Academic Appointments

  • Basic Life Research Scientist, Biology

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  • Mail Code: 5020

All Publications

  • Maintenance of cytoplasmic and membrane densities shapes cellular geometry in Escherichia coli. Nature communications Chure, G., de Silva, R. T., Sharma, R., Lanz, M. C., Cremer, J. 2025

    Abstract

    Microbes precisely control their composition and geometry across diverse growth conditions, yet the mechanisms coordinating these processes remain unclear. Here, we integrate quantitative proteomics, microscopy, and biochemical measurements to reveal a biophysical principle linking these properties in Escherichia coli: cytoplasmic and membrane protein densities maintain a tightly conserved ratio across growth conditions, while the periplasmic density varies. Building on this observation, we develop a mathematical model demonstrating that maintaining this density ratio constrains the surface-to-volume ratio as a nonlinear function of proteome composition, specifically the ribosomal proteome fraction and partitioning between cellular compartments. The model holds under guanosine tetraphosphate perturbations that alter ribosome levels, further demonstrating that cellular geometry is not strictly determined by growth rate. These findings provide a biophysical framework for geometry control, underscoring density maintenance as a key physiological constraint that shapes cellular phenotypes.

    View details for DOI 10.1038/s41467-025-67553-3

    View details for PubMedID 41429793

  • Community coalescence reveals strong selection and coexistence within species in complex microbial communities. bioRxiv : the preprint server for biology Walton, S. J., Xu, Q., Sharma, R., Gellert, H. R., Yeh, C. F., Cremer, J., Xue, K. S., Petrov, D. A., Good, B. H. 2025

    Abstract

    Complex microbial ecosystems harbor extensive intra-species diversity, but the fitness consequences of this genetic variation are poorly understood in community settings. Here we address this question by competing in vitro gut communities derived from different human donors, revealing the emergent fitness differences between conspecific strains as they competed within larger communities. Most pairs of strains experienced strong and context-dependent selection, even when their parent communities were originally selected in the same nutrient environment. However, these fitness differences typically attenuated over time due to biotic interactions within the community, leading to extended coexistence within many species, and competitive exclusion in others. These results support the view that conspecific strains can fulfill distinct ecological roles when competing within a diverse community, even when their genomic diversity exhibits the hallmarks of a single biological species.

    View details for DOI 10.1101/2025.11.06.687011

    View details for PubMedID 41278818

    View details for PubMedCentralID PMC12637602

  • Quantifying the varying harvest of fermentation products from the human gut microbiota. Cell Arnoldini, M., Sharma, R., Moresi, C., Chure, G., Chabbey, J., Slack, E., Cremer, J. 2025

    Abstract

    Fermentation products released by the gut microbiota provide energy and regulatory functions to the host. Yet, little is known about the magnitude of this metabolic flux and its quantitative dependence on diet and microbiome composition. Here, we establish orthogonal approaches to consistently quantify this flux, integrating data on bacterial metabolism, digestive physiology, and metagenomics. From the nutrients fueling microbiota growth, most carbon ends up in fermentation products and is absorbed by the host. This harvest varies strongly with the amount of complex dietary carbohydrates and is largely independent of bacterial mucin and protein utilization. It covers 2%-5% of human energy demand for Western diets and up to 10% for non-Western diets. Microbiota composition has little impact on the total harvest but determines the amount of specific fermentation products. This consistent quantification of metabolic fluxes by our analysis framework is crucial to elucidate the gut microbiota's mechanistic functions in health and disease.

    View details for DOI 10.1016/j.cell.2025.07.005

    View details for PubMedID 40744013

  • Quantifying the varying harvest of fermentation products from the human gut microbiota. bioRxiv : the preprint server for biology Arnoldini, M., Sharma, R., Moresi, C., Chure, G., Chabbey, J., Slack, E., Cremer, J. 2025

    Abstract

    Fermentation products released by the gut microbiota provide energy and regulatory functions to the host. Yet, little is known about the magnitude of this metabolic flux and its quantitative dependence on diet and microbiome composition. Here, we establish orthogonal approaches to consistently quantify this flux, integrating data on bacterial metabolism, digestive physiology, and metagenomics. From the nutrients fueling microbiota growth, most carbon ends up in fermentation products and is absorbed by the host. This harvest varies strongly with the amount of complex dietary carbohydrates and is largely independent of bacterial mucin and protein utilization. It covers 2-5% of human energy demand for Western, and up to 10% for non-Western diets. Microbiota composition has little impact on the total harvest but determines the amount of specific fermentation products. This consistent quantification of metabolic fluxes by our analysis framework is crucial to elucidate the gut microbiota's mechanistic functions in health and disease.

    View details for DOI 10.1101/2024.01.05.573977

    View details for PubMedID 40672209

    View details for PubMedCentralID PMC12265668