How To Support Your Gut When Taking Antibiotics

support gut antibiotics

The more I learn about our microbiome the more I appreciate it. That’s why I’m not such a big fan of the overuse of antibiotics. That said I do recognise that antibiotics play an important role when it comes to saving life and limb. After the second round of herbal antimicrobials failed to treat my Blastocystis and Dientamoeba gut infections I did consider circling back to antibiotics. Thankfully the third round of herbs was successful. Still, after that experience I have loosened my opinion on when antibiotics are indicated. Now I would consider their use to save life or limb and when herbal antimicrobials have failed multiple times and the patient is still symptomatic.

This article will cover what to do if you need to take antibiotics including during and after use.

Further Reading


The Gut Microbiome

The millions of different microbes, including bacteria, archaea, fungi, protozoa and viruses, living on and inside our body makeup our microbiome. The members of this ecosystem and their relative numbers influence health and disease in a number of different ways. They contribute to health and beneficial functions of our body by contributing to energy homeostasis, metabolism, the health of our gut lining. They can assist in tuning our immune function and even play a part in neurological (brain) function (1). The key here is balance.  The implications of an altered gut microbiome in disease is a hot topic in science at the moment. While it is still unclear whether the altered gut flora is a side effect of the different disease states or whether it is a driving factor it still crops up consistently in a number of different diseases. Previously we have covered an altered gut microbiome in

One paper I recently came across has correlated the microbiome with a number of other diseases including rheumatoid arthritis, systemic lupus erythematosus (SLE) and Sjogren’s syndrome (2). Does the disease stem from a disrupted gut microbiome, is it a driver, or simply a side effect of some other dysregulation in the body? Currently my thinking is that a disrupted or dysbiotic gut microbiome is a driver along with intestinal permeability and other environmental triggers.


Consequences of Antibiotics

So what to do if you find yourself in the unfortunate position of having to take antibiotics. Previously I had antibiotics placed in the ‘save life or limb’ basket. There is a whole materia medica full of herbal antimicrobials that come in handy when one is considering whether antibiotics are necessary. Not only are many of them selective in their antimicrobial function (as opposed to many broad spectrum antibiotics) all herbs also have a range of supporting, secondary actions. We discussed this when we covered one particular herbal medicine used to help treat Klebsiella infections Further Reading

You don’t need me to tell you that antibiotics are a popular drug of choice. One paper described them as one of the top most prescribed medications in the world (3). While they do have an important role to play in medicine many have criticised their overuse bordering on abuse. The same review outlined the associated health concerns from antibiotic use including

  • A disrupted gut flora
  • Antibiotic associated diarrhea (which we will be covering today)  
  • Electrolyte imbalances

They note that antibiotic associated diarrhea (AAD) has slowly been rising to a whopping 30% in some cases. Generally antibiotic associated diarrhea is self limiting but in about 10-20% of cases Clostridium difficile infection is to blame. This particular bacterial infection is really quite serious. In the United States it is responsible for more deaths than all other gut infections combined and infection rates are on the rise (4).


How Do Probiotics Help

Probiotics can help fend off antibiotic associated diarrhea and Clostridium difficile infections in a number of different ways. One systemic review listed a number of mechanisms including

  • Competing with pathogenic and opportunistic microbes for nutrients and space. This beneficial mechanism has been dubbed competitive exclusion.
  • They can interfere with the communication lines between pathogens known as quorum sensing.
  • Probiotic bacteria also have the ability to secrete antimicrobial compounds that can help knock down pathogenic microbes.
  • Finally, and this is a good one. Many different probiotics modulate and stimulate the immune system.

The same review recommended a number of different probiotics including

  • Lactobacillus rhamnosus GG
  • A multi-strain formulation of  – Lactobacillus rhamnosus GG, Lactobacillus acidophilus LA-5, Bifidobacterium lactis BB-12

Another meta-analysis found Lactobacillus rhamnosus GG, and the yeast probiotic Saccharomyces boulardii to be helpful in prevention of antibiotic associated diarrhea. But, and here is the interesting bit, they only found Saccharomyces boulardii to be helpful in antibiotic associated Clostridium difficile. One systematic review with meta-analysis (very high level science) concluded that ‘Moderate-quality evidence supports a large protective effect of probiotics in preventing CDAD (Clostridium difficile associated diarrhea)


Take Away Points On Probiotics During Antibiotic Use

Numerous systematic reviews with meta-analyses have found co-administration of probiotics along with antibiotics to reduce antibiotic associated diarrhea and Clostridium difficile antibiotic associated diarrhea as well. There are a number of different probiotic strains that have been assessed but a few that crop up consistently include Lactobacillus rhamnosus GG, Bifidobacterium lactis BB-12 and Saccharomyces boulardii (unfortunately the strain here wasn’t specified although I would hazard a guess that it is the legendary Saccharomyces boulardii Biocodex strain aka HANSEN CBS 5926 which we covered for Blastocystis infections.) One probiotic mixture supplied by Metagenics is almost the complete package. It supplies Lactobacillus rhamnosus GG, Bifidobacterium lactis BB-12 and Saccharomyces boulardii in one capsule ready to go. Unfortunately the Saccharomyces boulardii strain is not specified so the product isn’t a complete slam dunk. If you have come to the point where there is no way around taking antibiotics then supplementing with the Metagenics Ultra Flora Intensive can help to reduce your chances of antibiotic associated diarrhea and the possible complications associated with opportunistic overgrowths that stem from a disrupted gut microbiome.


Now over to you. Do you have any experiences with probiotics when taking antibiotics? What was your experience?


References and Resources

  1. The Gastrointestinal Microbiome: A Review
  2. The microbiome–systemic diseases connection
  3. Probiotics for antibiotic-associated diarrhea: do we have a verdict?
  4. Increase in Adult Clostridium difficile–related Hospitalizations and Case-Fatality Rate, United States, 2000–2005
  5. practical guide for probiotics applied to the case of antibiotic-associated diarrhea in The Netherlands.
  6. Meta-analysis of probiotics for the prevention of antibiotic associated diarrhea and the treatment of Clostridium difficile disease
  7. Probiotics for the prevention of Clostridium difficile-associated diarrhea: a systematic review and meta-analysis.
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1 comment

  1. Hi Todd, great article. Are there herbal ways to treat mild C Diff? I often hear that antibiotics are absolutely required. Eager to hear your thoughts on this.

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