Modelling Fusobacterium lifestyles transitions by integrating transcriptomics and growth data

TL;DR

This paper creates a detailed metabolic model of Fusobacterium nucleatum to understand how it adapts to the colorectal cancer environment.

Contribution

The novel contribution is an experimentally validated genome-scale metabolic model of F. nucleatum integrated with transcriptomic data and growth experiments.

Findings

Adhesion to host cells triggers metabolic rewiring, reducing branched-chain amino acid catabolism and increasing methionine and serine uptake.

Invasion activates central carbon and nitrogen pathways, suggesting adaptation to the tumor microenvironment.

Shifts in short-chain fatty acid production and redox balance may support bacterial persistence in CRC.

Abstract

•Reconstructed and curated of the genome-scale metabolic model (GEM) of Fusobacterium nucleatum.•Experimental data used to refine and validate the GEM, including biomass formulation with BOFdat (Biomass Objective Function from experimental data).•Integrated transcriptomic data to build context-specific metabolic models.•Metabolic rewiring links Fusobacterium adaptation to colorectal cancer (CRC) context.•Provides a systems framework to explore host-microbe metabolic interactions.

Reconstructed and curated of the genome-scale metabolic model (GEM) of Fusobacterium nucleatum.

Experimental data used to refine and validate the GEM, including biomass formulation with BOFdat (Biomass Objective Function from experimental data).

Integrated transcriptomic data to build context-specific metabolic models.

Metabolic rewiring links Fusobacterium adaptation to colorectal cancer (CRC) context.

Provides a systems framework to explore host-microbe metabolic interactions.

Bacteria living inside the tumoral micro-environment play a crucial role in the development of cancer and its progression. Enrichment of Fusobacterium nucleatum in colorectal cancer (CRC) tissue has been acknowledged as a major driver of its proliferation and mortality. Representatives of the F. nucleatum species exhibit a remarkable variability, being linked to a growing list of diseases. In this process, cellular metabolism plays a key role, allowing bacterial cells to efficiently cope with an ever-changing environment. To date, however, a mechanistic understanding of its relationship(s) with virulence and/or cancer-associated phenotypes is missing. In this work we characterize the basal physiology of this bacterium by reconstructing an experimentally validated genome-scale metabolic model (GEM) to simulate the major phenotypical features of F. nucleatum in different nutritional conditions. Further, we used gene expression data obtained from in vitro models to contextualize this metabolic reconstruction and simulate relevant phenotypes such as its interaction with human cells. Our analyses revealed that adhesion triggers a metabolic rewiring, with suppression of branched-chain amino acid catabolism and increased uptake of specific nutrients (e.g., methionine and serine), while invasion leads to a partial reactivation of central carbon and nitrogen pathways. Moreover, we identified shifts in short-chain fatty acid production and redox balance that may contribute to bacterial persistence and modulation of the tumor microenvironment.

Image, graphical abstract

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