Acquisition of Stickland-metabolizing bacteria during infancy prevents Clostridium botulinum infection

The mechanisms by which maturation of the infant gut microbiota promotes resistance to pathogen colonization remain poorly understood. Infant botulism, a potentially fatal disease caused by intestinal colonization by Clostridium botulinum, provides a striking example of age-dependent susceptibility to infection1. Although the gut microbiota has long been implicated in protection against C. botulinum2-6, the responsible bacterial species and underlying mechanisms have yet to be elucidated. Here, we show that acquisition of Stickland-metabolizing Clostridia during infant gut microbiota maturation confers resistance to C. botulinum colonization through competition for shared amino-acid-dependent nutritional niches. In human fecal microbiota-transplanted mice, longitudinally collected infant microbiotas exhibited a clear transition from susceptibility to resistance. Intestinal metabolomic analysis identified 5-aminovalerate as a hallmark metabolite of the resistant microbiota, implicating Stickland metabolism, an amino acid metabolic pathway also utilized by C. botulinum. Guided by this finding, metagenomic analysis revealed enrichment of Stickland-metabolizing Clostridia in resistant microbiotas, including Clostridioides difficile, a bacterium frequently carried by healthy infants. Intestinal metabolic signatures of C. botulinum and infant-derived Stickland-metabolizing Clostridia suggested competition for shared amino-acid-dependent nutritional niches. Consistent with this model, C. difficile suppressed C. botulinum expansion through nutrient competition. Together, these findings identify nutritional niche competition as a mechanism by which microbiota maturation promotes resistance to C. botulinum colonization. This work demonstrates how acquisition of specific microbial metabolic functions during early life can shift the gut microbiota from a susceptible to a resistant state.