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

Kobayashi, N.; Kodaira, Y.; Yang, J.; Matsumura, T.; Yamaguchi, A.; Arai, Y.; Takahashi, D.; Toriumi, H.; Komiyama, S.; Iwata, K.; Haga, N.; Nishida, Y.; Saito, K.; Motooka, D.; Matsumoto, Y.; Nakamura, S.; Wada, T.; Fukuda, S.; Hase, K.; Fujinaga, Y.

doi:10.64898/2026.06.23.734129

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bioRxiv · 10.64898/2026.06.23.734129

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

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Abstract

Infant botulism is caused by intestinal colonization with Clostridium botulinum, whereas healthy adults are resistant. Although the gut microbiota has long been implicated in protection against C. botulinum, its bacterial basis has remained unknown. Here, we show that specific amino acid-metabolizing bacteria confer resistance to C. botulinum colonization through nutrient competition. Longitudinally collected human infant microbiotas exhibited a transition from susceptibility to resistance after transplantation into germ-free mice. 5-Aminovalerate marked the resistant microbiota, implicating Stickland metabolism. Resistant microbiotas were enriched in Stickland-metabolizing Clostridia, including Clostridioides difficile. Metabolomics revealed overlapping amino acid utilization, and C. difficile suppressed C. botulinum expansion through amino acid competition. These findings demonstrate that acquisition of Stickland-metabolizing Clostridia during infancy prevents C. botulinum infection through competition for shared amino-acid-dependent nutritional niches.

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Kobayashi, N., Kodaira, Y., Yang, J., Matsumura, T., Yamaguchi, A., Arai, Y., Takahashi, D., Toriumi, H., Komiyama, S., Iwata, K., Haga, N., Nishida, Y., Saito, K., Motooka, D., Matsumoto, Y., Nakamura, S., Wada, T., Fukuda, S., Hase, K., Fujinaga, Y.. 2026-06-24. Acquisition of Stickland-metabolizing bacteria during infancy prevents Clostridium botulinum infection. https://doi.org/10.64898/2026.06.23.734129

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