How to Help Your Gut After a Stomach Bug
Quick note
This guide is for general education only. It is not medical advice and doesn’t replace care from a doctor.
What’s a “stomach bug”, or Gastroenteritis?
When people say “stomach flu” or “stomach bug”, healthcare workers usually call it gastroenteritis.
Gastroenteritis simply means the stomach and intestines are inflamed, often causing the following acute symptoms:
nausea
vomiting
diarrhea
cramping and/or abdominal pain
Common causes of gastroenteritis
Most cases of gastroenteritis are caused by:
Viruses: especially norovirus and rotavirus (very contagious, they often spread in schools, daycares, nursing homes, cruise ships).
Bacteria: like Salmonella, Campylobacter and some strains of E. coli, often from contaminated food or water.
Parasites: such as Giardia or Cryptosporidium, more common with contaminated water or poor sanitation.
Most people recover within a few days, but your gut and microbiome can feel “off” for weeks if you don’t support them.
How a stomach bug can throw off your gut
Even though gastroenteritis is usually short-lived, it can have a bigger impact on those who already have IBS, SIBO, SIFO, an IBD (Crohn’s or Ulcerative colitis), or just a sensitive gut.
Here’s what happens in your gut:
Diarrhea flushes out microbes
Fast, watery stools don’t just remove the “bug”, they also wash out beneficial bacteria and their protective compounds, like short-chain fatty acids (SCFAs).
Inflammation irritates the gut lining
The infection (and sometimes the toxins from the bug) can damage the gut barrier, making it “leaky” and changing the environment good bacteria need to thrive.
The microbiome has to rebuild
After a stomach bug, your gut bacteria usually recover in stages:
In the first few days: more oxygen-loving microbes show up (like Enterococcus, E. coli).
Over the next 1–4 weeks: Bacteroides and butyrate-producers like Roseburia and Faecalibacterium tend to come back and things gradually rebalance.
How fast this happens depends on how severe the infection was, how healthy your gut was before catching the bug, and what you do during recovery.
When a stomach bug leads to longer-term issues
Most people bounce back from gastroenteritis without much trouble. I unfortunately was not in that group after I got infected in 2009 with a pathogenic strain of E. coli in Peru. That’s also typically not the case for people I tend to work with. A smaller group of people develop ongoing gut symptoms such as:
1. Post-infectious IBS (PI-IBS)
Some people will continue to have:
bloating
abdominal pain
gas
diarrhea, constipation, or mixed stools
…for months or years after a stomach infection. This is called post-infectious IBS.
➜ About 10–15% of people develop IBS after a significant episode of bacterial gastroenteritis.
According to the systematic review, the risk is higher if:
you are a woman;
the initial illness was severe or lasted longer than typical; and
you already had anxiety/depression at the time of the infection.
2. Increased risk of IBD
Large studies suggest that people who’ve had severe gastroenteritis have a slightly higher risk of developing Crohn’s disease or ulcerative colitis later on, especially if they have other risk factors (family history, smoking, etc.).
That’s one reason it’s worth supporting gut repair, and not just “waiting it out”.
What to do during the acute phase
Your first priority should be to avoid dehydration. Vomiting and diarrhea can dehydrate you quickly, especially in children and the elderly.
Signs you need urgent medical care
Call a doctor or go to urgent care / emergency if you notice:
very little or no urine
very dry mouth, tongue, or lips
dizziness, confusion, or extreme weakness
blood in stool or black/tarry stools
high fever or severe pain
symptoms lasting more than a few days
What to drink to rehydrate
1. Homemade oral rehydration solution (ORS)
This is an alternative to store-bought formulas like Pedialyte that often contain dyes and artificial flavours or sweeteners. The following recipe is similar to what the WHO recommends for diarrhea:
4 cups (1 L) clean water
2 tablespoons sugar or honey
½ teaspoon salt
optional: squeeze of lemon or a bit of orange juice
Stir until dissolved and sip slowly throughout the day.
2. Coconut water
Gives fluids and a good dose of potassium, and is usually easier to tolerate than plain water.
3. Ginger tea
Ginger can help reduce nausea and vomiting, especially with acute gastroenteritis.
4. Broths and soups
Chicken, vegetables, or bone broth help replace sodium and fluids and are usually gentle on the stomach.
Hydration tips
Room temperature or warm fluids are often easier than icy drinks.
Whenever possible, alternate between the different options for rehydration.
Sip regularly instead of chugging large amounts at once.
Eat gentle foods while your gut is upset
During the acute (worst) phase, focus on simple, bland, low-fibre foods:
broth and broth-based soups
plain rice, rice crackers, or toast (if tolerated)
mashed potatoes (no heavy cream or cheese)
bananas or stewed apples
plain oatmeal or cream of rice
This is often known as the BRAT Diet (a simpler form, easier to remember):
B > Banana
R > Rice
A > Apple sauce
T > Toast
As symptoms settle, slowly reintroduce:
cooked veggies (carrots, zucchini, pumpkin, peeled potatoes)
small amounts of cooked protein (chicken, fish, eggs)
healthy fats (olive oil, avocado in small amounts)
Avoid the following, at least early on:
alcohol
caffeine
very spicy or greasy foods
large amounts of dairy (especially if you’re not used to it)
Supplements for gut recovery after gastro
Saccharomyces boulardii
Saccharomyces boulardii is a probiotic yeast (not a bacteria) that’s been well-studied for acute infectious diarrhea and prevention of C. difficile during antibiotic treatment.
S. Boulardii:
Binds and neutralises toxins (e.g. from E. coli, C. difficile)
Supports secretory IgA and gut immune defence
Helps beneficial bacteria recover more quickly
I certainly wish I knew all this when I got infected back in 2009! Alas, no one told me about this probiotic yeast back then, so I ended up on antibiotics (IV and pills) for three long weeks. My gut was never the same.
Brands with clinical data include Florastor and other S. boulardii CNCM I-745 products like Yomogi.
Note: I tend to avoid Florastor as it contains lactose (although in small quantity) and a few of my clients are either lactose intolerant or allergic to dairy. I recommend Floramyces by Designs for Health instead. You can easily get it in Canada, USA and Australia.
Zinc
Zinc is a mineral essential for both immunity and the gut lining. Best food sources for zinc are mainly animal-based: meat, shellfish, eggs, dairy; although legumes, nuts, and seeds provide some zinc as well.
The WHO and multiple trials show that zinc + ORS reduces the duration and severity of diarrhea in children, and may lower risk of another infection in the next 2–3 months.
Note: High doses of zinc can cause nausea or vomiting, so it’s usually better for the recovery phase, once vomiting has settled. I recommend taking it with a meal.
Butyrate
Butyrate is a short-chain fatty acid normally made by your gut bacteria when they ferment fibre. It is the main fuel for colon cells and is key for gut barrier health. Both human and animal studies show that butyrate:
reduces gut inflammation
supports tight junctions
helps repair the intestinal lining
maintains a healthy, low-oxygen environment in the colon, which beneficial microbes love
Note: we don’t have large human trials on oral butyrate supplements specifically for acute gastroenteritis yet, but the mechanisms and early data in other gut conditions (like IBD and IBS) are promising.
Colostrum and SBI
You can think of Colostrum and serum-derived bovine immunoglobulins as “borrowed” antibodies for the gut. These are known to bind and neutralize microbes and toxins in the gut, support gut barrier repair and help calm down post-infectious diarrhea.
Two options that can support the gut lining after infections:
Bovine colostrum: the first milk from cows after calving. It contains dairy proteins and lactose.
Randomized trials show bovine colostrum can reduce the duration and severity of acute infectious diarrhea in children, including cases from rotavirus and E. coli.
Serum-derived bovine immunoglobulins (SBI): purified antibodies from bovine serum. SBI is usually better tolerated in dairy-sensitive individuals but is more expensive.
Clinical studies of serum-derived bovine immunoglobulin (SBI) in people with diarrhea-predominant IBS (IBS-D) show improvements in stool frequency, stool form, and abdominal symptoms.
Typical doses used in studies:
Colostrum: 5–20 g/day in divided doses
SBI: 5 g twice daily in adults
Again, use under practitioner guidance in children or people with complex medical histories.
Supporting the Gut–Brain Axis to Prevent PI-IBS
We now have solid data showing that stress, anxiety, and depression around the time of an infection increase the risk of developing post-infectious IBS.
Why?
Stress changes gut motility
Alters the microbiome
Raises gut sensitivity
Affects immune responses to infections
Supporting the gut–brain axis is therefore not trivial, it’s protective.
Helpful tools:
nervous system-based practices (breathwork, gentle yoga, walking, somatic work)
regular sleep schedule
social support
therapy when needed
Long-term gastro prevention
To build resilience:
Eat a mostly whole-food, fibre-rich diet to nourish butyrate-producing bacteria
Stay well-hydrated (hint: with minerals)
Use S. boulardii, zinc, and/or colostrum/SBI strategically:
when travelling
when a family member has a stomach bug
during and after an antibiotic course
Work on stress and nervous system health to protect against PI-IBS and flares of existing gut issues.
Giving Your Gut What It Needs to Fully Heal
Recovering from a stomach bug isn’t just about waiting it out — it’s about helping your gut bounce back, rebuilding your microbiome, and lowering your risk of lingering symptoms like bloating, pain, or post-infectious IBS.
With a few simple steps: hydration, gentle foods, targeted probiotics, zinc, butyrate support, and basic nervous system care, you can shorten the course of illness and support a stronger, more resilient gut afterward.
Your digestive system has an incredible ability to heal. Giving it the right support before, during, and after gastroenteritis can make the difference between a quick recovery and weeks (or months) of unsettled digestion. With the strategies in this article, you can help your gut recover fully and confidently prevent long-term complications.
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