Note: The Prescript-Assist supplements discussed in this article are no longer available. Please click here to learn more about a substitute, the Daily Synbiotic from Seed.
I wrote this a while back when I had more time, thinking it might come in handy during the book tour. I was right!
A few years ago, I wrote an article about the often devastating effects that antibiotics can have on the gut flora. While it’s extremely important to avoid unnecessary antibiotic use, what about those who have carefully considered their options and decided that antibiotics are necessary in their situation? Is there no hope for recovering a healthy microbiome?
Need to take antibiotics? You need to read this article.
While having to take antibiotics is never ideal, there are many cases where it is absolutely necessary, and don’t worry – the situation is far from hopeless. It will take some time and effort, but there are many things you can do both during and after a course of antibiotics to minimize the damage and encourage regrowth and diversification of your gut flora.
Probiotics
To some, taking probiotics during a course of antibiotics might seem contraindicated. After all, won’t the antibiotics just kill all of the probiotics anyways? First, keep in mind that probiotics don’t need to actually colonize the gut to be beneficial; even transient strains can have powerful therapeutic effects.
For example, a study on 135 hospital patients taking antibiotics found that only 12% of the probiotic-receiving group developed antibiotic-associated diarrhea, compared with 34% of the placebo group. (8) Additionally, while 17% of the placebo group developed diarrhea specifically from C. difficile, nobody in the probiotic group did.
One interesting study tracked changes in gut bacteria in three different groups of people receiving antibiotics, with one group receiving placebo, one group receiving probiotics beginning after the antibiotic treatment ended, and the third group receiving probiotics both during and after antibiotic use. (9) The group receiving placebo had significantly higher levels of facultative anaerobes (their chosen marker for gut dysbiosis) 20 days after finishing antibiotics compared with baseline, while the two groups receiving probiotics had no significant difference. But even though both of the probiotic groups ended up back at baseline levels, only the group taking probiotics during as well as after antibiotic treatment maintained stable levels of facultative anaerobes throughout the experiment. In the group receiving probiotics only after completion of antibiotic treatment, facultative anaerobes increased significantly during antibiotic treatment, and decreased only after beginning probiotic supplementation. This clearly demonstrates the importance of taking probiotics during antibiotic treatment, as well as after.
Most of these trials used different strains of Lactobacilli, Bifidobacteria, or Saccharomyces boulardii. Lactobacillus and Bifidobacterium are two of the most common genera used as probiotics, so these supplements are readily available in most health food stores or vitamin shops. S. boulardii is actually a beneficial yeast rather than a bacteria, so it’s particularly useful during antibiotic treatment because the antibiotics can’t kill it. S. boulardii is also preferable under these circumstances because there’s no risk of it harboring genes for antibiotic resistance and later transferring those genes to pathogenic bacteria. (10)
Another option for probiotics is a blend of soil-based organisms, such as Prescript Assist. I haven’t located any studies on their effectiveness in conjunction with antibiotics, but based on my clinical experience, I believe they’re a great choice.
As with anything else, the best probiotic to take will depend on a person’s particular circumstances (such as the antibiotic they’re on and the state of their digestive system), but the two supplements I recommend most often are S. boulardii and Prescript Assist. If you don’t do well on either of those supplements or just wish to add more variety, feel free to add in a supplement with strains of Lactobacillus and Bifidobacterium. Do your best to take any probiotic supplement as far away from your antibiotic dose as possible.
Prebiotics
As I’ve mentioned before, prebiotics are much more effective than probiotics at promoting the growth of beneficial bacteria in the gut. Thus, prebiotics are an incredibly important part of any regimen to protect or rebuild a healthy microbiome.
However, one type of insoluble fiber that can be extremely helpful for supporting healthy gut flora is resistant starch. (11) I’ve talked about resistant starch before here and here, and the easiest way to get a concentrated dose of RS is to use Bob’s Red Mill unmodified potato starch. As with any supplemental prebiotic, it’s a good idea to start with a small amount and work your way up. In this case, you could start with 1 teaspoon and work your way up to 2-4 tablespoons per day. If you find that RS doesn’t work well for you, you might consider trying an inulin-based prebiotic.
If possible, introduce any prebiotic supplements before beginning the course of antibiotics so your body can get used to them. That way, you won’t have to deal with possible side effects from introducing the prebiotic on top of possible side effects from the antibiotics.
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Supporting diversity
As I mentioned in my article about the impact antibiotics have on gut flora, the main difficulty after a course of antibiotics isn’t recovering the number of flora present; it’s recovering the diversity. As we’ve seen, probiotic supplements can be incredibly helpful for preventing antibiotic-associated diarrhea and lowering the risk of a gut infection, and I recommend continuing with probiotic supplementation for a period of time after finishing your treatment. However, you can’t expect manufactured probiotic and prebiotic supplements to achieve the diversity of an ancestral microbiome on their own.
These can include kefir, beet kvass, sauerkraut, kombucha, kimchi, and other fermented vegetables or fruits. Keep in mind that foods like yogurt and kefir will probably only have a handful of bacterial strains if you buy them from the store, so homemade is best.
Another way to diversify the bacteria you’re exposed to is by gardening or otherwise getting your hands dirty, although I haven’t seen any research on whether that exposure translates to a more diverse set of gut bacteria.
As far as prebiotics go, just try to get as much variety in your plant foods as you can, in addition to supplementation with resistant starch or another prebiotic formula. Some of the best sources of soluble fiber include carrots, winter squash, summer squash (especially peeled), starchy tubers, turnips, rutabagas, parsnips, beets, plantains, taro, and yuca. Green bananas and unripe plantains (which you can dehydrate to make chips) are good whole-food sources of resistant starch.
Support for the Gut and the Liver
When antibiotics throw your gut flora into turmoil, the gut lining and digestive function as a whole take a hit too. To soothe your digestive system, it’s a good idea to ramp up your consumption of bone broth and other glycine-rich foods while you’re on antibiotics, and continue to consume these foods after the treatment is finished to promote healing.
If you experience nausea or other digestive upset from the antibiotics, ginger can be extremely helpful for reducing inflammation and calming the digestive system. (12, 13) It’s best to use fresh ginger, and you can easily make ginger tea by slicing it and simmering it in water until the tea reaches your desired strength.
Antibiotics can also take a toll on your liver, particularly if you’re on them for an extended period of time. Not only is the liver is responsible for processing and detoxifying medications, it also has to deal with extra circulating lipopolysaccharides from the increased bacterial death and intestinal permeability. Milk thistle is one of my favorite supplements for supporting liver health, and can be taken in a pill (like this one) or as a tea. (14, 15) Glycine is also important for liver detox, so be sure to drink that bone broth!
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Thanks for putting this information out there. I need to start antibiotics today for strep throat and want to minimize the damage.
I can’t thank you enough for all your articles and time. I don’t think you will ever know the full reach of your work and how many people you have helped. Thank you for everything you’ve done to help me without even knowing it. I am forever grateful.
My baby suffers from vesicoureteral reflux and was on a daily small dose of antibiotics since he was 5 days old.(to protect from possible urinary tracts) We stopped the antibiotics when he was 12 months old (today he is 18 months old) but the doctor prescribed no probiotics or anything to protect the gut after the treatment and I myself was unaware that anything like that was necessary until I started reading some articles in the internet. Do you think that the baby should take any prebiotics or probiotics(don t knowthe duifference) now or is it too late and whatever is done is done? Pls note also that the baby has been breastfed and is still breastfed until today. Pls help and thank you for your valuabke time in advance
Dr Mercola has something on how to improve gut flora in children
http://articles.mercola.com/sites/articles/archive/2013/07/18/autistic-children-gut-flora.aspx
btw Vaccines are the number one health danger for children. keep your child away from them.
Thank you !
I have to be on IV antibiotics during labor, which I’m a bit nervouse about. Can you recommend any specific regimen to take before/during/after to keep myself and my newborn from having too many issues? I plan to breastfeed as well and worry about antibiotics passing through the milk.
I would think about taking coconut oil before and after. It will keep the many bad guys in check from getting out of control. Start off with small amount and work way up to 2-3 tablespoons. I think antibiotics can set off all sorts of fungus diseases – one of the most ignored group of infections out there.
Thank you for this article, it’s very informative.
After a case of Rheumatic Fever this past summer, the specialists have said I will be on antibiotics for 5 years…I tried taking probiotics but they made me sick. So now I just drink a probiotic yogurt daily which I’m sure is not enough. I’m also pregnant now (11 weeks). Do you have any suggestions as to what I can take to keep my body healthy? Thank you so much!
i assume you are on low dose penicillin. i recall studies of people with cellulitis infections fared pretty well many years on penicillin. You should look at what happens to people on penicillin that long to understand what you may have to do.
Ok, thank you for your reply.
Hey,
Great article as always. I took bio-kult (I’m on GAPS), but I am now on PA. I can’t find any information about the best time to take probiotics, PA. With food or without? Read about probiotics not surviving the hcl in the stomach if taken on an empty stomch. Is this true? Does timing even matter?
Thanks!
You take with food. I could imagine that some of the probiotic may not survive.
For those of you looking for a probiotic to give infants, believe it or not, Gerber has a good option. Gerber recently bought the company Bio Gaia (who made a very expensive probiotic for infants) and Gerber has basically relabeled the BioGaia probiotics as their own!
The product is called “Gerber Soothe Colic Drops.” They are over the counter and approved for use in infants.
What about someone having a kidney transplant? There are more restrictions on what they can and can’t take, what would you suggest for them to protect if antibiotics needed? For the last 6 months they have been eating 2 big mouthfuls of fermented kraut and kimchi daily. Thanks!
After a long hard battle with a severe ear infection, we finally ended up having to give our 10 month old son antibiotic injections. It has been stressful and very disappointing to say the least. We first tried seeing a naturopathic doctor, tried waiting it out–but the infection continued to progress and was causing 103 degree fevers. It got a little scary.
I currently give him Pharmax HLC Mindlinx, plus cod liver oil. Is there anything else I can do to repopulate his gut? He is still primarily breastfed but we do give him soft meats, cooked vegetables, poi, and some fruits (no grains, no dairy so far). I was thinking of starting raw kefir (cow), and maybe seeing if he would eat raw sauerkraut, etc. What would you do for Sophie if she ever ended on a course of antibiotics? With babies, there are less food options to offer them until they start eating more.
The most critical thing you can do to protect a baby’s health is makes sure you DON’T vaccinate the baby.
The second thing is try to make sure the food is non GMO.
I don’t have any diet recommendations.
http://healthychild.org/five-natural-remedies-for-ear-infections/
Hi N Boyd,
I know you asked Chris, but I figured I’d chime in too. We have three kids. Our second and third started on bone broths and milk kefir before a year. And sauerkraut is a great idea too. Both girls (2 and 3) love sauerkraut, salt brine pickles and beet kvass. I think starting them so young really helped.
Also, FCLO and grass fed gelatin.
Don’t get too discouraged. It sounds like you’re doing all the right things. If you continue on this path, you’ll be surprised at how much you can repair. When I was pregnant with my first (who is now 6), I ate mostly vegetarian and had horrible gut flora (but didn’t know it). He is so wonderfully healthy and hasn’t taken an antibiotic for 5 years.
You may want to check out Oregano essential oil as an alternative to antibiotics for the future.
And kombucha for beneficial yeasts is especially helpful after antibiotics. It contains S Boullardi.
Thanks Megan! I appreciate the info and encouragement.
Chris, what do you think of Probiotic-3, specifically of Streptococcus faecalis strain there?
Chris, I love all of your articles . . . and I used to be a big fan of Milk thistle – used it effictively for years during cleaning fasts. However an ND told me last year that milk thistle is now recognized as only beneficial for protecting the liver from long-term damage, and not beneficial for short term liver cleansing. Does that sound right?
I was diagnosed with strep throat 5 days ago and prescribed amoxicillin. I hate taking antibiotics and have only been taking 1-2 per day, as opposed to the recommended 3/day. I caught hell this morning from some coworkers, one of which who called me selfish for not taking my meds as prescribed and possibly putting the rest of them at risk. The other one told me that I need to be careful because strep can affect my heart. I feel fine, haven’t had a fever since Friday, my sore throat is gone, and I feel otherwise healthy (aside from a very slightly stuffy nose). Is there any kind of middle ground with antibiotics, where I am receiving the strep-fighting benefits but not wreaking as much of havoc on my gut? I felt ill-prepared with my rebuttal and really should have just kept my mouth shut.
Additionally, I am taking elderberry syrup, colloidal silver, bone broth, vitamin C, and probiotics.
There are views that state that taking antibiotics for strep throat are useless. It doesn’t make any difference in recovery. What many people have done is just let the strep throat clear itself. I did get strep throat a year ago and took amoxicillin but on hindsight I wouldn’t take them again. My inner sense says that they made no difference.
As far as people’s reaction, you have to understand the standard advice. I don’t think a short term stint on amoxicillin is going to harm you so I’d compromise and either take the antibiotic or just plain lie and tell them you are taking it so there are no political problems and for their psychological comfort.
I do think strep is communicable so you shouldn’t go to work if you are still sick. If you are well then I wouldn’t worry about it. Maybe just wash your hands during day at work for a week or so as a safety precaution since you are more likely to spread it by touch.
Are the above mentioned prebiotics and probiotics safe in children who are prescribed antibiotics? My 11 month old is battling yet another ear infection and I’m beyond reluctant to utilize antibiotics without some natural assistance. Any help is greatly appreciated.
Klaire labs has a probiotic for kids under 2. You should also find a Chiro who is experienced with adjusting kids.
Chris, do you have any information about the effects of a colonoscopy (specifically, the colonoscopy prep) on the gut microbiota? Is it as devastating to the gut flora as antibiotics? It has been 10 years since my last screening colonoscopy, and my doctor has been bugging me to schedule another. I have a reasonably happy gut at the moment, after a certain amount of effort with careful diet, probiotics, fermented foods, resistant starches, etc., and I hate to think of it all going down the drain, so to speak. I assume that your tips for antibiotic use would apply to any disturbance from a colonoscopy. Any other suggestions?
My seven month old son keeps getting ear infections and we are trying to avoid antibiotics but are now on our second round in a month. If I take a probiotic and/or prebiotic will any of the benefits be transferred to my son if I am breast feeding? I’ve seen Culturelle for kids but it is recommended for age one and up.
Valerie, try breast milk directly in your little one’s ear to help with healing. I also gave my child both Bio Gaia Probiotic Drops and Baby’s Jarro-Dophilus before she was one.
Middle Ear Infections
“90% of upper respiratory infections, including children’s ear infections, are viral, and antibiotics don’t treat viral infection. More than 40% of about 50 million prescriptions for antibiotics each year in physicians’ offices were inappropriate.” CDC
“I have treated many hundreds perhaps thousands of cases of ear infections with echinacea and I know it works. I rarely have to give antibiotics or use tubes to clear up these infections.” Doctor Jay Gordon, Pediatrician Cedars Sinai MC
“The best way to prevent allergy in infants is to breast feed them. Children who are allergic to foods often have fluids in the ear tube leading to infections.” Prevention
“We found in our clinical practice an over 90% reduction in middle ear problems with the kids using xylitol for their teeth.” Doctor Lon Jones D.O. Note Doctor Jones also had good results using xylitol with colds, allergies, ear infections, sinus infections and dental health.
“I hope with the publication of this book more pediatricians will get their earache patients using xylitol.” Doctor Lon Jones D.O.
Giving a child Drug Antibiotics for a middle ear infection is almost never a good idea. Anti-biotics are vastly over prescribed presumably to induce the placebo effect in the paying stiff. Fine, use SUGAR PILLS, please. Believe it or not Drug Anti-biotics are STILL given for viruses. But please don’t YOU be so foolish as to accept this insane “Prescription”.
http://healthyprotocols.com/3_antibiotic_1.htm
Fungal infections are the most under reported infection around. They are implicated in COPD, emphysema, bronchitis, asthma, sinusitis etc. People who have cured themselves used an anti-fungal approach.
Hi,
This is a great article. I am so excited to see this! I have been considering Prescript Assist for several months, but have been hesitant because I’ve read some warnings against it because the SBOs are spore-forming, and apparently, they can take over and cause problems because of this. I am wondering what Chris Kresser’s response is to this.. AND… feedback from anyone else who has tried it.
Thanks!
Read my previous response about “spore-forming” here: https://chriskresserlac-shopify.helpjuice.com/questions/47699-Prescript-Assist-and-*spore-forming-organisms*
Thanks for referring to the article. It was very helpful.
I’ve been drinking a mass-produced kombucha available at grocers – I would appreciate any feedback on whether or not it is worthwhile from a gut flora perspective , or just a marketing gimmick?
Some people have chosen to not take Kombucha due to the high flouride content. Some have changed to Kefir soda. Suppose to taste like cream soda. You can make your own. Kefir is a very good probiotic also.
I haven’t looked into the issue too much but one needs to distinquish between natural fluoride and synthetic fluoride (for lack of a better term). One perspective is that natural fluoride is beneficial to the body.
My only position on fluoride is that the kind in water supply damages ones health but I haven’t done enough research to decide about Konbucha.
These are the things you need to look into.
Up until a few years ago commercial kombucha was umpasteurized. If I’m not mistaken the feds started requiring that it be pasteurized, so I assume it has no live bugs left in it. (I know that live cultures are ADDED BACK to yogurt and kefire after the pasteurization, I don’t think this is the case for commercial kmobucha). Maybe somebody can confirm this for us.
Best to make your own. Avoid commercial products. Use raw milk if you can. The reason raw milk was banned was to increase death and disablement in the population.
Pasteurization is acceptable if your going to boil or cook the milk.
Do intravenous antibiotics have the same (more? less?) devastating impact on gut flora than oral antibiotics?
It is my understanding that since they bypass the digestive track, they don’t impact the gut flora.
Do they not impact the gut flora at all? I’ve heard that side effects are not as bad, but since they are running through the bloodstream, wouldn’t they still have some effect? I’m actually not sure, but wanted to get more feedback.
Chris Kresser should give the definitive answer.
i found this comment by someone
————————–
Its the route out that counts.
Some like IV vanco will be filtered by the kidneys and peed out and not reach a “theraputic” level in the gut
Others like IV flagyl will be filtered by the liver and be excreated in faeces meaning the gut gets a “theraputic” dose of antibiotics.
———————-
I would think the antibiotic would be more diluted if it goes through the body hence less impact on the gut if any does and up there
Chris Kresser, could you comment on this one? What effect do IV antibiotics have on gut flora verses oral antibiotics?
Thanks!
I have had constipation for almost 70 years. I have an artificial aortic valve and take coumadin. Any time I need dental work I have to take a three pill antibiotic all at once. I am suspicious that I severely lack bowel motility. Right now I take a heaping Tbsp of ionic citrate of magnesiun, nightly. That keeps me pretty regular and I do drink 70 oz of water every day. I do Crossfit four days a week, eat Paleo. Any suggestions? I have used the prebiotics and probotics but do not notice any change. My CF coach suggested some sort of fresh, liquid p. biotics but I can’t find any. Help!
Coumadin is a very bad drug to be on. It is one of the four drugs responsible for 25% of visits to emergency. It causes damage to ones health in long run. It is better to take nattokinase which has no side effects.
I have been writing down the suggestions and looking up all the ideas. I only need the antibiotics when I see the dentist, for instance. The concern is not to let clots form on the artificial valve. I was thinking that needing them several times a year was interfering with the natural biota in the colon.
Thanks for all the ideas, I will post when I try one or several with the results.
Sally,
google up Resistant Starch. I believe Chris has covered this somewhere, and there’s oodles of rather uncouth, but amusing and useful, information over at FreetheAnimal. I tried it and it worked like a charm in about a week. Main advice would be to start veeeery slowly and up the dose gradually.
Umm, you’d better also discuss the possible effects of RS on coumadin with your doctor, before starting.
When you say “beneficial bacteria is found in … peeled fruits” do you mean fruits with edible peels or do you mean fruits from which you have removed the peel.