The prion concept postulates that seeded aggregation results in the recruitment of soluble protein monomers and their assembly into amyloid filaments with the same structures as those of the seeds. He...

MemBrain v2 enables streamlined analysis of membranes in cryo-electron tomography by providing user-friendly tools for membrane segmentation, membrane protein localization and spatial analysis, suppor...

Early enthusiasm for the “cellular revolution” in cryo-electron tomography (cryo-ET) was largely driven by the promise of resolving protein structures…

Using cryo-electron tomography, the authors reveal how plasmodesmata (plant cytoplasmic bridges) are gated by cell wall remodelling and how helical protein assemblies scaffold internal membranes, with...

Microbial interactions unfold within environments structured by physical transport and chemical gradients. Yet most mechanistic studies rely on well-mixed systems that mask the reciprocal influences of environmental heterogeneity on metabolism and ecology. Here, we investigate how the physical environment modulates the interaction between the gut commensal Bacteroides thetaiotaomicron and Escherichia coli . In anoxic liquid culture, cell-resolved isotope imaging and genetic perturbations reveal exploitative cross-feeding, where E. coli consumes diffusible sugars released by B . thetaiotaomicron during starch degradation. When exposed to intestinal-like oxygen gradients in microfluidics, the interaction is restructured by spatial organization. The species self-organize into complementary niches: E. coli locally depletes sugars and oxygen, thereby expanding the anoxic niche required by B. thetaiotaomicron . A reactive transport model confirms that this organization arises from coupled feedback between physical transport and metabolic reaction rates. Together, our results reveal how physical structure and chemical gradients convert an exploitative cross-feeding interaction into a dynamic niche-construction process that generates emergent spatial organization and stabilizes coexistence. ### Competing Interest Statement The authors have declared no competing interest.

Nature Methods - ROCKET improves experimental structure elucidation by integrating implicit structural knowledge from OpenFold, a trainable reimplementation of AlphaFold2, with X-ray...

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Cryo-electron tomography (cryo-ET) visualizes 3D cellular architecture in near-native states. Recent deep-learning methods (CryoCARE, IsoNet, DeepDeWedge, CryoLithe) improve denoising and artifact cor...