What To Do If You Need To Take Antibiotics

thyroidmedication

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. There are quite a few randomized, placebo-controlled trials that have demonstrated the effectiveness of probiotic use during a course of antibiotics for reducing side effects and preventing gut infection. (1, 2, 3, 4, 5, 6, 7)

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. During and after antibiotic use, focus on getting plenty of soluble fiber, which feeds beneficial bacteria and is found in starchy tubers, squash, and peeled fruits. It might be best to avoid too much insoluble fiber while your gut is in a compromised state, since it can be irritating to the gut lining.

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 such as this one.

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.

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.

One of the best ways to expose yourself to more diverse beneficial bacteria is by consuming fermented foods, so I highly encourage you to experiment with a variety of different ferments. 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!

I hope you found this article helpful. As always, I’d love to hear from you in the comment section; just be mindful that I’m busy with my book tour right now, and may not be able to reply to your questions. But many of my readers are extremely knowledgable, and I encourage you to take advantage of the free forum in addition to the comments section to bounce ideas and experiences around.

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  1. PillPopper says

    I’m on the Antibiotic Protocol for a serious autoimmune disorder for the past 3 1/2 years. The treatment has helped my condition tremendously and the alternative is deadly, so I am not likely to give it up.

    What do you suggest I do in terms of probiotics? I currently take either one Culturelle daily or 2 PB-8s. Is that enough?

    • Chris Kresser says

      I made some suggestions for probiotics in the article. Prescript Assist and saccharomyces boulardii are good choices when you’re taking antibiotics.

      • Tracy Anderson says

        I have IBS and use Prescript-Assist with great results. Regarding the Prebiotics I use a product called Heather’s Tummy Fiber, which is Acacia Senegal Fiber. I had tried Inulin, metamucil and it made my cramping worse. I now take Acacia Fiber daily with good results. I now only need to take the Prescript Assist three times a week. At least unless I really have to take antibiotics again!

        • prioris says

          Aloe Muciliginous Polysaccharide (AMP) capsules is a highly concentrated form of Aloe Vera and a natural antibiotic. Use that for IBS. It is used for Diverticulitis also. It works.

        • Jennifer says

          I use Heather’s Acacia senegal (aka Tummy fiber) as a prebiotic as well. I have IBS symptoms and it helps tremendously. Thanks for posting this. I’m wondering what Chris Kresser thinks of Acacia senegal as a prebiotic.

      • Jeannie Ology says

        Prescript Assist is wonderful.

        I had C-Diff and it was cured with a fecal transplant. After 14 months of being clear — I’m presently in a bout of diverticulitis infection — I was put on antibiotics. The thought of taking them terrifies me. Every pill is a major anxiety attack — literally.

        I am taking Florastor and Prescript Assist 2x a day in between doses of ABX. It’s giving me a little piece of mind. Not much, but some.

        I also have Nexabiotics in the fridge.

        • prioris says

          you can use AMP instead. see my posts under diverticulitis topic. they will cure the diverticulitis. no need for antibiotics.

    • Noel says

      Look at VSL#3, expensive but very effective. Once you settle with VSL#3 and you are off antibiotics, Nexabiotic routine is also a good thing.

      Personally, I use VSL#3 DS, Nexabiotic, Probiotic-3 and Prescript Assist. I have Ulcerative Colitis. As stated, I don’t use all of them all the time, VSL#3 to prime and rest for maintenance.

  2. says

    Is stock the same thing as broth? We get boxes of “Swanson 100% Natural Beef Broth” where the primary ingredient is “beef stock”. I’m sure homemade is much better, but is this stuff at least in the ballpark? It says that it’s fat free, which doesn’t inspire confidence…

    Also, your “getting your hands dirty” link points to http://www.apple.com. I guess you’re an Android fan? :)

    • Chris Kresser says

      We’ll fix the link, thanks.

      Unfortunately store-bought broth is not remotely the same as homemade, largely because the benefits of stock are primarily in the fat and from the bones, skin, cartilage it’s cooked with. You can add gelatin to store-bought broth to make it more nutritious, but homemade is much better. The good news is it’s fairly easy to make.

        • Carneiros says

          You can buy really nice broth at the store that is just as good as the homemade stuff. I’ve seen some at my local health food store that even contains gelatin. Unfortunately, they cost like $6 per quart. 3lbs of grass fed beef bones costs about that and you can make maybe 10 qts of broth from it, if not more.

        • says

          Anthony,
          Making your own bone broth is really incredibly easy. All you need is a crock pot (slow cooker) and a chicken carcass. After you eat your roasted chicken, take the carcass and toss it in the slow cooker. Add all sorts of chopped veggies to it, especially onion, carrots, celery, add a bay leaf and some whole black peppercorns, a little sea salt, and cover it all with filtered water. Set the cooker on low for 12 hours. Turn it off, allow to cool for a few hours, then strain. Voila! you have bone broth. The color is magnificent. No store-bought stock/broth will ever come close to the richness and delicious flavor of homemade. Give it a try.

          • says

            Thanks. Maybe I’ll give this a try. I had read recipes saying to cook for 24-48 hours on the stovetop, which sounds like a hassle and I don’t like the idea of leaving the stove on for that long; the crockpot seems much more appealing for this. I’m more interested in beef broth than chicken broth, though; I wonder if just 12 hours would be sufficient for beef bones?

            • Bet says

              12 hours would be enough for beef bones. For beef you are supposed to roast them a bit first, but I’ve done it without roasting. When you buy the bones (preferable grass fed bones) you want to get joint bones that have some cartilage in the so you will get the nice gel from it. If you can let it go more than 12 hours, that’s good too. You will see the meat and cartilage come off the bones and that means it’s done.

              • Rebekah says

                I would recommend 3 days on the beef broth! 12 hours is not even enough time for chicken broth. A very low boil is all that is needed. Do not forget to skim the scum off the too in the beginning.

        • Brian Klein says

          Wise Choice Market makes bone broth that they claim is like homemade. It seems we would be able to take them at their word. It’s much more expensive than making your own though.

      • says

        It really is easy to make. And so totally worth it. I love to cook but never realized what I was missing by buying store-bought broth. Since I’ve been making my own, it’s taken my soups to a new level. In fact, it’s so darn good, sometimes just a cup of the broth makes a great “snack”.

      • Peg says

        Chris, I’ve recently started making bone broth with grass-fed bones. You mention fat as being one of the benefits, but one large bone generates an enormous amount of fat. (I just pulled a 2″ plug of solid fat off the top of my jar of broth).

        So what do you do with all that fat? I couldn’t eat it in a soup. Any way to cook with it?

        thanks,
        Peg

        • says

          Hi Peg!

          If you’re using beef bones, the fat you have from making the broth is beef tallow, which is great for cooking! I usually just pull it off the broth once it’s solidified, re-melt it on the stove, strain it (if needed; usually it’s already clean enough for me!), and store it in a jar in the fridge. You can use it to cook pretty much anything savory, but I especially like it if I want to “deep-fry” things. It’s not actually deep-frying, but I use a decent amount of fat when I’m making things like hash browns, and I like using the tallow because it’s very stable and it’s cheap!

        • Sybil says

          The farm where I buy my meat and eggs from sells “homemade” chicken stock. Just a thought ….check the farmer’s market if you don’t want to make the stock.

      • Lynn says

        Gotta hunch this won’t fly for stock, but I usually use Knorr Bouillon Cubes when making soup. Is there any nutritional value for them? Anything detrimental?

        • Serenity says

          Sorry, but those are no good and will give you none of the benefits of homemade broth. Here is the ingredient list: INGREDIENTS: Salt, Monosodium Glutamate, Beef Fat, Partially Hydrogenated Cottonseed Oil, Yeast Extract, Caramel Color, Dehydrated Beef Stock, Dehydrated Vegetables (Onion, Carrots, Parsley), Turmeric, Disodium Inosinate and Disodium Guanylate, Spices.

          Hydrogenated fats, msg, fake coloring, tons of sodium and a bunch of other industrial ingredients. I’d ditch this fast. Homemade broth really is easy to make and you can make a large batch and freeze small amounts in freezer bags.

      • Jeannie Ology says

        BTW I have a pot of bone broth cooking right now to help heal my intestines.

        Any ideas on how to prevent this from happening again?

  3. Heather says

    Your website is informative and I enjoy it very much. However, it is reading my iPad mobile signal and automatically giving me the mobile content rather than the desktop version I would prefer for the iPad. It would be a wonderful improvement if you could offer the choice of either mobile or desktop content on the website rather than an automatic load (and I would have posted this somewhere else, but there does not appear to be another way to contact you). Thanks.

    • Andrew Pautler says

      Heather, I’m glad you like the site. Unlike some sites that offer a more minimal mobile experience, we are currently loading all of the content on the site regardless of your screen size. That said, given the more limited space on mobile devices, we have to make some layout adjustments as the screen size decreases. One suggestion for you would be to flip the orientation of your iPad. If you view the site in landscape mode (instead of portrait) it will look almost identical to what it would on a desktop. Let me know if that helps!

      • Heather says

        I have been viewing it in landscape and ever since I posted a comment it no longer gives me the sidebar information (popular or recent posts, etc.). Now I have to scroll to the end of articles to see that. Also, I can no longer see the website header, just the article title. Maybe it is just an “error in chair” situation, but I can’t figure out how to get the content to show up in safari the way it did previously.

  4. Tarah says

    My cat, Moccasin, recently had to have antibiotics, and I hated to give them to her and ruin her little gut, but it was necessary in her situation. However, I have done some cursory research online, and found that pets can have probiotics, too.

    I opened up a capsule of acidophilus and sprinkled some on her wet food, and I also gave her a little full-fat plain Greek yogurt. Do you think pets on antibiotics could also have prebiotics? Do you have any pets, Chris?

    • Adam says

      Tarah, Google: Are cat probiotics the same as human probiotics. My understanding is that cats microbiome is populated with different strains than humans so human probiotics may not be the best. I found an article by Dr. Becker on Dr. Mercola’s site that stipulates that. Indeed when I’ve had probiotics sent home with my cat I did not recognize the strains from the zillions of probiotics I’ve take over the years. My vet told me not to use human probiotics for the cat. Additionally it is my understanding that dairy products are not good for cats either as they are intolerant not having the ability to break down milk ‘sugar’. Lactose.

      • Marissa says

        Yogurt does not have much lactose and I give my cats some regularly with no ill effects. I have even seen cheese and dried milk on the labels of some cat foods.

        • Peg says

          Just because a manufacturer puts that into a product, doesn’t guarantee it’s good for cats. Sometimes ingredients are included to seduce the buyer of the cat food, not the cat. Just sayin . . .

    • Gabriella Kadar says

      Wellness cat kibble is sprayed down with probiotic bacteria. 80 million colony forming units/pound. Check out the information on the bag. At the beginning, just give the cat a little of this because it may cause loose stools. One of my cats is presently on a 42 day course of doxycycline for mycoplasma. He gets live culture yoghurt every day as well. No diarrhoea.

  5. says

    Hi Cris,

    I am from Slovakia (in the middle of europe). We call here potato starch solamyl as well. According to you it is solamyl safe and appropriate source of rezistant starch. What is your opinion. Thanks in advance.

  6. Peter says

    Chris,

    Great article. I am suffering from Lyme disease and have been cycling on and off antibiotics for over a year. Do you have any advice in terms of timing for both prebiotics or probiotics (on a daily basis)? Some protocols have me taking antibiotics 3 times a day so it becomes increasingly difficult to space out 5 pills (assuming I am taking probiotics twice) and potentially 6 pills/mixes if I intoduce a prebiotic into the mix (which I will do per your advice). At this point does timing make much of a difference? Finally, I have been following your auto-immune protocol would the potato starch as a prebiotic be a bad call to introduce at this point? Basically should I just go with the Prebiogen? Thanks for all the great work. You have been a life saver. Looking forward to starting your new book. Best of luck with everything.

    Regards,

    Peter

    • Chris Kresser says

      There’s no need to take probiotics 2x/d. Given your med schedule, I’d suggest just doing it once a day.

  7. says

    Interesting studies. Thanks for providing the links. I’ve been treating chronic Lyme disease and other systemic infections for several years with herbal and nutritional support. Although I didn’t want to, in the last few months I found it necessary to start taking oral antibiotics and now on daily IV antibiotics as well. Surprisingly, my digestion and bowels have been better and more normal than they’ve been in a long time. I’ve found that probiotic supplements along with a good variety of fermented and cultured foods like you mention has benefited me the most, even while taking so many antibiotics. I think the best you can do while on antibiotics is to take supplemental probiotics spaced out as far away from the antibiotics as possible and try to get some type of fermented foods all throughout the day, even if only in small amounts. Klaire Labs Therbiotic Complete, Florastor, and foods like beet kvass, pickles, sauerkraut, yogurt, kefir and kombucha have helped me quite a bit.

  8. Isabel says

    I am taking massive doses of antibiotics currently 1,500 twice a day, for 2 weeks for H pylori. I was reluctant to take them but was told that H pylori can lead to stomach cancer. Have been on GERD med for +10 years, doc wants me off it. I have had no issues with my gut, thankfully. Am I just one of the lucky ones or is my gut compromised and I just don’t know it? Thank you for the information on prebiotics. I take neither pre nor pro but was thinking of starting to take the pro. However, I will research your website for more details and likely change that idea to the prebiotics.

    • Lynn says

      If you are taking proton pump inhibitors they reduce the acid, obviously, but that can lead to B12 deficiency and allow bacteria that the acid would kill to have a chance to take hold – H.pylori is the prime example. I have had a few clients with this same issue and they take deglycyrrhizinated licorice, zinc carnosine, aloe vera and L-glutamine for the H.Pylori. For the acid reflux, I would check with someone who does visceral manipulation to help pull down your stomach – if you have a hiatal hernia. Then I would drink Kombucha or apple cider vinegar and eat sauerkraut along with the bone broth. Home brewed is best because pasteurization destroys the health benefits.

  9. joyce says

    Dear Chris,
    I am a 53 y/o otherwise healthy woman who has been eating paleo for one year. Hip replacement surgery infection at incision site has caused me to be on oral cipro and massive doses IV Vancomycin for six weeks. Side effects are joint swelling, soreness and unusually slow recovery time. Wondering if you had any further suggestions?

    • Michele says

      Cipro is a fluoroquinolone antibiotic and for some who are genetically susceptible can cause major health problems. Google search for floxies, check out Dr. Jess Armine’s site. He works with floxies a lot. Hope you find some help :)

  10. Kevin says

    Chris,

    Great book!

    As far as Pre-Script, it would have been my first choice, but the ingredient label states it “contains a proprietary blend of Leonardite and the following microorganisms…” I have yet to convince myself of the safety of Leonardite (humic acid, or more accurately, up to 90% humic acid). Fulvic acids are a particular type of humic acids; see here for an article on the safety — or lack thereof — of fulvic acid:
    http://drcrinnion.com/is-fulvic-acid-effective-for-heavy-metal-removal-is-it-safe/

    Any thoughts on this?

    Thanks and keep up the great work!

    -Kevin

    • anonymia says

      What you have been told about ‘many things’ – is only to Educate YOU – To the Degree “Someone Else” wants You to Know!
      Leonardite – named as such, is really “Lignite” – the Ore Structure which is ‘above’ Coal – but fondly named after the N. Dakota University professor Dr. Leonardite – who conducted a small library of research on this Miraculous “Ore” structure.

      As far as Prescript-Assist is concerned – this “Carbon-based Mineral Complex” is the Prebiotic Food Source – providing a readily available food source to the broad spectrum of microorganisms in P-A. Why is this significant? To balance – or ‘regain’ the high ground in the “biological terrain management’ – for to maintain, or re-establish ‘homeostasis’ one of four things must occur – to prevent a “Pathogen” from Taking Over.
      1) Multiply fast enough (called Binary-fission, as to make two organisms, from one) to “Crowd Out” the Pathogen.
      2) During multiplication – there is the necessity to consume ‘food’ – and if the microbes consume the food of the Pathogen – it cannot proliferate.
      3) During Proliferation – and in consuming surrounding food sources… often the Pathogen will be Consumed… and thus – will no longer be controlling the Biological Terrain.
      4) Emit a “metabolite” – or antibiotic – AKA Myco-toxin… which will kill / control (inhibit the further growth) of the Pathogen…. Look Up the Story of “NYSTATIN” – as to how the Streptomyces noursei bacteria came into medicine.

      Other probiotics lack these four ‘basic’ functionality principles – and thus are not even in the Same Galaxy – as is P-A… and yet, Leonardite is important for other factors, as it is a ‘natural chelating agent agent… as it’s heavy metals (if present) are “bound” and will not be absorbed by the body – but as to the contrary – they bind with other heavy metals and transport then from the body. Do your research, and you will substantiate these facts for yourself – and then you will have answers supportive as to why P – A is the World Class Probiotic – Prebiotic, that it is… Bar None!

      When you think – or see – Prescript-Assist…. think “Biological Terrain Management” – and with this comes Harmonization of Gastrointestinal Function.

      • Kevin says

        Did you read the link I sent? Because you didn’t respond to any of the issues raised in it. The question is still open to an answer with supporting evidence.

    • Chris Kresser says

      Therbiotic Infant from Klaire Labs if they’re under 2 years old. Same recommendations in this article if over 2 years old.

  11. cami D. says

    After learning, couple of years ago, about the devastating effects of antibiotics, I kept asking myself how did I end up having such a healthy digestive system (and good overall health), no intolerances or allergies ever. Growing up in Eastern Europe in the 80’-90’s, I used to take at least two rounds of antibiotics per year, usually more, prescribed by my doctor for sore throat infections. I even took some kind of antibiotic shots (very painful) for about 3 years on and of, at age of 10, for “preventative measures”. Antibiotics are sold over the counter there and people are popping them as candy for simple colds and coughs, even thinking that it’s straightens they’re immune system.
    After reading your article, I now have an idea: we grew all our vegetables, and during the spring and summer I used to play almost every day in the garden and snack on whatever was growing, green apples, peas, tomatoes, carrots, without washing them of course. We consumed lots of pickled vegetables, tubers, yogurt, broths and some kind of fermented drink, similar with kombucha, all of them homemade of course.
    About 8 months ago, being pregnant I had to take antibiotics for a massive tooth abscess. My now 6 month old daughter, has cradle cap and eczema flair ups, recurring colds also a big red spot at the crease of her neck that would not go away with over the counter anti-fungal cream (recommended by her pediatrician).
    I recently learned that it might be due to antibiotic use during the pregnancy.
    I would love your opinion on this.

  12. Joyce says

    Thanks, Chris–it is great to know that when you take antibiotics all is not lost if you take probiotics. This is the first time I have actually seen this in writing anywhere and I won’t get as stressed out next time I need to take antibiotics–usually for a bladder infection.

    • Chris Kresser says

      Joyce, while all is not lost probiotics and prebiotics do not restore the microbiota to the same state it was in before antibiotics. They are a way to mitigate the harm, not erase it. So it’s still wise to avoid them whenever possible, and only take them when necessary.

  13. Julie says

    I recently was started on triple antibiotic therapy (to continue for a minimum of 3 years ) for a Mycobacterial lung infection. Unfortunately because I have chronic SIBO I have avoided probiotics in general. Do you know if there is a good probiotic choice for me that would be helpful in preventing antibiotic associated diarrhea or Cdiff but will not exacerbate the SIBO?

    • anonymia says

      I have some knowledge – by way of experience – with what many of you are asking, as to all of these conditions – and for which most are representative of the untoward (not good) side effects of antibiotic interventions.

      Antibiotics can – and do – “Save Lives” – depending upon the type of infection. If, for example – you suffer a puncture wound, where pathogens are directly introduced into the body – antibiotics are your best answer to prevent – or abort an infection. However, and that being said – the same does not apply to a waterborne – or food borne infection – because here – it is “once again” about biological terrain management, and by way of example – ‘fully one third of all gastrointestinal poisonings are “Viral” and taking an antibiotic – will whack the Immune System – and could lead to death.
      Any overgrowth… whether SBIO – or otherwise – is an ‘Imbalance of Biological Terrain Management – and the singular best response is Prescript-Assist. OH… and I am speaking as Flight Crew Member to the World’s largest Airline… for which I fly ‘exclusively’ to foreign Countries – and for all of us who use P-A (as it is fondly called) – maybe thinking of a Physician Assistant… or Prescription Assistant – we ‘never’ have gut issues – while eating and drinking ‘just about anything’…. Oh Yes… .we may experience a little diarrhea, if we eat something that is quite contrary – but all we do, is to take a few more P-A – and as we say: “Be On Our Way”…. and that is “Not to the Hospital” – but Back to Work.

      Remember: Crowd Out the Pathogen, Consume the Food of the Pathogen, Consume the Pathogen for Food – or emit a metabolite – to Control the Pathogen… End of Story!

    • Chris Kresser says

      Yes, Prescript-Assist is safe to take with SIBO which is one reason I recommend it. The same can’t be said for lactic-acid probiotics like acidophilus.

  14. Nancy says

    I’ve just landed in bed with what appears to be the flu. Home remedies that REALLY work please? I hate taking medicine, and obviously flu shots.

    • Peg says

      Salt-water gargles for the throat. Tylenol for muscle aches, but no more than 3000 mg per day, (assuming you’re not allergic to Tylenol). Lots of chicken soup, hopefully made with bone broth. Lots of fluids in general. As much rest as you can get.

      If your temp drops after a few days, then a few days later rises steeply, plus you’re feeling short of breath, consider this: one of the worst complications of flu is bacterial pneumonia following in the wake of the virus. Time to see your doc.

  15. Christine Grace says

    Thanks for the info! My baby (10 months) is on Amoxicillin for a severe ear infection. We did everything we could to avoid it. We waited to see if she could clear it herself, and used red light therapy on her ear. It spread to the other ear and she started losing weight, so we had to do it. I HATE that her perfect little belly is now ruined. She used to be the happiest baby in the world and now she won’t sleep, and fusses all day. I think her ears are better, so I don’t think the fussiness is from pain. I know the link between digestive health and the brain, so I’m worried this has effected her personality.

    We spent a long time fixing my 3 year old twins’ digestive systems due to prematurity (which resulted in food allergies/damaged gut lining) and I really don’t want to go through all that again with her.

    She still breast feeds and I plan to for a long time. If I eat the fermented foods, does that translate into the breast milk for her? I am giving her an infant probiotic but it does not have S. boulardii. Is S. boulardii safe to give her? Also, I’ve heard soil based probiotics can be dangerous for some people. Any thoughts on this? Should I/she take them? We’ve used Prescript Assist before for my 3 year olds, but that was before I heard about the possible negative effects.

    Any suggestions for babies?? Please help!! (Btw, my 3 year olds were on Amoxicillin too for the same reason, but I’m more worried about the baby’s digestive health at the moment. I suppose I could do for them what I do for the baby).
    Thanks!!

  16. Megan Oien says

    This article is very helpful. Thanks for the pro biotic recommendations.

    I thought I would add that many people use Oregano oil as an alternative to antibiotics. No one in out family of 5 (ages 35, 34, 6, 4 and 1) has needed an antibiotic in 6 years. We use therapeutic grade Oil of Oregano (usually topically and if serious internally) for everything that would normally require antibiotics. I have cured numerous bouts of mastitis with Oregano oil. Oregano is also an antifungal, which kills Candida, so yeast overgrowth doesn’t tend to occur as it does in antibiotics. There are numerous studies on PubMed.

    • Christine Grace says

      Good to know, Megan. Do you have any recommendations for using the oil for ear infections? My kids are 10 months and 3 (twins) and they all recently had ear infections for the very first time. The inner ear was infected, so I’ve heard that drops or anything put into the ear doesn’t reach that part. Do you know what to do in this case? They all had Amoxicillin and I hated giving them antibiotics, especially the baby. What are some other uses for Oregano in order to avoid antibiotics? How did you use it with mastitis? Topically? Internally? Thanks!

      • Beth says

        For children with ear aches, you can get immediate results with the help of a classical homeopath. I’d also see the comments above for probiotics for children.

        • Christine says

          Thanks Megan and Beth! I just recently started purchasing Young Living Essential Oils. Oregano will be my next! We do a lot of bone broths and probiotic foods too. I have an appointment with our nutritionist this Friday to help get recommendations specifically for infants.

          Megan, is the Melrose Oil good for fighting infections? I’ve heard of using Oregano, but I don’t know much about Melrose. I am fairly new to using essential oils. Does rubbing it on the skin still have a pretty powerful effect internally?

          Thanks again!

          • says

            Hi again Christine :)
            Yes, I do find that most often applying them topically is enough. They are very powerful.
            Melrose is a blend of Tea tree, rosemary and clove (maybe more- I can’t recall). And Oregano would work behind the ear as well.
            Good luck finding answers.

      • Megan Oien says

        Hi Christine,

        We do a lot of what the articles says already- bone broths and tons of probiotic foods as our base. I am a minimal interventionist, so I prefer to let things play out on their own or treat them minimally. On myself and kids, i usually use essential oils topically. I do use them internally, if I feel it necessary.

        My experience with ear infections is rather limited. I think between my three kids, we’ve only dealt with ear infections 5 times, so I wouldn’t say I’m an expert or anything. I do consider it a success that none of them has ever taken an antibiotic for an ear infection. When they are very young and breastfeeding I squirt breastmilk in their ears. I have also used ear oil (garlic, mullein, thyme and tea tree) in the ear canal. I rub Young Living’s Melrose blend behind their ears at the first sign of infection and then 2-3 times daily for 3 days after symptoms resolve. I also rub Oregano oil diluted 1:4 with olive oil on their feet.

        If I want to give my children an oil internally (I use Thieves blend), I make a paste with honey and powdered slippery elm and then add 2 drops eo to each “lozenge.” Or I simply put a drop of eo on a spoonful of honey.

        For mastitis, I apply tangerine, geranium and oregano topically to my breasts. If the mastitis seems to be getting away from me, I take oregano internally- just a few drops under my tongue, 2-3 times daily.

        I have used it with success on my dog who had an infected bag of fluid on his neck that the Vet lanced and then prescribed an antibiotic for. I gave the puppy one dose which he vomited up and then decided to use Oregano. I gave it to him diluted in capsules for 2 weeks and he healed completely. I have used it for my sick chickens as well. It really is incredible.

        The reason, I started using essential oils was to treat persistent thrush/Candida that not even rx antifungals would kill- but Oregano oil did. The thrush came on after I took an antibiotic for mastitis just after the birth of my first son. I have had mastitis at least 6 times since (because of my tendency towards oversupply) and have always used Oregano with success. Although it is comparable to a broad spectrum antibiotic, I personally feel that it is far less damaging to gut flora. I have not experienced any ill effects and I’m pretty aware of my body. Hope this helps.

  17. Jessica says

    Thanks for another informative article, Chris!

    Just curious…if you recommend potato starch for resistant starch, why can’t one just eat potatoes? Is it due to the saponins (which I believe are largely concentrated in the skin)? Would potato starch have saponins?

    Again, thank you for all of the info!

    • says

      Potatoes that have been cooked and then cooled for 24 hours contain resistant starch, but I think the resistant starch is degraded as soon as you heat them up again. So I think eating 24-hour cooled potatoes is an option for RS, as long as you like cold potatoes! (Potato salad, perhaps?) Not sure how much RS is in a potato though, compared with the potato starch.

      Along the same lines, be sure your potato starch is unmodified, and don’t heat it. Otherwise, it probably won’t contain RS.

  18. says

    Always interesting to read your articles. Thank you.
    I was wondering what you thought of the Klaire Labs brand (Biotagen) for probiotics and prebiotics ?

    • Chris Kresser says

      Biotagen is a good prebiotic that I use in my practice. Klaire makes a number of probiotics. I use their Therbiotic Infant with kids under 2 years old, but I prefer Prescript Assist for adults.

  19. Sarah P says

    I recently had a baby and had to have a c-section due to placenta previa. I took sacc. b, Prescript Assist, and FemDophilus double doses daily for a week afterwards. I also stored my fecal microbiome in the freezer to transplant back to myself afterwards. 8 months later it’s still in the freezer, hehe! I think we should all store our microbiome in the freezer every 6 months or so just in case of an emergency where we would need antibiotics. I also an an organic gardener and made a point during and after pregnancy to sample some compost, and my baby loves to do the same.

    My baby got HLC Neonate the day he was born. So far so good, no autoimmune stuff like older sibling was showing soon after birth.

    Thanks again Chris, you have really helped me to have a healthy pregnancy and baby.

  20. Katy says

    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.

  21. Sally says

    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!

    • prioris says

      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.

      • Sally says

        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.

    • Peg Nicholson says

      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.

      • Peg Nicholson says

        Umm, you’d better also discuss the possible effects of RS on coumadin with your doctor, before starting.

  22. Robbie Bone says

    Do intravenous antibiotics have the same (more? less?) devastating impact on gut flora than oral antibiotics?

      • Jessica says

        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.

        • prioris says

          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

          • Jessica says

            Chris Kresser, could you comment on this one? What effect do IV antibiotics have on gut flora verses oral antibiotics?

            Thanks!

  23. Amy C. says

    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?

    • prioris says

      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.

    • Adriana says

      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.

      • prioris says

        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.

  24. Jessica says

    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!

  25. Valerie says

    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.

    • Amy says

      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.

    • says

      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

      • prioris says

        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.

  26. Danae says

    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?

  27. Jamie Griffin says

    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.

    • Lola says

      Klaire labs has a probiotic for kids under 2. You should also find a Chiro who is experienced with adjusting kids.

  28. Amy says

    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.

    • prioris says

      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.

  29. QueenJellyBean says

    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?

  30. N. Boyd says

    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.

    • Megan Oien says

      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.

  31. Lori says

    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!

  32. Carolina Lamp says

    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.

  33. anna says

    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!

  34. Raelene Nielson says

    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!

    • prioris says

      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.

  35. Andrea says

    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.

    • prioris says

      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.

  36. Jina Ps says

    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

  37. Danielle V says

    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.

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