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Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags.

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.

SUBMITTER: Daniel BBJ

PROVIDER: S-EPMC10994841 | biostudies-literature | 2024 Apr

REPOSITORIES: biostudies-literature

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Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags.

Daniel Benjamin B J BBJ Steiger Yves Y Sintsova Anna A Field Christopher M CM Nguyen Bidong D BD Schubert Christopher C Cherrak Yassine Y Sunagawa Shinichi S Hardt Wolf-Dietrich WD Vorholt Julia A JA

Nature microbiology 20240319 4

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 sho ...[more]

PMID: 38503975

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Dataset Information

Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags.

Publications

Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags.

Similar Datasets

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