Restoring Gut Flora After Diarrhea



Everyone at some point in their lives will experience the joys of diarrhea. Yes, this entire post will be discussing diarrhea. Specifically what it is, how and why you get it, plus how to restore your gut flora after the onslaught of constant bathroom breaks is done.

Having diarrhea chronically is just as bad as being chronically constipated. Before we get into chronic and acute diarrhea, let’s discuss exactly what diarrhea is, shall we?


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Diarrhea is characterized as loose, watery stools or the frequent need to have a bowel movement. Diarrhea can be acute or chronic.



There are many causes that result in diarrhea.

  • VIRAL INFECTION: Rotovirus is a common cause of childhood diarrhea. This is a viral infection that causes diarrhea and vomiting. Initial symptoms of rotovirus are fever and vomiting followed by three to eight days of watery stools.
  • BACTERIAL INFECTION: several types of bacteria can enter your body through contaminated food or water and cause diarrhea. Common bacteria that cause diarrhea are E. Coli, Salmonella and Campylobacter. These are all foodborne illnesses that you can get from contaminated food.
  • TRAVELLERS DIARRHEA: this is another foodborne illness caused by eating food or drinking water contaminated with bacteria, viruses or parasites. Travelers diarrhea is usually acute and clears up fairly quickly.
  • ADVERSE REACTION TO MEDICATION: many medicines may cause diarrhea. Medicines that may cause diarrhea are antibiotics, antacids and some cancer treatments.


Acute diarrhea usually only lasts a few days. This type of diarrhea could be from a viral infection or from something that you have eaten or a reaction to medication you are taking. This type of diarrhea is fairly common and clears up fairly quickly. Some examples of acute diarrhea: viral infection, bacterial infection, travelers diarrhea, adverse reaction to medications.


Chronic diarrhea lasts longer, at least 4 weeks. Chronic diarrhea is usually the result of an intestinal disease or disorder. Some examples of intestinal disease that may cause chronic diarrhea are:

  • SIBO (small intestine bacterial overgrowth)
  • IBS (irritable bowel syndrome)
  • FOOD ALLERGIES: could cause chronic diarrhea. Some examples of food allergies that may cause diarrhea are:
    • lactose intolerance
    • fructose intolerance
    • sugar alcohols: sorbitol, mannitol and xylitol may cause diarrhea in some people.
  • ABDOMINAL SURGERY: you may develop chronic diarrhea after abdominal surgery. This type of surgery includes:
    • gallbladder
    • large intestine
    • small intestine
    • spleen or stomach
  • LONG TERM USE OF MEDICINES: medicines taken for a long time may cause chronic diarrhea. Medicines such as antibiotics, can change the gut flora and cause bacteria overgrowth of opportunistic bacteria which can cause chronic diarrhea.



Drinking Water

What do you do when you have diarrhea? How do you treat it? While you are dealing with diarrhea, the best thing to do is to replace lost fluids. Drink water and an electrolyte supplement to help replenish lost electrolytes as well as lost fluids.

If the situation becomes serious and you become severely dehydrated, then you will need to be hospitalized and put on an IV to get fluids into your body.

If a bacterial infection is causing the diarrhea then your doctor may need to prescribe you antibiotics.

My oldest daughter contracted salmonella when she was six years old.

She was a thumb sucker.

One day she went on a field trip with her class to see baby chicks at a farm. They all washed their hands after touching the baby chicks however my daughter had also been sucking her thumb before washing for hands.

I did inform her before the field trip to NOT put her thumb in her mouth until AFTER her hands were washed but she was a six-year old at the time and it was such a habit to put her thumb in her mouth that she did it without even thinking.

Salmonella works fast let me tell you! She felt sick by the time she got home that afternoon and by that evening she had a fever and was throwing up!

Then came the diarrhea!!

It went from bad to worse to so disgusting that it didn’t even look like diarrhea anymore.

The poor little girl!

She had so much pain and cramping. I can’t remember if she had to go on antibiotics, but I know it was at least seven to eight days of nasty loose, bloody-swamp-water-looking stools, before the diarrhea started to clear up.

If I knew then, what I know now, about the importance of balanced gut flora, I would have started implementing some flora replenishing steps as soon as she was feeling even just a little better.

Once she was no longer infected with salmonella, she was still very weak and pale. It took her months to look and feel better. Now I know this was because her intestinal tract was depleted of all good bacteria and very unbalanced. At the time, I went back to feeding her, her regular diet, which wasn’t an unhealthy diet by any means. However, she could have used some extra help in the rebuilding of good gut flora.

Here is what I would do now to help restore gut bacteria after diarrhea. I would feed her foods that helped to replenish her gut bacteria.


Once your body has healed and the diarrhea has stopped, you can now begin to replenish your gut with good, helpful, beneficial bacteria.

All the good and bad bacteria have been pretty much wiped out with that bout of diarrhea.

It takes about one month for your gut microbiome to recover after having diarrhea. You will want to take care of your intestines during this time and help to re-establish a healthy balance of your gut mircobiome.

The foods you eat following a bad case of diarrhea will have a big impact on how quickly your guts recover. Let’s look at some foods to eat that will help to replenish beneficial bacteria in your gut.



How To Heal Gut Flora After Antibiotics

  1. FERMENTED AND CULTURED FOOD: some examples of fermented and cultured foods are; sauerkraut, kimchi, keifer and naturally pickled vegetable. Try to eat a variety of fermented foods as this will provide your gut with bacteria diversity which will help to restore your gut faster.
  2. PREBIOTIC FOODS: you will want to feed your new beneficial bacteria. These bacteria LOVE fiber rich foods. Foods high in soluble fiber are considered prebiotic and will work best at feeding your good gut bacteria. Here are some examples of prebiotic foods: broccoli, chia seeds, beans and legumesraw-vegetables
  3. RAW VEGETABLES: organic vegetables are best as they won’t have pesticides on them. These pesticides will kill off the good bacteria basically working against what you are trying to do! Raw veggies are a great source of fiber. If your body is having a hard time with raw veggies, then steam them. Steaming cooks the veggies slightly making it easier for your body to digest.

Of course, once you are feeling better, you usually go back to your regular way of eating, However, keep in mind that if you want to restore your gut microbiome to a healthy balance, you will need to avoid these three foods.


  1. SUGAR: it’s always good to limit your refined sugars to no more then 25grams a day. However, when you are rebuilding your gut flora, you will want to avoid sugar altogether. Opportunistic bacteria thrive on sugar and we want to limit the production of these bad bacteria as much as
  2. RED MEAT: limit your red meat (pork, beef) to once or twice a week while your gut heals. Too much red meat can lead to an unfavorable shift in your gut bacteria.
  3. UNDERCOOKED EGGS OR SEAFOOD: avoid raw eggs and seafood (sushi) while your gut flora is rebuilding a strong population of friendly bacteria.raw-seafood



You now know what causes diarrhea, and how to heal your gut flora after a bout of diarrhea.

So how do you go about making sure you don’t get diarrhea again? Here are a few tips to help prevent diarrhea.


  1. WASH YOUR HANDS: to help prevent spreading a bacterial infection that causes diarrhea, wash your hand frequently with soap and water.
  2. THAWING FROZEN FOOD: always thaw your frozen food in the refrigerator
  3. LEFTOVERS: refrigerate leftovers right away. Do not leave out.
  4. FOOD PREPARATION: wash cooking areas and food preparation areas frequently


If you have read any of my previous posts, then you will start to notice a trend. Our guts NEED bacteria to keep us healthy. But in order to have the good, high quality bacteria, we have to nourish our body with foods that feed the BENEFICIAL bacteria and starve the OPPORTUNISTIC bacteria.

This is why it is so important to be mindful of the food that you put in your body.

I would love to know your thoughts. Have you experienced gut issues after a bad bout of diarrhea and if so, what did you do to help heal your gut?


The Gut Nerd


8 thoughts on “Restoring Gut Flora After Diarrhea”

  1. Wow, what a great post you. Have written on restoring gut flora after diarrhoea, when I was young I contacted this sickness form one of my classmates and then I was told to drink some water to immediately but I think it was a chronic one then so I had to be hospitalized, many might contacted it they won’t know, some might wanna contact it but with this post I think we all captured the knowledge of it and how it works so we will stay abstained from it , thanks 

  2. I thought that diarrhoea was mainly down to a bad diet or essentially eating something that doesn’t agree with you.

    Especially at this time of year I somehow manage to eat a lot of rubbish food in the form of sweets and chocolate but that said Im more than capable of eating rubbish food all year round and I’m not very good at eating my 5 a day, in fact I’d struggle to do 1 a day.

    Personally I think one of the best ways to cleanse the gut is to drink a lot of eater throughout the day and when I’m in the mood to do this, I can easily get through several pints of water but then thats a habit that needs to be adopted.

    I find that sugar rush food will bring on a bout of diarrhoea which then takes a couple of days to get solid again. What is the cause of your faeces smelling real bad when emptying your bowel?

    • Yes! Water is a great way to stay hydrated and help keep things moving in the gut! Also drinking water will help to keep you hydrated if you are struggling with diarrhea. 

      As for the smell of your faeces, usually if it’s really stinky, that means it’s been up in your large intestine for quite awhile.

  3. Oh dear, traveller’s diarrhea, that happened to me twenty years ago when I was in Colombia, I must have eaten something bad on my second last day, because on the day before going back home I got very sick … I remembered that we were joking about it, saying that it was a sign that was telling me to stay 😉 I also had salmonella three years ago, but it strangely didn’t affect me in my gut but in my throat, that’s why I didn’t recognize it as salmonella, and when the doctor gave me the diagnosis I was shocked. 

    Sauerkraut is delicious and now that I know how good it is for the gut flora, I will definitely eat it more often. I also know how to make sauerkraut, so I’ll do that again soon 🙂 I also eat a lot of vegetables, so that’s good too as I can see in your recommendations. 

    I always wash my hands before I prepare food and also before I eat. I learned that the hard way 😉 I also hardly buy anything from the street, since I do not trust the hygiene of all foods sold by street vendors + the car exhaust and dust flying up … I rather pass.

    This post is important, diarrhea can be deadly if it goes on too long and if it is not treated. Even if some readers may be a little put off by the topic, it is a very important topic. Thanks for sharing this!

    • Thanks for the comment! I’ve never heard of salmonella in the throat! Crazy! That must have hurt really badly! Salmonella in the guts is nasty and VERY painful.

  4. hello Anna;
    I appreciate your article because you touch there a common problem, I received one evening of the fruits (mangoes) of my neighbor whom he had just gathered in his plantation and in haste I sucked one without taking the care of washing it, I do not tell you the rest, I have two weeks hospital center because of a dysentery amebienne so I appreciate the value of the tricks that define here, it is as useful for the parents that we are only for our dear children.
    thank you.


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