The first weeks of life are a period of extraordinary microbial change. As newborns acquire bacteria from their surroundings, their intestinal microbiome develops rapidly, influenced by birth conditions, feeding, medications and hospital exposure. At the same time, antibiotics—often essential for treating or preventing serious neonatal infections—can reshape this fragile ecosystem. A systematic review published in Pediatric Research examines whether probiotics influence the collection of antibiotic-resistance genes found in neonatal stool, a genetic landscape known as the faecal antibiotic resistome.
The study, led by C. Rath, A. Fursule and F. Wong and published under the title “Influence of probiotics on faecal antibiotic resistome in neonates: a systematic review,” focuses on a question with consequences far beyond digestion. The resistome includes the full set of antimicrobial-resistance genes carried by microorganisms in a particular environment. Some of these genes may never affect human health, while others can enable bacteria to survive antibiotic treatment or pass resistance traits to disease-causing organisms.
For newborns, the issue is especially sensitive. Neonates may receive antibiotics because clinicians must act quickly when sepsis is suspected, even before laboratory tests confirm an infection. Such treatment can reduce dangerous pathogens, but it may also disturb beneficial bacterial communities and alter the abundance of resistance genes. Because the intestinal microbiome is still being established, changes during this period could influence microbial development and the movement of resistance determinants within the gut.
Probiotics are live microorganisms administered with the intention of providing a health benefit. Common probiotic organisms include strains of Lactobacillus, Bifidobacterium and the yeast Saccharomyces boulardii. In neonatal care, probiotics have been investigated particularly in relation to intestinal health and necrotising enterocolitis, a severe inflammatory disease that primarily affects premature infants. Their possible influence on antibiotic resistance adds a more complex dimension to the debate: a microbial intervention might alter the gut ecosystem in ways that affect both beneficial functions and the persistence or transfer of resistance genes.
The resistome cannot be assessed simply by counting bacteria. Two organisms belonging to the same broad bacterial group may have very different genetic capacities, including different resistance genes. Researchers can investigate these genes by analysing faecal samples with molecular techniques such as polymerase chain reaction, targeted gene panels or high-throughput DNA sequencing. Metagenomic approaches sequence genetic material from an entire microbial community, allowing investigators to identify resistance genes without first growing each organism in the laboratory. However, detecting a gene does not always prove that it is active, expressed or capable of causing clinical resistance.
That distinction is central to interpreting research on probiotics and neonatal resistance. A change in the number of resistance genes detected in stool may reflect a change in bacterial population, altered gene abundance or differences in the way samples were collected and analysed. It may not directly predict whether a newborn will develop an antibiotic-resistant infection. The clinical meaning of a resistome profile therefore depends on several factors, including the specific gene involved, the bacterial species carrying it, whether the gene is located on a mobile genetic element and whether it can be transferred to another organism.
Mobile genetic elements make the problem particularly important. Resistance genes can sometimes be carried on plasmids, transposons or other pieces of DNA that move within or between bacterial populations. When a resistance gene is linked to such mobile elements, there is a greater biological possibility of horizontal gene transfer—the exchange of genetic material between bacteria rather than inheritance from parent to offspring. The gut, where dense microbial communities coexist in close contact, provides an environment in which such exchanges may occur, although the detection of a mobile gene still does not establish that transfer has happened in a particular infant.
As a systematic review, the paper brings together findings from existing research rather than reporting the results of a single new neonatal trial. This approach can reveal patterns across studies, but it also exposes the difficulties of comparing them. Neonatal populations can differ substantially in gestational age, birth weight, feeding method, antibiotic exposure and underlying illness. Probiotic preparations may contain different species or strains, administered at different doses and for different durations. Even the timing of stool collection can affect the apparent composition of the microbiome and resistome.
These variations mean that the influence of probiotics cannot be reduced to a simple claim that they either increase or decrease antibiotic resistance. The direction and significance of an observed effect may depend on the strain used, the infant’s clinical condition, the antibiotics received and the microbial community present before treatment. A review of this field is therefore valuable not only for identifying possible benefits, but also for clarifying where evidence remains incomplete and where future studies require more consistent definitions and laboratory methods.
The research arrives as antimicrobial resistance continues to challenge hospitals worldwide. Newborns, particularly those born prematurely or requiring intensive care, can be highly vulnerable to infection while also being exposed to multiple medical interventions. Understanding how probiotic supplementation interacts with antibiotic-resistance genes could help clinicians weigh potential advantages and risks more precisely. For now, the key scientific message is one of careful interpretation: probiotics may influence the developing intestinal ecosystem, but changes in the faecal resistome must be studied alongside bacterial activity, gene mobility and actual clinical outcomes. The systematic review highlights the need for rigorously designed neonatal studies that connect genetic signals in stool with the infections, treatments and long-term health of the infants behind those samples.
Subject of Research: Influence of probiotics on the faecal antibiotic resistome in neonates
Article Title: Influence of probiotics on faecal antibiotic resistome in neonates: a systematic review
Article References: Rath, C., Fursule, A., Wong, F. et al. Influence of probiotics on faecal antibiotic resistome in neonates: a systematic review. Pediatric Research (2026). https://doi.org/10.1038/s41390-026-05356-y
Image Credits: AI Generated
DOI: 10.1038/s41390-026-05356-y
Keywords: probiotics, neonates, antibiotic resistance, faecal resistome, gut microbiome, antimicrobial resistance, systematic review
