Dangerous microorganisms. Seamless patternIf you’re taking an antibiotic, you can either wait until the course of treatment is over before beginning probiotic supplementation, or, you can take probiotics during the course of antibiotic treatment.

WHY should you take probiotics during or after antibiotic treatment? Because nature abhors a vacuum! This means that the risk of secondary or opportunistic infection is greatly increased when your gut has been cleared of bacteria.

If you take probiotics during antibiotic treatment, the probiotics will help to further encourage the exit of undesirable bacteria from your gut and will also simultaneously inhibit the overgrowth of yeast, fungi and parasites – which can flourish in the absence of good bacteria (which have been killed off by the antibiotic).

If you know you have a Candida albicans problem, for example, then you definitely want to take probiotics during your course of antibiotics, to prevent an explosive proliferation of this yeast that will then be difficult to control.

Remember, antibiotics ONLY kill bacteria; they do not kill yeast, fungus, parasites or viruses.

So you really want to be adding in a LOT of good bacteria to keep these other pathogens at bay both during and after antibiotic treatment.

Note: I’m going to give you dosage instructions for Natren probiotics here as that is the brand I use myself and recommend for my readers.

If you’ve supplemented with potent probiotics prior to antibiotic treatment, then take your probiotics as follows:

  • Two hours after you take each prescribed dose of antibiotics, take 1 tsp. of each Natren brand probiotic (Megadophilus, Bifido Factor, Digesta-Lac) mixed in 6-8 ounces of room temperature, filtered water (not tap water) on an empty stomach (15-20 minutes before food, or 2 hours after food).
  • Then take an additional dose (1 tsp. of each) before bed. When your course of antibiotics is finished, do Jini’s Probiotic Retention Enema and take 1 tsp. of each powder on an empty stomach (15-20 minutes before food, or 2 hours after food) three times a day for three months and then once or twice a day (always on an empty stomach) for the following three months. If your bowel movements are normal, or you tend towards constipation, then you can take the probiotics in capsule form, if you prefer. If you use the Healthy Trinity capsules, then you do not need to take them on an empty stomach.

If you haven’t supplemented with probiotics prior to antibiotic treatment, then you may want to proceed more slowly to avoid the Herxheimer Reaction :

  • Two hours after you take each prescribed dose of antibiotics, take 1/4 – 1/2 tsp. of each Natren brand probiotic (Megadophilus, Bifido Factor, Digesta-Lac) mixed in 6-8 ounces of room temperature, filtered water (no tap water) on an empty stomach (15-20 minutes before food, or 2 hours after food).
  • Then take an additional dose (1/2 tsp. of each) before bed. When your course of antibiotics is finished, do Jini’s Probiotic Retention Enema and take 1 tsp. of each three times a day on an empty stomach (15-20 minutes before food, or 2 hours after food) for three months. And then take 1 tsp. of each powder once or twice a day (always on an empty stomach) for the next three months as well. If your bowel movements are normal, or you tend towards constipation, then you can take the probiotics in capsule form, if you prefer. If you use the Healthy Trinity capsules, then you do not need to take them on an empty stomach.

Diagnostic Or Exploratory GI Procedures

When undergoing a digestive diagnostic or exploratory test (stomach, small or large intestine), you should also immediately follow it with probiotic supplementation.

These tests are all very disruptive to bacterial flora and you leave yourself wide open to infection by yeast, bad bacteria, viruses and fungi following these procedures.

If you’ve already been taking probiotics regularly, then follow any of these procedures (gastroscopy, colonoscopy, barium enema, etc.) with 1 tsp. of each Natren brand probiotic (Megadophilus, Bifido Factor, Digesta-Lac) in powder form mixed in 6-8 ounces of room temperature, filtered water (no tap water) on an empty stomach (15-20 minutes before food, or 2 hours after food), three times a day for three months and then 1 tsp. of each powder (or 1 Healthy Trinity capsule) once or twice a day (always on an empty stomach) for the following three months.

If you haven’t been taking probiotics prior to the diagnostic/exploratory tests, then you should proceed more slowly with supplementation to avoid the Herxheimer Reaction. Take 1/4 tsp. of each Natren brand probiotic powder (Megadophilus, Bifido Factor, Digesta-Lac) mixed in 6-8 ounces of room temperature, filtered water (no tap water) on an empty stomach (15-20 minutes before food, or 2 hours after food), two to three times a day for two weeks, then 1/2 tsp. of each three times a day for two weeks, then 1 tsp. of each powder, three times a day (always on an empty stomach) for the following three to six months. If you don’t have loose stools, or tend towards constipation, you can also take one Healthy Trinity capsule before bed, on an empty stomach, if you prefer.

I also have detailed instructions for how you can protect both your gut mucosal lining and your gut flora, before and after a colonoscopy, in my free colonoscopy report.

Re-Populating the Gut with Probiotics After Antibiotic Usage

33 thoughts on “Re-Populating the Gut with Probiotics After Antibiotic Usage

  • Unfortunately like a lot of folks, I only learned of this after both antibiotic usage and after my colonoscopy. Now, my GI is in a very precarious state. I need to do the gut infection/oregano oil protocol but I have severe leaky gut and fistulas so need to start the IBD diet too. However one requires that I eat and the other requires that I don’t. What to do?? Or what have others done since the most common answer seems to be that you can’t give “medical advice”?

    1. Hi Liana, Yes, unfortunately we are legally prohibited from giving personal health advice. However, we certainly can share personal experience, or stories of what others have done. So the IBD Remission Diet – where you START the infection/oregano protocol at the same time you start the Diet, ramping up slowly of course – has been used in clinical trials with patients with leaky gut, ulceration, fistulas, etc. It is the elemental (pre-digested) nature of the shakes and broths that are different from regular food.

  • Thanks for your reply Jini. Unfortunately I’m still confused. If I’m on the elemental diet, I’m not eating any food. According to what I thought I read, it is pointless to take probiotics while not eating and one should not be taking oregano oil without taking probiotics so the two diets/protocols sound mutually exclusive to me. What am I missing?

    1. It may help to think of elemental shakes like breastmilk. Breast milk is most certainly a nutritious food. But even if you weren’t eating ANY food at all, it would still be beneficial to take probiotics.

    1. Hi Mei,

      We have not heard that and have seen no credible evidence suggesting that. If you have a link or a source we’d be interested in checking it out. Here are some links to other posts Jini has done about probiotics if you’d like to read more:


      And if you would like a free eBook about probiotics, visit the link below and sign up in the little pink box on the left side of the page:


      Kind regards,
      Customer Care

  • I have purchased both Healthy Trinity and Oregano oil…Problem is, both are to strong for me…Healthy Trinity gives me sharp cramps and the oregano oil causes my stomach to hurt in a spot where I previously had an ulcer…I really need to take both, but how??? Is there any way to accomplish this? I have been drinking a Absorb Plus every day and Udo’s Oil. Both I can tolerate…but I know I need the probiotics and Oregano Oil…By the way I was pooping marbles for two months until I started using Metamucil…works wonders for a proper bowl movement…I am a suffer of Diverticulitis and IBS…my bowel hurts every day…I know its inflamed and I am afraid of another Diverticulitis attack…

    Thank you

    1. Hi Mark,

      Jini recommends olive leaf extract for people who aren’t able to tolerate wild oregano oil so you may want to try that instead. For more info about that, check out this link:


      Regarding the probiotics, it isn’t uncommon for some people to have difficulty with using all three types of probiotics from the beginning. If your gut is proving to be particularly sensitive to probiotic supplementation, you may want to try the “Cautious/Sensitive Approach” outlined on page 175 of Jini’s Listen to Your Gut book.

      If you have any additional questions please don’t hesitate to ask! You can also reach us during normal business hours in the live chat by clicking the little blue box on the bottom right of your screen, on the phone at 888-866-7745, or via email at service@listentoyourgut.com

      Kind regards,
      Customer Care

  • What’s your advice for people who can’t stand the taste of the probiotics mixed with water? I started with 1/4 teaspoon on Bifido and it makes me gag so I’m not sure how I’ll survive the 1 teaspoon of all 3 strains!

    Can they be taken in apple juice/shakes instead or does that not count as an empty stomach?

    Also, can they be taken right before or right after the aloe vera juice (they both are supposed to be taken before bed on an empty stomach but not sure how much time to wait between them)?

    1. Hi Sara,

      There are two options we would recommend:

      1. You could switch to the probiotic capsules instead since they are flavorless.
      2. You can certainly mix your probiotics in with shakes (Absorb Plus, for example). Natasha Trenev, the founder/owner of Natren gave us these directions if you decide to do so:

      – Whip/shake up your Absorb Plus shake in the blender/shaker first as usual.
      – Take out 2 ounces of shake and mix in your probiotics with a spoon, to form a smooth paste.
      – Add the paste mixture back to the rest of the shake and stir well with a spoon to mix thoroughly.
      – Drink as usual.

      You can also open the probiotic capsules (again, get the single-species capsule version, not the powders) and mix them into milk, chocolate milk, yoghurt, or diluted apple or pear juice.

      For more details on juggling various supplements, check out the link below to another blog post Jini did about that:


      Kind regards,
      Customer Care

  • Thanks Justin.

    Doesn’t mixing the probiotics in the shake mean your stomach is no longer empty since there’s a shake in it? And if mixing with milk or yoghurt wouldn’t your stomach still have the milk or yoghurt in it, meaning it would no longer be empty as well?

    Thanks for clarifying.

    1. Hi Sara,

      Sorry for the confusion! Jini recommends taking probiotics either 20 minutes before food or 2 hours after. What I meant by taking the probiotics with Absorb Plus was, Natren’s founder told us that it was fine (likely because it’s an elemental, pre-digested product). But it’s not 100% ideal like the 20 before/2 after guideline. However, for many people, it makes sense to do this from a time management perspective. Likewise, probiotics have traditionally been cultured on dairy products, so they do work fairly well as a carrier – not ideal, but better than not taking them! Mixing with diluted non-acidic juice or dairy products will still produce a beneficial result.

      Kind regards,
      Customer Care

  • I was wondering if it was okay for me to drink raw milk during my elemental diet? Of which, I’m only in week one. Or should I wait till the time when when I repopulate my intestines with good bacteria since raw milk is a live substance? Thanks so much!

  • Keep in mind Miranda – that IF you want to keep your diet 100% elemental – then raw milk is not allowed. See the IBD Remission Diet book for all the allowable substances on an elemental diet. But if you’re just doing an easily absorbed healing diet, then Justin’s response is great.

  • Thank you very much for your informative responses! 😀 This elemental diet, your absorb plus and your IBD remission diet are helping me tremendously. However, my intuition is telling me to layoff till it’s over. I’m going to do the 100% elemental diet. I am looking for bowel rest as I have a tear in my large intestine that needs to heal. Thanks bunches!

    As the universe is such a funny wonderful place, I have ‘randomly’ met two people with other digestive problems/stories and recommended they read your book and your blog. I spread info only when it feels right. I wish you and your hubby blessings!!

    1. Hi Miranda,

      Thanks for spreading the word! We’d love to hear how the diet works out for you and please let us know if you have any additional questions along the way.

      Kind regards,
      Customer Care

  • Hi
    My son is 7 years old he is talking antibiotics for the day one very low dose bec he dont hav spleen. Here v can find probiotics in kefir.
    I gav him every day .plz guide me what to do bec i noticed that my son is having some stomach prob now he hav laktose allergi.
    Plz guide me.


    1. Hi Sana,

      I’m afraid that we’re unable to guide you as we aren’t health professionals and not qualified to do so. Jini has protocols for all of the things your family is dealing with in terms of GI tract issues and the best place to start is at her symptom section here:


      You mentioned that you read the 8 steps for healing your husband’s Crohn’s naturally; these are a summary of Jini’s protocol for that and you can find more details and instructions in her Listen to Your Gut book here:


      If you have any questions about any of the protocols or recommendations please let us know!

      Kind regards,
      Customer Care

  • Hi jini
    I hav IBS and recently my husband is dignosed with Crohn doc says that CT scan has shown signs of inflammation in segmentsof the small bowel and some enlarged intraabdominal lymph nodes. Recently ileo colinscopy was performed and ab edmatous, red mucosa with small ulceration in the terminalileum was found. Histology from the ileum shoeed eosinophilic inflammation (100 per HPF) without granulomas.
    Plz guide us i read ur 8 steps.

    Do u thing my husband need full elemental det. Sometimes he is having dierrhea. Discomfort in his stomach all the time

    As i told u i hav IBS i used oregano oil but my syptoms is still not fine its on and off i hav used Ntren probotics powderform but i m still not feing gud.
    Bec of n my husband now i m worried abt my kids they both hav starting sime stomach issue they hav lactose allergi.
    My daughter is having some gas issues her stool is not normal i told doc but he run some blood test and stool test they all r fine just lactose prob.
    But still i m worried my while family is having some stomach issue.
    I liv in Nireay plz guide me tell me wat to do i m worried abt me n my family.


  • Is natren trinity probiotics capsule safe for kids 3.5 years old? Since I take that capsule before going to bed every night, my little one wants to take it too? She has no issues but some basic constipation some times and she is a picky eater.

    1. Hi Purvi,

      Healthy Trinity is Natren’s most potent probiotic so it might not be the best choice for a child of that age. Natren recommends their Life Start product up to age 4 so you may want to consider starting off with that one instead. Another potential option would be to employ Jini’s “cautious/sensitive approach” to probiotics from her Listen to Your Gut book. If you have specific questions about probiotic usage with children we recommend contacting Natren directly.

      Kind regards,
      Customer Care

  • Hi, My husband suffers from diverticulitis, and has had his 3rd flare up. He went to the hospital and also found out he had c-diff. It is a result from the previous attack 6 weeks before. (I thought he had the flu) He is ready to come home and is finally listening to his body, but I want to put him on the right supplements that your team recommends. I know you are not doctors,…he is working with doctors, but I also want him to be on supplements…Like what Probiotics..capsule preferably for him, the Absorb Plus and maybe he should also be on olive leaf extract? I have not read your book yet but I am meaning to just gathering information. I thank you for your time.
    Thank you ,Marcela

    1. Hello Marcela,

      Thank you for the inquiry. That is a great idea to get your husband set up to work on healing when he gets home. So, we would need more information on his symptoms to give you more specific recommendations. However, the book gives a lot of specific information on the products and diets for the different symptoms, and you can purchase it as a eBook to start right away if you would like:

      We would recommend to check out these links than let us know what questions you may have:

      You can also contact us at any of these options as well for any further questions: http://listentoyourgut.com/contact.html

      Kind Regards,
      Customer Care

  • Here is another Perspective. Please watch the interview with Prof. Borody from the 2017 MAP Conference 5:56 – 6:52

    Prof. Thomas Borody, BSc (MED) (HONS), MBBS (HONS), MD, PhD, FRACP, FACG, FACP, AGAF. Medical Director, Gastroenterologist CDD Australia

    “With respect to probiotics, we don’t use probiotics because probiotics have never been shown to be any better than placebo because they are small in number and they’ve been cultured, as soon as you culture probiotics over and over, they are damaged goods, they don’t implant. We use fecal flora from people because it implants, probiotics have never ever been shown to implant.

    One exception is in babies using Lactobacillus GG, so probiotics….there are still a lot of doctors who feel that oh! you’ve taken a course of antibiotics, you should take some probiotics to replace it, and that is completely false and uneducated thinking. They just don’t replace what you’ve taken and we shouldn’t have probiotics of Lactobacillus and Bifidos, we should have bacteroides, firmicutes, they don’t exist in the shops. So unfortunately, probiotics are not worth using, it’s just spent money.”


    1. Hi Kevin, Yes, I interviewed Bianca James – who pioneered the fecal infusion protocol with Dr. Borody in Sydney – a few years ago. And then Dr. Silvio Najt took that and opened a clinic in Buenos Aires that only did fecal infusion/implant for all kinds of auto-immune conditions (sadly, he passed away this year). There is some good data supporting it, but there is also a ton of data supporting the use of food-cultured bacteria. Have you tried fecal infusion yourself?

      1. Hi Jini, No I have not tried fecal microbiota infusion but considering stopping amat triple antibiotics and doing FMT soon. I currently take probiotics VSL#3 DS, RenewLife Ultimate Flora, Klaire Labs Biospora, Saccharomyces Boulardii. I’ve tested positive for mycobacterium and have been on 3 antibiotics at high doses daily for nearly 3 years now and doing relatively well after the first 9 months. A company OpenBiome offers FMT capsules. There are patients and parents on the Crohn’s MAP support facebook group who have had success with fecal infusions. Jini what are your thoughts on probiotics and/or FMT after reading the above from Prof. Borody?


  • Need some advice here. I took 4 doses of cipro before bad reaction. Been reading horror stories about it. Private messages Jini, she said if it were her she would do HIGH doses of p robiotics. Couldn’t tell me how high, I understand she can’t legally. My question is I am on her wild of oregano oil protocol with nighttime nstren p robiotics. I’m up t o 2 of each of the healthy trinity starter pack, any suggestions for how high with pr obiotics..most importantly I heard if you take angstrom magnesium right away after the cipro, you can protect yourself from cipro damage aftermath…I really need advice on this..what supplements of Jini can help with the cipro issue…so worried I’m sick about it! Thanks in advance

    1. Hi Wendy,

      Thank you for contacting us here. As Jini is not a medical professional she is unable to comment on prescription medication. What I would do is ask myself how much of these strong substances my body can take. The Oregano oil is a strong substance, and so as the Cipro. So you have to Listen to your Gut if you can take these two together, or wait until the course of treatment is over before beginning the Oregano protocol.

      For probiotics, Natren Trinity is already considered as high dose probiotic supplementation, since 1 caps contain 3 species with total of 30 billion CFU. Just make sure to take this away from any type of substances: Oregano and Cipro. Atleast 2 hours away from each other, before and after.

      Kind Regards,
      Cris B
      Customer Care

  • Today I started on an antibiotic for a 10 day period.I also have been taking Natren Trinity Probiotics capsules for the last several weeks. What would you recommend as far as continuing the one capsule I take each morning?

    1. Hi Bob,

      As per this blog post, Jini recommends a tsp. of each strain ( 1 capsule of Trinity is also fine) 2 hours after you take your prescribed dose of antibiotics. Then take an additional dose (1 tsp. of each) before bed – she recommend powder form of Probiotics, however, Trinity capsules is also fine if you prefer this.

      Also note that Healthy Trinity and the powders are two very different applications, and taken for different reasons.  Powders are taken on empty stomach, a time when acids are at their lowest, so they have less to combat while the Healthy Trinity needs to be taken with food/snack to help break down the capsule and begins to distribute the strains through the GI tract, where HT does its work. Please let us know if you have any additional questions or concerns.

      Kind Regards,
      Cris B
      Customer Care

    2. Hi Bob,

      I would recommend reading Jini’s blog post about repopulating your gut flora after using antibiotics: https://blog.listentoyourgut.com/re-populating-the-gut-with-probiotics-after-antibiotic-usage/

      If the probiotic capsules have been working for you, that is great! Natren is the only brand that Jini recommends and uses through years of research and experience, and is the only one with all the requirements (probiotic strain selection, manufacturing, storage, and other factors effecting potency and efficacy). You can have many strains of bacteria in a product, but if they are not the right kind, they won’t help you.

      Jini has discussed probiotics with Natren founder, Natasha Trenev, as well – and you can watch her Q&A videos by clicking on the links below:


      Please let me know if you have any additional questions or concerns.

      Kind regards,
      Savannah B
      Customer Care

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