Predicting competition and substrate preferences for targeted microbiome alteration
Summary
Microbiome science has greatly expanded our understanding of microbial life and its roles in the environment and human health. Yet microbiome science often relies on descriptive, correlation-based approaches that limit causal insight and intentional intervention designs. Moving toward predictive and mechanistic understanding requires functional characterization of microbial interactions and metabolic preferences. Here, we present microbial interaction and niche determination (MIND), which
Content
# Predicting competition and substrate preferences for targeted microbiome alteration
*Published: 2026 Apr 17*
Microbiome science has greatly expanded our understanding of microbial life and
its roles in the environment and human health. Yet microbiome science often
relies on descriptive, correlation-based approaches that limit causal insight
and intentional intervention designs. Moving toward predictive and mechanistic
understanding requires functional characterization of microbial interactions and
metabolic preferences. Here, we present microbial interaction and niche
determination (MIND), which quantifies mRNA translation prioritization to infer
substrate preferences and competitive interactions in complex communities.
Applied to synthetic communities, soil, human fecal samples, and a mouse model,
MIND predicted microbial competition and substrate preferences, guiding
precision prebiotic and probiotic interventions to selectively modulate
community composition. Currently focused on competition and substrate
utilization, MIND could be further extended to capture additional interactions
and ecological niches. By linking functional measurements to ecological
outcomes, MIND offers a broadly applicable framework for targeted microbiome
manipulation and rational intervention design rooted in functional insight.
DOI: 10.1016/j.cell.2026.03.036