How Gut Health Affects Your Health, Weight Loss, and Mood

You might not have a noticeable digestive issue, but focusing on your gut (AKA microbiome) might be the biggest change you can make to significantly improve your health. 

Everything we know about diet and weight loss is being challenged by bacteria. Not some foreign infection, but — rather — the little bugs that live within your body. And the most promising part of it all: understanding how foods impact your gut could be the best weight loss trick you’ve ever tried.

Take one small example: do you find that you’re constantly craving sweets or not satisfied after you eat? It could be the doing of your microbiome — the army of microorganisms living inside of your digestive tract. These microscopic bugs fight to control your thoughts from a “second brain” located in your gut. And we’re not talking about urges caused by feeling hangry.

Diving into the (still young) research and you start to see interesting patterns, such as:

How is all of this possible? There are 10 times more bacteria living in your digestive tract than there are cells in your entire body.

There are 10 times more bacteria living within your digestive tract than there are cells in your entire body.

As a result, your body makes alliances and enjoys a symbiotic (that’s science-talk for “win-win”) relationship with the majority of the organisms within your microbiome. Gut bacteria aid in digestion and even produce an important nutrient, Vitamin K2 (think cardiovascular and bone health).

But not all of those bugs are so eager to be friends. There is such a thing as “bad” gut bacteria too. Even the “good” ones can turn on you and become harmful when things like the use of antibiotics, illness, stress, bad dietary habits, or other lifestyle factors shake up your digestive ecosystem. (Yup, basically living life is all it takes.) That’s when things can get rough, and why one of the biggest areas of research is trying to understand the relationship between your microbiome and medical issues such as inflammatory bowel disease (IBD), obesity, and maybe even cancer.

So how do you make sense of all the microbiome buzz? We know it’s important, but there’s a lot of misinformation swirling around and far too many claims that we can’t yet support (time will tell because we need more research). While “solutions” like probiotics may be helpful for some — and are definitely good, in general — there are many other accessible (and less expensive) things you can do to keep your microbiome healthy.

Microbiome 101: Simplifying the Science

We’ll be honest, anything about gut health can become a little too confusing, so it’s best to think in big picture terms: what it is, why it matters, and what you can do about it.

Your microbiome is the collection of all the microbes and microorganisms that populate your body.

There are unique groups of microorganisms living in many different regions of your body—your skin, mouth and digestive system, to name a few. Your gut microbiome (the “microbiota”) is home to millions of unique bacteria. Experts believe that having a wide spectrum of different bacteria in your GI tract is beneficial to your health (researchers are now trying to understand exactly what role they play in everything from your immune function, to macronutrient metabolism and absorption, and even your mood).

Diversity is a good thing. And research suggests that having less diverse gut bacteria might be linked to health issues like irritable bowel disease, cancer and obesity. While many questions about how and why still exist, there’s enough of a relationship that scientists are trying to figure out how you can best take care of your gut bacteria.

A Healthier Microbiome: Probiotics and Prebiotics

Probiotics are helpful bacteria in your gut. Think of them as adding backup troops when your frontline is a little weak. Probiotics can be found in fermented foods like yogurt and sauerkraut, and in drinks like kefir and kombucha. The beneficial bacteria from probiotics provide numerous health benefits including enhanced immune function, better digestion, a barrier against microbial infections, and much more.

Prebioticsmeanwhile, are foods that feed the microbes that are already in your body. And there’s been a growing awareness that they are also important because they affect the bacteria in your digestive system in such a way that it might improve your well-being and health. Basically, you help the bugs (by feeding them), and the bugs help you (by protecting you from bad bugs, keeping inflammation down, and so on).

Exactly why this happens isn’t fully understood, but prebiotics are carbohydrates that resist digestion in your small intestine. They reach your colon intact, where they wind up getting fermented by the bacteria there. That can shift gut flora in a positive way.

Some common foods that have prebiotic effects include bananas, whole grain wheat, garlic, leeks, and onions.

How the Microbiome Affects You

Remember how we referred to a “second brain?” That’s where the microbiome becomes more and more interesting for your overall health goals. The gut-brain axis is a two-way line of communication within your body between your brain and gut (at least they made the name easy to remember).

Your brain affects your gut, and your gut health affects your brain.

Each one can affect the other — for better or for worse. When your gut bacteria is out of whack, the signals that get relayed back up to your brain might cause or worsen anxiety or mood disorders, including depression. And stress—you know, what you feel when you’ve got looming deadlines or worries about paying the bills—can impact your gut microbiota negatively, and shift it in a less-than-favorable direction

Gut Dysbiosis describes what happens when you have an imbalance of gut bacteria favoring the more pathogenic (potentially harmful) microorganisms. This sort of imbalance is associated with a number of different problems including digestive disorders such as inflammatory bowel diseases (IBD), ulcerative colitis and Crohn’s disease. Those can manifest in many different ways, from consistent abdominal pain or diarrhea, fatigue or weight loss. Some skin problems like rosacea can potentially be linked to gut health issues. These types of medical issues will be much easier to notice, so don’t freak out or believe people that want to sell you expensive supplements or cleanses. As always, if you are worried about a medical condition, see a doctor and have the problem diagnosed.

While current research is still developing and learning about the many roles that gut bacteria play in our body, here are some of the things that we do know — and what you can do about it.

How Your Body Processes Calories and Nutrients: There’s growing evidence that shows your gut bacteria impact what you’re able to extract from your food, both in terms of the total number of calories absorbed and the nutrients you take in—and even in determining how much food you want to eat.

There are a number of complex mechanisms that make this possible, so here’s one example of how your microbiome affects energy balance: Gut bacteria break down previously undigested carbohydrates called polysaccharides into smaller bits known as short-chain fatty acids (SCFAs). When your body’s fat cells sense an increase in SCFAs, they release a hormone called leptin, which essentially sends a signal to the brain that says “We’re full, thanks. You can lay off the nachos.” This is a good thing. But, if you’re not releasing enough SCFA because of a break in your microbiome, then the opposite can happen and you never feel full.

This is part of the reason why some researchers believe there’s a strong link between the condition of the gut and obesity. There’s even some research showing that obese and non-obese people have differing levels of bacteria. (It’s worth noting, however, that no one is suggesting that your microbiome is the only factor causing obesity. Diet and exercise matter, and, certainly, also impact that healthy — and unhealthy — bacteria in your body.)

What Foods You Want to Eat: While most people chalk up their cravings to willpower (this is something that’s repeatedly proven to be incorrect), many researchers now believe that your gut bacteria might be manipulating you “like microscopic puppetmasters” to get what they want.

There is an internal battle in your microbiome where different bacteria in your digestive system are constantly competing for resources (food). Here’s where it gets crazy: these bacteria can create food cravings or generate feelings of dissatisfaction (mood) that can be alleviated by consuming the foods that benefit them. And it can work for good or bad. Your body might be telling you to eat more protein (yay!) or it could be pushing you for endless amounts of sugar (aw shit!). There are four main mechanisms that play a role in this ongoing battle:

  1. Microbes (just a fancy name for the bacteria in your stomach) could alter your taste receptors, making certain foods taste better. (And no, they aren’t working to make you like broccoli. Bad-news bugs thrive on bad-news fuel sources like those high in sugar.)
  2. Microbes could release toxins that can affect mood negatively, which can make you want to eat.
  3. Microbes could influence whether or not you find certain foods rewarding. (That happens by influencing an important part of the endocrine system known as the hypothalamic-pituitary-adrenal axis.)
  4. Microbes could “hijack” the vagus nerve, which is a major signaling pathway within the body.

Your Immune System: Your gut bacteria can assist your immune system by preventing potentially harmful pathogens from entering into the digestive system. You can think of the good bacteria as bouncers setting up velvet ropes along the walls of your intestines. They won’t let bad bacteria ruin the party. This helps protect the intestines against inflammation and prevents pathogenic bacteria from forming colonies.

What’s “Good” or “Bad” for Your Gut Health?

The colonization and development of your gut bacteria began at your birth and continues to evolve throughout your life. Some of the things that can adversely affect the microbial diversity in your gut include:

Antibiotics. Let’s be clear: We are not advocating against antibiotics. They can be potentially lifesaving drugs that absolutely have a time and a place for use. Antibiotics, however, indiscriminately kill the microbes in your body, which can lead to a disturbance of gut flora that you will need to work to rebalance and improve. The takeaway: Save the antibiotics for when you’re really sick. (But when a doctor says take them, take ‘em.)

Stress. Stress comes in many shapes and forms, but, on a basic level, stress is anything that removes your body from homeostasis or equilibrium. That stress can be psychological (worry, anxiety), physical (sleep deprivation is a physiological stressor that can negatively impact your gut bacteria), to social (feeling like a “loser”). All of them can disrupt the composition, diversity, and number of microorganisms in your digestive tract.

(Too Many) Processed Foods. A high-fat, sugar-rich diet feeds the pathogenic bacteria in your gut. Note that eating some sugar, or processed food here or there, isn’t a problem (We’ve discussed the overblown fear of sugar). It becomes problematic when you eat too much of them, combined with too little fiber — and most Americans get far less than the recommended 25 grams of fiber per day.

Diets that are high in processed foods, and low in fiber, have been shown to wreak havoc on gut microbes in trials in mice. Obviously, mice aren’t human, but similar results have occurred regularly enough that Dr. Justin Sonnenburg, an associate professor of microbiology at Stanford University, says simply: “It’s now evident that everybody should be eating more dietary fiber.”

Can You Test Your Microbiome?

Where there is a health problem, you can usually find a business offering a solution. This is not necessarily a bad thing (we all need cures to problems), but sometimes business interests come before practical applications. In other words: people are happy to sell you something based on theory and not on proof.

There are many new tests that claim to give you insight into your microbiome (most involve you sending your poop to a lab, so don’t be surprised when that’s the request). The problem: you will provide science with more (much needed) data…but it won’t really help you get more answers.

As discussed in a recent New York Times article (that we highly recommend), here are a few important takeaways about the big limitations of personalized microbiome testing:

  • “It’s not ready for prime time.” (referring to personalized microbiome testing) -Dr. Rashmi Sinha, a senior investigator at the National Cancer Institute 
  • “You’ll get an enormous amount of data that is basically uninterpretable,” -Dr. Martin J. Blaser, director of the Human Microbiome Program at New York University, though he added, “there are people who will be very happy to take your money and tell you they can interpret it.”
  • “What you can do with the information at the moment is limited. It’s very much a science project, not a diagnostic test.” – Dr. Rob Knight, director of the Center for Microbiome Innovation at the University of California, San Diego

Translation: we know the microbiome is important, but interpreting your microbiome, knowing what will or won’t have and impact, and how those changes will help your health is all still being investigated.

While that doesn’t help you figure out if you have a healthy (or unhealthy microbiome), it’s good to know that if you spend your money on any “microbiome services” it’s not likely your best use of money. The value from these tests will come with time and more clarity and understanding. But that doesn’t mean you can’t improve your microbiome.

How You Can Improve Your Gut Health

Three cups of fermented foods: sauerkraut, pickles and yogurt.
Fermented foods are great, but don’t forget the fiber, fruits and veggies.

The good news is many basic practices that are good for your body are also good for your gut health. While you can’t assess those changes directly, there’s enough evidence to suggest that the recommendations below are good general practices for a healthy microbiome.

  • Eat more fiber. We’re not trying to beat a dead horse, but carbohydrates and fiber are the most important sources of energy for the beneficial bacteria living in your colon. The fermentation of carbs and fiber in your digestive system helps lower its pH and therefore helps limit the bad bacteria. So you’d do well to consume more fiber-rich foods like:
    • Fruits such as raspberries (8 grams of fiber per cup), apples (4.4 grams per medium-sized piece), bananas (3.1 grams), oranges (3.1 grams), and strawberries (3.0 grams per cup)
    • Vegetables such as peas (8.1 grams of fiber per cup), broccoli (5.1 grams). Brussels sprouts (4.4 grams), corn (3.6 grams), or a baked potato (2.9 grams)
    • Grains such as barley (6 grams per cup), oats (4 grams) or brown rice (3.5 grams). Whole-wheat spaghetti has 6.3 grams of fiber.
    • Beans, whether they’re black, kidney, pinto, or you-name-it, are glorious sources of fiber. A cup of any one of them will give you a double-digit dose of fiber.
    • Nuts, especially almonds (3.5 grams per ounce, or about 23 nuts), pistachios (2.9 grams) and pecans (2.7 grams).
  • Cook more at home. Research shows that food eaten away from home tends to have less fiber on a per-calorie basis. Pressed for time? This approach to meal prep may help you simplify things and get more done in less time.
  • Eat fermented foods that contain probiotic bacteria, such as yogurt, kefir, sauerkraut or kimchi.
  • Aim for 7-9 hours of sleep. Having trouble getting to sleep? Here are some non-obvious solutions you may want to try.
  • Try to keep your stress levels in check. (Obviously, easier said than done, but something like meditation or journaling might help.)


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  1. This is a great post. I had no idea gut health was related to so many other areas of your health. It’s impressive what we can do when we understand how our body works.

  2. Great article, very informative. Thank you. Quick question, been dealing with a sickness and was prescribed 10 days of antibiotics, would I continue taking probiotics during those 10 days or just wait till after and then up my initial doses of them? How about the fermented foods, change any of the ways I am consuming them while taking antibiotics?
    Just curious. Thank you.

  3. Speaking as someone with IBS – if you have gut issues, consuming more fiber can be literally crippling (esp. during a flare-up). Cooking my own foods and not eating out, avoiding onions and garlics and complex carbs that literally make me double over from the stomach cramps are all key for me though. Being aware of which foods are fodmaps-friendly has been helpful. I’d strongly recommend to anyone having chronic issues that they try an elimination diet.

    It is really easy to just consume easily digestible foods like simple carbs when you’re having issues but there are veggies and fruits out there that won’t cause pain. Great article, overall good advice. As far as the fiber goes… i’d only say proceed with caution. there’s a very thin line that easily turns into terrible, terrible cramps.

  4. Gut health is so connected to many areas of our bodies. I started working on my gut health and my skin changed forever. Before I suffered from acne, dull skin, and scars. Now, I won’t say it’s perfect again, it’s much better than before.

  5. Couldn’t agree more about eating more fiber! I still try to keep carb intake low but making sure i have enough fiber to compensate!

    thanks for the read!

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