Exchange of metabolic pathway intermediates as the origin for cross-feeding interactions in E. coli auxotrophic co-cultures
Year: 2026
Type: preprint
Abstract: A large fraction of microbes in natural environments are auxotrophs that rely on metabolite exchange for growth. The Black Queen hypothesis and related frameworks explain gene loss and reliance on shared metabolites. Yet it is not fully understood how metabolite cross-feeding emerges and gives rise to experimentally observable community performance. Here, we propose that exchange of biosynthetic pathway intermediates provides a mechanistic route for the emergence of metabolite cross-feeding. Building on prior work demonstrating intermediate exchange in E. coli auxotrophs, we investigated co-cultures between a methionine auxotroph (ΔmetA) and a panel of histidine auxotrophs. Among these, only ΔhisD exhibited efficient co-culture growth with ΔmetA, suggesting a unique role for the final step of histidine biosynthesis, which converts histidinol to histidine. We found that ΔmetA-ΔhisD co-cultures accumulated high levels of extracellular histidinol (>200 µM), suggesting a mechanism for metabolite exchange. Spent media from these co-cultures supported growth of all histidine auxotrophs except ΔhisD, confirming that histidinol, rather than histidine, was the dominant exchanged metabolite. Furthermore, we observed that ΔmetA efficiently converted histidinol to histidine only under methionine-limited conditions, suggesting that nutrient limitation promoted overflow of converted histidine to the extracellular environment. To quantitatively assess whether histidinol exchange could account for the observed co-culture behavior, we constructed a mechanistic model that links extracellular histidinol dynamics to co-culture growth through independently measured conversion capacity of the ΔmetA strain. Rather than fitting growth empirically, we used experimentally derived parameters to predict co-culture growth from the measured histidinol-to-histidine conversion flux. The model accurately recapitulated the timing and magnitude of growth and population dynamics, supporting the idea that accumulation of histidinol enabled the conversion-driven supply of histidine that sustained ΔhisD, while coupling growth between the two strains. Taken together, these results suggest that metabolite cross-feeding in syntrophic co-cultures can emerge from the accumulation of pathway intermediates and their conditional conversion under nutrient limitation, providing a plausible mechanism for the rapid establishment of mutualistic interactions.
Authors: Yijing Cai, Maciek R. Antoniewicz
Institution: University of Michigan
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7221321761