Our gut microflora protects us from the dangers of the world around us, but who protects those that are born too soon? What is done for infants that don’t have time to develop a strong microbiome in defense of the diverse world of microbes?
Life in the NICU
Premature infants (those with a gestation period of <37 weeks) are often given broad-spectrum antibiotics (drugs that are effective against a wide range of bacteria) to prevent neonatal sepsis, a bacterial infection in the bloodstream of newborns that has high mortality rates due to their weak immune systems (Tripathi et al, 2011). These infants tend to spend the first few weeks of their lives living in the hospital, particularly the neonatal intensive care unit (NICU). Given that 10 percent of infants are born premature (World Health Organization) and the majority are prescribed one or more of these antibiotics, this is a significant amount of early-life antibiotic distribution. The use of antibiotics in children and infants is highly debated. More studies are emerging to highlight the consequences of antibiotic usage in infants, including fungal infections, intestinal tissue damage, late-onset sepsis (the very infection they’re trying to avoid), and antimicrobial resistance (Tripathi et al., 2011).
Antimicrobial resistance is becoming increasingly difficult to tackle. This is when bacteria become resistant to certain antimicrobials or antibiotics, which makes treating infection much more difficult. Everyone has their own resistome, or collection of genes that either can or do contribute to antimicrobial resistance. Considering the amount of antibiotic use in the population of preterm infants, they are an understudied and undervalued group when looking at the impact of antibiotic use. The 2025 study by Kiu et al, focuses on this population. They investigate the impact of antibiotic usage in low birth weight, pre-term infants on the gut microbiome and resistome. They were concerned as to how the use of these drugs could change the composition of the microbiome and contribute to antimicrobial resistance. In addition to their initial inquiry, they wanted to investigate the impact of probiotic supplementation on infants’ microbiomes, regardless of antibiotic usage. Studies have shown that probiotic usage in infants can mollify the impact of antibiotic administration, but this prospect isn’t well represented in research (Guitor et al, 2022).
Central Question
The central purpose of this article is investigating the impact of probiotics and antibiotics on the gut microbiome in low birth weight, pre-term infants. This observational study compares the species diversity and richness of the microbiome in very low birth weight (less than 1500g), pre-term infants. They also analyze the impact of probiotics on these preterm infants, regardless of antibiotic use.
Study Design and Findings
The study started with 34 preterm infants, split into two groups: probiotic-supplemented (PS) infants and non-supplemented (NPS) infants. Both of these groups included infants not being treated with antibiotics and those being treated with antibiotics. All 34 babies were fed breast milk, were under 1500 grams, and were born at <34 weeks of gestation. Stool samples were collected each week for 3 weeks (the duration of their neonatal ICU stays) and sequenced. They found that antibiotic use did not have a significant impact on the microbial diversity of these preterm infants. They did find that the use of probiotics significantly impacts the composition of the microbiome. For our purposes, microbial diversity is defined as the number of different species of bacteria found in a sample.
Bacterial samples were isolated from fecal samples and cultured. DNA was extracted from these samples. The researchers used shotgun metagenomics to analyze the DNA. This process consists of breaking down DNA into individual pieces, then assigning codes to each piece that act as a tag to identify samples. The tiny pieces are then ‘sequenced’ via software that tells us where each portion came from and what it is.
After sequence analysis, they found that the gut microbiome differed significantly between supplemented infants and those who weren’t. NPS were much more diverse and rich (define richness), whereas the PS infants were dominated by Bifidobacterium. It took two weeks for the difference in variety to show up. Figure 1a and 1b (Kiu et al, 2025) illustrate the sheer difference in diversity between the two treatment groups. While the NPS microbiomes were more diverse, the PS group stood out in terms of relative abundance. This means that they had fewer types of bacteria, but they have a huge relative quantity of the bacteria that they do possess.
Figure 1b) Difference in abundance of species of bacteria broken down between the two treatment groups. (Figure 1e from Kiu et al, 2025)
In terms of antimicrobial resistance, antibiotic usage did not have much of an impact, if any at all. Antimicrobial resistance in this study is defined as the number of antimicrobial genes in the sequenced genome, also called ARGs. When comparing the PS and NPS groups, the PS groups had significantly fewer ARG counts, suggesting that probiotics have an impact on antimicrobial resistance. When comparing the sequences of the infants provided antibiotics and not medicated, there is no significant difference in ARG count. These findings are highlighted in Figure 2 below.
What Now?
This observational study opens up a whole world of possibilities in multiple realms of science. Having a baseline set of data such as this one provides a starting point for more researchers to further explore the impact of early life antibiotic usage.
Would having a longitudinal study be beneficial? Does early antibiotic use in infants contribute to permanent or long lasting changes in the microbiome? Looking into the first 6-12 months of these infants microbiome could reveal some interesting information about the longterm impact of antibiotics on microbial composition.
From a medical and clinical standpoint, this research serves a significant purpose. Could we start implementing probiotics in the NICU? Would we be able to get to a place where we can discontinue the use of antibiotics in preterm infants? Further research would need to be done to reach these goals, but this research makes such ideas possible.
Something that was touched on in this paper was nosocomial transmission, or transmission of bacteria/illness that originates in a hospital setting. Researchers could build on the information in this study to mitigate infection risk and identify the sources of the most common infections.
Further Reading
If you’re interested in reading more about this topic, here are some resources:
1. Antibiotic exposure is associated with minimal gut microbiome perturbations in healthy term infants
This 2025 article by Benitez et al., similarly discusses the effects of early antibiotic use on the gut microbiome, but focuses more on healthy infants that were full term. It serves as an interesting comparison to the premature infant research.
2. The Effect of Antibiotics on the Infant Gut Fungal Microbiota
This 2022 article by Ventin-Holmberg, et al., discusses the effects of early antibiotic use in infants. Instead of focusing on the bacterial microbiome, it focuses more on fungi and how antibiotic usage impacts the fungal biome of infants.
3. Antibiotic use in infants within the first year of life is associated with the appearance of antibiotic-resistant genes in their feces.
This article addresses the concerns about antibiotic resistance. It highlights the sheer number of antimicrobial resistant genes in infants and why this is becoming a more pressing issue.
References
Benitez, A.J., Tanes, C., Friedman, E.S. et al. Antibiotic exposure is associated with minimal gut microbiome perturbations in healthy term infants. Microbiome 13, 21 (2025). https://doi.org/10.1186/s40168-024-01999-3
Guitor, A. K., Yousuf, E. I., Raphenya, A. R., Hutton, E. K., Morrison, K. M., McArthur, A. G., Wright, G. D., & Stearns, J. C. (2022). Capturing the antibiotic resistome of preterm infants reveals new benefits of probiotic supplementation. Microbiome, 10(1), 136. https://doi.org/10.1186/s40168-022-01327-7
Kiu, R., Darby, E. M., Alcon-Giner, C., Acuna-Gonzalez, A., Camargo, A., Lamberte, L. E., Phillips, S., Sim, K., Shaw, A. G., Clarke, P., van Schaik, W., Kroll, J. S., & Hall, L. J. (2025, August 14). Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants. Nature News. https//doi.org/10.1038/s41467-025-62584-2
Milani C, Lugli GA, Duranti S, Turroni F, Mancabelli L, Ferrario C, Mangifesta M, Hevia A, Viappiani A, Scholz M, Arioli S, Sanchez B, Lane J, Ward DV, Hickey R, Mora D, Segata N, Margolles A, van Sinderen D, Ventura M. Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut. Sci Rep. 2015 Oct 28;5:15782. https://doi.org/10.1038/srep15782
Tripathi, N., Cotten, M., & Smith, B. (2011, January 3). Antibiotic Use and Misuse in the Neonatal Intensive Care Unit. Clinics in Perinatology. https://doi.org/10.1016/j.clp.2011.12.003
Ventin-Holmberg, R., Saqib, S., Korpela, K., Nikkonen, A., Peltola, V., Salonen, A., de Vos, W. M., & Kolho, K.-L. (2022). The Effect of Antibiotics on the Infant Gut Fungal Microbiota. Journal of Fungi, 8(4), 328. https://doi.org/10.3390/jof8040328
World Health Organization. (2023, October 6). 1 in 10 babies worldwide are born early, with major impacts on health and survival. World Health Organization. https://www.who.int/news/item/06-10-2023-1-in-10-babies-worldwide-are-born-early–with-major-impacts-on-health-and-survival#:~:text=1%20in%2010%20babies%20worldwide,impacts%20on%20health%20and%20survivalhttps://pmc.ncbi.nlm.nih.gov/articles/PMC4623478/#:~:text=Both%20the%20adult%20and%20infant,carbohydrates%20in%20an%20infant’s%20diet.