Welcome to the MICROBIOME 
Written by Fritz Nugent

Take a look at the picture at the top of this post. It’s not only beautiful – it’s educational. This is a real image of the microbiota interacting with us and comes from The Center for Human Microbiome Studies at Stanford. This gut bacteria lab is run by husband and wife scientific duo Erica and Justin Sonnenburg. They are just one lab which drives the cutting edge of gut bacteria research. We are on our way to learning more about our “gut buddies” that we literally could not live without.

In the image, the pink and yellow-colored blips are gut bacteria in our colon feeding on mucus. The vibrant green barrier is where we begin and they end, the one-cell-thick layer which allows the transportation of nutrients across and restricts bacteria. Within the blue area, we can see human cells. Inside and outside our body – there’s the fine green line between us and them. And also notice how much larger our human cells (light blue orbs in the lower right corner) are compared to the  tiny yellow and red bacteria.

What are humans made of?

You think that you are human? How much of you is human, and how much is not human? Scientists estimate that we contain more bacteria cells than human cells. So we’re outnumbered there. Outside of our bodies on our skin, bacteria reside. They also live in massive colonies inside our gut, mostly within our colon. 

Now let’s talk genetic material. Humans have 20,000 to 25,000 genes. Those genes control all of our physical structure and much of our function. The bacteria that live within us contain almost 50 million genes. So if you crunch those stats, we are less than 1% human. Crazy, right? 

We literally could not exist without our “gut buddies”. There’s the fine green line between us and them. And also notice how much larger our human cells (light blue orbs in the lower right corner) are compared to the  tiny yellow and red bacteria. Treat them well and they will treat you well. We will get into more details about our microbiome (gut bacteria), how to eat to ensure both their success and ours, pre- and probiotic talk, and where the research is headed. 

What is the Microbiome?

The microbiome is a collection of trillions of microorganisms that live on and within us. They have been a part of us for so long, that many of these bacteria specialize in humans, meaning that they are found nowhere else on earth. And they are passed from mother to child at birth, arguably having lived as passengers on and within us for millions of years, evolving as we evolve, changing with the conditions of our environments, and supporting our endeavors so they may exist within us. Some scientists go so far as saying that humans are simply intelligent tubes which house bacteria.

What do our microbiome bacteria eat?

When we eat food, the particles that we (humans) cannot digest, namely fiber, which has recently been termed MACs (Microbiota Accessible Carbohydrates) are fermented by bacteria in our colon. That’s what the microbiota consume – our undigested scraps. In return, they provide the cells of our intestines with short chain fatty acids (SCFA’s) to use as fuel. That is just one of many thousands of interactions that our gut buddies have with our cells.

A Happy Microbiome – Your Mom Was Right

“Go outside and play!”

“Eat your vegetables!”

“Go to bed!” and “Wake up!” 

These are the big three for improving physical wellness. When we were kids, my mom would make us go outside and play. We had to eat our vegetables and fruits. We had to get to bed at a decent hour, and we had to wake up on-time. These demands are simple and they contain nearly everything we need to stay physically healthy and live well. There are also psychological benefits here.

  • When we go outside, we recharge vitamin D and physical activity.
  • When we eat fruits and vegetables, we obtain nutrients and energy.
  • When our sleep schedule is sound, our recovery is bolstered and our body systems are optimized.

This ALL has a direct relationship with the function of our microbiome, our “gut buddies”.

  • Exercise seems to increase the diversity of helpful microbes within us while also improving their function
  • Eating a broad range of fruits and vegetables provides many different food sources for our microbes, allowing our body’s ecosystems to flourish
  • Like us, our gut buddies also perform better on a regular sleep schedule

The Rain Forest Analogy

In the book, The Human Superorganism“, by Rodney Dietert, he compares microbiome function to a rainforest. Every species matters and all are connected. As diversity decreases, the ecosystem collapses. Even creatures that comprise a small percentage of the ecosystem play important roles which affect the whole system. Similarly, our microbiota function well in large quantities and high diversity, providing a robust immune system to us, their host

How do we keep our microbiome healthy?

Within each of us, there are hundreds of different bacterial species. As researchers dig deeper here, they uncover increasingly intricate interactions. The particles produced by our gut buddies resemble pharmaceutical drugs and each have specific functions within our bodies.

Here are some ways to keep your gut buddies (and you) functioning well:

  • Eat lots of fruits and vegetables
  • Get regular sunlight
  • Sleep on a regular schedule
  • Do not take antibiotics unless you ABSOLUTELY HAVE TO
  • Minimize the use of *antibacterial cleansers

* Minimizing the use of antibacterial cleansers – THIS ONE is probably ill-timed with today’s COVID-19 situation. Outside of a pandemic, reducing our personal and familial use of these bacterial-killing chemicals will allow the bacteria on our skin and inside our bodies to thrive.

Are cooked or raw vegetables better for gut bacteria?

Some people have a microbiome which does very well fermenting raw vegetables, and some people do not. For most people, starting with cooked vegetables and adding in small amounts of raw veggies can help acclimate the gut to digesting raw vegetables. 

Both cooked and raw are valuable, so once again, make it a semi-controlled scientific study of one: you. Test a food out, cooked or uncooked, and see how it goes for you. Retest. Take notes or commit to memory, then move on to others. If you haven’t eaten a lot of fiber, which is food for bacteria, and then one day you eat A LOT of fiber, your digestion speed, which is largely controlled BY YOUR BACTERIA will slow down. You don’t think that they would let you poop out a huge amount of undigested fiber which they could continue to feast on, do ya? Moderation is key. Gradually increase your fiber intake. This process could take years. Patience here is useful, similar to almost every other area of your life.

What’s the best way to cook vegetables for gut health?

There is no “best” way to cook vegetables. There are benefits and drawbacks to each cooking method. Cooking can reduce the available fiber and nutrients in some foods while increasing the fiber and nutrient availability in other foods. So a good rule of thumb here is to eat a wide variety of fruits and vegetables, cooked and raw, in a wide variety of combinations. Like your training, keep it intelligently varied for great results.

Should you eat fermented foods to boost gut health?

Start slowly. If your goal is to improve your gut health, start slowly with fermented foods. Try ONE at a time and see what happens to your motility (bowel movements). Possible responses:

  • bloating OR reduced bloating
  • distension OR reduced distension
  • diarrhea OR constipation OR brown S-shaped poops
  • nausea OR feeling fine

The real answer here is that we don’t know how YOU will feel with a particular food until you try it without mixing a bunch of new stuff together. Doing so will increase the difficulty in narrowing down which exact food works well/not so well for you. 


Marketers have literally been ramming probiotics down our throats for a while now, but are they even beneficial? Let’s first take a look at the definition of a probiotic. This is important.

Probiotics are “live microorganisms which, when administered in adequate amounts, confer a health benefit on the host”. (Food and Ag.)

So is your yogurt really a probiotic? How about that kombucha, or your sauerkraut? No, they are not. Are they beneficial to you? Perhaps. But they are not probiotics because they may or may not contain live microorganisms, and they most certainly have NOT been studied and proven to confer a health benefit to the host (you). This definition was created in 2001, but the supplement industry in the United States is widely unregulated and frequently touts supplements as probiotic when they clearly are not.

So be careful what you put in your body. Like everything else in this world, the benefits exist along the journey for those who are patient and consistent. There are no “quick fixes”. Go outside, move, eat things that grow in the ground, and sleep well. Hopefully that’s all you need. But if it’s not, we Seed is the only brand we recommend.

Is bone broth good for the microbiome?

After a quick review, no hard science could be found to support the idea that bone broth is good for the microbiome. There are homeopathic websites pushing this idea, however it is not backed by science, yet. There was one study which involved bone broth as one small nutritional option for participants, but the study was later retracted, meaning that the data and conclusions are not scientifically viable. If you want to try to make your own bone broth for it’s other benefits or because you love sipping on some soup, here’s a recipe for you.

What are signs of an unhealthy microbiome?

There are many symptoms. The main issues that people experience:

  • Digestive issues – ranging from lack of bowel movement regularity to bloating, distension, constipation, and diarrhea.
  • Food cravings – namely sugar
  • Psychological concerns – Mood problems, Anxiety, and Depression
  • Autoimmune conditions – skin, thyroid, hormonal, arthritic, and digestive issues

Microbiome & Digestive Issues

When you eat, you should not eat to fullness or feel bloated or distended after eating. If you do, this suggests you are eating too much OR eating the wrong foods for you. You should be pooping. Some people poop three times a day. Others, three times a week. Anywhere around or between these extremes seems to be ok. Check the Bristol Stool Chart:

As you can see, the chart flows from hardest to softest poops. Hard and dark-colored poops (types 1-2) are associated with constipation and caused by too much fiber for your body to utilize in a healthy manner, and dehydration. You should shoot for types 3-4. Brown and soft. Types 5-7 progress from too soft to diarrhea. These end types suggest a lack of fiber and a very unhappy gut. If you experience types 1-2, your gut is unhappy and probably needs a larger variety of fiber from many different colorful vegetables, but COOKED. Give your gut time to acclimate to the new changes. If you are experiencing types 5-7, you may need more fiber and can try both cooked and uncooked vegetables. For more reading on poop, check out this article. 

What are fecal transplants?

There have been studies performed where scientists perform a fecal microbiota transplant (called FMT), switching the gut bacteria from obese mice to healthy mice and vice versa. The healthy mouse becomes obese and the obese mouse loses body fat. This illustrates the power of our microbiome! Now, FMT is performed in humans with success. However, we are not suggesting you go get a FMT. We do suggest eating well, sleeping enough, moving a bit, and managing your personal stressors.

Food Cravings & Microbiome

Food cravings (we’ll focus on sugar here) can occur when specific types of bacteria in your gut become accustomed to sugar. If you don’t feed them, you may feel moody and tired. All it takes is 3-5 days of staying strong and NOT giving into your cravings, and they will subside for as long as you stay away from the sweets.

Psychological Concerns & Microbiome 

Psychological concerns can be microbiome-related, ranging from mood swings to anxiety and depression. This is a tricky subject because the science here is not yet clear. However, we touched on how gut bacteria can affect mood via food cravings, and sugar is the main culprit. Anxiety and depression are immensely more complex than moodiness. The short answer here is to work towards getting more vegetables and fruits into your diet. Increasing variety and amount of fruit and vegetable intake will support a robust microbiome and will give you the best chance at living a life unhindered by psychological issues.

How does our microbiome influence our psychology?

Our microbiome acts as an agent of our nervous system and influences disorders such as anxiety and depression (Clapp et al., 2017). While scientists have trouble disentangling correlation and causation, they hypothesize that some microbiotal environments affect inflammation and the adrenal-cortisol axis (stress response), influencing meekness versus aggressiveness in mice, dogs, and hamsters, depression and anxiety in humans, and other psychological responses. A study on aggressive dogs revealed similarities in their microbiomes which are different when compared to less aggressive dogs (Kirchoff et al., 2019). 

Autoimmune Disorders & Microbiome

There are many purported mechanisms underlying autoimmune disorders. “Leaky gut” is the big one that everyone talks about. Even though it’s a common issue, we can address leaky gut ourselves with food, sleep, movement, and sunlight. Eat more diverse fruits and vegetables (seeing a theme here yet?), sleep a lot and stick to a sleep schedule, move with intention, and get out in the sun each day. It’s truly that simple. 

Can my microbiome affect my waistline?

The short answer is yes. Here’s an interesting tidbit. Did you know that during pregnancy, the mother’s microbiome changes composition to one which can extract more caloric energy out of the same amount of food? This facilitates necessary body fat accumulation to insulate their growing fetus while also providing nourishment from the extra calories. 

Do you know how amazing this is? It makes clear evolutionary sense. Let’s say 200,000 years ago, food was a bit scarce. Those mothers whose microbiomes were more efficient at extracting extra calories from their sparse intake delivered healthier babies. 

What about this is interesting? Did anything jump out at you? How about the part where two people can eat the SAME FOODS in the same quantities, and one person gets fat while the other, not fat. Same foods, same amounts. The gut microbiome significantly influences absorption. The main takeaway here is that ingestion does not equal absorption, meaning what you eat does not necessarily make it INTO your body. 

In Summary…

Specific microbes in your gut specialize in various foods. Feed them vegetables and fruits, and they will function well. Feed them large amounts of fat and sugar, and they can make you overweight/obese, depressed, and anxious. We really are just now scratching the surface of the microbiome’s effect on us. 

Go make your gut buddies happy! Get some sun and movement. Eat some new foods you haven’t had in awhile, or ever. Stick to your sleep schedule even though it’s the weekend! You may have more questions about the microbiome and I’d be happy to answer them! Send them my way in the comments! 


  • Clapp, M., Aurora, N., Herrera, L., Bhatia, M., Wilen, E., & Wakefield, S. (2017). Gut microbiota’s effect on mental health: The gut-brain axis. Clinics and Practice, 7(4). https://doi.org/10.4081/cp.2017.987
  • Kirchoff NS, Udell MAR, Sharpton TJ. 2019. The gut microbiome correlates with conspecific aggression in a small population of rescued dogs (Canis -familiaris) PeerJ 7:e6103
  • Food and Agriculture Organization and World Health Organization Expert Consultation. Evaluation of health and nutritional properties of powder milk and live lactic acid bacteria. Córdoba, Argentina: Food and Agriculture Organization of the United Nations and World Health Organization; 2001.


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Candy Olkey
Candy Olkey
May 14, 2020 2:44 am

Outstanding read Fritz!! I have had the worst trouble with bowel movements, gas, bloating, etc. in the past couple of years. I’ve talked with my doctor and she has run tests and comes up with nothing. I rarely feel like I have emptied out when I go, meaning, I always feel like I still need to go, but can’t. My movements on the most part are some were between 4-6 on your scale. I exercise 5-6 days a week (thank you Invictus!), I eat real home cooked food, lots of veggies (I’m not much into fruit). Don’t get me wrong… Read more »

May 14, 2020 6:28 pm
Reply to  Candy Olkey

Thanks for your comment, Candy! Definitely quit your job… just kidding. Your sleep schedule could be the culprit for increases in body fat, low energy, or increased moodiness. However, I wouldn’t be quick to jump on blaming sleep alone for the gas and bloating that you are experiencing. It sounds like you are eating a few foods that are disagreeing with you. When combining these foods with less-than-optimal sleep, together, they could create your symptoms. I have to preface this next statement with a disclaimer: I am not a doctor or nutritionist, but instead am a microbiome nerd. Ok, here… Read more »

Candy Olkey
Candy Olkey
May 15, 2020 2:35 am
Reply to  Fritz

Interesting enough….I have read a lot of Dr. Gundry’s articles and looks like I will be reading his book now too. It’s been a couple of years, but I explored the lectin-rich food issue and even took Dr. Gundry’s recommended Prebiothrive for about a month. I didn’t see a significant change and discontinued use and the lectin-free diet. But after reading your article I should have stuck with it because change won’t happen overnight. I am fairly certain you are leading me down the correct path, just thinking about a few things that should have just jumped out at me… Read more »

May 19, 2020 8:59 am
Reply to  Candy Olkey

Candy! I’m glad that you’re familiar with Gundry. Too bad about the peanut butter and eggplant. At least you know a few foods to avoid. I am not a supplement fan. If you have tried Gundry’s supplements and they have been helpful to you, then go for it. I am a big believer that the right foods in the right amounts at the right time is the most powerful approach we have, especially when all other factors are upheld (sleep, sun, movement, and stress). Do a nutritional audit and see which foods you are eating might be causing your gut… Read more »

May 13, 2020 8:41 am

This is so interesting! Question for you – if we are taking a probiotic should it be the refrigerated kind to support a living microorganism? Or is there one you’d personally recommend (or maybe not and just stick to a variety of vegetables and fruits)? Thanks!

May 13, 2020 9:15 am
Reply to  Nichole

Thanks for reading, Nicole! If your supplement is indeed a probiotic with live cultures, most likely it will require refrigeration. To reiterate the article though, the definition of a probiotic is not JUST a supplement which contains microorganisms. Those live cultures must be specific and present in a large enough quantity to confer a health benefit to the host, you. So when you take a supplement containing microorganisms, make sure it’s helping you! Let your mood, energy, and stool be your guide 🙂

May 13, 2020 9:43 am
Reply to  Fritz

I love letting my stool be my guide!! Wonderful lol!