Antibiotics and bacterial dysbiosis

by 2565 · October 04, 2013 at 03:53 PM

I have all the symptoms of bacterial dysbiosis (bloating, pain, fatigue, brain fog, etc) and probably SIBO. I've tried every kind of probiotic you can imagine and I actually either feel worse after taking it or not affected at all. I've read that if you have SIBO, taking probiotics can make things worse since you already have too much bacteria growing in your upper gut and adding more in concentrated doses won't help until you've reduced the overgrowth already present. Some health practitioners recommend taking a course of antibiotics for this followed by probiotics to repopulate the gut, so I was thinking of doing that. However, I've also read some recent research suggesting that after antibiotics our good bacteria don't come back for a long time, and sometimes never come back http://www.wired.com/wiredscience/2011/08/killing-beneficial-bacteria/. I was wondering what everyone's thoughts on this are, and if I take antibiotics, how long should I take it for?

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I have been diagnosed with SIBO via a breath test, and matching symptoms to yours. I have battling it for over 3 years. I have tried EVERYTHING, so I might be kind of helpful to you, at least in ruling out things to try.

-Probiotics are hell for me and a huge waste of money!!!

-The Mark Pimentel protocols referenced by another answer was USELESS. I have taken two rounds of rifaximin at his suggested dose. (Plus another round of a different antibiotic). There was zero effect, including while I was on it -some people experience relief while on the antibiotic but not after). Mine was neither. Also I read somewhere that he has his hand in the honeypot for that drug. (Here is the article).

-Regarding Cliff's answer about the Peat carrot salad. I have been doing eating it daily, along with the pro-thyroid Peat diet for over 4 months with No effect.

I have literally tried everything from GAPS, to autohemotherapy, cleanses, chinese medicine ,eliminated everyfood (drank coffee and ate ice for weeks at one point in desperation to take a break from my damn digestion issues), consumed digestive enzymes to the tune of $200 a month worth, coconut oil every day for years....

What I am doing now is still the Ray Peat thing...however I am looking at SIBO strictly from a thyroid spin. Peat says that having chronically low thyroid allows bad bacteria to slowly creep up the digestive system, and a sure sign is small intestinal bacterial overgrowth. He also says that someone can have low thyroid but test normal, because of the expansive normal standards skewed by generations of low thyroid people. Going by the symptoms of low thyroid (including body temp and pulse rate), I have been experiencing low thyroid for years if not decades. It has taken a few months to get to the right dose of thyroid, and I have only been on the right dose for 2 weeks. But I feel like a different person -full of energy, warm, positive mood :except for my damn digestion!

So now, I am pinning all my hope that having a super great thyroid (and supporting it and my liver with the Peat diet suggestions), will allow my body to naturally get rid of the SIBO. I will keep you updated, and good luck!!


For me, reducing carbs to less than 25g/day had a good effect on dysbiosis at first, in that the symptoms entirely went away. Unfortunately, I had to up the carbs (to address cortisol from the stress response resulting from low carb). A few weeks later, the dysbiosis started up quite badly. Just before the dysbiosis blew up, I increased magnesium supplementation a lot. I suspect this made the gut environment more alkaline and encouraged the overgrowth. I also suspect I started to get too liberal with the potatoes in the evening. I have cut back on the carbs and magnesium and I am seeing some improvement.

I read somewhere on PH that unlike fungi, bacteria can't use ketones - if so, low carb/ketosis shouldn't give overgrown bacteria any kind of leg-up (over the beneficial ones)?

What helps me with some of the symptoms, brain fog, particularly, is molybdenum, which is a co-factor with the enzyme that deals with aldehydes. Glutathione is supposed to be good for aldehydes and brain fog but I am not sure it makes a difference. I remember once trying glutamine and it seemed to help a lot with brain fog and sore tongue. I was nervous about continuing it because of the excitatory effects, but I'm thinking of trying it again.

It will be good to hear how you get on - please keep posting on progress.


The human digestive track is a carnivorous one and doesn't rely on bacteria outside the colon. People can live without a colon, so that should tell you something. The appendix serves as a reservoir of colonic flora.

My experience with probiotics matches yours.

An alternative to antibiotics is a diet that will starve the bacteria. That means VLC/low residue or zero carb, unless you're ok with having to drink glucose filled liquids for weeks.

Walter Voegtlin talks about a similar diet - one that is optimal for human digestion and eradicating fermentative gut flora - in "The Stone Age Diet", which is available here.

The "Cedars Sinai" SIBO protocol by Mark Pimentel uses rifaximin for about a week... look into his book "A New IBS Solution".

There is more information on http://www.siboinfo.com/ and the author will release a new book on the topic next year.


Hi Chris,

This is highly empirical and theory-based. I would suggest the following (consult with your doctor first!):

  • Broad-spectrum antibiotics. This should help "resetting" the gut microbiota and reduce potential colonization resistance.
  • Concomitant supplementation with probiotics (Bifidobacteria and Lactobacillus). There are differences between strains, but most available probiotics use the strains known to compete with enteropathogens. Aside from direct competition, some produce anti-microbial molecules.
  • Supplementing with potential biofilm disruptors. There is an interesting laboratory which uses several enzymes shown to disrupt bacterial biofilms (1). However, I haven't seen hard evidence yet. Some natural plants can inhibit quorum sensing, like oregano, basil, rosemary, turmeric, berries, among other.

These measures, coupled to a healthy diet should help in SIBO.

11648 · ABOUT 17 HOURS AGO

I'm not a doctor, and this is not medical advice, but this is how I got rid of my SIBO/IBS-D problem.

Avoid antibiotics UNLESS you have mutated microbes that can't be dealt with diet (e.g. protozoal, CDiff, H.Pylori, gardia parasites). You need to test for these specifically. Only get antibiotics if you have something like that. Most "normal" bacteria and yeast overgrowth can be dealt on with diet.

So, follow a strict Paleo diet (including offal, bone broths, coconut oil), and if you do dairy, only do goat dairy, and only lactose-free (home-made probiotic yoghurt, hard cheeses). Then, eat probiotic foods: sauerkraut, the goat yoghurt mentioned above, raw & unfiltered local honey, Yogi kombucha green tea decaf, and eat some prEbiotic foods too (list of prebiotic foods on wikipedia). Last but not least, supplement with D3+K2+Mg (and Ca if you don't do dairy), and alternate it daily with krill oil and a multi-vitamin (Nature's Way Alive is the one I use). Get a multi-probiotic pill (I prefer iFlora) just before you go to bed. Probiotics will make you feel worse for a week, but then your body learns to deal with them.

With this regime, I went from 4-5 diarrhea episodes a day, to having one solid, healthy stool every day, within 20-45 minutes of waking up. I saw changes within the first few days, but it took about a month to get there overall.

32177 · ABOUT 17 HOURS AGO

If it were me, I'd try some high dosing of Vitamin D for a week (Acts like an antibiotic in high dosages.) and avoid FODMAPS, going vlc for 3 weeks.

Then I would add back in some carbs one at a time to see what you tolerate. Kombucha works for me as a food-based probiotic that you could try, too.

77322 · ABOUT 17 HOURS AGO

Try all the metabolic avenues, but at the same time find a neuromuscular therapist in your area who has been trained to do organ massage, aka visceral manipulation. The physical component of dysbiosis is EQUAL to the functional side. Dysbiosis is facilitated by physical "kinks" and stagnations throughout the digestive system. Then, if you find the right metabolic fix, , a complete recovery can be thwarted by pockets resistant to treatment. You can even work the intestines yourself. Google search brought up a lot of junkie stuff, so that's no help. Just go sqaure inch by square inch with two or three flattened fingers on each hand in a counter clockwide motion. You will feel many many area of hardness and discomfort. Work at a level of MILD discomfort. the Pain will go away. Not only are you "dekinking" the system, the visceral manipulation is mixing good bacteria from unobstructed areas with bad bacteria from obstructed areas. Intead of introducing exogenous probiotics, which many people here and elsewhere doubt works or can ever work. Can probiotics survive the stomach acid? In this case you're using the good bacteria that's already in the gut. Endogenous good bacteria. As long as you have some good stuff, squish it around and have them fight the bad guys. A bacterial Civil War. It works for me every time. It may take more than one "battle" , but the war can be won.


Antibiotics is one of the main cause of dysbiosis so it's like adding fuel to the fire, imo. Often times, it encourages other diseases to enter your body. Ever notice why the use of antibiotics are restrained even more today? People are learning that you don't mess with antibiotics cause it may heal an isolated problem in your body but can put your overall health at risk. Diet is the biggest role to cure you of dysbiosis. Eat foods that are HIGH IN FIBER. Try any or all of these effective natural stuff as well: astragalus, olive leaf extract, medicinal mushroom extract, and oil of oregano. Btw, do you know what kind of dysbiosis you have? The type of diet advisable for you depends on the category of your dysbiosis.


Are you sure it's dysbiosis, or only dysbiosis? Those are also symptoms of adrenal fatigue. I'd take the questionnaire here http://www.adrenalfatigue.org/take-the-adrenal-fatigue-quiz You might be surprised.

0 · October 04, 2013 at 01:40 PM

Antibiotics are medicine that kills bacteria or slows the growth of bacteria. They are used to cure diseases. Antibiotics do not harm people. Penicillin is a popular antibiotic. Antibiotics started to be produced in 1939. Antibiotics cannot stop a virus. Antibiotics are not the same thing as antibodies.


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0 · August 12, 2013 at 03:31 AM

don't do a low residue diet. i tried it. it's ridiculous and gives you a false positive. of course most of your flatulence and bloating will decrease because you don't have anything to feed it. but that does nothing for the underlying problem such as a damaged gut that got you to where you are to start, or a lack of good bacteria. soluble fiber is good for you but i agree it can be problematic by feeding the bad bacteria. this is easily fixed by ingesting probiotics alongside your soluble fiber. a much better approach! this is from experience. try acacia fiber. i find it very agreeable!

0 · February 13, 2013 at 08:00 PM

You're not alone, millions suffer from gut dysbiosis.

The major turning point for me was a grain, dairy, nut, nightshade, coffee, and yeast FREE diet (Paleo Autoimmune Diet).

Taking hydrochloric acid (Betaine HCI) every time I ate.

I originally thought probiotics were a scam, and many are for that matter, but some are also lifesavers. There are HUGE quality differences in probiotics, Jarro's brand was the only brand that worked for me after trying many, many different probiotic supplements.

Amazon's Reviews:


0 · January 25, 2013 at 09:43 PM

Not related to dysbiosis in particular (but includes it) is eating the wrong foods for your blood type. All you need to do is know your blood type, go to this website http://www.dadamo.com/typebase4/typeindexer.htm and for a large list of foods, each food for each type is categorised at beneficial for your health, neutral (safe to eat) or a food to avoid. I've been on it mostly by avoiding red meat and pork (I'm type A and live at home) and have noticed a large improvement in my bowel movements, little indigestion, much more energy and feeling healthier overall.

578 · December 26, 2012 at 04:31 AM

The best thing you can do is to avoid eating lots of fermentable fiber(Soluble fiber, prebiotics) that feed bacteria. You gotta starve it out, they need to die off. I agree with Dean. Go on a low carb/fiber diet and eat a more a higher fat/animal protein diet. Avoid all fruits, high fructose vegetables, simple refined sugars and sweeteners, starches, lactose and most FODMAPS. Eat mostly fish, seafood, eggs, beef, lamb, chicken, turkey, buffalo. Raw virgin coconut oil helps balance intestinal flora. Use olive oils, ghee, grassfed butter (kerrygold), avocado oils and eat some nuts and seeds occasionally. If all else fails, get medical help. I hope your condition improves and you feel better. It sucks going through life feeling crap all the time:(. You know what else might help? high quality Colostrum.

12804 · ABOUT 17 HOURS AGO

Make a daily salad of raw grated carrot and eat it alone between meals. Also Minimize starch unless you eat it with a lot of fat or just stick to fruits(preferably ones with low fiber).

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