How to Mitigate Antibiotic Side Effects
- Feb 24
- 7 min read
Updated: Jun 29
This is for educational purposes only and is not medical advice. Always consult your trusted healthcare provider before making medical decisions.
It can take up to a year or more to recover after a single round of an antibiotic!!
Giving an antibiotic shouldn’t be taken lightly, but sometimes they are needed. And there ARE things you can do to mitigate side effects and protect/rebuild the gut.
Saccharomyces boulardii: for gut support
The first thing you want to get is a Saccharomyces boulardii probiotic. This is a probiotic yeast (not a bacterium), which allows it to survive antibiotic treatment and prevent antibiotic-assocaited diarrhea, gut dysbiosis, and C. diff. It helps protect the gut microbiota and supports immune function.
You can get Florastor on Amazon or at any drug store/pharmacy/grocery store.
HOW TO TAKE:
Take 1 packet twice a day, taken 2 hours away from antibiotic for the full course of the antibiotic. For me, doing 2 hours after taking the antibiotic is easiest to remember. If I have Florastor left after the antibiotic course, I finish it and then switch back to my normal probiotic. But you could continue with the Florastor for another pack, if you wanted. If you don’t already take a probiotioc daily, you should be on one at least 6-8 weeks after an antibiotic.
Scutellaria baicalensis: for antibiotic effectiveness
Scutellaria baicalensis (Chinese skullcap) contains active compounds baicalin and baicalein that have shown the ability in lab studies to enhance the effectiveness of certain antibiotics.
Research suggests these compounds may help restore antibiotic sensitivity in some resistant bacterial strains, meaning they can make bacteria more susceptible to treatment when used alongside conventional antibiotics and combat against antibiotic resistance.
HOW TO TAKE
If going with Desert Oak Apothecary (code ALEX10 for $ off)
1 drop for every 2 lbs of body weight; 3x/day
If going with Supreme Nutrition
20 pounds 2-5 drops 3x per day
30 pounds 2-6 drops 3x per day
50 pounds 5-10 drops 3x per day
100 pounds 10-25 3x per day
100+ pounds 30 drops 3x per day
It doesn’t matter when you take it, but take it during the full course of the antibiotic and 6-8 weeks after.
HOW TO TAKE
20 pounds 2-5 drops 3x per day
30 pounds 2-6 drops 3x per day
50 pounds 5-10 drops 3x per day
100 pounds 10-25 3x per day
100+ pounds 30 drops 3x per day
3x/day ideal
Very gentle. Can put a drop on the nipple for breast-feeding baby, or a drop directly in the mouth. Mom can also take while breast-feeding for baby to get the benefit that way, too, in addition to putting in the mouth.
Biofilm Buster
Biofilms are slimy protective layers that bacteria and fungi can build around themselves to help them survive. These layers can make it harder for the immune system (and sometimes treatment like antibiotics) to fully reach and remove the germs. Because of this, some infections may linger or keep coming back. If you struggle with recurrent infections, no matter what you try, this might be one piece of the puzzle.
Biofilm busters are exactly what they sound like. They help breakdown the protective film so the immune system and/or treatment can better reach the microbes that are contributing to the infection.
Biofilm Buster - NAC
Based on research and clini use,
N-Acetylcysteine (NAC) is widely recognized as the most thoroughly studied and understood biofilm buster.
N-Acetylcysteine (NAC) is a compound derived from the amino acid cysteine that helps thin mucus and support the body’s production of glutathione.
In biofilm research, NAC is thought to help break apart the sticky protective matrix that holds biofilms together, making it harder for microbes to stay protected and hidden.
NAC Dosing with FNP Jessica Bunkelman
0-2yr: 150mg
2-5yr: 300mg
5-12yr: 450mg
^ FOR A MONTH
13yr+: 1200mg for a month, then stop; or can decrease and continue at 600mg
Fav NAC Brands
Capsules - Pure Encapsulations
Powder - Trace Minerals
For Nebulizing - Bulk Supplements
There are also many herbal biofilm busters used in functional medicine. We’ll get into those next. I would personally take NAC + 1 (or 2) herbal busters - depending on budget and supplement threshold.
Biofilm Buster - Scutellaria/Chinese Skullcap
Scutellaria baicalensis (Chinese skullcap), is one of the more researched herbs when it comes to biofilms and antibiotic resistance.
Some studies suggest its active compounds may help break down biofilms, weaken certain bacterial defense systems, and help antibiotics work more effectively against stubborn bacteria.
Because of this, this would be my top choice if an antibiotic is part of treatment.
Scutellaria/Chinese Skullcap Dosing
If not taking an antibiotic - take for 2-3 weeks
If taking an antibiotic - take for 6 weeks
If going with Desert Oak Apothecary (code ALEX10 for $ off)
1 drop for every 2 lbs of body weight; 3x/day
If going with Supreme Nutrition
20 pounds 2-5 drops 3x per day
30 pounds 2-6 drops 3x per day
50 pounds 5-10 drops 3x per day
100 pounds 10-25 3x per day
100+ pounds 30 drops 3x per day
Biofilm Buster - Usnea
Usnea (also called old man’s beard) is a lichen traditionally used for respiratory and throat support because of its natural antimicrobial compounds, especially usnic acid.
In lab research, it has shown activity against certain bacteria and may help disrupt biofilms,
It’s especially popular for strep throat support since some research suggests activity against Streptococcus bacteria commonly associated with strep infections.
Usnea Dosing
If not taking an antibiotic - take for 2-3 weeks
If taking an antibiotic - take for 2-3 weeks, then switch to Scutellaria and continue with that another 3-4 weeks
If going with Desert Oak Apothecary (code ALEX10 for $ off)
1 drop for every 2lbs of body weight; 3x/day
If going with Supreme Nutrition
20 pounds 2-5 drops 3x per day
30 pounds 2-6 drops 3x per day
50 pounds 5-10 drops 3x per day
100 pounds 10-25 3x per day
100+ pounds 30 drops 3x per day
Antifungal of choice: for preventing yeast overgrowth
Antibiotics can lead to yeast overgrowth because they kill off the beneficial bacteria that normally keep fungi like Candida in check. When those protective bacteria are disrupted, yeast has less competition for space and nutrients and can multiply more easily, especially in the gut, mouth, or vaginal microbiome. This imbalance is why some people develop thrush, yeast infections, or digestive symptoms during or after antibiotic use.
Scutellaria Baicalensis: safe for any age, very gentle, breastfeeding safe, pregnancy safe
This is my go-to since I'm usually already taking/giving it for antibiotic effectiveness + herbal biofilm buster. 3in1!!!
Oil of Oregano (2yr+) and Garlic: But if you find you need something stronger, or if you’re prone to candida, these are greay considerations.
You can also just eat raw garlic. For an adult, I would do 1 clove 3x/day (3 cloves total) for the course of the antibiotic. For a child, use your best judgement, but 1-2 cloves a day should be fine during the course. Either way you can then switch to something more gentle like Scutellaria for 6-8 weeks following.
Vaginal probiotic (IF taking antibiotic for UTI)
Top evidence-backed strains for UTIs:
Lactobacillus rhamnosus GR-1
Lactobacillus reuteri RC-14
These are the most studied combo for recurrent UTIs and have been shown to reduce recurrence and help restore healthy vaginal flora
Very promising (especially for prevention)
Lactobacillus crispatus: BioDoph-Fem or Fem-Dophilus
Strong evidence for reducing recurrence, especially when it successfully colonizes the vaginal microbiome
Finish the bottle, or consider making it part of your daily routine it you experience recurrent UTIs.
Whole Food Considerations
Fermented Foods: Fermented foods like sauerkraut, kimchi, plain yogurt, and kefir are another great way to get additional probiotic benefits. Fermented foods contain live microbes that help replenish good bacteria, support the gut lining, reduce antibiotic associated diarrhea, and lower the risk of yeast overgrowth. Eating them during treatment can help maintain balance, and continuing afterwards helps rebuild the microbiome.
High Protein Foods: High protein foods are helpful during and after antibiotics because they provide essential amino acids (glutamine) that the body needs to repair tissues and rebuild the gut lining. Amino acids help make enzymes, antibodies, and structural proteins like collagen that aid in healing. Meat, seafood, eggs, and dairy are the best sources since they are a complete protein, meaning they contain all essential amino acids in forms that the body can easily absorb. Be careful with processed dairy, as it can be inflammatory. Plant sources include: quinoa, soy foods, buckwheat, hemp seeds, and chia seeds.
Bone Broth: Bone broth provides easily absorbed amino acids like glycine, proline, and glutamine that help repair the gut lining and aid in tissue healing. It also contains collagen compounds and minerals that nourish the digestive tract and be gentle to consume when appetite is low during/after antibiotics, or when digestion is sensitive.
Prebiotic Foods: Prebiotic foods help probiotics work better because they act as fuel for beneficial gut bacteria. They’re types of fiber and plant compounds that humans don’t fully digest but gut microbes do, which helps those good bacteria grow, produce beneficial compounds, and rebalance the microbiome during and after antibiotics. Prebiotics are naturally found in foods like garlic, onions, bananas, asparagus, oats, and apples, or can be taken as supplements.
Raw or manuka honey, cod liver oil, and whole-food vitamin C sources like acerola cherry or camu camu can support the body during and after antibiotics by helping regulate immune function and inflammation during recovery. Honey provides natural antimicrobial compounds and soothing support for mucosal tissues. Cod liver oil supplies vitamins A and D plus omega-3s for immune balance and tissue repair. Whole-food vitamin C supports antioxidant defenses and healing. You can choose to do all three daily, rotate them regularly, or simply pick and choose based on what works best for you.
This is not a free pass to take antibiotics willy-nilly. Antibiotics should only be used when truly necessary. Even with supportive measures, they can disrupt the gut microbiome and immune balance, and overuse contributes to antibiotic resistance. Taking them “just in case” can do more harm than good.
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