Do You Have a Stinking Gut? (And Why You Should Want One)

Do you have a stinking gut?

Hippocrates was once quoted for saying “all disease begins in the gut.” Time is proving Hippocrates to be a pretty smart guy, and science is even now linking poor gut health with a myriad of health problems.

From eczema to poor immune health, it seems that our gut health influences much more than we previously realized. If all disease beings in the health, it is logical to realize that perhaps optimal health begins here as well.

Ever had a “gut” feeling? There may be more to it than your realize. It is now estimated that over 3/4 of our immune system resides in our intestinal track, with over 500 species of bacteria present.

Overall, there are ten times the number of bacteria in the body as actual human cells, and this colonization of bacteria (good or bad) can weigh up to three pounds. With such a large concentration of bacteria in our bodies, it is logical that we depend rather heavily on them for health.

Traditional diets around the world have typically included raw and fermented foods teeming with bacteria, including many beneficial strains. From yogurt, to kefir, to sauerkraut, to fermented fish, cultures around the world are not afraid of a little bacteria.

In our modern society, we’ve effectively managed to pasteurize, irradiate, and process out any naturally occurring beneficial bacteria while at the same time feeding harmful bacteria with a feast of processed starches and sugars.

On top of that, we sanitize our children from the moment they are born, afraid to ever let them encounter bacteria, good or bad, which are necessary for immune development. Besides the fact that research has found that antibacterial soap is no more beneficial than regular soap and water and might be harmful, raising our kids with Lysol in hand may not even let their digestive systems develop properly.

It has now been found that babies are born with a completely sterile digestive system, since in utero, they don’t need gut bacteria for the breakdown of food as all nourishment comes from mom. During the rather messy birth process, the baby’s digestive system begins to colonize bacteria based on the mother’s existing bacteria (good or bad!).

The baby’s bacteria further develops during breastfeeding thanks to certain strains of immune boosting beneficial bacteria found only in breastmilk. Since the baby depends on the birth process and on breastmilk for this balance of bacteria, it makes sense that babies born naturally and then breastfed have lower rates of eczema, allergies, and illness.

Babies born by cesarean or who are formula fed are not doomed from the start, but it is good for parents to be aware of this need for probiotic bacteria and consider supplementation and natural sources.

After the infant stage, toddlers naturally supplement probiotics by putting everything, dirt included, into their mouths. If given the proper resources, these beneficial bacteria grow and flourish, boosting immunity and allowing proper breakdown of food.

Unfortunately, this isn’t the norm anymore. More often, the balance of good bacteria is altered by an abundance of starches/sugars/vegetable oils in the diet, or destroyed completely by antibiotic use or other pharmaceuticals. Lack of exposure to bacteria in environment and food further aggravate this problem.

In fact, in our Clorox cleaned world of processed foods, many of us might benefit from a good dose of healthy bacteria. The digestive track as has almost as many nerve cells as the spinal cord, and research is increasingly linking digestive health to overall health.

Beneficial bacteria is necessary to properly digest food (especially starches) and to absorb nutrients. It plays a big role in overall immunity. With the rise of digestive problems like IBS, Crohn’s disease, Celiac Disease, colitis, allergies, etc., a good dose of beneficial bacteria certainly wouldn’t hurt.

The good news is that while outside sources are constantly working against our good bacteria these days, there are ways to boost good bacteria naturally, even for those of us not still nursing or fond of eating dirt.

An Ounce of Prevention…

Grandma said it and it still holds true. One of the best ways to keep beneficial bacteria from becoming depleted is to avoid the things that deplete it in the first place, including:

  • antibiotic use (especially if it can be avoided or natural alternatives can be used)
  • use of antibacterial soap
  • overuse of harsh cleaning chemicals to sanitize environment
  • consumption of processed and refined foods
  • consumption of sugars or excess of starches
  • any sources of stress on the body that can be avoided (lack of sleep, overexertion, etc.)

Building Up Good Bacteria in the Digestive System

Fortunately, even if you’ve depleted your beneficial bacteria by some of the methods above, there are ways to increase it and help balance the bacteria in your digestive system. Chances are, unless you already consume a lot of fermented foods, garden barefoot a lot and eat some dirt, your probiotic balance could use a boost.

Here are some tips for boosting your probiotic balance:

  • Don’t Eat Sugars/Grains/Excess Starches/Vegetable Oils– These foods deplete beneficial bacteria very quickly and can consequently suppress immunity and lead to a variety of health problems. There is no need to eat these foods, especially in processed form, so for the sake of your guts… avoid them!
  • Eat Lots of Real Foods- Eating foods like vegetables, proteins and fats will help support beneficial bacteria that feed on certain types of fiber in foods like veggies. They will also support the body in culturing additional good bacteria, as will…
  • Consume Fermented Foods and Drinks– Foods like Sauerkraut, Kimichi, Fermented Salsa, Fermented Veggies, Natural Yogurt, Kefir, Naturally Aged Cheeses, etc. are natural sources of probiotics and eating a variety of these will help get in all the beneficial strains of bacteria. Cultured drinks like kombucha and water or milk kefir also provide probiotics.
  • Use natural soap and water instead of antibacterial– Antibacterial soap kills bacteria, good or bad, and some suggest that overuse of antibacterial soap may be contributing to the rise in resistant strains of bacteria like MRSA. Use a quality natural soap and warm water to clean hands.
  • Start Gardening– Believe it or not, the benefits of dirt that ring true for kids are still beneficial to adults. If you aren’t fond of mud pies, take up gardening. It is a way to get your vitamin D and probiotics in while producing your own food… a win-win!
  • Don’t Overuse Antibiotics– There are certainly cases when it is best to use antibiotics, but for mild illnesses that can be left to run their course or treated naturally, consider skipping the antibiotics, which will deplete all gut bacteria, including the beneficial strains. If you do need to take antibiotics, make sure to take a high quality probiotic at the same time and for a while afterward to help replenish bacteria.
  • Take A Probiotic Supplement– Many of us need more help in the probiotic department than simple dietary changes can provide. That being said, supplementing probiotics without a change in diet and lifestyle is just a waste of money! If you are already eating real foods including fermented foods/drinks and using other ways to replenish your bacteria, consider supplementing probiotics, at least for a while. This is also an important recommendation if you are currently using or recently have used antibiotics. Children with eczema, allergies, digestive disturbances or those who were formula fed can often benefit from probiotics as well.
  • Try to GAPS/SCD diet– These diets are specifically focused on healing and rebuilding a digestive system that has been harmed over time. If you have specific or acute symptoms, one of these diets may be the fastest/best way to help your body recover.

What do you think? Do you get enough good bacteria? Ever realize your guts did so much work? Tell me below!

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Reader Comments

  1. What should I look for when buying probiotics?


    • You want it to have a variety of live strains, and preferably a
      number in the billions! I’ve hear that Bio Kult is a really good
      brand, though I’ve never used them myself.

      • Which ones are you using then? You stated in your other article about vitamins and supplements for children, that you use Bio Kult probiotics?

      • Hello. I have a question. Is there a way four me to extract honeysuckle extract from the flower to put in my organic homemade lotion? By the way, so glad I’ve found you!

  2. Hello! Thanks for all your inspiration & insight! I am a first time mom, and my five month old son is – at this point – strictly breastfed. However, he is allergic to nuts, dairy and eggs. Long story short, I think there are a couple reasons that I might have a gut in need of a little repair – could that be influencing his health? What would you recommend I eat to help him (us)? I attempted to take a probiotic supplement, but Will had a strong allergic reaction due to the lactase… Thank you very much!

    • You are definitely wise to think that your gut may need some help,
      and really, his might too! I haven’t tried it myself, but I’ve heard
      that Bio Kult probiotics have virtually no dairy and don’t affect
      those who are lactose intolerant, though you’d want to check on that
      for sure with the company. You could also try making water kefir or
      kombucha and drinking those yourself to get the probiotics, and
      neither of those should have dairy in any amount. You could also try
      the GAPS diet for yourself, and the child version when you start your
      baby on foods (minus the one’s he can’t tolerate!).

      If you/he tolerate coconut, you could buy or make coconut yogurt for
      probiotics or coconut kefir. I suspect that if he has these issues
      already, you do need serious doses of probiotics, but also that there
      is a likely grain intolerance as well. I’ve never seen these not
      connected in working with clients. The good news is, with many of the
      people I’ve worked with are eventually able to tolerate dairy, nuts,
      eggs, etc after a year or more grain free and focusing on rebuilding
      the gut lining. It is great that he is still exclusively breastfed,
      since you’ll have a blank slate to work from with his diet. If
      possible, avoid ever giving him sugar or processed foods, and work on
      getting rid of these yourself if you haven’t already.

      Other things that might help: If you can find one (they do exist!)
      take a quality probiotic without dairy in it
      -drink enough water
      -start including probiotic rich dairy-free drinks for you and for him
      once he starts on other foods/drinks
      -include fermented foods in your diet and his once he starts eating
      -avoid sugar and processed foods, which will feed the bad bacteria
      -avoid juices for the same reason

      Hope that helps some! Let me know how it goes!

      • Wonderful! Thank you, Katie. This is a huge help. I must admit… I am a health nut, and the grain free thing is challenging… But, I am VERY intimidated looking at the GAPS diet! A couple more questions for you: Do you buy only organic meats (and fish)? Also, do I simply take the probiotic myself? Or do you recommend I give it to Will, as well? In researching, it appears some advocate pumping and putting the probiotic right in the milk. What are your thoughts?

      • Hi Katie I was just reading all these comments and Im so lost. I can’t find any doctors that DONT just wanna throw a bandaid on my health problems. They give me tons of antacid and tell me I might have food intolerances. Which I think I do but now it’s everything I eat that makes me dizzy, nauseated, cold chills, no energy, muscle pains, headaches etc. I have constipation from any grains, unable to digest meat(stays on my stomach all day), diarrhea with severely undigested food. I do have lots of mineral and nutrient deficiencies such as vitamin D, magnesium, vitamin b, etc. My health deteriorates every day. Now I have mood swings now as well cuz of pain. My upper middle to right side of my stomach. Oh I’ve had my gallbladder out about 3 years ago btw. Never had trouble till this year. Things have drastically gotten bad in the past month and it’s scary. Can you please help? Where do I start? I want to try betaineHCI cuz I just cannot digest food properly anymore but should I take a probiotic with it? Should I try these two things or something else?

        • It sounds like you have IBS. One of the first things to do would be to have a colonoscopy, to rule out any other issues.

          If you do indeed have IBS, then first you should really learn and become an expert on the human microbiome.

          Second, you should begin your research and learn what a microbiome transplant is. It’s going to sound “yucky”, but the truth is, it works, and it can reverse IBS.

          Third, you could try visiting the IBS self help and support group, you might learn some things.

  3. I was sick for a long time and kept getting one illness after another.  When my doctor’s advice was “Hand sanitizer–put a bottle in every bag and every room,” I decided to do the opposite and now make my own fermented vegetables, brown rice, sourdough, and yogurt.  I also no longer take birth control or other unnecessary prescriptions and use herbs instead of antibiotics, but it is a hard battle to achieve good health these days.

  4. Would probiotics be helpful with acid reflux and heart burn? I eat a whole food/paleo diet and have tried going off the Prilosec or Zantac, but the acid is still so bad. What could be the cause of the excess acid or the reflux?

    • Antacids are probably doing the opposite of what you want. You actually need more stomach acid if you’re having heartburn. Start taking raw Apple cider vinegar 5 min (1-3 tsp) before each meal and again after as needed. This has been one of the biggest game changers for my health!

  5. “Overall, there are ten times the number of bacteria in the body as
    actual human cells, and this colonization of bacteria (good or bad) can
    weight up to three pounds.” How is this possible when the brain alone weighs 3lbs? Adult skin weighs 9-15 pounds…

    • Because billions of bacteria don’t weigh very much. The entire amount of bacteria weighs that total, even though it is made of of many, many bacteria…

    • It’s because we have 100 trillion of these bacteria in and on our body, and their collective weight adds up to that.

  6. I have been taking the Lady Soma Probiotics for about 1 year now and I can’t belive the difference it makes in my digestive health! My OB/GYM reccomended Lady Soma. I have had stomach/instestinal problems my whole life and I have diagnosed with IBS. since taking the probiotics I have seen alot of improvement.

  7. Do you have a recipe for the coconut yogurt?

  8. Great article but I think I missed the tie-in with the title lol what is a stinking gut? Is it called that because of eating fermented foods?

  9. Wellness Mama, this is one of the best flows of information for probiotics. I am doing a presentation today on making kombucha green tea and had a few kinks in the flow and this really helped focus and provide the clarity that I was looking for.

    Dr. Patrick Garrett

  10. I am really disappointed, as I found out I will have to be on antibiotics during delivery of my child due to Group B strep. I know this is a preventative, but I am really worried about killing off the good bacteria for my baby. Do you have any idea on how long it will take my system to recover after this antibiotic dose? I plan to breast feed, but don’t know how long it will take for my child to start receiving “good bacteria” from my breast milk. Any help is appreciated.

  11. Wellness mama or anyone do you know if acetaminophen is bad for gut health? thanks I am new to this and have been trying to get my body healthy.

    • Yes, avoid medicine. If you have a belly ache or headache, try peppermint instead

  12. From what I’ve read, grains aren’t necessarily all bad, but you should soak them in water and cider vinegar or lemon juice or plain yogurt to break down the anti nutrients and enzyme inhibitors. You can do this with oatmeal, brown rice, but of course try to avoid white rice and other processed grains because they won’t be good for you anyway. Also, buying a sourdough starter and using spelt flour to make bread is a good way to cut processed white flour and yeast from your diet.

  13. I have a one week old baby girl. She is EBF but has smelly gas (like rotten egg) and doesn’t poop everyday. Her last two poops have been smelly as well and aren’t yet yellow even though I think they are finally beginning to change over. I had an epidural and pitocin during labor. We declined the vitamin K injection and instead were going to do the drops. My husband administered less than a drop into her mouth on the day of her birth. Since then I’ve read that could have compromised her gut health. If that’s the case, what can I do for her? She doesn’t seem to be bothered by it or in any discomfort. Could it be a side effect from the drugs I was given in labor? Or the vitamin K? I’m hesitant to continue her dosage. Thank you for any help you can provide! I should also note that before I got pregnant I suffered from IBS issues.

  14. Aside from the grimy spoon problem, the probiotic pill is beneficial for those that are vegan, and/or do not such as the structure of yogurts, also the dairy-alternative selections. Me, I LIKE yogurt– specifically the Greek style that’s now popular, and I have no compunctions about dirtying spoons. Plus, popping supplements such as this has that weird, sci-fi “nutrition-in-a-pill” ambiance taking place, at the very least for me. I like to know my probiotics are coming from real meals and not a research laboratory. Something to note: 1) those who can not digest cow’s milk extremely well could have much better good luck with goat’s-milk yogurt, which I, personally, discover tasty. It has far less casein (a healthy protein discovered in cow’s milk) in it that will certainly disturb sensitive digestive tracts. 2)I also make certain and acquire natural. RBGH and RBST have actually been related to creating problems with women’s endocrine systems. So, if unsure, get your yogurt as in your area as you can– or better yet, get some simple natural yogurt (I suggest the Kalona brand if you live in Iowa, like I do), a yogurt-making set and make your very own. I don’t have the area to do the last, sadly– otherwise I would!;-).

  15. Hi Katie,
    I have a two week old infant who was born by c-section and she is being bottle fed. Long story short I could not breast feed and I am extremely disappointed by this. What type of probiotic do you suggest I use for a newborn? I feel like we are behind in gut health! Any input would be really appreciated! Thanks!

    • With my preemie, I used top quality ones like biokult and spread a little in his mouth before feeding him to help his gut bacteria culture.

  16. Aloha wellness mama:-) I have a question…I am a super natural holistic mama-homebirth clean diet etc I never take medicine not even Advil 4 month old is exclusively breastfeed..I am really upset bc my wisdom tooth got infected and I am in severe pain and the doc have me an anti biotic that is compatible w breastfeeding I know antibiotics will mess up my gut flora and I am planning to take probiotics etc but will taking the antibiotic and breastfeeding affect my babies gut flora ?? Thank u so much ~ blessings

  17. I hear so much about the benefits of yogurt because it supposed to put back and balance gut bacteria yet, all yogurt in our stores are pasteurized. If pasteurization kills the bacteria, what or where is the benefit?

  18. I’m a mom of a 2-year-old who has very mild eczema. He also has a bit of a nut allergy (I say “a bit” because he tested negative for it, both blood and skin tests, and yet, whenever he is exposed to nuts, especially sesame seeds, he gets a rash on his cheeks). Our pediatrician has told us to just avoid nuts. My son’s diet is very healthy, but he eats some of the things on your list that doesn’t promote healthy gut bacteria. I want to incorporate some probiotic yogurts into his diet, and am starting to research what kinds/types/brands would work best for a toddler. And after reading this article, I just want to clarify: Am I to understand that even if my son is taking probiotics regularly, it won’t do anything to promote a healthier gut?

    • Probiotics can help and I gave my kids Bio Kult at that age because they could chew them. For yogurt, have you thought about making your own? It is hard to find even a natural brand without sweeteners or fillers.

  19. may i know do our body need bad bacteria? Some doctor advice say we need both and good and bad bacteria in our body ..which i do not understand why we need “bad bacteria”. Does “Extra Virgin Coconut oil” kills all bad bacteria in our body? What happend to our body without bad bacteria? Thank you very much !

    • All of us carry some bad bacteria. The important thing to remember is : our good, helpful bacteria normally keep them from causing us problems by out-competing them. It’s when we take antibiotics or other medications that the good ones are killed off or disturbed, thus giving the bad ones a chance to attach to the intestinal wall, and then give us problems.

  20. Hi, I’ve recently returned from America where I was prescribed azithromycin for a sore throat. Since then I have been having bouts of nausea, loose stool and loud noises. So you suppose this is a typical case of lack of good bacteria? Also I’ve been told that too greater dose of probiotic can be bad for the stomach, is that correct?

  21. Hello, just curious does our body produce natural probiotics or is it completely down to what we eat and or ingest?

    • The body does make some, especially if there is already a healthy balance of bacteria, but it does need prebiotics found in fresh vegetables, fruits and healthy starches to feed these beneficial bacteria.

      • Was just doing some interesting research…….. When we ingest natural, fresh fruits they often have microbes on them, the good, helpful ones that we want. The same goes for natural, fresh vegetables, they also have good microbes on them. So, besides getting the good vitamins, we are also helping our microbiomes. Even raw honey has good microbes in it.

        Therefore, one of the things we can do, just like this article says, is to consume lot’s of fresh fruits and vegetables. The fresher the better. Any just maybe we shouldn’t try to wash off all of these good guys before we consume the food either.

        Growing our own garden, is another thing we can try to add. Growing fruit trees, and various berries too. Fresh is best !

  22. Hello Katie,

    I’m a male in his 40s; Have 2 boys 9 and 7. My wife as of now is skeptical about most of the natural and organic stuff- basically the antithesis if most women visiting your site.

    Me, I’m willing to try anything that can potentially break the cycle of us eating bad foods. I do want to try pribiotics- but as you’ve said- one needs to change lifestyle and diet first.

    I want us all to change, but it’s going to be a hard road since I’m the breadwinner and work a lot of long hours. Is there a place in your blogging or communication where one can track progress and exchange updates often?

    Sorry if this is misplaced. I know you’re doing a lot with your family and all. I just wanted some total beginner guidance/direction to start with.

    Thanks so much for all the great tips!

    • My heart goes out to you RJ… that is so tough. It is still not announced yet, but I’m working on building a free private membership part of where readers can privately and confidently share advice and information with each other. Hoping to be able to share about that in a month or so.

  23. It’s nice to find someone else that has been studying and knows about the Human Microbiome. It’s incredible how important this is to our lives, and how a disturbed or damaged microbiome is associated with so many different disease conditions.

    For those with disease conditions, I suggest they start by studying the human microbiome. When they have a really good background in this, then they should move on to studying a microbiome transplant. It’s like the ultimate probiotic. They work.

    Another thing : I have read in my research that “probiotics don’t attach to the intestinal wall”. It has something to do with the processing or manufacturing process. So, we only get a temporary relief at best. Sorry, but this is from a medical researcher, and it honestly agrees with my personal experience. Also, taking a probiotic with a handful of strains is pretty futile. We have to realize that we have millions of species of helpful bacteria living in our gut. The chances of our getting the right bacteria strains to relieve our symptoms are like one in a million, even if they could attach.

    So, what can we do ? Well the fact is, there are beneficial microbes on fresh, raw fruits, and fresh, raw vegetables, and nuts, and even raw honey. We are doing our microbiomes a favor by consuming these, with every meal, and avoiding processed foods. Planting blueberries, and apple trees, etc. etc. are good steps, along with a garden, with a variety of vegetables. Why a variety ? Well, different beneficial microbes can be associated with different vegetables. And don’t necessarily wash off all those good microbes either. (Of course, we need to avoid any fruit or vegetable that has been contaminated by animal feces.)

    Do your research, and nourish your microbiomes

    Treat your microbiome right ; eat fresh and AVOID antibiotics as much as you can. (they’re invaluable for lifesaving situations, but the truth is, we overuse them)