Babies who are given antibiotics early may have lower levels of antibodies and reduced immune responses to vaccines in later infancy, possibly due to changes in the gut microbiome, Australian scientists have suggested.
They have reassured parents, however, that there is no need to “worry unduly”.
Their study tracked 191 healthy babies from birth, and found that those who received antibiotics in the first few weeks of life had significantly lower levels of antibodies against multiple vaccines at seven and 15 months, reports The Guardian.
Of the babies, 111 were exposed to antibiotics in the newborn period – either through direct treatment (32 newborns), or indirectly through mothers who took antibiotics during labour (49), or the first six weeks postpartum (30).
The study, published in the journal Nature, assessed the infants’ microbiomes around the time of their first routine vaccinations at six weeks, and found that those directly treated with antibiotics at birth had less of a group of beneficial gut bacteria known as Bifidobacterium.
The reduction in Bifidobacterium was linked to lower antibody levels against multiple components of the pneumococcal vaccine, as well as Haemophilus influenzae type b, at both seven and 15 months.
Professor David Lynn, a programme director at the South Australian Health and Medical Research Institute, who co-led the research, said that Bifidobacterium was commonly found in the healthy infant gut in the first weeks of life.
“They are particularly well adapted to metabolising human milk oligosaccharides 9a type of carbohydrate) in breast milk, and so you’ll see high rates of those bacteria in infants that are breastfed,” he said.
Lynn, also a professor of systems immunology at Flinders University, said the bacteria gave the immune system “an extra kick”, priming it for an optimal antibody response to vaccines.
“What we think is probably most important is the composition of the microbiome around the time of vaccination,” he said.
“Antibiotics can disrupt the normal colonisation by Bifidobacteria and allow other types of bacteria to colonise the intestine instead.”
The research also studied immunity in germ-free mice, finding that antibody responses to the pneumococcal vaccine strongly depended on the presence of Bifidobacterium and improved when the mice were given a probiotic containing the bacteria.
Labour
The study, involving researchers from 12 institutions across Australia, did not find reduced vaccine responses in babies whose mothers received antibiotics during labour, suggesting direct antibiotic treatment in newborns had a more persistent impact on the gut microbiome.
Lynn said the study results should not “unduly worry” parents of newborns treated with antibiotics. “There’s usually very good reason for giving the neonates those antibiotics, given that infections and sepsis in that critical early life period can be serious.”
The antibiotic-treated newborns still mounted “pretty decent responses to all of the vaccines”, he said. “Around that seven-month time point, most of the infants are above what’s called the seroprotective threshold, so they will be expected to be protected against infection.
“What does seem to happen is that, over time, those responses wane a bit quicker in the infants that directly have antibiotics.”
The study had a “relatively modest” sample size, the authors noted, and did not include any who had been born via Caesarean section.
In the coming months, the researchers will start a clinical trial to test whether giving antibiotic-treated newborns a probiotic containing Bifidobacterium would improve antibody responses to routine vaccinations.
The probiotic is safe and already widely used in hospitals to protect preterm infants against a condition called necrotising enterocolitis.
Study details
Bifidobacteria support optimal infant vaccine responses
Feargal J. Ryan, Michelle Clarke, Miriam Lynn et al.
Published in Nature on 2 April 2025
Abstract
Accumulating evidence indicates that antibiotic exposure may lead to impaired vaccine responses; however, the mechanisms underlying this association remain poorly understood. Here we prospectively followed 191 healthy, vaginally born, term infants from birth to 15 months, using a systems vaccinology approach to assess the effects of antibiotic exposure on immune responses to vaccination. Exposure to direct neonatal but not intrapartum antibiotics was associated with significantly lower antibody titres against various polysaccharides in the 13-valent pneumococcal conjugate vaccine and the Haemophilus influenzae type b polyribosylribitol phosphate and diphtheria toxoid antigens in the combined 6-in-1 Infanrix Hexa vaccine at 7 months of age. Blood from infants exposed to neonatal antibiotics had an inflammatory transcriptional profile before vaccination; in addition, faecal metagenomics showed reduced abundance of Bifidobacterium species in these infants at the time of vaccination, which was correlated with reduced vaccine antibody titres 6 months later. In preclinical models, responses to the 13-valent pneumococcal conjugate vaccine were strongly dependent on an intact microbiota but could be restored in germ-free mice by administering a consortium of Bifidobacterium species or a probiotic already widely used in neonatal units. Our data suggest that microbiota-targeted interventions could mitigate the detrimental effects of early-life antibiotics on vaccine immunogenicity.
Nature article – Bifidobacteria support optimal infant vaccine responses (Open access)
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