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.