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      Is All Bacteria Harmful for Babies?


      Is All Bacteria Harmful for Babies?

      Read time: 3 minutes

      Explore the impact of bacteria on babies and their immune system. Learn about “good” and “bad” bacteria for babies and why exposure to germs can help your baby’s immune system to mature.

      Exposing My Baby to Germs

      The moment your baby is born is likely to be the first time your baby’s immune system has been exposed to bacteria from the outside world. Not all bacteria are harmful, and we have many bacteria (known as the human microbiome) which live in our gut and on our skin, which don’t cause us any harm. There are a number of ways in which your baby may be exposed to bacteria after birth.

      Birthing Method

      Babies born vaginally are more likely to develop a pattern of gut bacteria which reflects their mum’s gut bacteria. For babies born by caesarean section, their gut bacteria is likely to reflect their mum’s skin bacteria. The development of an infant’s immune system is influenced by this early exposure to bacteria, which could have life-long impacts on health1.

      Living Environment

      After birth, the type of environment you live in will also affect your baby’s exposure to bacteria.  For example, children who live in farming communities and who have close contact with farm animals have been found to have lower rates of asthma in childhood when compared to children from farming communities who do not have close contact with farm animals2.

      Food Preparation

      For formula fed infants, correct preparation of their milk is essential, as it can help to prevent bacterial infections, particularly diarrhea and vomiting. Ensure you wash your hands and sterilise your baby’s bottles and follow the manufacture’s preparation instructions on the pack very carefully to prepare the formula. Dispose of any formula which is left over after you have fed your baby3.

      "Good" Bacteria for Babies

      Studies have been done to find out whether providing beneficial bacteria in the diet, known as probiotics, can benefit babies in early life. Giving mothers or their baby probiotics has been shown to result in a lower risk of eczema in young children4.

      Bacteria in Breast Milk

      Human breast milk contains its own pattern of beneficial bacteria which help with the development of a baby’s immune system. Breast milk is also rich in human milk oligosaccharides (HMOs) which these beneficial bacteria thrive upon5. The quantity and type of HMOs in breast milk varies a great deal between women6. You can read more on breast milk nutrition here.

      "Bad" Bacteria for Babies

      Why Can’t Babies Have Honey?

      It’s important that we protect babies from exposure to harmful bacteria. Babies under the age of 12 months should not be fed honey – it may contain bacteria which produce botulism toxin, which can be very harmful to young children7.

      Vaccinations and Childhood Illness

      Once your baby has arrived, make sure they have the childhood vaccinations and immunisations recommended by the NHS as these will protect them against both bacterial and viral illnesses. For example, meningitis is a serious and life-threatening childhood illnesses caused by meningococcal group B bacteria. Rotavirus is a common childhood illness with symptoms of diarrhea and vomiting which is caused by a virus, and vaccination reduces the number of children who have serious infections requiring hospitalisation8.

      Dr. Caroline Childs

      Dr Caroline Childs is a Registered Nutritionist and a lecturer in Nutritional Sciences at the University of Southampton. Her research includes nutrients such as dietary fatty acids, probiotics, and prebiotics.

      1. Dogra, S et al. Rate of establishing the gut microbiota in infancy has consequences for future health. Gut microbes 2015, 6,5:321-5. Doi:10.1080/19490976.2015.1078051. Available at:
      2. Ober, C et al. Immune development and environment: lessons from Amish and Hutterite children. Curr Opin Immunol 2017;48:51-60. Doi:10.1016/j.coi.2017.08.003. Available at:
      3. NHS. How to make up baby formula [Online]. 2019. Available at: [Accessed November 2020]
      4. Zuccotti, G et al. Probiotics for prevention of atopic diseases in infants: systematic review and meta-analysis. Allergy 2015;70,11:1356-71. Doi:10.1111/all.12700.  Available at: 
      5. Lawson, MAE et al. Breast milk-derived human milk oligosaccharides promote Bifidobacterium interactions within a single ecosystem. ISME J 2020;14:635–648. Doi: Available at:
      6. Ruiz L et al. What’s Normal? Immune Profiling of Human Milk from Healthy Women Living in Different Geographical and Socioeconomic Settings. Front Immunol 2017;8: 696. Available at: 
      7. NHS. Foods to avoid giving babies and young children [Online]. 2018. Available at: [Accessed November 2020].
      8. NHS. NHS vaccinations and when to have them [Online]. 2019. Available at: [Accessed November 2020].

      Important notice:

      Breastfeeding is the best form of nutrition for babies and provides many benefits to babies and mothers. It is important that, in preparation for and during breastfeeding, you eat a healthy, balanced diet. Combined breast and bottle feeding in the first weeks of life may reduce the supply of your own breastmilk, and reversing the decision not to breastfeed is difficult. Always consult your healthcare professional for advice about feeding your baby. If you use infant formula, you should follow manufacturer’s instructions for use carefully.

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      Your baby's future health begins here

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