Why Antibiotics Can Make Acne Worse (And What Actually Works for Clear Skin)

Why microbiome health is the key to lasting skin results

"The microbe is nothing, the terrain is everything." - Antoine Béchamp

Summer's almost here, and if you're like many people I know, you're probably standing in front of your bathroom mirror wondering why your skin looks worse despite using half the products at Sephora. Maybe you've been down the rabbit hole of skincare forums at 2 AM, hoping someone's miracle routine will finally be the answer. Or perhaps you're that person who's tried everything... the fancy serums, the dermatologist visits, the elimination diet... and you're starting to think your skin just hates you.

I get it. I've been there. And here's what I wish someone had told me years ago: the real answer to your skin struggles probably has less to do with which products you're putting on your face, and everything to do with how those products are affecting the invisible ecosystem living there.

I know how desperate you can get when your skin is acting up. When you're canceling plans because you can't bear to leave the house without makeup. When you're avoiding eye contact because you're convinced everyone is staring at your breakouts. When you've tried everything 'natural' and you're sitting in a dermatologist's office thinking, 'Just give me something that works.'

So when your doctor suggests antibiotics for your acne, of course you say yes. Here's what happens: those antibiotics travel through your entire system to reach your skin. Along the way, they're carpet-bombing the beneficial bacteria in your gut, your mouth, everywhere. They might clear up your breakouts temporarily by killing the bacteria causing inflammation. But they're also wiping out all the beneficial bacteria that were keeping your skin balanced in the first place. Not only that but they are decimating the gut bacteria that were supporting your immune system, mood, and overall health.

It's like using Roundup on your entire garden because you spotted a few weeds. The weeds die, but so do all the beneficial bacteria in the soil, the helpful insects, and even some of the plants you were trying to protect.

Which is why so many people find their skin comes back angrier than before, often accompanied by digestive issues, mood changes, and a whole host of other problems they didn't have before.

There is another way to think about this. What if instead of trying to kill the 'bad' bacteria, we focused on creating an environment where the good bacteria could thrive?

What Is Your Skin Microbiome

Your skin is not only a barrier between you and the world, It's also a bustling ecosystem, home to trillions of bacteria, fungi, and other microorganisms that are working 24/7 to keep you healthy. This is your skin microbiome, and when it's happy, your skin glows. When it's not? Well, that's when things get complicated.

But here's where it gets really interesting: your skin microbiome is basically best friends with your gut microbiome. They're constantly texting each other (okay, not literally, but they're in constant communication). When your gut is struggling, your skin knows about it. When your skin barrier is compromised, your gut feels it too.

Think about it—have you ever noticed your skin breaking out when you're stressed? Or getting worse after eating certain foods? ...or getting sick after a sunburn? That's not coincidence.

How Birth and Childhood Shape Your Skin Health

This whole microbiome story actually begins the moment you're born. If you were born vaginally, you got what researchers call a "microbial bath"—basically, your mom's bacteria became your bacteria. It was like getting the starter culture for your entire body's ecosystem. And there's another piece to this birth story: that white, cheese-like coating babies are born with called vernix caseosa (usually just vernix).

Most of us thought it was just something to wash off quickly, but vernix is actually an incredible biological gift. It's loaded with protective compounds that help seal and protect the newborn's skin while supporting the establishment of a healthy microbiome. The longer it stays on, the better start that baby gets.

If you were born via C-section, you missed out on both that initial microbial seeding and often the vernix protection, instead getting colonized by whatever bacteria happened to be hanging around the hospital that day. Neither scenario is good or bad—it's just different starting points for your microbial journey.

But here's what really shaped your microbiome: being a gloriously dirty kid. Every scraped knee, every unwashed apple, every time you pet a dog or played in the dirt... that wasn't poor hygiene. That was microbiome education. Kids who grew up getting dirty, having pets, and being exposed to diverse environments often have more resilient skin as adults.

Somewhere along the way, though, we decided bacteria was the enemy.

Why Antibacterial Products Are Making Your Skin Worse

Walk down any cleaning aisle and you'll see products proudly proclaiming they "kill 99.9% of bacteria." But here's the thing that would probably shock most people: less than 1% of bacteria can actually make you sick. The other 99% are either neutral or actively helping you stay healthy.

Scientists have identified only about 1,400-1,500 bacterial species that can infect humans, out of tens of thousands of known bacterial species. When you consider all the microbes on Earth—likely millions of species—the proportion that cause human diseases is vanishingly small. The bacteria living on your skin right now are busy crowding out potential pathogens, maintaining your skin's pH, and even producing compounds that keep harmful microbes at bay. Your gut bacteria are breaking down food, synthesizing vitamins, and training your immune system to recognize real threats.

Yet we've spent decades systematically destroying this bacterial diversity in our homes and on our bodies. We sanitize everything, use antimicrobial soaps, and wonder why our skin is reactive and inflamed. The irony is heartbreaking: the more our skin struggles, the more products we buy to "fix" it, often making the underlying problem worse.

Summer Skin Problems: Heat, Humidity, and Microbiome Imbalance

Summer brings its own challenges. More heat means more sweating, which changes your skin's pH. Air conditioning dries everything out. You're using more sunscreen (which you absolutely should if you are going to be out for a long time in intense sun), but if you're not removing it properly, it can clog pores.

When your skin microbiome is already out of balance, these summer stressors become magnified. The beneficial bacteria that should be protecting your skin can't keep up, leaving space for the troublemakers to move in.

The Gut-Skin Connection: Why Your Digestive Health Affects Your Complexion

While you're focused on what's happening on your face, your gut microbiome is quietly running the show. When your digestive system is out of whack from stress, processed foods, antibiotics, or just modern life, it sends inflammatory signals throughout your body.

Your gut bacteria help process nutrients, regulate inflammation, and even produce compounds that affect your skin health. I've seen people spend thousands on skincare who finally cleared their acne by focusing on their gut health instead.

Natural Ways to Support Your Skin Microbiome

So what's the solution? It's not about throwing out everything in your bathroom cabinet (though you might want to simplify and gradually replace the remaining products with cleaner ones). It's about working with your body's natural intelligence instead of against it.

Start from the inside: Feed the good bacteria with fermented foods like sauerkraut, kimchi, and kefir. If you've taken antibiotics recently, consider probiotics. Pay attention to how different foods make your skin feel. Your body is constantly giving you feedback.

Be strategic about products: Your skin's natural pH is slightly acidic, which helps good bacteria thrive. Many conventional products are alkaline and disrupt this balance. Look for gentler options that support rather than strip your skin's natural defenses.

Rethink "clean": This doesn't mean abandoning hygiene, but maybe you don't need to sanitize every surface. Maybe you can garden without gloves occasionally. Maybe not every minor cut needs antibiotic ointment. And as Kiran Krishnan, a well-known research microbiologist, recommends, go outside and work or play and come in and sit on the couch with the clothes you wore outside to inoculate your household with a diverse set of microbes.

Consider your environment: If you live in an area with heavily chlorinated water, a shower filter might help. Your skin is absorbing that chlorine, and it's not doing your microbiome any favors.

The Bigger Picture

The pursuit of perfect skin often misses the point entirely. When you support your microbiome, both gut and skin, you're not only potentially improving how you look. You're supporting your immune system, your energy levels, and your overall resilience.

Your skin is trying to tell you something. Those breakouts, that dryness, that sensitivity are not personal failures. They're information.

This summer, instead of declaring war on your skin, what if you approached it like tending a garden? With patience, wisdom, and respect for the complex relationships that create health from the inside out.

Because the most beautiful skin isn't the most controlled skin, it's the most balanced skin. And balance, it turns out, has a lot more to do with invisible microbes than $200 serums.