners survive as food became scarcer during the winter, but now it just makes us fat. It’s also why I tell people that a calorie is not a calorie, and that even when people say “this salad has more calories than a big mac,” the salad is still a much healthier option because it helps feed the good bacteria in your microbiome. Eating healthy foods changes the composition of your microbiome which protects your body and your brain from obesity, autoimmune diseases, mood disorders, and all other kinds of disfunction. I’ll get more into what foods and behaviors lead to positive changes later.


Germs aren’t good or bad, they’re selfish

I’ll use words like good and bad bacteria throughout the article, but ultimately any microbe could cause harm if they breed out of control or escape from the places where they are supposed to reside. Why doesn’t our immune system take them all out, both good and bad? Because as long as they hang out in the mucosal layers where they belong, they are part of your immune system. We consume all kinds of microorganisms every time we eat, drink, breathe, or touch something (it’s unavoidable), and your microbiome is one of the first lines of defense. Why? It’s not because they love us, but actually because they’re selfish. They want to keep their home safe by releasing helpful metabolites your body can use to build mucosal surfaces (basically a germ-wall invaders can’t cross). They work to drive off any competition by releasing antimicrobial agents that kill intruders. They even stabilize your mood and keep you happy because a happy host is more likely to interact with other people and give them the chance to spread to new environments. In return, our immune system recognizes them as harmless and let’s them stay. In fact, these microbes interact with your immune cells and help them hunt down other invading organisms by regulating the release of T-cells that either promote or reduce inflammation. A proper amount of inflammation kills intruding microorganisms, but too much starts to hurt our cells as well. Maintaining the right balance in your microbiome helps your body maintain the right balance in it’s immune response.

Things get out of balance when you don’t provide your microbiome the foods it needs. All those various microbes have a specific diet and you need to feed them to keep them healthy and happy. If they don’t get the food they need, some may die off which leaves plenty of vacant space for more harmful microbes to swoop in and colonize, or even worse, they may start consuming the same mucosal cells that they previously helped build up. This is where you get the “leaky gut syndrome” people refer to. It’s when your strong germ-wall breaks down and the bacteria that should be contained to the digestive system travel about the body causing a constant inflammatory immune response. This also contributes to food allergies because whole proteins are allowed to enter your bloodstream instead of the properly digested amino acids that your body was meant to handle. Your body sees proteins in your blood as microorganism invaders that need to be destroyed rather than food to be digested.

The DO’s and DON’Ts of microbiome management

Now that I’ve gone over why it’s important to maintain a healthy microbiome, I’ll go over what will help keep it (and you) healthy, and what you should avoid in order to keep yours in proper balance.


DO Probiotics

I’ve found that many people have heard of probiotics, but they’re often surprised to hear that there are more sources than just yogurt. Probiotic foods actually contain live cultures of good bacteria. They are used to partially ferment the foods they’re in which not only provides the bacteria your microbiome needs, but many vitamins and metabolites that were otherwise locked away. Don’t assume that all manufacturers of these foods provide probiotics. Our all-germs-are-bad culture pasteurizes many of these foods to make sure all bacteria are destroyed. This not only extends the shelf-life but kills off dangerous microbes that might have been introduced by poor food-handling practices. Check the label to make sure they say they contain live and active cultures. Most probiotic foods tend to be on the sour side. They’re usually more of a side dish than a main one, but you can always dress them up with spicier prebiotic foods (see below) to give your microbiome an extra boost.

1. Active-culture yogurt: The reason everyone associates yogurt with probiotics is because we’re been bombarded with advertising from yogurt companies for decades. Once again, that doesn’t mean all these brands actually contain active cultures. Check and make sure that it says live and active cultures on the label. I also suggest avoiding the “lite” versions because they’re higher in added sugar. Don’t fear the fat. The fat in dairy is filling and it does not contribute to weight gain (which I will explain later).

2. Fermented cabbage: Foods like sauerkraut and kimchi are made by partially fermenting cabbage with active cultures. Some of these cultures remain, but once again, only if they don’t pasteurize the final product (check the label).

3. Sour pickles: Most any kind of pickled fruit or vegetable will do, but only if they’re pickled in brine instead of vinegar. Vinegar will kill off any active cultures and sterilize the batch.

4. Miso: This fermented soy bean paste is typically made into a healthy, low-calorie soup.

5. Kefir: Similar to yogurt, this thick drink is made by fermenting goat’s milk with a combination of good yeast and bacteria.

6. Tempeh: This is another probiotic food made from fermented soy. Many people actually like to use it as a meat substitute since it is a complete protein containing the full array of essential amino acids.


DO Prebiotics

I’ve said many times before that we aren’t herbivores and we’re not good at digesting whole fruits and vegetables, yet I recommend they form the majority of your diet. For one, they are extremely filling, yet from the standpoint of weight control, they basically count as zero calories. The other reason is because one of the primary food sources for a healthy microbiome is fiber. You may not be able to digest it, but your microbiome can eat it just fine. Remember, you’re not just one organism, you’re the landlord for trillions of others, and if you want to keep all your tenants from trashing the place, you need to keep them well fed. While some sources are better than others, just increasing your fruit and vegetable intake will help tremendously. An imbalanced microbiome contributes to obesity and repairing that balance makes it much easier to change your body’s metabolic environment to one that encourages fat loss instead of fat storage.

A study by the Stanford University School of Medicine shows that not only do low-fiber diets decimate the diversity of bacteria within the microbiome, but the loss of variety is passed down through the generations. We’re already seeing this loss of important bacterial species in industrialized societies, which is why we’re also witnessing a steady rise in the disorders mentioned above. Add some of the foods below to your daily diet to improve the diversity of your microbiome and try to eat a decent variety to give all those good bacteria cultures a chance to thrive and protect you.

1. Leafy greens: We’ve said for years that leafy greens were an important part of a healthy diet, but we were never sure why. It’s true they provided many vitamins and minerals, but if that’s all that mattered then you could simply eat crappy processed foods, take some daily vitamins, and be fine. Obviously that hasn’t worked so what is the secret in leafy greens that really seems to promote health and help you maintain a healthy weight? Researchers recently discovered that leafy greens contain a unique sulfur-containing sugar called sulfoquinovose that fuels the good bacteria in our microbiomes. Sulfur is also important for building proteins, so the bi-products from breaking down this sugar likely also serve as important nutrients for other bacteria species in your microbiome.

2. Inulin: Inulin is a natural storage carbohydrate found in over 36,000 species of plants. Some great sources for inulin are asparagus, onion, garlic, Jerusalem artichoke, chicory, dandelion root, leeks and even many whole grains like wheat and oats. Food companies have found that it is easily extracted from various plants which is why they are increasingly using inulin in a lot of supplements and processed foods. Aside from it’s benefits for the microbiome, it also helps with calcium absorption and blood sugar control.

3. Fructo-oligosaccharides (FOS): This prebiotic is found in many of the same foods as inulin because it is actually produced through the degradation of inulin. This is another prebiotic used more and more in processed foods because of it’s sweetness and healthy properties, but in general, I recommend avoiding processed foods when it comes to gut health. Manufacturers are jumping on the prebiotic bandwagon to differentiate their products. They see FOS as a “natural sweetener” that’s healthier than sugar. Sugar is perfectly healthy too if you eat the small amounts found in whole foods, but it is incredibly damaging to your body (and your microbiome) in the doses found in processed foods. Inulin and FOS are helpful in whole foods but not magical once your strip them out and stick them in a box. Focus on getting your prebiotics from fiber-rich sources like berries, bananas (when they’re slightly green), onions, chicory root, garlic (this is a good one in particular because it’s been shown to have antimicrobial properties for many bad species of bacteria while serving as a prebiotic for many good species), asparagus, jícama, and leeks. You can also find them in some grains and cereals like wheat and barley. A recent study found that the improvements to the gut microbiome from barely in particular improved people’s metabolism for up to 14 hours after consumption, decreased their blood sugar and insulin levels, increased insulin sensitivity, and improved appetite control.

4. Galacto-oligosaccharides (GOS): Something that surprised me a few years ago during my research was finding out the saturated fat in dairy tended not to lead to weight gain. Of course, you could ruin it’s naturally protective effects by eating a lot of crappy processed foods with it, but in general, something in dairy prevented fat storage. One of the reasons is the fat-clearing effects of calcium and the other is the fact that our bodies can process lactose into a prebiotic known as galacto-oligosaccharides. I’ve heard many people theorize on the subject of lactose intolerance by saying that we aren’t meant to drink it and it’s strange that we drink the milk of another animal because no other creatures do that in nature. While it’s true that many people lack the enzymes to process lactose, millions of others have evolved the ability to handle it. In fact, many scientists have been baffled by the mystery of how this trait evolved in humans so rapidly. Perhaps close proximity to cows helped those early agricultural humans acquire the beneficial bacteria that expressed this advantageous mutation. That’s just conjecture on my part, but we’re learning that our traits do not just come from the passing of our genes, but from the passing of our hologenomes (the collection of our genes and our microbiome’s genes). Regardless, if you are lactose intolerant, you can still receive the prebiotic GOS through plant sources like lentils, chickpeas/hummus, green peas, lima beans, kidney beans, Jerusalem artichoke, broccoli, Brussels sprouts, cabbage, cauliflower, collard greens, kale, radishes and rutabaga. One study found that this particular prebiotic helped produce bacteria that reduced the release of cortisol in humans, which reduces feelings of stress and anxiety.


DON’T Use Antibiotics So Casually

Antibiotics are another miracle of modern medicine that has saved millions of lives and extended our overall lifespans, but they’re not magical. There is no free lunch in nature, and every medication comes with side effects. If the benefits outweigh the side effects, then we prescribe it, but don’t think any medication is consequence free. I’ll get into the consequences to an individual’s microbiome in a minute, but first I want to address another good reason to limit your usage of antibiotics.

Massive overuse of antibiotics for livestock, antimicrobial soaps (shown to be no more effective than regular soap), and the overprescription of antibiotics for human diseases like colds and the flu (where they serve no benefit) has led to a frightening rise in antibiotic-resistant diseases. The reason our microbiome can evolve so rapidly due to dietary changes is because of the speed at which they reproduce. The generations of some species pass in minutes which allows rapid-fire evolution. Low doses of antibiotics (like in the soaps or given to livestock) leave behind living bacteria that have proven themselves to be strong enough to resist those chemicals. These survivors then flourish and spread their antibiotic-resistant genes. Our casual use of antibiotics could lead us to a post-antibiotic world where simple infections and illnesses go from being easily-cured to as lethal as they were to our ancestors.

Antibiotics also don’t discriminate in the bacteria they kill. I’ve already established that diversity of species is vital to a healthy microbiome and a single course of common antibiotics can kill up to one third of the species in your body (some of which may never come back). One study found that the alterations to the gut microbiome took up to a year to return to normal, and worse yet, genetic testing revealed that many bacteria species present developed antibiotic-resistance after a single treatment. We’re only just beginning to understand the importance of the microbiome for our health, so perhaps we’ve misjudged just how bad the side effects of antibiotics truly are.

When I tell people that 90 percent of antibiotics consumed in the United States goes to our livestock, most assume it’s because our factory farm system is so unsanitary. That’s part of it, but the main reason is because it makes the animals grow larger and fatter on less feed. Humans also tend to gain weight after a course of antibiotics. In fact, one review not only showed this same growth could be seen in humans after undergoing treatments with antibiotics, but they also surmised that the growing use of antibiotics in farming over the past 20 years and the growing incidences of obesity in that same timeframe were related. They theorize residual exposure from all these antibiotics in our food may in part be responsible for rising obesity rates. We’re not sure on the residual antibiotics in our food, but a recent study showed a linear relationship between the number of doses of antibiotics given to children and their body mass, and that this relationship actually got worse as the children got older. There’s definitely enough evidence to show the importance of the microbiome in preventing or causing obesity, and it seems antibiotics tend to kill off species that help prevent it.

All that said, antibiotics are still life saving. I’m not saying that you should avoid them all together, but you need to really understand all the consequences and measure them against the illness you’re hoping to cure. Diseases like the cold and flu are completely unaffected by antibiotics, yet many people take them anyway. For too long, we’ve looked at antibiotics as all upside with no downside and that is simply not true. We’ve ignored the consequences for too long which has led to greater ones that we all now need to worry about.


DON’T Be So Clean

Eating a variety of fruits and vegetables tends to be a concept that most people feel comfortable with, and I generally don’t get much pushback there. However, I tend to get a lot of resistance from people when I give this next little bit of advice. As I mentioned above, our typical low-fiber western diet mixed with rampant antibiotic use, and general germ-phobia has helped decimate the variety of species in our microbiomes. Lack of variety can cause even good bacteria to breed out of control and cause disfunction. You can’t simply eat prebiotics to restore your those bacterial colonies that were completely wiped out. That’s why some of these prebiotic foods cause gas, bloating, diarrhea, and other digestive issues in people that have an unbalanced microbiome. In order for prebiotics to successfully restore the diversity of your microbiome, you first need to seed your body with a variety of species, and to do that, you’re going to need to get a little dirty. Let me be perfectly clear first. Wash your hands after using the bathroom, handling raw meat, touching someone that is ill, or other behaviors we know bring you into contact with virulent pathogens. There are plenty of harmful germs out there still, but I’ll list some behaviors that will introduce some less harmful ones back into your microbiome without you needing to get a fecal transplant.

1. Open Windows: We’ve known for a long time that we tend to get sick more often in the winter than the summer. Is it due to cold temperatures? Closer contact with other people? Vitamin D deficiencies from less sunlight? All kinds of theories abound, and while they all hold a little truth, our new understanding of the microbiome has shined light on another cause. One study examined the diversity of bacteria present indoors and outdoors. Not only did they observe much less diversity in indoor environments, but the genetics of the ones they found inside were more closely related to bacteria that are pathogens in humans. These same pathogenic bacteria species didn’t even exist outside. Opening the window will not only bring a greater variety of beneficial microbes into your home, car, office, etc, but it will help clear out the ones that will make you sick.

2. Play in the Dirt: Just as there are a greater variety of beneficial microbes in the air outside, there are even more in the soil (especially in gardens). It’s actually beneficial to get your hands dirty in the soil and then eat without washing them. This is also one of the reasons why people with dogs tend to have less seasonal and food allergies. If you’re not willing to play in the dirt, your dog will do it for you and bring those beneficial bacteria all over the place.

3. Be Around People: This is one of the hardest concepts to beat out of people after a lifetime of being told otherwise, especially during cold and flu season. Yes, more exposure to more people can get you sick, but total avoidance is not only bad for your emotional health, but your microbiome as well. You don’t need to kiss everyone you meet, but close proximity increases your likelihood of sharing beneficial microbes. One study of chimpanzees looked at their microbiome during the social wet season when food is plentiful compared to the barren dry season when they tend to go off of their own. They found that when the chimpanzees were in social groups, their microbiomes contained 20 to 25 percent more species. If someone is sick, then by all means wash your hands, but don’t be afraid of a few sniffles when you could “catch” bacteria that improve mood, weight management, and your overall immunity. As strange as it sounds, this is also one of the things that I point to as a benefit of working out in the gym as opposed to staying home. Exposing your microbiome to people that have generally adapted a healthy lifestyle can only help. There was a study on rugby players that claimed that exercise increased the diversity of their microbiomes more than most people, but it could have had as much to do with playing outdoors or the close proximity to other players as it did with exercise.

4. Hand Wash Dishes: Being too clean is not a good thing and dish washing machines are great at sterilizing your plates completely. We’ve always thought this was a good thing, but studies on food allergies in children show a reduced likelihood of developing food allergies when dishes were washed by hand.

5. Throw Out the Antibacterial Soaps: I thought people gave up on these when the FDA announced that they not only were no more effective than soap and water, but they also increased the risk of thyroid problems, disrupted the endocrine system, and helped create drug-resistant bacteria. That’s all in addition to likely disruptions of your microbiome. Just because you’re putting it on your skin doesn’t mean it isn’t getting into your body. One study found that 75 percent of people excreted the antibacterial ingredient, triclosan, in their urine. Low-grade antibiotics increase your risk of harboring drug-resistant pathogens in your body, so at the very least, you’re actually increasing your risk of a life-threatening illness rather than reducing it. Just use regular soap, it works.

DON’T Eat Processed Foods

As I’ve said many times before, if something has a nutrition label on it, then it probably isn’t very nutritious. Processed foods are designed with more than just taste in mind. They have all kinds of additives in them to create an appealing appearance and texture and to improve shelf-life. Even though they have been deemed safe by the FDA, as our understanding of biology improves, we learn to look at possible disruptions these additives might cause that we never considered before, like effects on our microbiome. Two good examples are the emulsifiers carboxymethylcellulose and polysorbate-80. These commonly used additives act as a bridge between oil and water in processed foods so the two don’t separate out later. A mouse study found that these additives that were classified as “generally regarded as safe” by the FDA disrupt the composition of the microbiome, degrade the mucosal layer in the intestines causing widespread inflammation, and induced metabolic syndrome, obesity, and colitis. In general, focus on real food and avoid the boxed stuff and you won’t need to deal with the unknown side effects of other “safe” additives.

DON’T Rely on Artificial Sweeteners

While many studies have shown that non-caloric artificial sweeteners like saccharin, sucralose, and aspartame help people lose weight and consume less calories, other studies show that these non-caloric substitutes somehow lead to weight gain anyway. There are many theories on the subject, but one mouse study found that these artificial sweeteners changed the composition of the microbiome which made the mice glucose intolerant and set them up for obesity and diabetes. The fact that this metabolic disfunction could be cured with antibiotics or transferred to other mice through fecal transplants made for a compelling argument concerning how changes to the microbiome ultimately caused the end results. Artificial sweeteners can still be a part of your diet as long as they are a small part. If you avoid fiber and other important prebiotics, you will limit the composition of your microbiome and exacerbate the problems of these sweeteners. They can work for you just fine if the rest of your diet is balanced. In other words, a diet soda or two is fine, but having them all day long probably will be counter productive and having them with a big mac and fries is basically pointless.

DON’T Diet and Binge

The microbiome can change quickly with a healthy diet, but it can also change back just as fast if you binge a few days later. A behavior I’ve seen all too often from people is to diet and eat healthy all week long and then binge during the weekend. They then ask me why their diet isn’t working. “I thought cheat days were fine.” A cheat meal or a cheat day is far different than a cheat weekend (which seems to be what cheat days typically turn into). I never expect people to be perfect (I’m not), which is why I think all or nothing thinking just doesn’t work. Have a treat here and a treat there instead of perfection followed by anything-goes insanity. Studies have shown that this cycle of dieting and binging leaves the microbiome as imbalanced and unhealthy as subjects that never ate properly in the first place. You need to build up some momentum first before you can start experimenting with cheat days. If you give your microbiome time to stabilize, you’ll be surprised to find that your desire to “go crazy” diminishes significantly. As I’ve mentioned above, a healthy microbiome positively effects your mood and stress levels, and that desire to comfort eat will slowly fade away as you restore the balance in your gut bacteria.

End Result: More Proof Why Real Food Leads to Real Results

While study of the microbiome is a fascinating new area of biology, the real reason I wanted to outline how it works was to emphasize advice I’ve been giving for a while. If you adopt a balanced diet with plenty of fruits and vegetables, healthy fats, and a good protein source, you’ll lose weight, improve your health and mood, and feel more energetic. It’s not about deprivation and starvation, it’s about giving your body the fuel it needs to work right. This also shows how your success builds momentum that leads to easier success. As your microbiome changes in response to your improved diet, you’ll find it easier and easier to stick to your healthier new diet for the long term. You can’t just eat better for a few months and then return to a crappy diet. That’s why people always say “diets don’t work.” They’re right and they’re wrong. It won’t work if you think it’s just a short term thing, but it’s easy to see great success if you’re willing to adopt changes you can live with for the rest of your life.

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