ANTIBIOTICS

The antibiotic effect in pregnancy and at birth

There is absolutely no doubt that antibiotics save lives. The world before they were discovered saw huge loss of life from what are now treatable infections, however, we now know that they come with a cost. Our microbes are crucial part of how we function as humans and while antibiotics can help fight infection, they disrupt all our microbes during the treatment.

"A single course of antibiotics can change the composition of oral and gut microbiomes for at least a year, according to a modelling study by UCL researchers. Moreover, this change leads to a decrease in the number and types of microbes found in the gut"

Antiobiotics account for 80% of all pres

This matters because antibiotics are among the most commonly prescribed medications in pregnancy. A 2025 review confirmed that antibiotics account for nearly 80% of all prescription medications during pregnancy, and approximately 20–25% of women will receive an antibiotic during pregnancy. The most common reasons are urinary tract infections, genital tract infections, and respiratory infections.

To be clear — if a pregnant woman needs antibiotics, she should absolutely take them. Untreated bacterial infections in pregnancy can be life-threatening for mother and baby. But this is exactly why caution in prescribing matters: the more we understand the impact on the developing microbiome, the better we can support recovery alongside treatment.

(Professor David Burgner and Dr Jessica Miller, University of Melbourne 2018)

Research from Denmark, that used data from over 770,000 children found when antibiotics were used late in pregnancy this increased the risk of infection in vaginally born infants.

"The overall increased risk occurred regardless of infection type; whether it’s invasive bacterial, viral, gastrointestinal, lower respiratory tract, upper respiratory tract, genitourinary, skin or soft tissue. ... A child’s gut microbiome is particularly important in gastrointestinal infections"

More recent research has also found:
2018 — Repeated prenatal exposure to antibiotics was associated with childhood obesity at age 7 years, with risk tending to increase with an increasing number of antibiotic exposures.
2019 — Prenatal antibiotic exposure in the second trimester was associated with an altered infant gut microbiome at 3 and 12 months, and with higher weight-for-length scores at 12 months.
2015 — Antibiotic use in the third trimester leads to an increased risk of childhood wheeze (no link was found with first trimester use).

Antibiotic resistance — a growing concern for babies

One of the most important and underreported consequences of antibiotic use in pregnancy and at birth is its effect on antibiotic resistance genes in the baby's gut. This is an emerging area of research with significant implications.

Every one of us carries a 'resistome' — a collection of antibiotic resistance genes in our gut microbiome. In adults, this is less of an immediate concern, but in newborns, whose gut microbiome is being assembled from scratch in the first weeks of life, it matters enormously.

Research has found that antibiotics given to the mother during labour increase the number of antibiotic-resistant bacteria passed to the baby. And the type of feeding after birth makes a real difference: one study found that formula feeding was associated with a 70% increase in antibiotic resistance genes in the infant gut compared to breastfeeding. Infants fed exclusively on human milk had both a more diverse gut microbiome and significantly fewer antibiotic-resistant bacteria.

A 2025 study went further, finding that Bifidobacterium longum — one of the most important beneficial bacteria in the breastfed infant gut — had a consistent protective effect, being negatively associated with 21 different antibiotic resistance genes at one month in breastfed babies. In other words, breastfeeding actively suppresses antibiotic resistance taking hold in baby's gut.

(Pärnänen et al 2022; Pan et al, Gut Microbiota 2025)

This adds yet another dimension to the importance of supporting breastfeeding after any antibiotic exposure in pregnancy or birth.

Remember that antibiotics absolutely are necessary sometimes and should not be avoided when needed. If you do need to take them, make sure you eat a really healthy diet and consider taking a supplement.

GROUP B STREP

GBS AND THE MICROBIOME

In many countries pregnant women are routinely screened for GBS (not here in the UK) and when there is a postive test, antibiotics are given in labour to reduce the risk of transmission to the baby. Of the approximately 25% of women who carry GBS, in a tiny number it will lead to infant infections resulting in serious illness and even death. Antibiotic treatment is an important prevention strategy in the treatment of GBS.

The trouble is that those antibiotics also disrupt the infant microbiome in early life. A study from McMasters University found that the infants who had the antibiotics in labour had "dramatically" altered gut bacteria in early life although this difference had narrowed by 12 weeks. Again this is significant as it's the early life microbia that train the immune system. More recent and larger studies have found the picture is more complex — and more concerning — than that early research suggested.

The impact on Bifidobacterium may last longer than we thought

More recent research has found that intrapartum penicillin given for GBS causes a persistent reduction in Bifidobacterium longum in the infant gut microbiome across the entire first year of life — not just the first 12 weeks as earlier research suggested. This is significant because Bifidobacterium species are among the most beneficial bacteria in the infant gut, playing a key role in immune training, gut barrier function and protection against harmful bacteria.

(Teuscher et al 2023)

Increased risk of autoimmune conditions in childhood

A major 2025 systematic review and meta-analysis published in BJOG — the most comprehensive to date on this topic — found that intrapartum antibiotic prophylaxis for GBS was associated with a significantly increased risk of autoimmune-related disease in children, with a relative risk of 1.73 across six studies. It also found associations with reduced gut microbiome diversity in newborns.

(Moradi et al, BJOG 2025)

A nuanced picture on infections

A 2024 large population cohort study brought an interesting and genuinely nuanced finding: maternal intrapartum antibiotics were associated with a small overall increase in the risk of later infectious diseases in the offspring — but there was also a long-term protective effect against severe infectious diseases caused by penicillin-susceptible microbes. This means there isn't a straightforward good/bad message, and it underscores the importance of individualised risk-benefit conversations.

(eBioMedicine / The Lancet 2024)

There is no easy solution here, and this page is in no way intended to discourage women from accepting antibiotics for GBS when they need them — the risk of serious neonatal infection from GBS is real and the antibiotics are effective at preventing it.

What research tells us is that:
The microbiome impact of GBS antibiotics is more significant and longer-lasting than was previously understood
Breastfeeding is one of the most important things a mother can do after receiving intrapartum antibiotics — both to support microbiome recovery and to reduce antibiotic resistance proliferating in the baby's gut
The microbiome impact should be part of the informed consent conversation when antibiotics are offered in labour
There is a real and pressing need for research into more targeted solutions — treatments that can address GBS specifically without the broad disruption to the developing microbiome that current antibiotics cause

What can you do?

If you have received antibiotics during pregnancy or labour, here are some evidence-supported steps to help support your baby's microbiome:

Breastfeed if you can — even one feed matters. Breastmilk actively helps restore beneficial bacteria and has been shown to suppress antibiotic resistance genes in the infant gut. This is the single most impactful thing you can do.

Skin to skin — promotes transfer of beneficial skin bacteria and has wide-ranging benefits for the newborn.

Eat a gut-friendly diet — fermented foods (live yogurt, kefir, sauerkraut), fibre-rich vegetables, oats, and legumes all support your own microbiome recovery, which in turn benefits your baby through breastmilk.

Consider probiotics — there is reasonable evidence for probiotic use after antibiotic exposure. Discuss multi-strain options with your midwife or GP. Food-based sources are always the best starting point.

Don't panic — the research shows increased risk, not certainty of harm. Knowing this information helps you make informed choices to support your baby's start.