Posts for category: Microbiome

By Dr. Marvin Singh, MD
October 14, 2018
Category: Microbiome
Tags: @healthygutmd  

What’s In Your Gut Virome?

The gut microbiome is a hot topic these days. It seems like everywhere you turn someone is talking about gut health and bacteria. But is it all about bacteria? What is the gut microbiome? Let me break it down for you.

The gut microbiome is basically the ecosystem of trillions of microorganisms that live inside of our intestinal tract, mainly in the colon. Some have estimated that there are about 100 trillion microorganisms that live in the gastrointestinal tract. By the way, this is just the gut we are talking about; there are even more organisms on our skin, in our mouths, and in many other parts of our bodies. These little bugs make up an intricate network and ecosystem and are largely responsible for our health (or lack thereof). There are ten times more microorganisms in our digestive tract than there are human cells on our body. The DNA from these organisms outnumbers our human DNA by a factor of 100 to 1. This is definitely a force to take seriously!

We often think about the gut microbiome in terms of bacteria. In fact, it is predominantly bacteria. However, there are also fungi, yeasts, parasites (in some cases), and viruses. It’s the viruses I want to spend some time talking about. We are probably going to discover in the years to come that certain viruses alter the ecology of the gut microbiome and this can lead to certain conditions. For example, a recent study suggested that infection with the Reovirus could trigger an inflammatory response to certain foods and lead to the development of celiac disease ( Another study suggested that infection with Rotavirus could lead to the development of non-celiac gluten sensitivity ( Even a decade ago, in the literature, researchers described the Epstein-Barr virus (the virus that causes mono) as being associated with autoimmune diseases like Lupus, Rheumatoid Arthritis, and Sjogren’s syndrome (

What some of us biohackers are discovering is that there are viruses that are living in the gut. For the most part, these happen to be plant viruses. For example, some people may have a cucumber mosaic virus living in their gut. This is a virus that was first discovered in 1934 and it was found to infect cucumbers and a variety of other plants. We probably don’t think too much about plant viruses when we are eating vegetables but maybe we should. Humans make a good go-between for a plant virus and when we ingest them they could potentially change the ecology in the gut microbiome before they depart the gastrointestinal tract. Although we don’t know too much about all these different viruses yet, it is generally felt that the more viruses you have, the more issues with health you may have as well. Some bacteria in the gut can inhibit viral infections while other bacteria can promote viral infections, so there is definitely an interaction there ( Remember, 70% of the immune system exists in the gut. When you take a snapshot of your gut microbiome and get it tested, it is hard to know if the viruses that are being detected are related to food recently eaten or persistent infections. Either way, it could be a sign that you are not eating the best quality vegetables. While it is unclear if the viruses are a part of the picture when it comes to food sensitivities, it makes sense to try to avoid a particular plant if you know you are infected with a virus that infects that plant.

What is even more interesting are the viruses that infect the bacteria. These are called bacteriophages. One of the more common ones is referred to as crAssphage or cross-assembly phage (I love the name, don’t you?). This is a common phage in the gut, actually. It is felt to predict infection to the family Bacteroidetes. While the function of this virus in human health is not really clear, it does make one wonder about its role in human health if it can infect certain kinds of bacteria. It also makes one wonder about particular drug or therapy targets in certain diseases or conditions that involve a virus at the root of its cause.

In the meantime, here are a few things you can do to help protect your gut from viruses:

  1. Make sure your produce is organic and comes from a reliable source. If the vegetable looks infected or just doesn’t look right, think twice before eating it
  2. If you know you have a particular plant virus living in your gut, consider taking a break from that plant at least for a while.
  3. Work towards eating plenty of colorful fruits and vegetables that come from a reliable source so that you can build the diversity of your gut microbiome.
  4. Reduce stress, exercise, avoid toxins, have fun in life, avoid sugars and processed foods; basically, do all the things that help build a strong resilient gut microbiome

We don’t yet have enough information about the gut virome but it is clear that there are viruses that live in the gut as well. It is fascinating how a plant virus can settle down in the gut microbiome. It is even more fascinating to wonder about what it is actually doing. In some cases, these viruses may be doing nothing. However, in other cases, it is possible they could be shifting the balance of the microbiome and contributing to significant health effects. While I wouldn’t lose too much sleep over this, I would definitely try to be more aware that it exists and perhaps pay more attention to the quality of plants we are eating on a regular basis. 

By Dr. Marvin Singh, MD
October 01, 2018
Category: Microbiome
Tags: @healthygutmd  

My Top 5 Tips on How to Detox Using Your Gut Microbiome

Detoxing is a big topic these days. Everyone wants to know how to detox. But what does it really mean to detox? Well, it means getting rid of the bad stuff and putting in the good stuff. It’s not entirely that simple but that is the basic concept to keep in mind. There are a few ways to help get the bad stuff out, besides not being exposed to the bad stuff. Three of the main ways that someone can flush the bad stuff out is via the digestive tract, urinary tract, and sweat. Of these three systems, the digestive tract is one of the most powerful. Why? Because the digestive tract is home to the gut microbiome, the ecosystem of trillions of bacteria, viruses, and fungi that live together with us, in sickness and in health.

The gut microbiome has been shown to have the ability to degrade chemicals and toxins such as pesticides ( In humans, chemicals such as plastics, pesticides, fertilizers, electronic waste, and food additives that are endocrine disrupting chemicals are felt to be associated with the growing rate of diabetes and obesity. An endocrine disrupting chemicals is basically a chemical or substance that disrupts the normal hormone balance in your body and throws things off. As a result, you suffer negative health effects such as diabetes, obesity, and a whole number of other conditions. We know that the gut microbiome, metabolizes these toxins ( This is such an important topic that I wrote a book chapter in the textbook of Integrative Environmental Medicine ( on this very topic: how the gut microbiome is involved and influenced by diet and environmental toxins.

Why should you care about all this? Well, what the gut is exposed to is very important. This is because when the gut microbiome gets imbalanced, various different diseases and conditions can occur such as Crohn’s Disease or Inflammatory Bowel Disease ( When the detox capability of the gut microbiome is on point, then maybe we are ok. However, when the detox capability of the gut microbiome is off, as a result of an imbalance, then we may suffer negative health effects. It’s like having a well-oiled machine that doesn’t work as well as it could because the parts used to build that machine are lower quality. If our gut microbiome is bombarded with toxins, we may reduce the quality of our detoxification systems and we may alter the composition of the ecosystem that could subsequently leave us vulnerable to other changes, effects, and conditions.

So, what should we do? How can we maximize our gut’s detoxification capabilities? Here are my top 5 tips:

  1. It makes the most sense to try to reduce and avoid toxins. There won’t be as much stress on the system if the load is not as large. This means using clean cosmetic products, cleaning supplies, cooking tools, and most importantly it means eating clean.
  2. Eat plants. Plants have a lot of nutritional benefit, chemicals, vitamins, and anti-oxidants. This will help us in our never ending detoxification endeavors. Some of my favorites are dandelion greens, celery, swiss chard, cilantro, broccoli, green tea, oolong tea, turmeric, ginger, and berries.
  3. Eat clean foods. This means avoiding processed and packaged foods. These foods generally contain food chemicals that are meant to improve shelf life and make the product “look nice” for as long as possible. While these chemicals often accomplish the goal of the company, it exposes our microbiome to extra unnecessary chemicals.
  4. Avoid unnecessary antibiotics. Antibiotics can be life-saving. They should be used but in the appropriate setting. Often, antibiotics are over-prescribed and being given for viral infections or other self-limited conditions that do not require antibiotics. What happens is that we also kill the good bacteria when we take a broad spectrum antibiotic and some of these effects can be long lasting on our inner ecosystem.
  5. Ensure regular bowel habits. If we are not going #2 on a regular basis, we impair the gut’s detoxification abilities. Some of the bacteria can take a detoxified chemical and make it a toxin again if it sits around too long. We want to make sure we have at least one or two regular, soft, formed bowel movements every day. The saying “better out than in” never made more sense! If you eat cleaner, increase your fiber intake, drink plenty of water, and optimize your lifestyle choices, you will find that the bowel habits just come along as part of the process. For those of you who need a bit of a boost, that’s okay too; my only suggestion would be to work with someone who is well versed in digestive conditions to optimize your choices in things you can use. Sometimes a prebiotic and probiotic supplement can help; speaking to your health care provider about which ones may be best for you is important.


We live in a toxic world. That’s just a matter of fact. Everywhere we turn or look, I would bet you could find toxins. However, this is not something to fear. We have to live our lives in this modern world. So, the point is not to be scared of everything. The point is to learn how to maximize that detoxifying machine in our digestive tract and help it do the job it was meant to do, the job it wants to do. If we build a resilient and diverse gut microbiome with all the arsenal it needs to fight off the bad toxins, we will be ready (as best as we can) to handle the common threats that come into our everyday lives. 

By Dr. Marvin Singh MD
September 03, 2018
Category: Microbiome
Tags: @healthygutmd  

My Top 3 Choices For Treating Heartburn Naturally

As an Integrative Gastroenterologist, heartburn or acid reflux is one of the most common topics of discussion. There are all kinds of news reports that acid reflux medications like PPIs (Proton Pump Inhibitors) can cause anything from kidney failure to dementia. Is there any truth to this? Is there anything else that can be done? Well, yes, there is definitely something that can be done. And there are definitely some associations with some of these conditions.

Acid reflux and heartburn are basically the same thing; we use the term interchangeably. It basically means that stomach acid and bile can flow up from the stomach to the esophagus (food pipe). This can be a really uncomfortable feeling and can cause burning under the chest. The traditional go to medications have been things like TUMS or Zantac (ranitidine). Now that several proton pump inhibitors (PPIs) are over the counter, these have become much more readily used although they are still, and have always been, very widely prescribed. A proton pump inhibitor (PPI) reduces the production of stomach acid. They help us feel better, so we take them. End of story? Not exactly…..

We need the acid in our stomach. We were born to produce acid in our stomach so that we can digest and process the food we eat. So, what happens when you do something to counter that effect? Well, there have been a whole host of health effects noted or found to be associated with use of these PPI medications. These include: B12 deficiency, osteoporosis, kidney dysfunction, dementia, low magnesium levels, small intestinal bacterial overgrowth (SIBO), increased risk of getting a stomach bug, and increased risk of a potentially significant diarrheal infection from Clostridium difficile. There have been reports of low magnesium induced low parathyroid function  ( While there is no definitive consensus on the role of PPIs in dementia, there is some information to raise suspicion that PPIs could play a role in the development of dementia, perhaps as a result of drug-drug interactions and/or effects on electrochemical gradients in neurons, among other possibilities ( Risk of acute kidney injury and chronic kidney disease is also something well described. I have personally seen patients develop kidney failure and no other reason could be determined besides the use of a PPI. It is well established that an allergic kidney injury called acute interstitial nephritis can occur. Although we need more research to definitively establish that kidney failure and chronic kidney disease can result from use of PPIs, there are enough reports demonstrating association that should raise our eyebrows (

The literature and reports go on and on. I could probably write a book on it! The point, though, is that these medications may have a role in management of some things but they were not truly meant to be taken for long periods of time. However, many of us do take them for long periods of time. The problem is that we are now learning about things that could happen that we didn’t anticipate would happen. What we are likely doing is manipulating our gut microbiome. The gut microbiome is the ecosystem of over 100 trillion bacteria, viruses, and fungi that live inside of our gastrointestinal tracts. We know that they play a role in many chronic diseases. When we chronically reduce the acid in our stomach, which is there for a purpose, and also which is there as a line of defense for our GI tract, then we leave the doors wide open for all kinds of other bacteria to get into the digestive tract. This can lead to an imbalance in the ecosystem which could potentially be a set up for all of these things that we are discussing here. That’s my theory. And it is certainly plausible and worth consideration.

So, what do we do? Suffer? Absolutely not! While nobody would argue that you avoid a PPI if you are in the hospital with a life threatening GI bleed from an ulcer, we certainly do not need to take these medications for a lifetime, outside of potentially reducing risk of Barrett’s esophagus (a precancerous change in the lining in the esophagus) from progressing to esophageal cancer and a few other special circumstances.

Here are a few initial tips:

  1. See if there are any medications you are taking that could be correlated with your reflux symptoms. Perhaps there could be an alternative if you identify something.
  2. Keep a food log or get food sensitivity testing to see if there are any foods that are triggers for you (it is not always tomato sauce or spicy foods; it could be bread!).
  3. Stop smoking
  4. Reduce alcohol consumption
  5. Don’t eat 2-3 hours before lying flat
  6. Avoid heavy, fatty meals (you should be doing this anyway!)
  7. Don’t over-eat (you shouldn’t be doing this anyway!)
  8. Make sure you talk to your doctor; it is possible you may need an upper endoscopy (EGD) or other evaluation to evaluate the esophagus and upper GI tract, especially if there are concerning symptoms like difficulty swallowing, pain with swallowing, and/or weight loss.

Lifestyle interventions are excellent ways to reduce acid reflux. Losing weight, eating healthier, exercising, modifying your habits and routine can all be great ways to improve your symptoms. Remember, your symptoms are probably happening for a reason. I have a few favorite natural treatments that I use to help control symptoms while working on the above. Make sure you consult a doctor who understands how to use these natural alternatives when trying to taper or wean off your PPI. Here are my top 3 natural alternatives for acid reflux treatment.

  1. DGL (Deglycyrrhizinated licorice). This is a mainstay in my practice. It comes in a variety of forms. Many people like the chewable DGL tablets but I am not so fond of the fillers and sugars that are in some of those formulations. I tend to prefer a pure powdered DGL. We want to make sure you don’t take a pure licorice for long period of time because doing that may have some important health consequences; however, taking DGL is different and safer than taking regular licorice. As always, be sure to discuss this with your doctor and make sure there are no interactions with other things you could be taking.
  2. Ginger. This is another favorite. Ginger has many health benefits. It can help reduce inflammation, improve arthritis symptoms, and fight certain infections. I love it as a natural treatment for nausea. It also works as a prokinetic which means it helps move things forward. It can help with stomach emptying, bloating, and constipation. So, it is a great adjunctive therapy for acid reflux.
  3. Slippery elm. This is another natural therapy that I use as an adjunct to the other therapies. It is particularly good for those that have upper throat and esophageal symptoms. It acts as a natural cooling blanket and helps coat the esophagus. I tend to prefer the lozenge form for minor esophageal symptoms.

While there may be a lack of definitive evidence correlating acid reflux medications with chronic health problems and diseases, there is definitely an ever-growing body of evidence hinting that there could be an association with PPIs and these conditions. My take on all this is that if there is no underlying major problem that could justify use of PPIs (most of the time there is not), we should do everything we can to minimize and eliminate their use and replace them with more natural therapies and lifestyle changes. This is what is best for us in the short term and in the long term!



The information contained in this article and on is informational and not meant to be medical advice or replace the advice of a physician. Please consult your doctor with regards to your medical conditions and management.





By Dr. Marvin Singh MD
August 27, 2018
Category: Microbiome
Tags: @thehealthygutmd  

My 5-minute gut healing meditation

Wait….what??!! How can a meditation be gut healing? Am I serious? The answer is a resounding YES!

Stress reduction is a cornerstone to obtaining gut healing, for people of all ages. Stress, even at an early age, can change the composition of the trillions of bacteria and microorganisms in our digestive tracts referred to as the gut microbiome. Infant monkeys (monkeys are quite similar to humans) who were separated from their mothers were shown to have reduced amounts of the key helpful bacteria such as Lactobacilli and Bifidobacteria. Instead, they had increased amounts of the Prevotella species; this is the species of bacteria that has been well established to be linked to imbalance in the gut microbiome and psychiatric disorders ( There is evidence in the scientific literature that different kinds of psychological stress can affect the composition of the gut microbiome and these organisms are pertinent to controlling overall stress, anxiety, and cognitive function (

Meditation is one of the most powerful medicines that I prescribe in my office. I consider meditation to be the forgotten magic potion to gut healing. There is an ever growing body of literature to support the health benefits of meditation. For example, meditation has been shown to improve cellular health, regulate stress response, improve immune function, reduce levels of cortisol (the stress hormone), reduce CRP (a marker of inflammation in the body), reduce blood pressure and heart rate, and reduce tumor necrosis factor alpha (another inflammatory marker that can play a role in a variety of diseases, including inflammatory bowel disease), among many others (

In my medical practice, I often see patients with chronic unaddressed stress who have abdominal pain, heartburn (acid reflux), bloating, constipation, diarrhea, and a number of other symptoms. They keep getting passed around from doctor to doctor and have normal work ups. Yet, the problems remain. Much of the time I find that stress plays a big role in how refractory these symptoms can be. The brain and the gut are connected to each other. Chronic stress can change pain circuits and alter motility in the gastrointestinal tract in addition to causing intestinal permeability (leaky gut) (

One of the main obstacles to meditating is time. People often say that they don’t have the time. Largely this is not true because there is always time. We often spend countless minutes flipping away on social media and other activities during our days and we don’t think twice about it. While there are tons of different meditative practices that you can use, I’ve created a quick 5-minute gut healing meditation for you to get you started and hopefully this will tune body in to the health benefits of meditation. I must say that it is most ideal to meditate for 20 minutes or more at a time. However, I always tell people that we have to get you there before we can keep you there; this means that we have to get you started before we can focus on the long term practice. Also, this is not a religious practice; it can be if you would like it to be but it absolutely does not have to be. This is often another misconception that I hear about. Meditation is a great way to give yourself a little break, focus your attention, and ground yourself.

If you are not meditating at this time, just the mere fact that you are reading this article and thinking about it is progress! Congratulations! Now, try this 5-minute meditation practice and start healing your gut!   

Dr. Marv’s 5-minute gut healing meditation:

  1. First, find a nice quite place. Sit however you like (on the floor, on a chair, on a bed, it doesn’t matter although the bed is probably not the most ideal place since you may be more likely to fall asleep).
  2. Close your eyes. Rest your hands on your lap.
  3. I like to start my meditative practice by saying a positive affirmation in my head such as “May this be of benefit.”
  4. Start by taking a few deep breaths and just observe yourself breathing. Breath in through your nose and breath out through your mouth. If you notice your mind already wandering, it’s ok; just gently redirect your mind to the breath without any judgement.
  5. Once you have gotten into a rhythm, do 4 cycles of the 4-7-8 breath. Dr. Andrew Weil taught me this breathing exercise ( and it has changed my life personally! Make sure you are inflating your belly when you take these deep breaths. Take a breath in through your nose to a count of 4. Hold it in your belly to a count of 7. Breath it out through your mouth to a count of 8. Do this at least 4 times and no more than 8 times.
  6. After you have done the 4-7-8 breaths, then go back to taking nice gentle breaths in through your nose and out through your mouth at a comfortable pace.
  7. Next, imagine yourself inhaling the positive energy from the earth and your environment. On the inhalation, you are taking in all that positive energy and strength. On the exhalation, you are blowing out all of that positive energy and strength to everyone and everything in your immediate surroundings.
  8. After one minute of doing this, your inhalations will be for the same purpose (taking in all the positive energy). However, on the exhalation you will be blowing out all of that positive energy to the entire planet. Really truly imagine with every inhalation and exhalation that you are using yourself as a beacon of energy and that you are delivering that positive energy to the rest of the planet. Remember, that we are all human beings at the end of the day. We all want to be happy and healthy. Everybody needs kindness and compassion. That’s how we are built.
  9. Once you have reached the approximate 5-minute mark you can stop or feel free to continue as long as you want. When you are ready to finish, take a nice deep breath in and raise your arms over your head in the shape of a circle. Then slowly lower your hands as you slowly open your eyes. Sit there for a moment and note how you feel. When you are ready, you can quietly and slowly get up and enjoy the rest of your day!

I find that this is a nice way to start your day and a nice way to end your day. It will be guaranteed to be awkward and difficult when you first start. Some of you may even fall asleep. That’s no big deal! Don’t criticize yourself over it. Enjoy the rest and keep doing it! Keep trying. Once you get into a good rhythm with this, you can graduate to trying some of the other meditative practices. You can even make up your own meditations! If you find that you cannot remember the steps in this guided meditation, then read the steps out loud into a recording device (you can use your smartphone or tablet, for example) in a quiet gentle voice and play it when you are ready to sit down and do it.

There is a wealth of healing in mindfulness, meditation, kindness and compassion. Definitely do not forget this important medicine when putting together your gut healing protocol!

By Dr. Marvin Singh MD
August 05, 2018
Category: Microbiome
Tags: @healthygutmd  

Five probiotic foods your kids will love (and thank you for later)

Everywhere you look these days it seems like there is some advertisement for probiotics or probiotic foods. A probiotic is a live microorganism that can have health benefits. The marketplace can make things challenging to figure out what is best with all the choices we have out there these days. We know that our adult gut microbiomes (the ecosystem of trillions of bacteria that live within our digestive tracts) are fully developed somewhere between 2 and 3 years of age and that there are a number of different things that can influence the gut microbiome of a child. These things can include the mode of delivery (c-section versus vaginal delivery), duration of pregnancy (term vs. pre-term), antibiotics, environmental exposures, among many others ( Don’t fret! There is definitely hope! I’ve put together a list of my top 5 probiotic foods that you and your kids can enjoy regularly. This way your whole family can heal their gut together!

  1. Kefir. Kefir is basically a cultured dairy product. Although, there are numerous amounts of non-dairy kefir products available these days (like water kefir or coconut kefir). Just be wary of the sugar content in some of these products because it may not be worth the extra probiotics if it means you are going to get 25 grams of sugar with it! Kefir has a whole host of health benefits. Some of them include improved cholesterol metabolism, antimicrobial activity, tumor suppression, help with speed of wound healing, and improvements in asthma and allergy ( I can’t think of very many medicines that can do all of those things, can you? Kefir makes a good snack especially when you are on the go and if you want to go to the next level, you can make your kids a smoothie with kefir as the base and pump them full of other great antioxidants and phytonutrients at the same time! Their brains and microbiomes will definitely thank you!
  2. Fermented Pickles. My kids love pickles. The fermented ones may take some getting used to but they do make a delicious side note to a healthy meal. Make sure you get truly fermented pickles. If it isn’t refrigerated, that’s one clue that you are about to pick up junk food, not a fermented pickle. A recent study showed that three unique strains of a bacteria called Bacillus from a fermented pickle showed good potential as a probiotic. These probiotics showed protective effects against bad bacteria (pathogens) and also had anti-oxidant activity ( I bet you never thought you could boost your kids’ immune system with a pickle, did you?
  3. Cultured ghee. Everything is better with butter isn’t it? Seriously, ghee is a form of butter that has great health benefits. When it is grass fed and organic, it is packed with even more nutrients. When you get a cultured product, you have the added bonus of a probiotic food that your gut will welcome! We know that grass fed butter has a higher Omega 3 content and it is higher in vitamin K2 which is great for the bone health of your growing children. Additionally, there is a beneficial fat called CLA or conjugated linoleic acid in grass fed butter; this healthy fat can help boost immunity and may have anti-inflammatory effects. In fact, some types of CLA have been suggested to show anticarcinogenic (or anti-cancer), antiobese, and antidiabetic properties ( Mix that with some good bacteria and have a recipe for wellness! For those who may be concerned about dairy sensitivity or allergy, you may want to consider if this food is really for you, but keep in mind that ghee is a casein and whey free product and you may tolerate it unless you are extremely sensitive since very pure ghee is around 99% pure butter oil.
  4. Sauerkraut. This is another great one. It is pretty easy to make at home too. My kids love it. Since the name sauerkraut may not be the most appealing to a kid, we usually call it “shredded pickles” and since they love pickles, it’s almost a no brainer that they would like this one too! One of the main bacteria that is present in functional foods such as sauerkraut includes Lactobacillus. There is some data to show that these bacteria can degrade certain pesticides and can also provide antioxidant power, make the gut barrier stronger, and reduce inflammation ( Even if you are already eating organic and non-GMO foods, pesticides are in our environment, parks, and other places. I’ll take an extra dose of detox anytime!
  5. Fermented carrots. This is another personal favorite. Fermenting your own carrots at home is super fun for the kids and the whole family. It is also incredibly healthy and pretty easy to do. All you do is dissolve salt in water and put carrot sticks in the jar and pour the liquid over the carrots. Then cover the jar with an airtight lid until they are ready to be eaten. Just make sure to release any excess pressure in the jar on a daily basis. We all know that carrots are full of Vitamin A, antioxidants, fiber, minerals, and other key nutrients. We can take this awesome food and turn it into a superfood with fermentation! Oh, and remember that it can be fun to mix it up with colorful carrots. It will make eating the carrots more fun for the kids and also give them a variety of other health benefits. For example, purple carrots have more anthocyanin and extra Vitamin A. And don’t leave out the white carrots just because they aren’t colorful; their health benefits come from their fiber content. As always, it’s good to eat the rainbow!

Side dishes and snacks can definitely be healthy and full of nutrients and vitamins. Helping your children (and whole family) build a diverse ecosystem of bacteria within their intestinal tracts can have long-lasting health benefits. Your kids will definitely thank you for this when they get older!

By Dr. Marvin Singh MD
July 29, 2018
Category: Microbiome
Tags: @healthygutmd  

What is gut health anyway?

So, what is gut health? Is this just another fad? It seems like everywhere you turn there is some advertisement, article, or post about gut health (this one included!). Many of you may be wondering what the big deal is. Should you even be interested? The answer is an “absolutely, yes!”

Let’s first start off by talking about the gut. What is the gut? Well, the gut refers to our digestive tract. The second you put something in your mouth the process of digestion starts from the enzymes in your mouth to the chewing with your teeth. Digestion progresses as the food is transferred into your food pipe (aka, the esophagus) and then down into your stomach. From there, it will travel through the small intestines (or small bowel) and finally end up in the colon (or large bowel). The final product that is expelled from our rectum is what we fondly refer to as poop. This is an oversimplified explanation of how things travel down; there are a lot of things that happen in between. However, I wanted to at least give everyone an idea of what the different parts of the gut actually are. Did you know that if you were to remove your digestive tract from your body and lay it down on the ground it would be about as long as a doubles tennis court? That’s a lot of ground to cover!

One of the reasons why it is important to be concerned about our gut health (or the health of our digestive tract) is because it is home to one of the most powerful entities in our bodies—the gut microbiome. The microbiome refers to the approximately 100 trillion bacteria, viruses, and fungi that exist together in our digestive tracts. These little bugs are important because they do a whole host of things for us. They can also make us sick if things get out of balance. Protecting the gut microbiome and helping to grow a resilient ecosystem can go a long way in the management of chronic disease.

In those with obesity and fatty liver, we know that there are changes in the inflammation levels in our intestines and changes in gut permeability (or leaky gut). Along with these changes come alterations in the gut microbiome ( There is also a suggestion that the gut microbiome can affect kidney function and play a role in acute kidney injury ( Not only does the gut microbiome play a role in metabolism and immunity, it also can influence your risk for heart disease ( The body of knowledge that we are accumulating regarding the gut microbiome is growing at a rapid pace and we are learning about associations with almost every medical condition, including diabetes, Parkinson’s Disease, Alzheimer’s disease, autism, ADHD, stress, depression, among many others. Just doing a PubMed (medical literature) search for the “gut microbiome” brings almost 11,000 articles.

We are still trying to figure out how it all works and which microorganisms do what but one of the clear messages is that a diverse and rich microbiome are key. It’s kind of like this….if you are the CEO of a major company, what kind of work force would you want? Would you want a bunch of people who have the same skill set, same educational background, identical cultural backgrounds, and same ideas? Or would you want a bunch of highly talented people that come from a variety of backgrounds, from different schools, different countries, and have their own unique personalities and ideas? I think the answer is obvious, right? So, as the CEO of your body (and your gut microbiome), it is our jobs to make sure that we have a diverse microbiome. This is another way of looking at the term “gut health.”

Here are a few basic tips on building a diverse, resilient gut microbiome:

  1. Eat a variety of (preferably organic, non-GMO) colorful vegetables and fruits, while avoiding processed foods, unhealthy trans-fats, fast foods, and excess sugar.
  2. Avoid toxins. This includes food toxins, environmental toxins (as best as possible), certain medications (if possible), tobacco, and excessive alcohol.
  3. Exercise. Movement on a regular daily basis is good for your gut too!
  4. Sleep. Shoot for 7 hours of sleep per night.
  5. Reduce stress. This is a big one. There is a direct mind-gut connection and stress can definitely weigh heavy on the gut and the gut microbiome.
  6. Social interconnections. Yes, this is definitely part of the program too. Our social connections, friendships, and relationships play a large role in our overall health and how we do, especially when we are sick. This is one of the keys to living a long healthy life. Our gut bugs can definitely feel the love!

I hope this helps clear up some of the confusion about gut health and what it is. At the end of the day, we should remember that gut health is important. It may actually be one of the most important parts of our bodies. We should be responsible CEOs to our gut microbiomes. In turn, they will help us be strong, healthy, and successful in many different ways!



By Dr. Marvin Singh MD
July 08, 2018
Category: Microbiome
Tags: @healthygutmd  

How many times have you heard people talk about good genes and bad genes? Even as a physician, I have had my own physicians tell me that I probably have a higher risk of heart disease because of my family history and genetics. Is this entirely true? Well, yes and no.

We do carry added risk for certain conditions that are inherited in our genes. However, we have the option to exercise control over those genes. Really? We can control our genes? Yes!

Our genes and our DNA are definitely an important part of our health. However, this is not the only factor that we need to consider. Our gastrointestinal tract or digestive tract starts from our mouth and goes all the way to rectum. Within these pipes lies a vast amount of power. There are approximately 100 trillion microorganisms that live inside of our inner pipes (Singh M, Mullin G. Diet and Environmental Chemicals and the Gut Microbiome. In: Vom Saal F, Cohen A, editors. Integrative Environmental Medicine. Oxford University Press. 2017). These can include bacteria, fungi, yeast, and viruses. We affectionately call these guys our gut microbiome. This basically refers to the ecosystem that lives within our gut. Not only are these little bugs responsible for making vitamins for us and helping us digest our food, they help control the immune system since 70% of our immune systems lies within the gut! Even more fascinating is that at least 90% of the serotonin in our bodies is stored in the gut as well. When we think of antidepressants we often think of increasing the amount of serotonin in our brains but this is only partially true. We have a whole pharmacy of antidepressants sitting in our gut. We just have to know how to open the door to get access to all this free medicine!

Our DNA and our gut microbiome work together and are influenced by our environment, exposures, stress levels, and hormones. One of these elements alone is not enough to control or manipulate our health. It is my belief that the human body was designed this way on purpose. Almost like checks and balances within the government. When everything works together nicely, our everyday challenges are dealt with effectively and problems are solved. When a few things start to get out of balance, the entire system can get out of balance. And if we have some underlying risk for a particular condition that is hidden within our DNA blueprint, our body may push the button to activate that condition when we don’t want it to.

Don’t get too worried, just yet! Our health is not that scary. The beauty of the whole system is that even if we have already started to walk down the path of sickness, we can do our best to get off that path. More importantly, we can do things to keep on a path of wellness!

Dr. Elizabeth Blackburn was awarded the Nobel Prize for her groundbreaking work on telomeres, which are the caps at the end of our DNA that help keep the DNA intact (almost like the plastic tips of your shoelaces that help keep the shoelaces from fraying). It turns out that we have an enzyme called telomerase that helps keep these caps intact and can even make them longer. This is important because once the caps get too short and the DNA starts to “fall apart” so to speak, the cell that contains that DNA starts to become senescent or senile and does things that you don’t want it to do such as send false signals that can be confusing to the other cells in your body. When I heard that The Telomere Effect by Dr. Elizabeth Blackburn and Dr. Elissa Epel was coming out I made sure I got a copy because I was very interested to learn about what their research showed regarding how we can live longer and be healthier. Guess what? The very same things I have been educating patients about in my practice about gut health are also important for telomere and DNA health! These include eating a balanced diet full of antioxidants, phytonutrients, colorful vegetables and fruits; exercising; avoiding toxins; reducing stress; sleeping the right amount; and having fun building friendships and relationships with people and the environment. Personalized lifestyle interventions are the cornerstone of optimizing our health (, not only because they are good for our DNA but because they are good for our gene expression, our gut microbiome, hormone balance, and our environment.

So next time someone tells you that your chronic illness is “all in your genes,” tell them and prove to them that they are not entirely correct. Your genes are not your destiny. We can change our environment (inside of our bodies and outside of our bodies) and harness the power of our beautifully intricate bodies to create positive changes in our health!

By Healthy Gut MD
May 29, 2017
Category: Microbiome
Tags: Untagged

There is a lot of press and chatter in the medical community about stool these days. Some of you may be wondering why and what the big deal is? 

Well, this is actually a very important topic. There are over 100 trillion microorganisms that live inside of our intestinal tract. They make up 10 times the amount of human cells on our bodies and have 100 times the amount of DNA compared to human DNA. It's no understatement that these tiny bugs that live inside of our gastrointestinal tracts are important. We are learning more and more about this ecosystem of microorganisms in our guts (referred to as the gut microbiome) and discovering new things on a daily basis it seems. We have found associations in gut imbalance with diseases such as Alzheimer's and Parkinsons to diabetes, heart disease, mental illness, and various cancers. We are seeing literature surface on stool transplants to help those with inflammatory bowel disease (Crohn's disease and Ulcerative colitis) and we have known for a while now that stool transplants for the severe bacterial infection in the colon called C.diff (Clostridium difficile) can be extremely helpful. What these stool transplants do is rapidly change the environment inside the colon to help reset balance very quickly so that you can regain health. This supports the notion that the composition of the gut microbiome is central to health. Just recently there was a study suggesting that infection with a particular virus (reovirus) could be contributory to an immune response whereby people can develop celiac disease and be symptomatic when eating gluten. 

These little bugs may be invisible to the naked eye but understanding their importance is paramount to preventing and managing various conditions and diseases. Manipulating the microbiome and shifting its abilities to produce various different substances is going to become a focus of medical care for patients in the coming times (in fact, it already is).  

So, in a nutshell....yes, your stool is important. It is very important. It is a reflection of your health. It is a reflection of your microbiome. It is a reflection of the inner you!

Cheers to your (gut) health!

--Dr. Marv

By Marvin Singh, MD
February 14, 2016
Category: Microbiome
Tags: Untagged

Many people have seasonal allergies and/or allergies to various types of foods (namely nuts). Most probably wouldn't flinch before taking an antihistamine to help reduce the nuisance of the watery eyes, runny nose, or sneezing that one might experience when it's that time of the year for allergies. What really causes allergies? Well, recent research suggests that the answer may be uncovered in your poo...yes, you got it...your poo!


Within our intestinal tract lives over 100 trillion microorganisms. This is refered to as the gut microbiome. It is essentially a powerful "organ system" that is being researched by many across the globe; we are uncovering many of the secrets to human life that were not really clear before. Now, there is still a lot of work to be done and a lot of things are not entirely clear but there is some exciting research coming down the pipelines.


I recently reviewed one study by scientists at the National Cancer Institute. They reviewed data from the American Gut Project ( What they discovered was that in those with allergies, especially seasonal allergies and nut allergies, there was "lower richness and altered composition of their gut microbiota." We know that one of the keys to gut health is having a microbiome that is diverse, which means a nice wide spread of different kinds of bugs. What this statement means is that they found that in those with allergies, there was less diversity in the bugs found in the participants' stool samples. This concept is called dysbiosis, which basically refers to an imbalance in the bugs in your gut. People with seasonal and nut allergies were also found to have higher amounts of Bacteroidales and less Clostridialis


So, what does all this mean? Well, it means that if you have allergies you may have an imbalance in your gut microbiome. It could mean that when you pop that allergy pill all you are doing is just covering up the problem instead of addressing the root cause of the issue, which is that your poo may not be well balanced. Certainly we need more research and studies into this particular issue. This was not a clinical trial and we need to investigate this concept further. We also need to understand how this dysbiosis is established? Does it have to do with being born vaginally or by cesearan section? Does it have to do with being breast fed or bottle fed? Does it have to do with what environmental exposures you may have had? An even more interesting question is, can allergies be prevented or symptoms reduced/eradicated with specific targeted treatment for this dysbiosis? We don't have all these answers yet. But this is definitely exciting new research. 


My take on it is that we are discovering more and more that there are a lot of conditions associated with alterations in the microbiome. What we can do to help ourselves is eat a healthy, diverse diet rich in colorful fruits and vegetables while including probiotic and prebiotic foods (See The Microbiome), avoiding chemicals and products that can have harmful effects on our gut bugs, and living a healthy balanced and centered life. The gut bugs are the keepers of our immune system. We need them to be happy!


Cheers to your health!


--Dr. Marv 



Shi J, et al. Allergy associations with the adult fecal microbiota: Analysis of the American Gut Project. EBioMedicine 3 (2016): 172-179.