Authors: Shaohua Gu, Zhengying Shao, Zeyang Qu, Shenyue Zhu, Yuanzhe Shao, Di Zhang, Richard Allen, Ruolin He, Jiqi Shao, Guanyue Xiong, Alexandre Jousset, Ville-Petri Friman, Zhong Wei, Rolf Kümmerli, and Zhiyuan Li.
Journal: Science Advances
DOI: 10.1126/sciadv.adq5038
Link: https://www.science.org/doi/10.1126/sciadv.adq5038
Published: Jan 15, 2025
Document Type: Research Article
Abstract:
Bacterial social interactions play crucial roles in various ecological, medical, and biotechnological contexts. However, predicting these interactions from genome sequences is notoriously difficult. Here, we developed bioinformatic tools to predict whether secreted iron-scavenging siderophores stimulate or inhibit the growth of community members. Siderophores are chemically diverse and can be stimulatory or inhibitory depending on whether bacteria have or lack corresponding uptake receptors. We focused on 1928 representative Pseudomonas genomes and developed an experimentally validated coevolution algorithm to match encoded siderophore synthetases to corresponding receptor groups. We derived community-level iron interaction networks to show that siderophore-mediated interactions differ across habitats and lifestyles. Specifically, dense networks of siderophore sharing and competition were observed among environmental and nonpathogenic species, while small, fragmented networks occurred among human-associated and pathogenic species. Together, our sequence-to-ecology approach empowers the analyses of social interactions among thousands of bacterial strains and offers opportunities for targeted intervention to microbial communities.