During pregnancy, your gut microbiome is doing much more than helping you digest food. The microbes living there produce a wide range of compounds, some of which enter your circulation and interact with immune and metabolic pathways. Researchers are now exploring how these signals may help shape the environment in which your baby develops.
The connection continues around birth, when a baby begins to acquire microbes from their mother and the world around them. Because this early microbiome develops alongside the immune system, there is growing interest in how the pregnancy microbiome, birth, feeding and maternal gut health may influence a child’s longer-term health. This guide explains what current research shows and offers practical, evidence-based ways to support gut health during pregnancy.
Key takeaways
- The maternal microbiome produces compounds that may influence immune and metabolic development during pregnancy.
- A baby’s microbiome begins taking shape around birth and continues to develop throughout early childhood.
- Birth mode can affect a baby’s early mix of microbes, but it does not determine their long-term health.
- A varied, fibre-rich diet can support gut health during pregnancy; increase fibre gradually if needed.
- Take antibiotics when prescribed, and seek professional advice before choosing a probiotic for a specific symptom.
What is the maternal microbiome in pregnancy?
Your microbiome is the community of bacteria, fungi, viruses and other microorganisms living in a particular part of the body, together with the substances they produce.
There is no single maternal microbiome. The gut, vagina and mouth each support a different microbial community. Gut microbes help break down parts of food that we cannot digest ourselves. The vaginal microbiome is usually much less diverse and, during a healthy pregnancy, is often dominated by Lactobacillus species. These bacteria produce lactic acid, helping to maintain the vagina’s naturally acidic environment.1,2
Greater diversity is often discussed as a positive feature of the gut microbiome, but it is not a universal goal. In the vagina, a stable Lactobacillus-dominant community is commonly associated with health.
How does the microbiome change during pregnancy?
Pregnancy brings hormonal, immune and metabolic changes, so the microbiome may respond too. Vaginal microbiota often become more stable and Lactobacillus-dominant. Findings from the gut are less consistent. Some studies report changes as pregnancy progresses, while others find that differences between women are greater than changes within the same woman.1
Diet, medication, geography and pre-pregnancy health can all influence the results. Researchers have not identified a single “ideal” pregnancy microbiome.
Does your microbiome affect your baby before birth?
The connection between your microbiome and your baby may begin before birth. During pregnancy, substances made by your gut microbes can enter the circulation and reach the placenta, where they may help to shape aspects of immune and metabolic development.1,5
Fibre is particularly interesting here. When gut bacteria ferment it, they produce short-chain fatty acids and other metabolites that act as chemical messengers around the body. These microbial signals appear to be one of the ways the maternal microbiome can influence the developing baby, while the baby’s own microbiome begins to establish around birth and continues to develop throughout early childhood.3,4
How does birth affect a baby’s microbiome?
Birth is when a baby’s microbiome really starts to take shape. During birth and the first weeks of life, babies pick up microbes from their mother’s gut, vagina, skin and breast milk, as well as from the people and environment around them. In one study, an average of 58.5% of a baby’s microbiota during the first month could be traced back to their mother.6
How a baby is born influences this early mix. Babies born vaginally tend to acquire more bacteria from their mother’s gut, including Bacteroides species. Babies born by caesarean tend to begin with fewer of these bacteria and more microbes associated with the skin or hospital environment.7
These findings describe general patterns across groups of babies. They cannot tell us how an individual baby’s health will develop, and a caesarean is often the safest way for a baby to be born. The microbiome also keeps changing after birth, shaped by feeding, antibiotics, gestational age and everyday contact with people and the home environment.
Some parents may hear about “vaginal seeding”, where vaginal fluids are transferred to a baby after a caesarean birth. This is not currently recommended outside a research setting because there is no clear evidence of benefit and it could expose the baby to harmful microorganisms.9
Why does the early microbiome matter for immune development?
During the first months of life, a baby’s immune system is learning how to respond to the world around it. Gut microbes are part of this process, interacting with immune cells and producing substances that help the immune system recognise what is harmless and when it needs to respond.
Researchers are particularly interested in whether the early microbiome may influence allergy risk and aspects of metabolic health later in life. It is one part of a much bigger picture, and it continues to develop in response to feeding, antibiotics and the baby’s everyday environment.8 Early differences are not necessarily permanent, and no single microbial pattern determines a child’s future health.
How can you support gut health during pregnancy?
Supporting your gut during pregnancy can begin with the foods you already eat. Fibre provides fuel for gut microbes and can also help with bowel regularity, which is particularly useful if constipation has become an issue.
Vegetables, fruit, wholegrains, beans, lentils, nuts and seeds all provide different types of fibre. As different gut microbes use different fibres, it is worth mixing things up where you can. This might mean adding beans or lentils to a soup, choosing oats for breakfast, or sprinkling nuts and seeds over yoghurt. If you do not currently eat much fibre, build it up gradually and drink enough alongside it, as increasing it too quickly can make bloating and wind worse.
When gut bacteria break down certain fibres, they produce compounds called short-chain fatty acids, including butyrate. These help to maintain the gut lining and are involved in immune and metabolic signalling. Research during pregnancy suggests that diet is one of the factors that shapes the maternal gut microbiome.10
Fermented foods can provide live microbes as well. Pasteurised live yoghurt and kefir are easy options during pregnancy. Kimchi and sauerkraut can also be included, although they can be high in salt and may not contain live cultures by the time you eat them. They are a useful addition if you enjoy them, rather than something you need to eat every day.
Digestion can also be affected by movement, sleep and stress. These are not always easy to manage during pregnancy, so work with what feels realistic. A gentle walk may help to get your bowels moving, while on a more tiring day, rest may be what your body needs.
What about antibiotics and probiotics in pregnancy?
Antibiotics can alter the gut and vaginal microbiota, and exposure during pregnancy or around birth is associated with differences in the infant gut microbiome.11 That is not a reason to avoid treatment when it is needed. Untreated infections can carry serious risks in pregnancy. Take antibiotics as prescribed and speak to your doctor or midwife if you have concerns.
Probiotic effects are specific to the strain, dose and outcome being studied, so positive findings for one product cannot be applied to every probiotic. There is currently insufficient evidence to recommend routine probiotics during pregnancy to prevent food allergy in children.12
If you are considering taking a probiotic for a particular symptom, check whether the exact strains have been studied for that purpose and ask a qualified healthcare professional whether it is suitable for you. More strains or a higher bacterial count does not automatically make a product better.
Pregnancy microbiome: the bottom line
Supporting your pregnancy microbiome is part of looking after yourself. A varied, fibre-rich diet helps feed your gut microbes while supporting digestion and providing many of the nutrients you need during pregnancy.
You do not need to get every meal right. Focus on foods that nourish you, suit your appetite and feel manageable in everyday life. These regular choices can support your health throughout pregnancy while giving your baby a healthy start.
Explore more Health & Her pregnancy advice.
Health information: This article provides general information and is not a substitute for personalised medical advice. Speak to your doctor, midwife or another qualified healthcare professional if you have concerns about your pregnancy, diet, medicines or supplements.
FAQs
Does my microbiome affect my baby?
Your microbiome may help shape some of the immune and metabolic signals your baby receives during pregnancy. Around birth, you also become an important source of the microbes that begin to populate your baby’s gut. This is only one part of their development, so your microbiome does not decide their future health.
How can I improve my gut health during pregnancy?
Try to include a good variety of fibre-rich foods, such as vegetables, fruit, wholegrains, beans, lentils, nuts and seeds. If you enjoy them, pasteurised live yoghurt or kefir can also be useful additions. Increase fibre gradually, particularly if bloating or constipation is already an issue.
Does a caesarean birth harm a baby’s microbiome?
Babies born by caesarean tend to acquire a different mix of microbes at first. Their microbiome continues to develop after birth, however, and is shaped by feeding, close contact with family, antibiotic exposure and the wider environment. A caesarean does not mean that your baby’s microbiome has been permanently harmed.
Should I take probiotics during pregnancy?
A probiotic is not automatically necessary during pregnancy. Different strains have different effects, so the right product depends on why you are taking it. If you are considering one for a particular symptom, ask your doctor, midwife or nutritional therapist whether there is evidence for the strains it contains.
Can antibiotics during pregnancy affect my baby’s microbiome?
Antibiotics can temporarily alter your microbiome and may influence the mix of microbes your baby encounters. Sometimes they are essential for protecting your health and your baby’s health, so always take them as prescribed. If you are worried about their effects, speak to the healthcare professional looking after you.
Reference
- Koren O, Konnikova L, Brodin P, Mysorekar IU and Collado MC. “The maternal gut microbiome in pregnancy: implications for the developing immune system.” Nature Reviews Gastroenterology & Hepatology. 2024.
- Gerede A and colleagues. “Vaginal microbiome and pregnancy complications: a review.” 2024.
- de Goffau MC et al. “Human placenta has no microbiome but can contain potential pathogens.” Nature. 2019.
- Kennedy KM et al. “Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies.” Nature. 2023.
- Gomez de Agüero M et al. “The maternal microbiota drives early postnatal innate immune development.” Science. 2016.
- Bogaert D et al. “Mother-to-infant microbiota transmission and infant microbiota development across multiple body sites.” Cell Host & Microbe. 2023.
- Shao Y et al. “Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth.” Nature. 2019.
- Stewart CJ et al. “Temporal development of the gut microbiome in early childhood from the TEDDY study.” Nature. 2018.
- American College of Obstetricians and Gynecologists. “Vaginal Seeding.” Committee Opinion. Reaffirmed 2022.
- Kunasegaran T et al. “Diet Gut Microbiota Axis in Pregnancy: A Systematic Review of Recent Evidence.” Current Nutrition Reports. 2023.
- Dierikx TH et al. “The influence of prenatal and intrapartum antibiotics on intestinal microbiota colonisation in infants: a systematic review.” Journal of Infection. 2020.
- British Society for Allergy & Clinical Immunology. “Nutritional supplements and allergy prevention.”
