ArticleCell systems2025
Subspecies phylogeny in the human gut revealed by co-evolutionary constraints across the bacterial kingdom.
Article in Cell systems, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
4 citing papers in PubMed.
- Pan-tumor spatial transcriptomics reveals conserved properties of tumor organization.Cell reports. Medicine · 2026Article
- Physiological architecture and evolutionary origins of cellular adaptability.bioRxiv : the preprint server for biology · 2026Article
- A data-driven universal gut microbiome health assessment: a machine learning framework trained on large metagenomic data.Frontiers in microbiology · 2026Article
- Statistical design of a synthetic microbiome that suppresses diverse gut pathogens.bioRxiv : the preprint server for biology · 2025Article
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Authors and funding
10 authors.
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Abstract
The human gut microbiome contains many bacterial strains of the same species ("strain-level variants") that shape microbiome function. The tremendous scale and molecular resolution at which microbial communities are being interrogated motivates addressing how to describe strain-level variants. We introduce the "Spectral Tree"-an inferred tree of relatedness built from patterns of co-evolutionary constraint between greater than 7,000 diverse bacteria. Using the Spectral Tree to describe over 600 diverse gut commensal strains that we isolated, whole-genome sequenced, and metabolically profiled revealed (1) widespread phylogenetic structure among strain-level variants, (2) the origins of subspecies phylogeny as a shared history of phage infections across humans, and (3) the key role of inter-human strain variation in predicting strain-level metabolic qualities. Overall, our work demonstrates the existence and metabolic importance of structured phylogeny below the level of species for commensal gut bacteria, motivating a redefinition of individual strains according to their evolutionary context. A record of this paper's transparent peer review process is included in the supplemental information.
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