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Genomic diversity landscape of the honey bee gut microbiota

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  • Kirsten M. Ellegaard

    (University of Lausanne)

  • Philipp Engel

    (University of Lausanne)

Abstract

The structure and distribution of genomic diversity in natural microbial communities is largely unexplored. Here, we used shotgun metagenomics to assess the diversity of the honey bee gut microbiota, a community consisting of few bacterial phylotypes. Our results show that most phylotypes are composed of sequence-discrete populations, which co-exist in individual bees and show age-specific abundance profiles. In contrast, strains present within these sequence-discrete populations were found to segregate into individual bees. Consequently, despite a conserved phylotype composition, each honey bee harbors a distinct community at the functional level. While ecological differentiation seems to facilitate coexistence at higher taxonomic levels, our findings suggest that, at the level of strains, priority effects during community assembly result in individualized profiles, despite the social lifestyle of the host. Our study underscores the need to move beyond phylotype-level characterizations to understand the function of this community, and illustrates its potential for strain-level analysis.

Suggested Citation

  • Kirsten M. Ellegaard & Philipp Engel, 2019. "Genomic diversity landscape of the honey bee gut microbiota," Nature Communications, Nature, vol. 10(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-08303-0
    DOI: 10.1038/s41467-019-08303-0
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    Cited by:

    1. Romuald Laso-Jadart & Christophe Ambroise & Pierre Peterlongo & Mohammed-Amin Madoui, 2020. "metaVaR: Introducing metavariant species models for reference-free metagenomic-based population genomics," PLOS ONE, Public Library of Science, vol. 15(12), pages 1-17, December.
    2. Vincent Somerville & Nadine Thierer & Remo S. Schmidt & Alexandra Roetschi & Lauriane Braillard & Monika Haueter & Hélène Berthoud & Noam Shani & Ueli Ah & Florent Mazel & Philipp Engel, 2024. "Genomic and phenotypic imprints of microbial domestication on cheese starter cultures," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    3. Trine Zachariasen & Jakob Russel & Charisse Petersen & Gisle A. Vestergaard & Shiraz Shah & Pablo Atienza Lopez & Moschoula Passali & Stuart E. Turvey & Søren J. Sørensen & Ole Lund & Jakob Stokholm &, 2024. "MAGinator enables accurate profiling of de novo MAGs with strain-level phylogenies," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    4. Haoyu Lang & Yuwen Liu & Huijuan Duan & Wenhao Zhang & Xiaosong Hu & Hao Zheng, 2023. "Identification of peptides from honeybee gut symbionts as potential antimicrobial agents against Melissococcus plutonius," Nature Communications, Nature, vol. 14(1), pages 1-11, December.

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