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Global branches and local states of the human gut microbiome define associations with environmental and intrinsic factors

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Listed:
  • Julien Tap

    (Danone Nutricia Research
    Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute)

  • Franck Lejzerowicz

    (University of California San Diego
    University of Oslo)

  • Aurélie Cotillard

    (Danone Nutricia Research)

  • Matthieu Pichaud

    (Danone Nutricia Research)

  • Daniel McDonald

    (University of California San Diego)

  • Se Jin Song

    (University of California San Diego)

  • Rob Knight

    (University of California San Diego
    University of California San Diego
    University of California San Diego
    University of California San Diego)

  • Patrick Veiga

    (Danone Nutricia Research
    Université Paris-Saclay, INRAE, MGP)

  • Muriel Derrien

    (Danone Nutricia Research
    Katholieke Universiteit Leuven)

Abstract

The gut microbiome is important for human health, yet modulation requires more insight into inter-individual variation. Here, we explored latent structures of the human gut microbiome across the human lifespan, applying partitioning, pseudotime, and ordination approaches to >35,000 samples. Specifically, three major gut microbiome branches were identified, within which multiple partitions were observed in adulthood, with differential abundances of species along branches. Different compositions and metabolic functions characterized the branches’ tips, reflecting ecological differences. An unsupervised network analysis from longitudinal data from 745 individuals showed that partitions exhibited connected gut microbiome states rather than over-partitioning. Stability in the Bacteroides-enriched branch was associated with specific ratios of Faecalibacterium:Bacteroides. We also showed that associations with factors (intrinsic and extrinsic) could be generic, branch- or partition-specific. Our ecological framework for cross-sectional and longitudinal data allows a better understanding of overall variation in the human gut microbiome and disentangles factors associated with specific configurations.

Suggested Citation

  • Julien Tap & Franck Lejzerowicz & Aurélie Cotillard & Matthieu Pichaud & Daniel McDonald & Se Jin Song & Rob Knight & Patrick Veiga & Muriel Derrien, 2023. "Global branches and local states of the human gut microbiome define associations with environmental and intrinsic factors," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-38558-7
    DOI: 10.1038/s41467-023-38558-7
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