7 Things Your Microbiome Wishes You’d Stop Doing

In recent years, research has confirmed what many in the health world have long suspected: gut health is foundational to overall health. From digestion and immune function to mood regulation and inflammation, the trillions of microbes living in your gut—collectively known as the microbiome—play a critical role in how your body performs and feels each day.

But supporting a healthy gut isn’t just about adding a probiotic or eating more yogurt. Daily habits—from what you eat to how you manage stress—can have a lasting impact on your microbial balance, for better or worse. Even the most health-conscious among us may unknowingly make choices that disrupt that balance.

So, what does your microbiome really need from you? Let’s start with what it doesn’t. Here are seven common habits that could be harming your gut—and how to swap them for ones that support a healthier, more resilient microbiome.

Related: Probiotics 101: A Beginner’s Guide to Gut Health

1. Living on Ultra-Processed Foods

Your gut bacteria love fiber-rich, whole foods. What they don’t love? A steady diet of packaged, low-nutrient processed foods loaded with additives, refined sugars, and artificial ingredients. These can feed the “bad” bacteria and crowd out the beneficial ones, throwing your gut out of balance.

Try this instead: Add more diversity to your meals with plants—fruits, veggies, legumes, whole grains. Aim for 30 different plant-based foods per week to support a healthy microbiome.

2. Overusing Antibiotics

Antibiotics can be lifesaving, but they’re also notorious for wiping out your good gut bacteria along with the bad. Taking them when they’re not necessary—or without replenishing your gut afterward—can lead to dysbiosis (microbial imbalance).

Try this instead: Only take antibiotics when prescribed, and after your course, rebuild your microbiome with probiotic-rich foods and prebiotic fiber. Consider a targeted probiotic if recommended by your healthcare provider.

3. Eating Too Fast

Mindless eating isn’t just a digestion issue—it can affect your microbiome, too. Rushing through meals can limit digestive enzyme production and increase bloating, gas, or indigestion.

Try this instead: Slow down. Chew thoroughly. Engage your senses. Eating mindfully can help improve digestion, reduce stress, and give your gut the time it needs to do its job.

4. Skimping on Sleep

Your gut has its own circadian rhythm, and pulling all-nighters or living on broken sleep messes with that internal clock. Poor sleep has been linked to reduced gut microbial diversity and increased inflammation.

Try this instead: Aim for 7–9 hours of quality sleep per night. Create a calming wind-down routine and try to keep your sleep and wake times consistent—even on weekends.

Related: Improve Your Gut Health, Improve Your Mood

5. Letting Stress Run the Show

Chronic stress doesn’t just mess with your mood—it alters your gut microbiome. Thanks to the gut-brain axis, high stress can lead to digestive issues, inflammation, and imbalanced gut bacteria.

Try this instead: Incorporate daily stress-relievers like walking, deep breathing, yoga, or journaling. Even 5 minutes of intentional calm can help your gut recalibrate.

6. Drinking Too Much Alcohol

Excess alcohol can damage the gut lining, reduce microbial diversity, and encourage the growth of harmful bacteria. It also disrupts sleep, which creates a double-whammy for gut health.

Try this instead: Drink in moderation—or opt for gut-friendly swaps like kombucha, herbal teas, or sparkling water with a splash of citrus.

7. Ignoring Fiber (Especially Prebiotic Fiber)

Fiber is your microbiome’s favorite fuel, but most people don’t get enough. Prebiotic fibers, in particular, feed the good bacteria and help them flourish.

Try this instead: Add foods like garlic, onions, bananas, oats, and asparagus to your weekly rotation. They’re all rich in prebiotic fiber and easy to incorporate into everyday meals.

Related: How Much Fiber Do You Need?

The Bottom Line

Your microbiome is the silent MVP of your overall health, and the good news is, small changes can make a big difference. Start with one or two of these habits and build from there. Your gut (and the rest of your body) will thank you.