How to Support Your Gut Microbiome While Taking Antibiotics

Antibiotics are dramatically overprescribed in our current medical system, and this takes the form of prescribing them when they aren’t necessary, prescribing wider-spectrum antibiotics than necessary, and prescribing longer courses than necessary. I was once prescribed 10 days of Cipro twice in rapid succession for urinary tract infections that I later learned only warranted a 3-day course. All of my autoimmune conditions were diagnosed in the following year. This makes me quite suspicious!

During the cold and flu season this winter, your doctor may prescribe you antibiotics for conditions that are caused by viruses, like cold and flu, or for sinus infections, which are much more likely to be fungal, not bacterial or viral. So if you’re offered an antibiotic for one of these conditions, you should definitely ask your doctor, first of all, is this really necessary? Now admittedly, there are some bacterial infections like strep throat that can be secondary to a viral infection, and those legitimately do need to be treated with antibiotics or herbal antimicrobials. If you go that route, you can see a naturopath for herbal medicines or instructions on which herbal products to use and when to seek out antibiotics if they aren’t working.

If you do have to go on antibiotics, one of the best things that you can do is to take probiotics both during the time you’re taking the antibiotics and then afterwards, to make sure that you protect and rebuild your gut. Note that most probiotics are just transitory and will not colonize your gut, but will protect you from pathogenic bacteria taking root (like C. Difficile) while you’re on antibiotics, will help select for healthier strains in your gut and will protect you from intestinal permeability or leaky gut, where the gut opens up and allows food particles, bacteria and toxins to escape.

So the first probiotic that I always recommend is S. Boulardii, (officially Saccharomyces Cerevisiae subspecies Boulardii), which is not actually a bacteria. It is a beneficial yeast. I like the Jarrow brand (5 billion CFU in 1 capsule; also available from my Fullscript Dispensary) because you can get a nice big bottle for a reasonable price. I would take those at least two or three times a day during the time you’re on antibiotics. As a yeast, the antibiotics won’t kill it. The nice thing about S. Boulardii is that it stops the reproduction of candida, which is also a yeast normally present in your gut. When you are killing off bacteria, the balance between the bacteria and the candida can get off, which can lead to an overgrowth of candida. I take S. Boulardii on a daily basis even when I’m not on antibiotics.

Then another type of probiotic you will want to consider are soil-based or spore-based probiotics, of which I’d take one serving/day. Some of the big names in spore-based are Megasporebiotic (also on Fullscript); likely the most expensive, most diverse and highest dosage one with 4 billion CFU and 5 strains in 2 capsules). Then there’s justthrive (3 billion and 4 strains in 1 capsule) and ProFlora 4R (on Fullscript; 3 billion CFU, 3 strains + Querticin, Aloe Vera and Marshmallow Root). And then there’s also a brand called Restorflora (on Fullscript) that has both 5 billion CFU of S. Boulardii and 2 billion CFU of 2 strains of spore-based probiotics. So I’d either go with the S. Boulardii plus a separate spore-based probiotic, or I would go with the combined one. But you may want to double up on RestorFlora to get as many of the spore-based as you would with another brand that was only spore-based strains. But of course, it’s not an exact science.

Another probiotic that I recommend as well is Equilibrium, which is really unique in the field of probiotics because it’s a human-derived probiotic with 115 strains. So these are strains that actually live in your gut. Again, I would go with maybe two or three of these a day during the time you’re on antibiotics or one/day starting right after you’re done, and keep that up until you’ve finished out 1-2 bottles. You could also go with Equilibrium Boost, which is basically 2 capsules of 10 Equilibrium combined into one, and then follow that by a regular bottle of Equilibrium right after you finish with the antibiotics. (You can use discount code HDH15OFF to get 15% off Equilibrium either at at the link above or on Amazon).

And then either at the same time or after you’re finished with your antibiotics, I’d also use food-based probiotics, something that has high levels of lactobacilli and bifidobacteria. If you want to go really high end, you can look at the Bifido Maximus, which is sold out of the Gut Institute and has 100 billion CFU per ¼ tsp. serving. Another good one is Renew Life Ultimate Flora that has 50 billion CFU per capsule. Of the food-based, I’d shoot for 100 billion CFU/day.

In terms of timing, all of the probiotics besides the S. Boulardii need to be taken separated in time from antibiotics. Otherwise the antibiotics will just be killing them. So for example, if you’re taking your antibiotics at breakfast and dinner, then take your probiotics at lunch and/or right before you go to bed, or if the antibiotics are three times/day, then take the probiotics between meals and/or at bedtime.

Another substance you might want to look at to help protect your gut is L-glutamine, which is a nonessential amino acid. Normally your body makes enough and it also comes from a lot of different foods like chicken, fish, dairy, tofu, cabbage, spinach, beets, peas, lentils and beans. But it can become deficient due to major infections, trauma, significant stress, radiation and chemotherapy, shock and vigorous exercise. So one way to protect your gut during these times of infections is to have a lot of bone broth, which has both L-glutamine and collagen, which is why of course grandma’s chicken soup was recommended. Note though that if you have histamine intolerance, bone broth is a source of histamine, so you wouldn’t want to go that route. Or you can take supplements of L-glutamine. The maximum dose is 30 grams a day split into five gram portions taken six times a day. But what I’d recommend is that you just start with a powder and work your way up to what seems to be a good dose for you. That helps seal the gut and keep it protected from becoming leaky.

Then you should also make sure you eat probiotic foods. So fermented sauerkraut, kefir, kim chee, etc. And the other thing that’s really important is to avoid sugar and processed carbohydrates during the time you’re on antibiotics and while you’re rebuilding your gut afterwards, because this is a time you’re going to be particularly prone to an overgrowth of candida. The more I see clients and people around me who are sick, the more I believe that a lot of these gut and autoimmune issues are traceable to the destruction of the gut microbiome due to antibiotics. You end up with an imbalance between the bacteria and fungi, including candida. So it’s really important that you get off the sugar and the processed carbs as much as possible. And that includes alcohol.

Then the other important part is to feed the body and its resident bacteria prebiotics and fiber. So just in case there’s any unclarity, probiotics are the bacteria and beneficial yeast, prebiotics are the food for the bacteria. I wouldn’t say it’s necessary to go for a prebiotic supplement, but just eat a lot of fiber from fruits and vegetables, like onion, garlic, beans, lentils and other legumes (the powerhouses of fiber).

And then you can also aim to get good resistant starch, which functions like soluble fiber, as a food for our bacteria. It helps us feel more full and controls blood sugar but we don’t digest it, our bacteria do. Good sources are tiger nut flour (a root vegetable, not a nut), green banana flour and banana skins. If you want to put banana skins into your smoothie, make sure you use organic bananas. You can also get resistant starch from heated and then cooled rice and potatoes. Once you cool them down, you get significantly fewer carbohydrates (or simple carbohydrates if you’re eating white rice) and 2½ to 3 times more resistant starch. Once you cool them, you can heat them back up to eat.

Finally, I did want to mention that if you took antibiotics a long time ago and you’re now dealing with what seems to be gut issues that followed on the antibiotic treatment, you can certainly try probiotics. You can go hard on them and see if it helps. But it may just be putting a bandaid on a bigger problem. So my recommendation is if it’s been a while since you took the antibiotics and you’ve been having gut issues, then you probably want to see what’s going on through testing. It may be parasites, it may be bacterial overgrowth like SIBO, it may be fungi like candida. It’s important to figure out what’s going on so that you can kill the appropriate thing, if there’s something to kill, and then rebuild with the prebiotics and probiotics. I think that’s a better route than trying to just put a bandaid on a dysbiotic gut.

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