Marks Daily Apple
Serving up health and fitness insights (daily, of course) with a side of irreverence.
20 Apr

What’s Up With Your Gut? – Beneficial Bacteria and Good Digestive Health

4197076733 2b2b540b4bEveryone knows (well, not everyone, but anyone who’s probably reading this) how crucial the early days of an infant’s life are for establishing good habits and healthy patterns for the rest of its life. What the mother eats while pregnant, what the child eats, delivery methods, breastfeeding duration, heck, whether you read to your children or plop them down in front of the TV – everything helps lay the groundwork for the rest of their lives. Exposure to bacteria is another growing concern for parents. Too little bacteria, and we risk allergies and significantly compromised immune systems later on. Too much isn’t as much of an issue, though we should avoid obviously harmful bacteria. It’s my general sense that most kids these days get far too little bacteria in their lives. They’re swaddled in protective clothing, forbidden from touching (or, perish the thought, licking) things, and doused in antibacterial liquid every other hour. How many kids play in the dirt nowadays? Build forts? Turn over stones in search of bugs? Roughhouse with friends? Far too few, I’d imagine.

While beneficial bacteria reside throughout our bodies, gut bacteria may be the most important of all. A substantial part of our immune system depends on these healthy flora (which will be the subject of a future post). People try to go about obtaining beneficial gut bacteria in ridiculous, counterproductive ways, but at least there’s a sizable public awareness of the subject. Most reasonably health conscious folks these days at least recognize the word “probiotic,” while many researchers are beginning to understand that the bacteria present in breast milk (Bifidobacterium) offers considerable benefits to an infant’s intestinal microbiota. Low levels of Bifidobacterium have also been linked to higher rates of eczema in human children, while giving chubby rats a Bifidobacterium supplement slimmed them down and improved their lipids. Breastfeeding has also been linked to lower rates of asthma in children – is Bifidobacterium involved here, too? There’s a good chance; the author of this study co-authored one last year that found “children who received antibiotics in the first year of life were at higher risk of developing asthma later on.” Obviously, antibiotics can kill both harmful and beneficial bacteria.

Gut flora is responsible for breaking down carbohydrates into short chain fatty acids. If you consider our gut flora to be foreigners – permanent alien residents, put another way – then you might say that humans cannot fully utilize starches without outside help. Technically, those gut organisms are foreign born, but a human without gut microbes is like America without its rich and storied history of immigration; immigrants made America and gut microbes make us whole. Indeed, we’re wholly dependent on our gut flora. You might even say we’re more microbe than man (gut flora outnumber the cells of our bodies by 10 to 1).

Until we’re born, the fetal gut is sterile. It’s just sitting there, accepting pre-digested nutrition from the mother, taking up space and generally living the slacker’s dream. But it works. The fetus doesn’t need a teeming, active gut, because all the work is done by mom’s gut flora. They’re breaking down the polysaccharides and the sugars, converting it into usable fuel, and diverting a portion of it all to the child. In a way, then, the kid is dependent on gut flora, just as much as you or I are. Once he (or she) is out of the womb, the child needs his own intestinal team. He’ll be eating, which requires digestion, and good digestion (especially of carbohydrate) just doesn’t happen without gut flora. He needs gut flora, and he needs it relatively quickly. That’s where the birthing process comes in.

Traditionally, birth allows the passage of microbes from mother to the sterile infant gut, a relatively quick process. Gut colonization isn’t exactly a “feature” of the birthing process, however, and it’s not like there’s a specific pathway designed for the flora to travel from mother to child. No, gut colonization arises organically. It’s common sense, really, if you consider what child birth actually is: a somewhat chaotic, unsanitary event, where fluids are being exchanged, stuff is sloshing around and mixing together, with this vulnerable baby in the midst of it. You’ve got a helpless infant sporting a fecund, totally accessible gastrointestinal tract and a perpetually open mouth. He’s just kind of lying there, maybe crying a bit, but he’s incredibly open to suggestion. To gut flora, this is prime real estate, ripe for the taking. By the time the cord is snipped and the infant’s butt’s got a handprint on it, the baby’s upper gastrointestinal tract has been partially populated with bacterial strains derived from the mother’s feces and the surrounding environment (the air, others in the room, etc). Breastfeeding provides another ongoing source of bacteria. It takes about a month for a newborn to establish a solid population of gut flora, and another year for it to resemble an adult’s gut contents. (Any wonder why C-section, bottle-fed babies might get off to a slow start?)

Raising kids isn’t just about bringing new organisms into the world. It’s also important to prepare them for what lies ahead, and the only way to ensure adequate preparation is with exposure and personal experience. Shortchanging kids now, whether by maintaining the ultra-sterile environment (Purel everywhere, no physical skin-to-ground/dirt/skin contact, zero exposure to the outside world, lots of antibiotics, etc) at all costs or feeding them a purely refined food diet, sets them up for poor health in the future. Getting enough gut flora is one huge step in the right direction, but there’s a bit more nuance, as researchers are learning. Getting a wide enough variety of gut flora is just as, if not more important in the path to good digestive health – and that goes for kids, teens, and adults, as well as infants.

Accelerated Evolution

Bacteroides plebeius is a common microbe that lives in the human gut, issuing various digestive enzymes to deal with various types of food. It’s a pretty basic example of gut flora, but researchers noticed something very strange while studying a marine species of Bacteroidetes. Zobellia galactanivorans, which lives on a type of red seaweed, contains a specialized enzyme designed for the cleaving of porphyran, a polysaccharide found in red seaweed. Simply put, this specific enzyme was meant to digest seaweed. The researchers searched the gene-sequence databases and found that the same enzyme was also present in human-borne B. plebeius. How did the digestive enzymes of an obscure marine microbe get incorporated into human gut flora? They looked a little harder and found that it was only present in Japanese B. plebeius, not North American. They had their answer.

When humans began arriving in Japan, around 40,000 years ago, seaweed became a staple. And, while most seaweed sold in stores is roasted (and therefore sterile), Paleolithic seaweed eating conditions were considerably less “sanitary.” Folks were eating lots of raw seaweed, teeming with bacteria, and those bacteria were communicating with the already present gut flora. We already know that bacteria enjoy accelerated evolution via gene transfer on a regular basis, but this was the first research to confirm that gut microbes learn from other microbes. They aren’t static. Our gut flora actually receives genetic information from foreign microbes passing through, borne by the food we eat, and they can alter their own genetic code to incorporate the new material.

That’s exactly what happened. Ancient human guts were exposed to new strains of bacteria with new digestive enzymes, and information was exchanged. Genetic code was transferred. And it happened really quickly; according to lead researcher Jan-Hendrik Hehemann, “a bacterium that can’t digest nori one day, can the next.” If those early Japanese had been eating grocery store nori, roasted and months-old, would they have been able to break down the prophyran? No. The seaweed had to be fresh, it had to be raw, and bacteria had to present and alive to survive the trip into the gut. Today’s sterile, refined fare is absent bacteria – good or bad. We irradiate, we pasteurize, we sterilize, and we roast everything that goes into our mouths. Is it any wonder we’ve got widespread health problems?

Clearly, humans evolved in a bacteria-rich environment. The food we ate, the ground upon which we slept, and even the water we drank sent a steady stream of microbial diversity into our bodies – and this went on for hundreds of thousands of years. It made for occasionally lethal infections, but it also made possible the digestion of a wide variety of foods, an ability that we continue to enjoy today. But that seems to be changing. Food is losing its bacterial kick, unless you go out of your way to incorporate microbes into your diet. In the past, as food became more “sterile” and we moved into cities and became successful with agriculture, fermented foods became staples. Nearly every traditional cuisine uses fermentation, in fact. Did they suspect something was missing with the increased refinement of the food supply? Maybe, but either way, they maintained a steady level of bacteria in their diets. We, for the most part, do not.

What Does This Mean?

This shows the probable arc of our evolutionary relationship with food. As we evolved and ate new foods, our gut flora evolved as well. It’s quite remarkable, really, and it shows just how fast evolution can occur. Humans don’t change that quickly, of course, but our gut microbes do, and we in turn change with our gut.

I think everyone of all ages, but kids especially, should eat a wide variety of foods. Avoiding refined foods isn’t enough. You’ve got to actively seek out new foods, “living” foods and raw foods. Don’t become a raw foodist, mind you. Just experiment. Try fermented foods, like kefir or sauerkraut. If most soil wasn’t filled with pesticides, heavy metals and other unknowns I’d probably even encourage you to eat some dirt. Since grubbing on dirt isn’t practical (or appetizing, for that matter) I also recommend supplementing with probiotics. If anything, we owe it to our next of kin to fill our bellies with tons of organisms.

What are your thoughts on gut health? Does it even cross your mind? Is this new to you? Or do you have a plan of attack to keep your gut happy? Fermented foods? Supplements? Share your thoughts in the comment board. Thanks, everyone, and Grok on!

AJCI Flickr Photo (CC)

You want comments? We got comments:

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  1. I need to add more fermented foods to my diet. I do not take a probiotic supplement and I do not eat any fermented foods that I know of.

    This article urges me to continue to learn more about gut bacteria as some other articles I have read recently has brought it to my attention.

    Todd wrote on April 21st, 2010
  2. Lets make it really easy, head for a Korean restaurant. They’re fewer in number but tend to be more authentic then other ethnic fare. Most meals come w/ kimchi and a load of fermented fare. First timers should head for the Bi Bim Bop.

    Michael wrote on April 21st, 2010
  3. Gut health is VERY VERY VERY important to me. I had a colectomy ONE YEAR (exactly) ago and my digestion really hasn’t been all that great since (or even before for that matter) but in order to keep my gut as “smooth” as possible I take digestive enzymes with probiotics and eat lots of healthy fiber!

    GiGi wrote on April 21st, 2010
  4. Do you have any thoughts about Kombucha fermented tea?

    Emily wrote on April 21st, 2010
    • Second Emily’s question — I threw out Kombucha above but no one has discussed. I have used it with success but my experience is entirely anecdotal. We tried making it for a while but the stuff from the store tastes way better and I did not take the time to sort out the tea / flavoring aspect. I split a bottle with my wife daily, we both think it essential to gut health + PH.

      eric wrote on April 21st, 2010
  5. Perhaps we shouldn’t discourage our kids from picking their noses! Seems like an instinctive reaction they inherit?

    Perhaps adults might benefit also?

    Auto-inoculation?

    George wrote on April 22nd, 2010
  6. 3 weeks into changing my diet so that my carbohydrate consumption dropped from maybe an average 300 + grams per day to below 80, I had a massive day long episode of diarrhea — the experince of which was so different from any I’d had in the past from infectious causes.

    I suspect that that, and occasional minor brief re-occurrences, may have a lot to do with massive changes in, maybe even death of, intestinal flora.

    Dave Riley wrote on April 22nd, 2010
  7. The sad thing is that most people do whatever they can to do the exact opposite. Slather themselves in anti-microbial concoctions, wipe down FOOD PREP areas with chemicals that kill bugs. Imagine what those cheicals do to us!!!

    My 6 year old (who loves the dirt and all things outside) was asked, along with the rest of her class to “bring 2 large bottles of hand sanitizer to class”. I asked about it and the teacher mentioned that it prevents the spread of germs. The staff were worried about getting sick. Keep limiting your exposure to these bugs, and catching the flu will be the least of your worries.

    Spence wrote on April 22nd, 2010
  8. Hi there
    Have you heard of the drink Kombucha? I drink one every day. It claims to boost metabolism, digestion, appetite control,weight control, cell integrity, anti-aging……

    peggy callahan wrote on April 22nd, 2010
  9. Lying Just to finally cover Kombucha, YES, it is full of probotics. Make it yourself if you don’t want to break the budget. It’s very easy to make:)
    Also, if anyone is really interested in the health of their gut, look up a guy named Konstantin Monastyrsky. He’s a wealth of knowledge on everything that has to do with guts and has been specializing and treating people with gut problems for many years.
    http://www.gutsense.org/author/author.html
    He has a few book out there and if you click on the “Store” link on his page, there is a product called GI Recover which contains a boat load of natural probiotics.
    I’m reading one of his books right now, Functional Diet, and it is very much in line with Primal Blueprint with one exception that the author doesn’t advocate a lot of vegetable consumption. Interesting stuff!

    chocolatechip69 wrote on April 22nd, 2010
    • How do you make the kombucha at home?

      peggy callahan wrote on April 22nd, 2010
      • We did it for a while. My wife got some of the culture and put it in a bin of tea and put it on the warming plate for a spell…don’t know the specifics but the folks we got the culture from loved what they made. We did not play around with juices and flavorings enough to get something that was really good, plus I always felt we were at risk of poisoning ourselves due to ineptness…so we buy it now but its $$$.

        eric wrote on April 22nd, 2010
  10. That way you keep him on your board in case things don’t work out with Westerman/Hegarty, while retaining an open spot if you do hit a home run on the OOS guys. If you’ve already filled his spot and he does get back into shape and demonstrates himself to be Texas caliber, tell him your very sorry but there’s a numbers issue and offer him a greyshirt. He should have a number of options by that point.

    H. Ghr wrote on April 22nd, 2010
  11. I just got back from a trip to Mexico, SICK AS HELL for eating street food on the last night there. My naturopathic doc has me on probiotics until I finish the bottle. I have a naturally sensitive digestive track that’s been ravaged by IBS most of my life. I LOVE kefir, but I figure I should probably eat more fermented foods.

    I was a pre-mature baby too (by three months!) AND a C-section birth too. No wonder I was always sick as a kid! Oh, and the onslaught on antibiotics I took as a child didn’t help either.

    Thanks for the article, Mark! As always :D

    pat wrote on April 23rd, 2010
  12. Awesome post, one issue with the rat study though. The rats were given bacteria that were genetically modified to produce a particular hormone (oxyntomodulin) that aids in weight control – rats given control bacteria that didn’t produce the hormone didn’t get the weight loss benefits. However, they did have significantly reduced plasma triglycerides when compared to rats that didn’t get any bacteria.

    meg wrote on April 26th, 2010
  13. As long as the mother and baby are both healthy, here is yet another reason to have a home birth. Think of the bad bugs lingering in a hospital and how all of those nice nurses colonize your baby’s gut with the germs they pass around. No thanks!

    Someone asked about the father’s bacteria. Yes good flora is important for him too. He passes fluids onto the mother and baby (kissing, sexual contact with mother) and it’s important for him to be healthy as well.

    Twyla wrote on April 28th, 2010
  14. a clean gut is a healthy gut :)

    Usman wrote on April 29th, 2010
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  17. Exercise is a powerful immune booster, not to mention a very important component of good overall health. Regular, moderate exercise has been shown to lower an individual’s likelihood of getting sick. It also boosts natural energy levels while relieving stress at the same time.

    John Smith wrote on June 20th, 2010
  18. A work out plan does not have to be strenuous it can be simple with numerous benefits. Aerobics and sports are the most common types of performed health and fitness exercises.But for good brain we can take some supplements to improve brain fitness.

    T. Eeth wrote on June 21st, 2010
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  22. Mark,
    As a Newbie I am curious if a cleansing diet would be beneficial; getting all the crap out of my body before embarking more seriously into this new(old)primal lifestyle?
    Thanks for all your words.
    Cheers,
    Kurt

    Kurt wrote on July 7th, 2010
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  24. Can we have more posts about food and stuff (sarcasm). We haven’t had a post on working out since the Brad Kearns post a month ago. Not counting the weekend links here and there. Just saying. It’s spring, good weather, for those of us who don’t live in Calf. And we’re itching to go outside and play, do new stuff. And you’re posting mostly about food? Really?

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  28. The intake of vitamins and minerals varies from person to person, but there are some groups who are more nutrient-lacking than others. New scientific studies are seeing that we even have a genetic code that tells what nutrients we need more of as individuals.

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  29. I’ve got some kraut brewing in the pantry right now..and I make all the yogurt my family consumes.

    zolpidem wrote on November 26th, 2010
  30. Mark

    I am curious about how the gut flora looks like for someone like you on your diet and lifestyle.

    Do you have a gut flora test done with some specialist labs like Genova or Diagnos tech and share it with us.

    Thanks

    Vestigal wrote on May 29th, 2011
  31. If all that’s true, my son should be immune to everything. When he was a toddler, he would chase the chickens until he caught one, then sit under a tree, in the dirt, with the chicken in his lap and pet it until he got tired of that chicken and then do the whole thing all over again. He used to come in the house more dirt than kid, but he was happy and never got sick.

    Katie wrote on September 9th, 2011
  32. I took daily doses of the probiotics sold on this site and after a few days I got cramps and diarrhea. So I went off them. Then a few weeks later I got a second bottle (thinking I may have had a bad batch) and I tried again with the same result. Any thoughts?

    Gene Banman wrote on October 17th, 2011
  33. i wonder what sorts of problems, if any, the guys on the international space station for a year had…..not many bugs floating around up there.

    Dan wrote on October 23rd, 2011
  34. I follow the GAPS diet by dr natasha campbell-mcbride. Below is a great video by her explaining gut health
    http://vimeo.com/m/10507542

    Rach wrote on December 10th, 2011
  35. a few questions– any guidance is appreciated: (1) there are some who claim that enzymes derived from plant-based foods are not used by the body to aid in digestion because stomach acids eventually destroy the plant-based enzymes. That the only enzymes we use are those that our bodies manufacture on their own. Can anyone shed any light on this? … (2) re gut bacteria- do the bacteria “produce” enzymes that the body can use? Or does the body’s enzymes use but bacteria somehow? It seems there’s a symbiotic relationship between our own enzymes and gut bacteria- is there any more info on that anywhere? …and last question (3)- does the good bacteria come from our food, and if so is there a list of the good bacteria/food sources that must be consumed on a regular basis for good health?

    rick wrote on December 19th, 2011
    • I heard that, although eating probiotic foods, and taking probiotics can improve your health, it is a temporary and limited improvement. I read, somewhere, that it is our resident bacteria that make the most significant difference to our health, and consuming other bacteria does not repopulate resident bacteria in adults. The conclusion I got was that consuming plenty of pre-biotics, which feed and protect our resident bacteria, is more important that consuming pro-biotics. And the best sources of pre-bioics were Jicama, and Jerusalem Artichokes.
      I also read that there have been cases of very sick people, with weakened immune systems, getting sicker when consuming probiotics, because they became overly infested by them.

      dipinmilk wrote on February 8th, 2012
  36. Hi! I may be completely crazy but in the UK mothers are told to avoid any foods with living organisms (yoghurt, unpasteurized cheese, kefir etc) during pregnancy so that diseased can’t pass to the unborn and vulnerable baby. However, this must influence her gut flora negatively and thus the bacteria that the baby ingests at birth is of a poorer quality. Could this be a reason why many babies today are not enjoying the full benefits of a sound gut flora?

    Tammy wrote on February 24th, 2012
  37. BS. Bacteria are bad for the body. All of them. Some are worse than others, thats why probiotics work is they are good relative to bad bacteria.

    Here is why baceria are bad:

    1. they make us fat. We absorb 25% more calories with bacteria present. Any wonder why we are obese?

    2. they make us sick. Virus’ are designed to infiltrate bacteria. Virus’ use bacteria to gain a foothold in the body to infect human cells. http://blogs.discovermagazine.com/notrocketscience/2011/10/13/beneficial-gut-bacteria-can-become-virus-collaborators/#.UQfz7Si9Kc0

    I use diatomaceous earth to mechanically kill the bacteria in my intestines and I can’t remember the last time I’ve been sick.

    Sure probiotics may be good if you don’t know of a way to keep all bacteria out consistently without antibiotics, but now you know how: diatomaceous earth. Make sure to take some metamucil with it to prevent constipation and get FOOD GRADE diatomaceous earth.

    Marcus wrote on January 29th, 2013
  38. From our birth our bodies know exactly what to do to best defend and heal itself. Our body is such a finely tuned machine that we’d be better off feeding it good food and getting ready for how good we would feel with all our cylinders firing. Take care of your body so your body can take care of you.

    jennifer wrote on April 7th, 2013
  39. The same flora that is in the intenstines, also populateo the vagina. Through natural birth the baby ingests fluids that contain the much desired bacteria.
    The first day the baby only drinks tiny portions of colonstrom which further help the proliferation of the bacteria.
    Babies born through c-section do not have the chance to get in contact with the much needed bacteria.
    The same applies to babies that have not breastfed.

    vsg wrote on June 7th, 2013
  40. I guess this article is several years old, but I just read it and it made me cry! My daughter is 6 years old and she has had chronic stomach and intestinal problems her entire life. When I was in labor, her heart rate dropped, so they did an emergency c-section. They had to knock me out because the epideral did nothing for me. By the time I woke up, my baby girl was already on a stealth dose of antibiotics to combat whatever it was that made her heart rate drop (they had NO idea what caused it to drop, but they apparently don’t need a reason to drug people). She was to spend the next 7 days in the NICU being fed intravenious antibiotics and living on formula. I did finally get to start breast-feeding, but maybe the damage to her gut had already been done? She already had 3 counts against her.

    Could this be one of the reasons she has problems now? I have tried so many things, with no help from her pediatrician. She’s gluten free. I did an elimination diet for dairy, too, and she doesn’t seem to have a problem with it, but maybe I should try again. I would love it if I could get her to be primal/paleo, but she’s far too picky an eater for that. I do make grain-free breads and other baked goods for her as often as possible, but she can’t have any kind of tree nut at school, which limits what I can pack for her that she’ll actually eat. She throws up a couple times a week and complains daily that her stomach hurts. I’ve done a food journal and there doesn’t seem to be any pattern to what makes her hurt.

    I haven’t really investigated fermented foods (which I will right now), but is there a way to get a healthy dose of probiotics into a kid who may need serious gut help? She can’t do pills.

    Cati wrote on April 2nd, 2014

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