How to Restore Gut Flora After Taking Antibiotics

There was no way around it. For one reason or another, you had to take a course of antibiotics, and now you’re worried about the aftermath of the attack on your gut flora.

Back in the day, doctors used to think that a healthy body is a sterile body, and that our immune systems are constantly fighting the microbes you come into contact with.

Now, the medical community understands that there’s a whole separate world of living organisms within your intestines, and keeping them balanced keeps you healthy. Colonies of beneficial bacteria in your digestive tract help you digest and absorb your food, they fight off germs that make you sick,^[1] and they even make a large portion of your serotonin, which helps keep your moods level.^[2]

How antibiotics impact gut health

Antibiotics kill off the bacteria responsible for the infection you’re targeting, as well as the friendly gut bacteria you’d rather leave alone. Best case, you have gas and diarrhea for a few days. Or, it can get so bad that the balance of your microbiome shifts, and you can end up with problems like:

• Malapsorption
• Acid reflux
• Irritable bowel syndrome
• Anxiety
• Depression
• Brain fog
• Acne
• Autoimmune diseases
• Candida (yeast) overgrowth and more

You don’t have to sit around and wait for your body to readjust. Read on to find out how to restore your gut flora and bounce back from antibiotics as quickly as possible.

Take probiotics to restore gut flora

Beneficial bacteria balance out microbes that slow you down. Every dose of antibiotics wipes out a large portion of bacteria in your entire system, including the good guys. After that, the good microbes and the unfriendly ones slowly rebuild, and if all goes well, they come back into balance. But, it takes time, and they don’t always colonize in balance. Sometimes, one or a few harmful strains takes over.

Supplement with probiotics: To keep the bad gut flora from winning, take probiotics while you’re taking antibiotics.^[3][4] Friendly bacteria don’t have to colonize in the gut to help you through a course of antibiotics. If you time it right, bacteria that are just passing through will keep the bad bugs in check. Even though the next dose will wipe out a lot of them, some will survive, and if the good guys hold their own, you’ll be in better shape when they build back up.

Timing and type are crucial: Make sure to take your probiotics at least two hours away from antibiotic doses in either direction. Also, watch for histamine-producing strains, like Lactobacillus casei, Lactobacillus reuteri, and Lactobacillus bulgaricus, if you’re sensitive. Instead, opt for Lactobacillus plantarum, Bifdocaterium lactis, and Bifidobacterium longum. These strains lower histamine levels, reduce inflammation, and improve digestion. More on the best types of probiotics here.

Use s. Boulardii during antibiotics: S. Boulardii is a beneficial yeast, not a bacteria, so antibiotics can’t touch it. In several studies, researchers found that s. Boulardii prevented antibiotic-associated diarrhea (AAD) when they administered it with antibiotics.^[5][6][7][8]

Cut sugar while you’re on antibiotics, and after

Without bacteria to keep them at bay, fungi have the opportunity to get busy during a course of antibiotics. You can attribute a lot of the problems that you experience after antibiotics — diarrhea, infections down there — to fungal overgrowth, particularly yeast. One problematic strain of fungus is candida albicans, which is especially prone to going haywire after antibiotics.^[9]

Candida thrive on sugar and simple carbohydrates (like bread and pasta) that your body quickly turns into sugar. Candida will flourish if bacteria aren’t there to fight back, and it will get sugar from the food you eat. To keep it from taking over, keep your sugar and carb intake to a minimum. They won’t get very far if they don’t have a substantial food source. Staying away from sugar is always good advice, but it’s especially crucial when you’re taking antibiotics.

Sip bone broth or take hydrolyzed collagen

The bacteria that line your digestive tract protect the membranes that keep intestinal contents on the inside where they belong. As they wear away, fungi have the chance to colonize in their place. When fungi grow, they shoot out hyphae, thin filament-like roots that dig into the intestinal walls. Essentially, they poke holes in your intestines which allows partially digested food particles to seep outside of the digestive tract and cause problems.

Giving your membranes what they need to stay strong won’t completely prevent fungi from shooting their roots into your intestinal walls, but it will make them more resistant to damage and more resilient when the antibiotics are done and it’s time to heal.

Collagen is the protein that holds your membranes together, and taking hydrolyzed collagen will give your cells all of the amino acids they need when it’s time to patch up. You can’t make collagen without vitamin C, even if you ingest collagen protein, so it’s a good idea to boost your vitamin C intake along with it.

Eat a lot of veggies

When a large portion of bacteria gets wiped out, they rebuild slowly. As with any population competing for resources, it’s a bit of a race to repopulate. While this is happening, you want to feed the good guys and starve the bad guys.

Cutting sugar will only take you so far. While you’re closing down the bar on the yeast party, why not serve the welcome guests?

The gut microbes that help you digest and absorb your food love vegetables. Makes sense, because they eat the portion of the veggies that humans do not break down, and convert those portions into nutrients that you wouldn’t otherwise get.

Pile your plate with the foods that friendly microbes eat, and more of the good guys will colonize your gut.

Resistant starch

Resistant starch gets its name because it is resistant to digestion. It ferments in your gut and feeds the beneficial bacteria in your gut.^[10] Well-fed friendly bacteria populate the gut lining, and keep unfriendly strains from taking over. This helps restore and maintain the integrity of your gut lining.^[11]

Sources of resistant starch include:

• Unroasted cashews
• Raw green bananas
• Raw plantain flour
• Raw potato starch

If you have IBS or Crohn’s Disease, resistant starch may cause digestive distress. Start slow, and build up to a few tablespoons. If you run into trouble along the way, it’s simple enough to stop taking it.

People who pop over-the counter and prescription pills for every minor thing are doing it wrong. With all the havoc they cause in the gut, you and your medical professionals need to be judicious about using them. There’s certainly a time and a place for antibiotics. For aggressive infections, surgery, and other instances, you have to have them, and as a society, we’re lucky to have access to medicine. For those times, it’s best to have a few preventive measures in your back pocket to keep your gut strong while you’re taking them and help it balance back faster when you’re finished.