High abundance of Bacteroides was associated with receiving antibiotic treatment 45-225 days later, while low Bacteroides abundance before treatment was associated with low alpha diversity and increased beta diversity post treatment, suggesting a key role of Bacteroides for susceptibility to infections and microbiome stability and resilience in early childhood.
Key Findings
Results
High early-life gut Bacteroides abundance was associated with receiving antibiotic treatment 45-225 days later.
1176 stool samples from 162 children were included in the analysis, of which 49 children received antibiotics.
Sample groups were defined based on antibiotic exposure: never-treated controls, 45-225 days pre-treatment (pre45-225), 0-30 days pre-treatment (pre0-30), 0-30 days post-treatment (post0-30), or >90 days post-treatment and age >540 days (post>90).
Generalized linear mixed models adjusted for age were used to identify associations.
The association was specific to the 45-225 day pre-treatment window, suggesting Bacteroides abundance may predict future infection susceptibility rather than being a direct consequence of illness.
Results
Low Bacteroides abundance before antibiotic treatment was associated with reduced alpha diversity following treatment.
Children with low Bacteroides abundance in the pre-treatment period showed lower alpha diversity in the post-treatment period (post0-30).
Alpha diversity reflects the richness and evenness of microbial species within a sample.
This suggests that pre-treatment Bacteroides levels may influence the capacity of the gut microbiome to maintain diversity after antibiotic disruption.
Analysis was performed longitudinally using the LoewenKIDS intensified subcohort in Germany.
Results
Low Bacteroides abundance before antibiotic treatment was associated with increased beta diversity post-treatment.
Children with low pre-treatment Bacteroides showed increased beta diversity in the post-treatment period, indicating greater compositional shifts in microbial community structure.
Beta diversity measures differences in microbial community composition between samples.
Increased post-treatment beta diversity in low-Bacteroides children suggests less stable microbiome recovery following antibiotic exposure.
This pattern points to a role of Bacteroides in microbiome resilience — the ability to return to baseline composition after perturbation.
Results
The study identified Bacteroides as a key taxon associated with both susceptibility to infections requiring antibiotic treatment and with microbiome stability and resilience in early childhood.
The study focused on children up to age two, a critical window for microbiome development and immune maturation.
Longitudinal stool sample analysis was conducted within the German LoewenKIDS intensified subcohort.
Associations were assessed using generalized linear mixed models adjusted for age.
The findings link a single bacterial genus to two distinct outcomes: likelihood of future antibiotic-treated infection and post-antibiotic microbiome recovery.
Background
Early childhood, up to age two, represents a critical period for microbiome development and balanced immunity later in life.
This framing motivates the longitudinal design of the study, tracking microbiota from early infancy through the second year of life.
The study design captured both pre- and post-antibiotic microbiome states, enabling assessment of resilience.
The post>90 days group was restricted to children older than 540 days to ensure adequate recovery time was assessed at a comparable developmental stage.
What This Means
This research suggests that the amount of a common gut bacterium called Bacteroides in the first two years of life may play an important role in how vulnerable young children are to infections and how well their gut microbiome recovers after antibiotic treatment. Scientists followed 162 German children and collected over 1,000 stool samples, comparing children who received antibiotics to those who did not. They found that children who had higher levels of Bacteroides in their gut were more likely to need antibiotic treatment within the next several months, possibly reflecting an underlying difference in infection susceptibility rather than a direct cause-and-effect relationship.
The study also found that children who had lower levels of Bacteroides before receiving antibiotics showed less microbial diversity and more disruption to their gut microbial communities afterward. This suggests that Bacteroides may help stabilize the gut microbiome and support its ability to bounce back — a property scientists call 'resilience' — after the disruption caused by antibiotic use.
This research matters because the early-life gut microbiome is thought to shape immune development, and disruptions during this window may have lasting effects. Understanding which bacteria are linked to infection risk and microbiome stability could eventually help identify children who might be more vulnerable and inform strategies to support healthy microbiome development. However, this was an observational study, so it cannot prove that Bacteroides directly causes these outcomes — further research would be needed to establish causation.
Hauptmann M, Gottschick C, Muthukumarasamy U, Klee B, Strowig T, Mikolajczyk R, et al.. (2026). High early-life gut Bacteroides links to microbiome stability, resilience, and risk for childhood infections.. NPJ biofilms and microbiomes. https://doi.org/10.1038/s41522-026-01022-7