The Problems with Antibiotics: Possible Alternatives and Damage Control

Are there any viable alternatives to antibiotics? I just spent the last few posts talking about all the bad things that stem from taking too many antibiotics, and you’re likely wondering if there’s anything you can do when an infection comes around. Although I wouldn’t suggest ignoring your doctor’s antibiotic prescriptions for some herb you found on some site online, there are potential alternatives. Not every alternative I list is going to work for you. To be honest, we have yet to confirm many viable alternatives that pack the punch of modern antibiotics. And in many cases, the wallop of conventional pharmaceuticals is exactly what the doctor ordered (in, um, every way). Sure, it could be said that every dose of antibiotics given out is exerting a selection pressure on billions of microbes that will ultimately lead to greater resistance, but when it comes down to it, you don’t want to be sick in the here and now.

So, once again, are there any viable alternatives to antibiotics, and if we have to take one, what can we do to mitigate the potential fallout?

First, the alternatives.

Fecal Transplants

Feces is mostly made up of living bacteria. That’s why poop-covered greens are often at the heart of these E. coli outbreaks you hear about – the bacteria lives on. Bad for those who like unwashed commercial spinach, but good for fecal transplants. Yes, fecal bacteriotherapy – the transplantation of fecal matter from a healthy human with healthy gut flora into an unhealthy human with unhealthy gut flora via enema or nasogastric tubing (through the nose directly to the gut) – is a promising new procedure. It’s particularly effective against recurring C. diff infections, showing “complete resolution” in 92% of 317 patients across 27 studies. C. diff is notoriously antibiotic-resistant (many C. diff infections happen because of antibiotics, in fact); only three antibiotics are currently even remotely effective at combating the nasty infection, but the fecal transplants displace the C. diff and replace the missing good stuff.

Unfortunately, but not surprisingly, fecal transplants are a bit of a hard sell. It clearly works, but since it smells of the dreaded “alternative medicine” and there is as yet no randomized controlled trial testing it, few physicians are even aware of or prepared to handle the procedure. Furthermore, most insurance won’t cover it. That they often blend the “fecal probiotics” with milk to form a “lactofecal slurry” (my choice of words) probably doesn’t help, either. Everyone loves a chocolate milkshake, but c’mon.

All hope is not lost. At-home fecal transplantation using a basic drug store enema kit has been shown to work just as well. (Of course it’s imperative that you work with your doctor if this is a route you think you might want to take.) And although most fecal transplant research centers on C. diff, it’s been shown to resolve antibiotic-related changes in short chain fatty acid production and increased diarrhea. I imagine we’ll see a lot more in coming years. Overall, I think fecal transplantation is the most promising antibiotic alternative.

“Natural” Antibacterials

To deal with pathogenic or competing microbes without pharmaceutical intervention, organisms have developed natural antibiotics. So it should come as no surprise that certain naturally-occurring substances have antibacterial properties. Modern and ancient medicine have identified many of these and isolated them, purified them, extracted them, and as I said in the first post, modern antibiotics like penicillin originally stem from naturally-occurring antibiotics that bacteria have been using against each other for millions of years. The problem with recommending natural antibiotics as a replacement is that there exists very little evidence in the literature supporting their efficacy. Plenty of antibacterial compounds exist, often in herbs and spices with long histories of medicinal uses, but that doesn’t mean that taking a pill of an extract of that herb or spice will kill whatever’s infected you. It might, and I wouldn’t be surprised if it did – heck, go through all my Smart Spice posts and you’ll see that just about every one has some sort of antimicrobial function – but I can’t recommend it because I simply don’t know.

One argument (to which I’m somewhat partial) in favor of natural, whole food/herb antibiotics is that they have a long track record of dealing with real-world infections and microbial attacks. That even though modern pharmaceuticals have isolated the compounds with the most powerful effects, whole foods contain a wider range of compounds working in concert and “attacking” the problem from different angles. Anyway, here’s the list of some (but not all) foods/herbs with natural antibacterial action, along with some relevant links. I tried to limit the list to only those substances showing efficacy in vivo:


Using doses between 1-3 mg/ml, garlic extract was effective against antibiotic-resistant Mycobacterium tuberculosis. In another study, garlic extract reduced the viability of methicillin-resistant Staphylococcus aureus in mice, and lowered inflammation associated with the infection. It’s worth noting, however, that a 2003 review (submitted before the other two studies were run) found garlic and other herbs/foods to be mostly ineffective as an in vivo antibiotic. It also concluded that while solid evidence for using herbal replacements is scarce, there’s enough in vitro evidence to demand further investigation.


As a topical antibacterial agent, honey has been used for thousands of years, a role which plenty of clinical studies have confirmed (PDF). Some studies have even found that topical honey works better than systemic/oral antibiotics in treating infected wounds. So, next time you’re infected with E. coli, do I recommend taking a tablespoon of raw honey? No, not quite. But you can certainly benefit from applying a dollop to a cut or open wound instead of reaching for the antibiotic ointment. That last link has guidance on how to apply honey to wounds.

Forsythia Suspensa

Forsythia suspensa is one of the 50 “traditional herbs” used in Chinese medicine, and a few studies indicate that it has antibiotic capabilities. In the only in vivo one I could find, oral extracts taken from the dried forsythia fruit proved effective in killing antibiotic-resistant Streptococcus suis, both alone and when combined with amoxicillin in a 4:1 forsythia:amoxicillin ratio. Of course, seeing as how most Chinese medicine sources I could find refer to forsythia suspensa as a broad spectrum antibiotic compound, it’s possible that it has systemic effects as well.

Coconut Oil

Coconut fat contains lots of lauric acid, a medium chain triglyceride. In the body, lauric acid turns into monolaurin, a monoglyceride with antibacterial properties also found in human breastmilk. Makes sense, huh? A baby’s immune system is pretty undeveloped, especially early on, and some delicious milky antibiotics from Mom are just the ticket. Hmm, I wonder if it works in adults…


Speaking of monolaurin, an in vivo study showed that a combination of monolaurin and oil of oregano was effective against staph infections in mice (60% survival rate), even slightly more so than vancomycin (50% survival rate), a type of antibiotic. An in vitro study showed that oregano oil makes conventional antibiotics more effective against E. coli, perhaps lowering the effective dose and subsequent side effects.

Cranberry Juice

It has proven effective at preventing urinary tract infections, but whether or not it can be an effective treatment remains to be shown.

Just be wary. Natural does not mean safe, nor does it mean “less powerful.” Think of red yeast rice, which is an over-the-counter statin analog (statin drugs came from it, actually), with all the potentially negative effects of Lipitor and Crestor. Go ahead and eat your garlic, add oregano to soups and stews, use coconut oil like normal – basically, treat food like food – but be careful when treating them like medicines (not that garlic is going to hurt you, of course). I’ve given you a list of foods with antibiotic properties, so now do your research or find someone who’s done theirs to decide if these are right for you. Don’t mess around with serious infections; instead, try these alternatives out when it’s a minor one, at least at first.

Vitamin D

A thought provoking article by the Vitamin D Council hints at the antibiotic potential of vitamin D megadoses. We already know that vitamin D is crucial for immune support, and numerous testimonials (in this forum and others) of folks taking large doses of vitamin D at the onset of a cold or infection and beating it abound, but the D Council article discusses a little-known role for vitamin D: the expression of the gene involved in producing endogenous antimicrobial peptides, or our body’s own antibiotics.

In the short term, megadoses of around 30-40,000 IUs are perfectly safe. Just don’t maintain that dosage for longer than a week.

Waiting It Out

For relatively minor conditions, like a middle ear infection, some doctors are recommending that patients simply “watch and wait.” A 2005 study put this to the test. Two groups of kids, each with ear infections. One group gets amoxicillin, the other goes home empty handed. The antibiotic group’s symptoms resolve quicker than the “watch and wait” group, but not by much. Both groups’ infections resolved. Plus, as time goes on, more members of the antibiotic group get sick again, this time with antibiotic-resistant bugs. After 30 days, both groups had essentially identical cure rates. Both were equally effective, but the “watch and wait” group got to keep their gut flora intact.

If it’s not life-threatening and it’s not impeding your ability to enjoy life, wait a little while. See how your body sorts it out. Check with your health provider first, though.

Maintaining Good Gut Health

Sometimes, antibiotics are necessary. Sometimes, alternatives simply won’t suffice and you (or someone you care about) just gotta take the stuff. When that happens (and even when it hasn’t happened yet), maintaining good gut health is paramount.

You should already be eating a variety of fermented foods, but the need for dietary probiotics grows more pressing when antibiotics enter the picture. And yes, take probiotics and eat fermented food during your course of antibiotics. Sure, some of them won’t make it out, but some will, and most studies show that concurrent probiotic/antibiotic schedules are helpful in avoiding antibiotics-related complications:

So, eat yogurt, kefir (real kefir, make your own, make coconut kefir (combo of monolaurin and probiotics?), search for “kefir grains” on Craigslist), sauerkraut, kimchi, and real pickles when you take antibiotics. Focus on variety. Continue to eat them after the antibiotics are done. Don’t stop.

Don’t always wash your produce (if it’s from a farm you trust, like your backyard) and eat some of it raw, because there’s a lot of interesting bacteria out there, and most of it – contrary to popular belief – will not kill you. This is a good way to introduce gut flora to your system.

Eat foods that contain soluble prebiotic fiber. You gotta feed the flora, keep it happy.

Go outside. Roll in the mud. Play in the dirt. Pet your pets. Don’t stress over washing your hands so much.

Speaking of stress, try to work on that. Chronic stress, whether it’s physical, emotional, financial, professional, or traffic-related, can negatively impact your gut flora.

Don’t despair.

I know I spent this post series talking about the negative ramifications of antibiotics on one’s gut flora. I know there have been some scary articles claiming that your gut flora may never return to normalcy. But really? It’s not always so bad. If you’ve taken antibiotics and are asymptomatic – that is, your digestion is normal, you’re not falling ill out of the blue – you probably have nothing to worry about. Continue to eat and live well.

But what if you’re one of those who took heaps of antibiotics? What if you’ve tried the probiotics, the prebiotics, you spend time outdoors, you get dirty from time to time, but you can’t shake the poor gut health? Talk to your doctor about the possibility of fecal transplants. Other than that, we could all wait around for small interfering RNA-wielding nanomachines, crafted by DARPA, and cold plasma jets to supplant antibiotics entirely, but I wouldn’t hold my breath.

Now I want to hear from you. What’s worked for you? What hasn’t? Would you consider a fecal transplant?

About the Author

Mark Sisson is the founder of Mark’s Daily Apple, godfather to the Primal food and lifestyle movement, and the New York Times bestselling author of The Keto Reset Diet. His latest book is Keto for Life, where he discusses how he combines the keto diet with a Primal lifestyle for optimal health and longevity. Mark is the author of numerous other books as well, including The Primal Blueprint, which was credited with turbocharging the growth of the primal/paleo movement back in 2009. After spending more than three decades educating folks on why food is the key component to achieving and maintaining optimal wellness, Mark launched Primal Kitchen, a real-food company that creates flavorful and delicious kitchen staples crafted with premium ingredients like avocado oil. With over 70 condiments, sauces, oils, and dressings in their lineup, Primal Kitchen makes it easy to prep mouthwatering meals that fit into your lifestyle.

If you'd like to add an avatar to all of your comments click here!