Bacteria, viruses and fungi. What do these three terms remind you of? Disease and badness most likely. But did you know that most of these microorganisms actually do you more good than harm. In fact did you know that as you read this blog you have more bacterial DNA in you swarming around than you have human cells!
In fact, it is estimated that there are about 100 trillion microbial cells in our body, about 3 times as many human cells!
So, lets talk microbiota.
Microbiota refers to a massive, diverse group of bacteria, viruses and yeast that live in your gastrointestinal tract (GI) shortly after you are born. For those of you who were born naturally, you ingested your first microbiota from your mother's birth canal ( trying to phrase this as none graphic as possible), for those of you who had to be cut out, you ingested your first microbiota from your mother's milk. And as you grow older and diversify your diet, you acquire your own unique set of bacteria and viruses that live in your GI tract. Some of this is genetic, but the majority of your unique microbiota depends on your lifestyle.
Your GI system starts from your mouth and ends at your anus. The mouth, stomach and early part of the small bowel are connected to the outside world via the mouth, hence the bacteria that live in these parts are mostly aerobic species (they use oxygen for life). But as the GI tract convolutes further away from the mouth oxygen levels drop, so the bacteria that live in the distal parts of small bowel. and most of colon are anaerobes (they do not depend on oxygen). In additoion, the food that is available to the microbiota varies from the mouth and stomach to the small intestine and colon. Early on there is various food types available from simple sugars, fats and proteins. But as we digest and absorb most of the food we eat. there is little left for the bacteria that live in the colon. Interestingly, most of the bacteria that live in our GI tract actually reside in the cecum, part of the colon. These bacteria have to feed on the left overs; what we did not digest nor absorbed. So, depending on what kind of food you eat, you promote the growth of certain bacteria that can utilize that particular diet. There are other factors that affect the microbiota. Stress, infections and antibiotics can all alter the composition of the microbiota. Infections and antibiotics tend to be transitory and for a short time, so their effect is not as long lasting.
But your diet, genetics and stress levels can have a more prolonged influence on the type of bacteria that reside in your GI system and make up your microbiota.
Fun Fact: Microbiota refers to the bacteria, viruses and yeast that live in our body. Microbiome refers to the genetic pool of these organisms. Now, did you know that there is more microbiome in you than your own human DNA!! Yep, you are made of more bacterial DNA than human DNA. So, be humble little creatures!!
Microbiota and your health:
It is estimated that the total weight of the microbiota is more than any one organ in our body. So, why do we carry such a heavy weight "organ" around all our life? It turns out that the microbiota have evolved to have a significant symbiotic relationship with their host, us humans. And although some of these benefits have been well established, some other ones are only starting to become recognized, hence the whole buzz about gut health.
So, lets first take a look at some known health benefits of the microbiota:
1) Microbiota play an essential role in our immune system:
We are born with passive immunity. This simply means that during the first few weeks of life, our immune system is just born and naive, so it has not produced any antibodies to foreign organisms. its essentially useless at defending us. What we have is the antibodies we eat from the mother's milk., these antibodies help protect the newborn during the first few weeks. But as time goes by we are exposed to more and more microorganisms (bacteria, viruses and yeast). Through these interactions our own immune system starts to diversify and mature its arsenal of antibodies. Our digestive system, being a conduit to the outside world, is lined with lymph nodes (immune centers, think of them as army bases) where immune cells are constantly surveying the contents of what comes through. This is a major conduit for our immune system to build up immunity. It turns out that the bacteria and viruses that reside in our GI tract from day one of life play a major role in providing these lymph nodes with practice targets. They help mature the immune system. Think of the lymph nodes as army bases, the immune cells as soldiers, and the microbiota as target ranges. Except the soldiers are using blank bullets. So the bacteria and viruses provide the stimulation our immune system needs to grow and mature, but our immune system learns to tolerate the normal microbiota as a friendly host. This becomes essential during infections, when foreign and harmful bacteria and viruses enter the GI system. They are immediately recognized as an intruder and attacked. In fact, on a daily basis you may be exposed to many foreign bacteria and viruses that you inadvertently eat, but the immune system kills them before they can cause serious infection. Without the microbiota, this immune system never matures.
2) Microbiota protect us agains harmful bacteria:
Not only do the host microbiota help our immune system grow and mature, but they also directly help us fight harmful bacteria and viruses. This is done through direct competition. When your GI tract is filled with healthy microbiota, invaders simply can not compete with the large healthy host for food and space, so they never get a footing and can not grow. This is why antibiotics can have serious complications. They kill the host bacteria, allowing opportunistic infectious bacteria to get a footing and cause trouble (have you heard of C-diff, a common nasty bacterial infection that is caused by antibiotics).
Friendly fact: This is one of the reasons why we don't just give out antibiotics for few days of cold symptoms. Antibiotics can have rare, but serious complications. I personally have treated and admitted patients for severe C-diff infection after antibiotic treatment.
3) Microbiota help us digest food: The bacteria that live in our GI tract digest some of the food we eat for their own fuel. But by doing this they also make by products that have health benefits. For example, some bacteria help digest food and release the vitamins in those food, which we then absorb.
Besides these well established benefits, we are now starting to uncover a whole slue of other health benefits that the microbiota have. The health benefits appear to arise from the metabolite by products of the bacteria in the colon.
As humans we can not digest fiber, a complex form of carbohydrate found in fruits, vegetables, whole grains and legumes. However, certain bacteria thrive on fiber. So, a diet rich in fiber promotes the growth of these bacteria in the colon. One of the major by products that these bacteria produce from consuming fiber is called short chain fatty acids (SCFA).
As it turns out, SCFA have tremendous health benefits for us humans. So, although we can not digest nor consume fiber, but by feeding fiber to the bacteria in our colon, we can utilize the by products. SCFA are thought to have many benefits such as anti-inflammatory effects, hence lowering risk of inflammatory diseases such as heart disease and Inflammatory bowel disease. SCFA also help lower blood sugar and protect over all gut health. If you had read my blog on Carbs you already knew that fibers are known to lower the risk of heart disease, diabetes and risk of colon cancer. Now you know why!
Another area of importance is microbiota and risk of cancer, particularly colon cancer. Epidemiological studies show that certain bacteria in the microbiota are associated with increased risk of colon cancer. These bacteria are more prevalent in those with diets high in saturated fat and low in fiber. These bacteria produce pro growth proteins that may stimulate growth of GI cells and also inflammatory by products. This in turn may promote growth of abnormal cells that eventually lead to cancer and other chronic diseases. Whether these pro growth and inflammatory by products have more systemic consequences are still being investigated.
So, now that you know what is microbiota and its importance, how do you make sure you got the right bacteria down there.
Some of this is genetic. So you are either blessed or not. But your lifestyle also has a tremendous effect on what kind of bacteria make up your microbiota. In fact just few days of dietary changes can significantly change the microbiota's composition.
A diet high in fiber seems to be the healthiest. But you already knew that. So food like fruits, vegetables, legumes, whole grains and oats should be a staple of your daily diet. .
On the other hand diets high in saturated fat appear to promote growth of harmful bacteria. So cut down on red meat and really cut down on fast food and processed food (but you already have done that because you have been reading my blogs). Now, this does not mean that you should become a vegetarian. In fact there is no cause and effect studies to show that a vegetarian diet leads to less cancer. Most studies are association, which has many confounding factors and does not establish a direct causality. For one, people who eat a total vegetarian diet tend to be more health conscious over all. But try to focus more on a high fiber diet and limit your red meat intake. This seems to be a recurrent theme on most of my blogs! SO you get the picture. Focus more on healthier meat options like fish. Some chicken and pork and less of red meat. But as long as most of your diet is rich in fiber, you are promoting a healthy gut. Aim for AT LEAST 3-4 servings of fruits and vegetables per day. Including a high fiber source of carb in your meals like vegetables, potatoes, healthy grains like brown rice, whole wheat pasta, quinoa, barley, farro and beans. For breakfast fruits like banana and apple, oranges, and healthy carbs like oats, quinoa and home made or bakery made whole grain bread.
A healthy fiber rich diet is the key to a healthy gut.
Lets wrap this one up with the latest hot topic in gut health: probiotics and prebiotics:
Probiotics: probiotics are pills that are packed with bacteria which are supposed to populate your GI system with healthy microbiota. But research so far has not shown any benefit from taking these pills except in special scenarios. Part of this reason is we still do not fully know the full extent of the bacteria that are beneficial. The microbiota is a very diverse and dynamic community and most likely there are many factors besides couple specific bacteria. We are only starting to explore this universe. Eating a healthy diet is a much more effective way of letting nature do its magic. Second reason is that most of these probiotics are not regulated, so the bacteria in the pill may not actually be as effective. There is also no evidence that the bacteria in a pill can replace your natural microbiota. Probiotics are now a multi million dollar business Eat a healthy diet, skip the pill and spend your money on something more fun.
Probiotics do have a role in certain at risk population such as patients on chronic antibiotics. If you are part of the at risk population, your doctor will tell you and in fact prescribe you the probiotic.
Prebiotics: these are pills supposedly packed with nutrients that promote healthy gut bacteria. I am not even going to expand on this. For heaven's sake, eat some delicious bananas, apples with a nice warm bowl of oats and skip the pill. There is no evidence that shows these pills do in fact promote health of healthy bacteria or lead to improved outcomes. You can not eat an unhealthy diet and hope that a pill will fix your problems. There is no research that shows a direct link between prebiotics and improved health outcomes.
The gut microbiota and human health is a new and of course trendy subject. There is still a lot to be learned and much we do not know. So I would be very skeptical of any pills that claim to improve your gut microbiota, or more importantly your over all health. As is usually the case, human physiology is much more complicated than one or two bacteria. Rememebr, there are trillions of organisms in there, and how these bacteria interact with each other and their human host is far more complicated than a couple of isolated strands of bacteria. This is like the human genome project. For those of you old enough to remember, when the human genome was cracked we all thought that we will soon cure all diseases and have individualized treatments based on our DNA. But it turned out that our genetic sequence was just a small part in a much more complicated cellular world. Same is with the microbiota. Just because we have isolated some bacteria from healthy gut flora it does not mean that those few bacteria are the whole picture. So my recommendation is to eat a high fiber diet, focus on healthy sources of fat and stay away from pills and supplements until we know more. And please, do not pay hundreds and thousands of dollars to get a bacterial map of your poop and then another hundreds of thousands of dollars to presumably fix the bacteria in your poop. For now there is no evidence, or in fact enough clinical and scientific data, to support any of this. Instead take that money and take a vacation to Costa Rica, eat lots of fruits from the trees and fish from the ocean, and your gut will thank you.
