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Getting a Good Gut

Along with being a mom to your little one, whether you realize it or not, you’re also mom to trillions of microbes who are making their home in baby’s gut. These tiny guys shape the way baby’s brain, immune system, and digestive system develop. And with a little nurturing know-how you can ensure they create long-term health benefits for baby from the get-go.

Factors that influence infant gut microbiome

Understanding your baby’s microbiome

Inside your gut is a world teeming with life. Trillions of microbes, including bacteria, fungi, and viruses, live and multiply within your gut. This microscopic world is your microbiome. A healthy microbiome is one that has lots of helpful bacteria in the right amounts, to help your body stay healthy.

The health of a microbiome has a ripple effect for overall health, and for about the first 1,000 days of your baby’s life their microbiome is developing.

A baby’s gut starts with 0 microbes, but quickly develops right from conception. Having a healthy microbiome creates a blueprint for:

A good metabolism

As we learn more about how our microbiome impacts our health, we’re starting to understand how an unbalanced microbiome may increase the risk of developing diabetes, obesity, cardiovascular disease, and other illnesses.

Brain and cognitive development

A healthy, diverse microbiome sends ‘positive’ messages to the brain which may improve baby’s motor skills, language development, and behavior.

Physical growth

We all know that good nutrition is key for baby to grow. However, what is also key is having a healthy, diverse microbiome which is needed for the absorption of these nutrients. A healthy microbiome also plays a role in producing the right amount of hormones baby needs to grow.

Strong immune system

Your immune system has a huge job to do, including destroying harmful microbes and looking after the good ones. A healthy microbiome supports the development of a strong immune system for life.

Microbiome under the microscope

If it’s been a while since your last school biology lesson, here’s a quick reminder of the microscopic world that inhabits everyone’s gut:


Bacteria are single-celled microorganisms and are the most abundant microbe of your microbiome. Most of them are helpful but there are a few harmful ones that, given the opportunity, flourish and make you ill.


Fungi are usually multi-cellular organisms that love warm and damp places. A healthy immune system supports the balance of good and bad fungi.


Protozoa are like bacteria and love moist environments such as soil and water. Some protozoa are parasitic and live in animals, plants, and people.


Viruses are little carriers of genetic material who invade other cells and use the cell structure to reproduce and spread. Not all viruses are harmful to us but sometimes they’re hard to treat and can easily spread.

The roles of the microbiome

Sharing our world with our family of microbes benefits us both. We need them to survive, and many of them need us to survive as well. It’s a perfect partnership—most of the time—and one that’s survived for millennia.

We’re still learning about how beneficial this relationship is for our health, but we know a healthy microbiome helps you with digesting food, regulating your immune system, protecting against disease-causing bacteria, and producing important vitamins.

Helping digest food

Bifidobacteria is one of the first bacteria to grow in baby’s gut that’s needed to break down breast milk and formula for baby’s body to use.

Regulating your immune system

Most of your immune cells are inside your gut. When baby’s microbiome is well-balanced and diverse, it can lower their risk of developing autoimmune conditions such as asthma, eczema, and allergies.

Protecting against disease-causing bacteria

A healthy microbiome provides a protective barrier between your bloodstream and any harmful bacteria in your gut. Without a healthy gut wall, bacteria can cross into your circulation where they can potentially cause illness or disease.

Producing important vitamins

Microbes help to break down food and supply the body with important nutrients, including the B vitamins and vitamin K.

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Boosting baby’s microbiome

During pregnancy

During pregnancy your microbiome changes to support the health of you and baby. Eating high-fiber and nutrient dense foods improves your microbiome, while processed, sugary, and fatty foods can unbalance the good and bad microbes and impact both short and long-term health.

At birth

From the moment baby is born, their world influences their microbiome. If born vaginally, their early microbiome is similar to yours as you pass your microbes to your baby from your birth canal and gut.  If born via caesarean section, their microbiome has more microbes usually found on skin and in the environment.

Antibiotics, either from exposure while in the womb or if baby needs them after birth, can also impact on the diversity of their microbiome.

After birth

If you can, breastfeeding is best for baby, and for you. Your breast milk contains all the nutrients baby and their microbiome need to stay healthy. 

While it’s still sensible for everyone to have good hygiene, don’t go overboard using lots of sanitizers or disinfectants. Remember exposure to bacteria helps build the microbiome and develop a healthy immune system.

Probiotics vs. Prebiotics

Whoever first said, “the best-laid plans often go awry” must have been a parent. Because if you’re like many moms or moms-to-be, you probably had ideas about how you wanted your birth and first few months with your little one to be. But life has a way of throwing us a few curveballs to keep us on our toes.

Maybe you had an emergency caesarean section or breastfeeding didn’t work out well, or perhaps you or your new baby needed to take antibiotics. Even if baby’s microbiome got off to a rocky start there are many simple ways you can improve their gut health including a diet high in probiotics and prebiotics.

What are probiotics?

Probiotics are ‘live’ bacteria and yeasts that help to maintain or improve the amount of good bacteria in your gut. Some yogurts and fermented foods are great sources of probiotics. There are probiotic supplements available for babies, you should discuss their use with your healthcare provider before starting your baby on any supplements.

Giving your baby a quality probiotic can help to improve the diversity and health of their microbiome, laying the foundation for good long-term health including:

  • Good digestion and metabolism of food;
  • Reducing the risk of developing food allergies;
  • A strong immune system; and
  • Lowering the risk of developing autoimmune conditions such as asthma and eczema.

By the time baby is enjoying smooshing their first birthday cake, they would’ve moved from a liquid diet (breast milk or formula) to eating a range of vegetables, fruit, and other family foods.

Even though the human microbiome is complex and still not fully understood, we do know two key probiotics, Lactobacillus and Bifidobacterium, can improve gut health. Together with a nutrient-dense diet you’re helping baby’s microbiome get off to a great start.

What are prebiotics?

Like every living thing, your microbiome needs food to survive. Prebiotics are the food source for good bacteria and are in many vegetables, fruits, and whole grains.

Prebiotics are a type of plant fiber your body can’t digest but your microbes can and it helps them to stay strong in your gut.

Breast milk is a rich source of prebiotics, so if breastfeeding is working for you and your little one, their microbiome will be making good use of prebiotics. Once baby starts eating vegetables and fruit they’ll benefit from the prebiotic fiber from food.

Prebiotics can also:

  • Digest carbohydrates your body can’t, helping good bacteria grow;
  • Help your body absorb calcium, needed for strong bones and teeth;
  • Break down some foods faster so they move through your gut quicker; and
  • Improve the health of your gut cells.

Antibiotics' influence on the microbiome

Taking antibiotics during pregnancy can cause changes to your microbiome and, therefore, changes to the initial microbiome of baby. As researchers learn more about the long-term effects of antibiotics on microbiomes, there’s evidence to suggest antibiotics early in life may impact on long-term gut health.

Antibiotics work by killing certain bad bacteria, but in the process they can also wipe out many of your microbiome’s good bacteria. This can mean a less diverse microbiome, giving bad bacteria more room to grow, and unbalancing your microbiome.

Antibiotics: the good and bad

You shouldn’t think of antibiotics as either good or bad. Like many things: wine, coffee, candy, taken in moderation they’re beneficial. But since antibiotics were first discovered by western medicine in the 1900s, their over-prescription and overuse has led to unwanted side-effects, such as antibiotic resistance and changes to our microbiome.

Before taking antibiotics, it’s important to know they:

  • Only treat bacterial infections, not infections caused by a virus such as the common cold;
  • Can alter your microbiome, and if you’re pregnant they can impact your baby’s microbiome;
  • Can be overprescribed and overused, increasing the risk of resistance and increasing the risk of infections in childhood; and
  • Can cause unnecessary side effects such as diarrhea, vomiting, rashes, and allergic reactions.

If you can, avoid regular antibiotic use for everyone in your family. But remember, taking antibiotics when necessary can help to treat, cure, and save lives. It’s a balancing act, but knowing how they can cause microbiome imbalance gives you the power to proactively look after your family of microbes during and after taking antibiotics.

Gut feeling

Now you know the simple steps needed to care for baby’s microbiome. These will soon become second nature, ensuring good microbes flourish and support the healthy development baby needs. So, when baby gives you that first magical smile you can be assured that if those tiny microbes could they would all be smiling too.

Disclaimer: The information provided is the opinion of Good Feeding, it has not been evaluated by healthcare professionals, and is for educational purposes only.  Before starting any new foods or feeding practices, please consult your baby's healthcare professional.

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Creating healthy and happy eaters

  • You provide, let baby decide. You provide what foods are on offer, and baby decides when they have had enough
  • Keep mealtimes happy and stress free
  • Remove unnecessary distractions such as TV or devices
  • Ensure baby is sitting comfortably and facing other family members
  • Role model healthy eating at every opportunity.
  • Respond to hunger and fullness cues and leave behind expectations of how much you want baby to eat. 
  • Feed slowly, encouraging baby to eat and never resorting to bribery
  • Avoid unhealthy foods you know baby will eat to ensure they ‘just eats something’
  • Only offer food for hunger and not for any other reason

Disclaimer: The information provided is the opinion of Good Feeding, it has not been evaluated by healthcare professionals, and is for educational purposes only. Before starting any new foods or feeding practices, please consult your baby's healthcare professional.

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Creating a veggie lover

  1. Pack in those veggies when you’re pregnant and breastfeeding

    Baby’s flavour journey begins in the womb surrounded by your amniotic fluid. Breastfeed if possible to continue the flavour journey through your breast milk.

  2. Begin Flavor training at around 4-5 months

    Flavor training starts before baby needs solids for nutrition. A ‘taste’, 1/2 teaspoon, is all that is required, after a milk feed.

  3. Vary your Veggies

    • Introduce a wide variety of vegetables spanning the whole flavor spectrum. Being sure to include plenty of bitter vegetables (broccoli, spinach, brussels sprouts).
    • Try offering a new ‘taste’ every 1-2 days In all different forms (warm, cold, puree and after 6 months as finger foods)
  4. No health by stealth

    Offer single vegetables where possible, especially in the first few months of flavor training. Avoid hiding ‘unliked’ foods in ‘liked’ foods.

  5. Repetition, repetition, repetition

    If baby doesn’t like it the first time offer again and again. It can take up to 10 times before acceptance. Don’t be put off by funny faces baby is just getting used to something new. Continue to offer again and again, throughout infancy, toddlerhood and the preschool years

  6. Be a healthy eating role model

    Be a positive role model at all ages and stages, show baby just how delicious those veggies are. Avoid allowing your own likes or dislikes, wants and expectations get in the way.

Disclaimer: The information provided is the opinion of Good Feeding, it has not been evaluated by healthcare professionals, and is for educational purposes only. Before starting any new foods or feeding practices, please consult your baby's healthcare professional.

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