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Caenorhabditis elegans populations shape their microbial environment

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Abstract

Nematodes represent one of the most abundant and ecologically significant taxonomic groups on earth, playing diverse roles in the cycling of organic matter. However, little is known about their effects on their microbial environment. To explore such effects, we took advantage of the bacteriovore free-living nematode Caenorhabditis elegans, which has been shown to assemble a characteristic gut microbiome from different microbial environments. Worm populations (initially germ-free) were raised in several microbially-distinct natural-like environments emulating the environment from which C. elegans are often isolated, allowing worms to go through four generations encompassing the typical boom-to-bust population growth cycle. Samples from worms, their environments, and from control environments without worms were analyzed using next-generation 16S rRNA gene sequencing. Data analysis showed that microbial diversity increased in the environment, either when worms were present or not, but that trajectories of change were different depending on the presence of worms. Importantly, the presence of worms led with time to convergence in the composition of their microbial environments, particularly affecting the abundance of members of bacterial families that are part of the C. elegans gut microbiome. Our findings reveal that C. elegans not only responds to environmental microbial changes but also shapes them, suggesting new roles for nematodes in modulating environmental microbial diversity and ecosystems.

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Data availability

Raw data is available in the NCBI SRA database with accession number PRJNA1116742.

Code availability

R-scripts used to generate figures are available at https://rpubs.com/MicroRB/Boom_Bust.

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Acknowledgements

We thank Dan Kim for assistance with DNA sequencing. Work described in this paper was supported by NIH grants R01AG061302 and R01ES034012.

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Authors and Affiliations

  1. Department of Integrative Biology University of California, Berkeley, CA, USA

    Rahul Bodkhe & Michael Shapira

  2. Department of Statistics University of Wisconsin, Madison, WI, USA

    Kris Sankaran

Authors

  1. Rahul Bodkhe
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  2. Kris Sankaran
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  3. Michael Shapira
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Contributions

R.B. and M.S. conceived the project and wrote the paper. R.B. set up all the experiments and analyzed the data. K.S. contributed to microbiome analysis.

Corresponding authors

Correspondence to
Rahul Bodkhe or Michael Shapira.

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Bodkhe, R., Sankaran, K. & Shapira, M. Caenorhabditis elegans populations shape their microbial environment.
npj Biofilms Microbiomes (2026). https://doi.org/10.1038/s41522-026-00975-z

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