ArticleNature microbiology2024
Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags.
Article in Nature microbiology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Metabolic strategies of Enterobacteriaceae gut colonization.Nature reviews. Microbiology · 2026Review
- Engineering rhizobacterial communities for soil and plant health.Microbiology (Reading, England) · 2026Review
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- Quantifying host-microbe interactions with bacterial lineage tracing.Science (New York, N.Y.) · 2026Review
- The Gfr Uptake System Provides a Context-Dependent Fitness Advantage to Salmonella Typhimurium SL1344 During the Initial Gut Colonization Phase.Molecular microbiology · 2025Article
- Salmonella multimutants enable efficient identification of SPI-2 effector protein function in gut inflammation and systemic colonization.Nature communications · 2025Article
- Applying ecological principles to microbiome engineering.Nature microbiology · 2025Review
- Human microbiome acquisition and transmission.Nature reviews. Microbiology · 2025Review
- Evaluation of Engineering Potential in Undomesticated Microbes With VECTOR.Microbial biotechnology · 2025Article
- Strain-specific galactose utilization by commensal E. coli mitigates Salmonella establishment in the gut.PLoS pathogens · 2025Article
- Interplay between chemotaxis, quorum sensing, and metabolism regulates Escherichia coli-Salmonella Typhimurium interactions in vivo.PLoS pathogens · 2025Article
- Building microbial synthetic communities: get inspired by the design of synthetic plant communities.The New phytologist · 2025Article
- Context-dependent change in the fitness effect of (in)organic phosphate antiporter glpT during Salmonella Typhimurium infection.Nature communications · 2025Article
- Monosaccharides drive Salmonella gut colonization in a context-dependent or -independent manner.Nature communications · 2025Article
- A microbial symphony: a literature review of the factors that orchestrate the colonization dynamics of the human colonic microbiome during infancy and implications for future health.Microbiome research reports · 2025Review
- Community standards and future opportunities for synthetic communities in plant-microbiota research.Nature microbiology · 2024Review
- Non-canonical start codons confer context-dependent advantages in carbohydrate utilization for commensal E. coli in the murine gut.Nature microbiology · 2024Article
- Commensal E. coli limits Salmonella gut invasion during inflammation by producing toxin-bound siderophores in a tonB-dependent manner.PLoS biology · 2024Article
- Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags.Nature microbiology · 2024Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Microbiomes feature recurrent compositional structures under given environmental conditions. However, these patterns may conceal diverse underlying population dynamics that require intrastrain resolution. Here we developed a genomic tagging system, termed wild-type isogenic standardized hybrid (WISH)-tags, that can be combined with quantitative polymerase chain reaction and next-generation sequencing for microbial strain enumeration. We experimentally validated the performance of 62 tags and showed that they can be differentiated with high precision. WISH-tags were introduced into model and non-model bacterial members of the mouse and plant microbiota. Intrastrain priority effects were tested using one species of isogenic barcoded bacteria in the murine gut and the Arabidopsis phyllosphere, both with and without microbiota context. We observed colonization resistance against late-arriving strains of Salmonella Typhimurium in the mouse gut, whereas the phyllosphere accommodated Sphingomonas latecomers in a manner proportional to their presence at the late inoculation timepoint. This demonstrates that WISH-tags are a resource for deciphering population dynamics underlying microbiome assembly across biological systems.
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