If you need to take antibiotics and are looking for ways to reduce the side effects, please see this article.
Maintaining proper balance of healthy gut flora is a crucial yet widely misunderstood component of human health. While the development of antibiotics has lengthened our lifespans, our excessive and inappropriate use of these drugs may be causing serious long-term consequences we are only now becoming fully aware of.
These consequences not only affect our individual health, but may even be causing permanent changes to the microflora of all people from generation to generation.
Martin Blaser’s recent (2011) article published in Nature highlights the potentially dangerous long-term consequences that arise from the rampant overuse of antibiotics. (1) He argues that changes in our microbiota may even be promoting the transmission of deadly organisms, as one of the important roles of an intact microflora is to resist colonization by pathogenic organisms.
Blaser also points out that not only does the individual use of antibiotics cause permanent changes in the gut flora, but that infants born to women given antibiotics during pregnancy, or the 30% of children delivered via cesarean section, may be starting life with a significantly altered and insufficient level of friendly gut flora. (2) This is a serious concern because lack of diversity in friendly gut bacteria has been shown to contribute to a large number of diseases and complications.
Unfortunately, even a single course of antibiotics can permanently alter the gut flora.
One study found that after a single treatment of intravenous antibiotics, fecal bacteria tests demonstrated a significant change in the variety of bacterial strains, and the development of the pathogen Clostridium difficile. (3) C. difficile colonization in the gut can lead to serious complications such as severe diarrhea and colitis. (4)
Another study demonstrated that a short course of the antibiotic ciprofloxacin reduced the diversity of the intestinal microbiota, with significant effects on roughly one-third of the bacterial species. (5) This study also found that while much of the diversity eventually recovered, there were still several species that failed to recover after six months, suggesting that even a short course of antibiotics may cause permanent changes to the community of friendly flora in the gut.
Antibiotics are known to cause diarrhea, which may be due to infection by antibiotic resistant pathogens such as salmonella, C. perfringens type A, Staphylococcus aureus, and possibly Candida albicans, as well the various metabolic consequences of reduced concentrations of fecal flora. (6) These results suggests that disturbance of the normal intestinal flora following antibiotic use may be responsible for the overgrowth of dangerous pathogens.
One study demonstrated significant changes in the primary intestinal flora of infants born through cesarean delivery, lasting at least six months. (7) Primary colonization of the newborn’s sterile intestinal tract normally happens during vaginal birth, and it is unknown whether an infant born with inadequate or unbalanced colonization will ever develop normal intestinal flora without intervention.
While breastfeeding can help restore some of the natural balance to the microflora, only about 44.3% of American women breastfeed (with only 14.8% breastfeeding exclusively) for the full six months that is recommended. (8, 9) Furthermore, breastfeeding alone may not compensate for the changes in flora associated with cesarean sections, suggesting that many infants may be at an even greater disadvantage when it comes to the proper development of a healthy, functional digestive tract. (10)
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Research from diverse fields demonstrates the negative effects of gut dysbiosis and inadequate friendly flora on a variety of health outcomes.
For example, resident bacteria of the normal flora are involved in intestinal mucosal inflammation and patients with inflammatory bowel disease (IBD) have higher amounts of bacteria attached to their intestinal mucosa than do healthy people. (11) Patients with Crohn’s disease and ulcerative colitis are found to have reduced concentrations of fecal Lactobacillus and Bifdobacteria, which protect against pathogenic bacteria, increase mineral absorption and induce the production of growth factor in the gut. (12)
An unbalanced microbiota in the gut is also a contributing factor in autoimmunity. (13) Infection with certain microbial pathogens can trigger autoimmune reactions in joints and other organs. (14) The destruction of healthy gut flora can make the mucosal lining more susceptible to leakage, which some researchers believe is a precondition for developing autoimmunity. (15, 16) It is well-established that the balance of gut bacteria plays a key role in the formation of a proper immune response. (17, 18) A lack of healthy gut bacteria is associated with allergies, IBD, and general autoimmune reactions when this immune modulation goes awry.
New research has linked changes in gut bacteria with obesity. One study found that the gut bacteria of obese subjects differs significantly in species type from lean subjects, and that low calorie diets, restricting either fat or carbohydrates, changed the gut flora and increased the abundance of the bacterial strains found more predominantly in the lean subjects. (19) Another study found that transplanting fecal bacteria from lean or obese mice into mice with sterile guts could affect whether these mice gained body fat, even when food intake was controlled. (20) Those mice implanted with fecal bacteria from obese mice gained a significantly larger percentage of body fat than those transplanted with bacteria from lean mice. The authors hypothesized that certain types of gut flora are associated with obesity due to the increased extraction of energy from the diet. I’ve written about this in more detail here.
These studies demonstrate the wide range of potential consequences caused by the improper development or destruction of the intestinal flora.
If antibiotics must be used (and there are certainly situations where this is the case), special care should be taken to not only restore their gut flora using probiotic foods and supplements, but to eat a diet that supports healthy gut microbiota with plenty of fermentable fibers from starch and the removal of food toxins.
To protect infants’ gut health, especially those infants born through cesarean section, it is crucial to exclusively breastfeed for at least six months, with breastfeeding continuing on-demand throughout the complementary feeding period (up to 2 years of age). I also recommend using a high-quality infant probiotic to help populate your baby’s gut with beneficial flora, as I explain in this article from my natural childbirth series.
Infancy is a critical time where the development of a healthy gut microbiota is essential for the long term health of your child. You can read more about protecting the gut health of your child in The Healthy Baby Code.
As I said in the beginning of the article, antibiotics save lives and have significantly lengthened our lifespans. But that benefit has come with a price, and it’s one that we’re only just beginning to understand the full implications of. My goal here is simply to raise awareness of this price – the harmful and potentially lasting effects of antibiotics – so that you can make a more informed choice.
What are some alternatives to antibiotics?
Mark Sisson wrote a good post listing some alternatives to antibiotics a few months back. In my practice I use a combination of botanical anti-microbials, biofilm distruptors (bacteria often live in extracellular matrices called biofilm, which protect them from our innate immune defenses and any external anti-microbials we might take), and probiotics – as well as micronutrients to support immune function, like vitamin C, iodine and selenium.
While these botanicals do have an impact on the gut flora, it is less pronounced than the effect of broad-spectrum antibiotics. Still, I recommend taking any strong anti-microbials under the supervision of a qualified health care provider.
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Hi
I have been on SCD for four months and have not been very sucessful. For the last four days I have had just ate protein and nothing else but my D has been the worst it ever has and it feels like my strictures are tightened again. I was wondering is this yeast die off or do I need to supplement with Betaine HCL. I was on it before but was afraid it was aggravating my stricture.
Any advice you have would be greatly appreciated
Thanks
Please help?. After taking antibiotics for 2 weeks for peptic ulcer. Feel worst than before. Alot of gurgling in my stomach, burning sensation and pain. I have try taking probiotics, enzymes, and change my diet. No good results.
Hi my name is Socorro Im from Mexico so my english istn good, but I need help
in february my 2 year old son got sick and his flora was damaged and now he can drink mil, because of lactose, I took my son to the pediatrician and he prescribe my son with probiotics, but he’s still having problem with the milk *lactose”, also the pediatrician said the he must avoid the sweet foods or candies
and that it could take hip a whole year to re establish his flora
could you help me please?
See “Fighting for autistic children: The endless battles” for an inside look at what happens when non-verbal autistic patients get staph in hospital settings. And why being a warrior mom or dad is critical in protecting these children.
Hi,
My son was blasted with antibiotics at birth (c-section). I never had a chance to say no. We believe this caused leaky gut for him. He has been covered in SEVERE eczema since he was 3 months old. We just found out he has at least 17 food allergies (neither of us have any allergies). He is now 14 months and I just weaned him from breast-feeding. Because of his limited diet from all the allergies he stopped growing and was put on formula. It’s called Elecare, it’s amino-acid based and has 55% corn syrup solids. I don’t know what to do! He needs nutrition to heal but, the corn syrup is a toxin. We’d like to try the rotation diet but he only eats a handful of foods. He takes probiotics, gets adjusted twice a week and eats lots of raw foods.
Do you have any suggestions? Thank you for your time.
Krystn
A Paleo diet or GAPS diet. You can learn more about the GAPS diet at http://gapsdiet.com. These would both be far, far better options than the formula.
Thank you so much for responding.
He is allergic to many of the foods and supplements on the GAPS diet (fish and shellfish, all forms of dairy, all meat except chicken, the top 8 allergens, beans, peas, all nuts, banana, avacado… The list goes on) the allergist says to introduce some of these foods but not the top 8. He becomes anaphylactic to those. On the contrary, most holistic doctors say remove all allergens.
Krysten,
My son had all of the same issues as yours, although he ended up with a feeding tube for a year after loosing tremendous amounts of weight around 18 months. He’s almost 4 and doing better, but we have a ways to go in terms of healing his gut. If I had known then what I know now I would have done my best to get him on the GAPS protocol, obviously avoiding allergens right away. We’re on a full GAPS diet and preparing for intro soon. All I can say is to start sooner than later. Now that he’s 4 he’s much more hard headed about eating, or not eating, certain foods. Remember that allergy tests are pretty inconclusive and the only way to really know if he’s truly allergic to something is to heal his gut.
Hi Diane,
Thanks for the insight. My son is now 22 months old and by rast allergy testing, blood tests, and eating the suspected foods we know he is allergic to at least 30 foods. These foods include almost everything on the gaps diet. He takes a good probiotic and eats a healthy diet of organic chicken, brown rice, quinoa, some fruits, and veggies and he’s never looked better. If we stray from the diet or try to introduce new foods (last week we tried grass fed beef) he breaks out and has diarrhea.
Anyone know how long it takes for one’s gut to recover from antibiotic use? My son takes probiotics but can’t eat any of the fermented foods suggested so I’m assuming his will take longer. I wish I could post a before and after picture to show you what we are dealing with.
Have you tried prebiotic supplements? They help the good bacteria to grow and seem to be more effective than probiotics. Look at reviews on Amazon.
My youngest son was given a ton of antibiotics for persistent ear infections btwn 9-18 months old( he breastfed). Then after major vomiting issues at 22 months, an endoscopy determined celiac.
Could antibiotic overuse in small children create celiac gut? No one else in family has celiac symptoms or labs.
Thx
Yes, it could predispose him to that. Diseases like Celiac are multifactorial, and have both genetic and environmental causes.
Chris,
I had the same thing happen after antibiotics, Celiac symptoms. Blood tests have been negative but I cannot eat grains long enough before testing.
Could someone have Celiac even with-out the genes?
Is it theory or proven that probiotic containing foods can help repopulate the gut? Also, Does the probiotic in the food tend to only help with digestion/utilization of similar foods as the item ingested?
Does the same scorched earth(gut) observation apply in cases where an inject-able antibiotic is used rather than oral? It seems to me since the gut is technically outside the body the affects of an antibiotic would be reduced than an oral antibiotic that would travel through the gut. I suppose where in the digestive system antibiotics are absorbed into our bodies would be good to know. Anyone?
Recent evidence suggests that the primary benefit from probiotics may be immune regulation rather than permanent repopulation of the gut flora. However, consuming fermented foods or probiotics on a daily basis does alter the gut microbiota (if not permanently) and the benefits of both are well-documented.
Does this mean that those of us forced to endure long-term antibiotic regimens (recalcitrant Rocky Mountain Spotted Fever) can never successfully repopulate our guts?
On another track, do you think that coffee enemas ruin gut bacteria? Before needing the abx, I occasionally used coffe enema to stimulate my liver. A lovely side effect was that it completely extinguished my horrible cravings for sweets, leading me to believe that my gut had been populated with unhealthy bacteria/fungus. I tripled my use of strong probiotics & thought I was doing okay, but then RMSF returned, again . . .
I have a question about my son, who is now almost a year old. I know looking back now that I had some underlying gut issues while I was pregnant with him (I’m now on the GAPS diet to try to heal), but I unfortunately didn’t really start learning about “real food” and such until after he was born. I tested positive for group B strep while pregnant and thus received antibiotics via IV during labor. We had a fairly standard, uncomplicated, vaginal hospital birth, and he was exclusively breastfed (I’m still breastfeeding). He’s also essentially been on a paleo diet (plus fermented dairy) since we’ve started solids, and I’ve recently been working hard to get him fermented foods and probiotics (I give him kefir grains and small doses of probiotic powder from Custom Probiotics).
He’s generally been a super healthy kid despite how many mistakes I made during pregnancy and birth–no skin issues (except heat rash), very few sicknesses, very active and energetic. Before solids, he would poop once every few days, but then that increased to once or twice a day on average after solids (all of which I think is normal). However, the one issue he has had is that he spits up a lot. For a while (before starting solids), it was often 10-15 times a day. It has gradually gotten better, but he still sometimes spits up once or twice a day, even though he’s almost a year old. It has never bothered him and he has never spit up while sleeping, and his weight gain has progressed normally. I know some amount of spitting up is normal for babies, but his has seemed excessive. It did seem to improve a bit when I cleaned up my diet and started GAPS, but that might have been my imagination :). Is this something I need to worry about? Do I just need to wait it out and keep it up with the clean diet and probiotics? Or is there something else I should try?
Three years ago I had outpatient foot surgery.
Four days later I had a visible MRSA/Staph infection.
I received an IV antibiotic – Cubicin – for two weeks….I was very lucky I was healthy before hand and it worked as fast as it did.
Though I still went on a tablet antibiotic for the next 6 or 8 weeks.
So far so good……uh, not really.
About nine months after that I started to get strange – for me anyway – symptoms.
Urination problems, prostatitis (with a discharge – yuck), constipation and low grade stomach pains.
So I went to a Urologist…and guess what ?….he put me on antibiotics.
It seemed to all get better (95%)….for a while anyway.
Then it all came back.
A friend gave me the number to her Chiropractor who deals with health issues with muscle testing.
I was on & still am on some specific supplements along with a change in diet….not that I ever had weight issues…I haven’t had a beer, yeast bread, cake, etc in over a year now.
Here I am today…everything is more or less okay…except I can’t put on weight.
All my blood test come out great.
I still have some Reflux that I mainly feel in the back of my mouth.
My Intestinal Flora has probably changed.
I don’t know what I’d do if I ever really needed an antibiotic again, or worse…what if I needed to get some kind of hospital surgery again ?
Deal with those issues if they ever come up, I guess.
In the meantime…keep taking my probiotics as it is a slight battle.
Thanks for your Blog.
a website you may enjoy, makes a lot of sense:
http://www.gutsense.org/gutsense/flora.html
Great article, Chris! Full of reminders of why nature does things a certain way (vaginal birth). Many people don’t think twice about popping antibiotics. Hopefully many new parents will read your article and take it to heart (or should I say gut?). 🙂
Chris,
Just had a thought and was hoping you could answer a question. I have begun supplementing with Iodine after reading Dr Brownstein’s book. Any thoughts about Iodine potentially killing the good gut bacteria?
Thanks!
Tim
Great information shared to aware people about use of antibiotics and substitute to antibiotics.
I have an upcoming endoscopy/colonscopy but one thing that is going to be tested on the tissue samples is h pylori, for which ill prob have to take antibiotics. If it does come up positive should I just take the prescribed antibiotics for it or take some alternative for it? I would like to fix the h pylori part but I don’t want to mess up anything else by taking some strong antibiotic and messing up my gut flora or more up.
As a Naturopath I have helped many clients who have taken antibiotics. Prevention is always key, if you do have to take antibiotics ensure you take a probiotic and continue for at least 3 months. Colloidal silver is an excellent alternative to antibiotics and the juice from garlic can be used for kids ear infections, there are many alternatives.
Many people have candida albicans after taking antibiotics, an overabundance of yeast in the body. A strict diet containing no sugar or yeast and supplements will cure this, although it takes 6 months or longer.
hi, I was wondering about a kidney infection, is there anything i can take besides Antibiotics? If not ,is there something i should be taking like pro biotic or? Is there a website or book that has the stuff you talk about i would sure love to read it. thanks
Sue Ann,
How do we kill H. Pylori? I gave in and after 3 days wound up in ER with allergic reaction to the antibiotics. Now they want me on Pylora.
Before all this I had Never taken an antibiotic in my life except for iv antibiotics in hospital after surgery.
Thanks
Chris,
Given that the vast majority of people in the developed world have taken antibiotics at some point or another, I hope that you will soon be offering some advice on restoring normal or normal-enough biota (besides a low-calorie diet as referenced in your post). I also hope you will share your thoughts on whether it was the reduced calories, or the change in macronutrient composition that “changed the gut flora and increased the abundance of the bacterial strains found more predominantly in the lean subjects.”
And thank you for a thoroughly researched post!
Chris – what about the issue of probiotics derived from soil bacteria vs. probiotics derived from milk?
And I think an earlier comment asked about your views on colloidal silver – I’d be interested in your response on that topic too.
Chris, Do you recommend probiotics – do you have a past post on the use of probiotics???? Love your blog.L.
Hi Lula,
Check out this post for details: http://chriskresser.com/9-steps-to-perfect-health-5-heal-your-gut
Hi Chris,
Let’s not forget the associated increased risk of various cancers with antibiotic use. For example: http://www.pmid.us/18704945.
This line caught my eye – “..lack of diversity in friendly gut bacteria has been shown to contribute to a large number of diseases and complications.”
Could the same apply if one regularly took a single strain of probiotic, eg Culturelle (Lactobacillus GG). Should one diversify when taking probiotics in other words?