Rebuilding Your Gut: A Post-Antibiotic Guide

As winter fades, some people may find themselves having taken antibiotics. Here at My Joy Body, we approach antibiotics with caution because while they are sometimes necessary, they also disrupt the gut microbiome, and rebuilding it is no small task.

Antibiotics can significantly reduce the helpful microbes in your gut—the ones that help digest food, support your immune system, and even produce mood-regulating chemicals like serotonin and GABA. Some bacteria may be shed in stool, and overall microbial diversity can drop. Recovery can take weeks to months, and without careful support, some strains may never return fully.

This microbial disruption often affects mood. Since much of our serotonin is produced in the gut, a depleted microbiome can leave you feeling flat, irritable, or foggy-headed. Teens, whose microbiomes are still developing, and women, whose hormonal cycles intersect with gut health, can be particularly sensitive.

Sugar intake plays a major role in recovery. Refined sugars feed opportunistic bacteria and yeast, slowing the return of beneficial microbes and increasing inflammation. Natural sugars from whole fruits and vegetables are better choices, especially when paired with fibre or protein to maintain steady absorption and support microbial balance.

“Your microbiome just survived a mass extinction event. Time to rebuild its little empire.”

Rebuilding your gut is like tending a garden. You need to feed the beneficial bacteria, avoid feeding opportunistic microbes, and create the right environment for growth. Prebiotic-rich foods—such as asparagus, leeks, onions, garlic, broccoli, cooled potatoes or rice, and legumes—feed good bacteria. Fermented foods like sauerkraut, kimchi, kefir, and yogurt introduce beneficial strains directly.

Supplements can further support recovery. Slippery elm, marshmallow root, and aloe vera soothe and protect the gut lining, while beta-glucan-rich mushrooms (reishi, shiitake, maitake) and prebiotic powders help nourish the microbiome. Probiotics from food or supplements help recolonise key bacterial strains, and nutrients like glutamine, omega-3s, and polyphenols from green tea, cocoa, and berries support repair and reduce inflammation.

A practical recovery timeline might look like this: in the first two weeks, focus on gentle prebiotic vegetables, fermented foods, and minimising sugar. In weeks two to four, gradually increase fibre variety and introduce probiotics. By months two to three, natural sugars can be reintroduced cautiously, with ongoing plant diversity supporting long-term recovery. Consistent care through diet, supplements, sleep, stress reduction, and gentle movement is essential.

Supporting your gut health in this way benefits digestion, immunity, mood, and energy, helping you move into spring feeling resilient, vibrant, and balanced.

Morning Routine

• Begin the day with a glass of warm water; optionally add a teaspoon of slippery elm powder or a small amount of aloe vera juice for gut lining support.
• Breakfast: high-fibre porridge with berries and a sprinkle of chia or flax seeds. Keep sugar minimal.
• Optional: probiotic-rich food like a small serving of unsweetened kefir or yogurt.

Mid-Morning

• Snack on fibre-rich vegetables, small portions of fruit, or a handful of nuts.
• Prebiotic support can be included: small amounts of raw garlic, leek, or onion in snacks or dressings.

Lunch

• Large salad with a variety of vegetables, legumes, or whole grains.
• Add fermented foods such as sauerkraut, kimchi, or miso.
• Dress with olive oil and apple cider vinegar for healthy fats and digestive support.

Afternoon

• Snack: a small serving of resistant starch (cooled potato or rice) or beta-glucan mushroom powder in a smoothie.
• Optional green tea for polyphenols.

Dinner

• Steamed or roasted vegetables with whole grains.
• Include a source of omega-3s: fatty fish, flax, or chia.
• Fermented side dish for ongoing probiotic support.

Evening

• Light herbal tea, optionally with marshmallow root for soothing gut effects.
• Gentle meditation, breathwork, or restorative yoga to support the gut-brain axis and stress reduction.

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Supplement Guidance

• Slippery elm, marshmallow root, aloe vera: gut lining support.
• Probiotics: multi-strain supplements or fermented foods.
• Prebiotics: inulin, resistant starch powders, beta-glucan mushrooms.
• Glutamine, omega-3s, polyphenols: repair and anti-inflammatory support.

Sugar Guidelines

• Minimise refined sugars for the first 4–6 weeks.
• Reintroduce natural sugars from whole fruits and vegetables gradually after week 4.
• Pair sugars with fibre or protein to prevent spikes and microbial imbalance.

Lifestyle Tips

• Prioritise sleep and consistent sleep-wake cycles.
• Gentle movement and mindful practices reduce stress, which supports microbiome recovery.
• Monitor mood and digestion; adjust diet and supplements as needed.

These protocols provide a structured yet flexible framework to support gut recovery, optimise mood, and enhance overall well-being after antibiotics.