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Universal gut microbial relationships in the gut microbiome of wild baboons.

Publication ,  Journal Article
Roche, KE; Bjork, JR; Dasari, MR; Grieneisen, L; Jansen, D; Gould, TJ; Gesquiere, LR; Barreiro, LB; Alberts, SC; Blekhman, R; Gilbert, JA ...
Published in: eLife
May 2023

Ecological relationships between bacteria mediate the services that gut microbiomes provide to their hosts. Knowing the overall direction and strength of these relationships is essential to learn how ecology scales up to affect microbiome assembly, dynamics, and host health. However, whether bacterial relationships are generalizable across hosts or personalized to individual hosts is debated. Here, we apply a robust, multinomial logistic-normal modeling framework to extensive time series data (5534 samples from 56 baboon hosts over 13 years) to infer thousands of correlations in bacterial abundance in individual baboons and test the degree to which bacterial abundance correlations are 'universal'. We also compare these patterns to two human data sets. We find that, most bacterial correlations are weak, negative, and universal across hosts, such that shared correlation patterns dominate over host-specific correlations by almost twofold. Further, taxon pairs that had inconsistent correlation signs (either positive or negative) in different hosts always had weak correlations within hosts. From the host perspective, host pairs with the most similar bacterial correlation patterns also had similar microbiome taxonomic compositions and tended to be genetic relatives. Compared to humans, universality in baboons was similar to that in human infants, and stronger than one data set from human adults. Bacterial families that showed universal correlations in human infants were often universal in baboons. Together, our work contributes new tools for analyzing the universality of bacterial associations across hosts, with implications for microbiome personalization, community assembly, and stability, and for designing microbiome interventions to improve host health.

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Published In

eLife

DOI

EISSN

2050-084X

ISSN

2050-084X

Publication Date

May 2023

Volume

12

Start / End Page

e83152

Related Subject Headings

  • RNA, Ribosomal, 16S
  • Papio
  • Microbiota
  • Humans
  • Gastrointestinal Microbiome
  • Bacteria
  • Animals
  • 42 Health sciences
  • 32 Biomedical and clinical sciences
  • 31 Biological sciences
 

Citation

APA
Chicago
ICMJE
MLA
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Roche, K. E., Bjork, J. R., Dasari, M. R., Grieneisen, L., Jansen, D., Gould, T. J., … Archie, E. A. (2023). Universal gut microbial relationships in the gut microbiome of wild baboons. ELife, 12, e83152. https://doi.org/10.7554/elife.83152
Roche, Kimberly E., Johannes R. Bjork, Mauna R. Dasari, Laura Grieneisen, David Jansen, Trevor J. Gould, Laurence R. Gesquiere, et al. “Universal gut microbial relationships in the gut microbiome of wild baboons.ELife 12 (May 2023): e83152. https://doi.org/10.7554/elife.83152.
Roche KE, Bjork JR, Dasari MR, Grieneisen L, Jansen D, Gould TJ, et al. Universal gut microbial relationships in the gut microbiome of wild baboons. eLife. 2023 May;12:e83152.
Roche, Kimberly E., et al. “Universal gut microbial relationships in the gut microbiome of wild baboons.ELife, vol. 12, May 2023, p. e83152. Epmc, doi:10.7554/elife.83152.
Roche KE, Bjork JR, Dasari MR, Grieneisen L, Jansen D, Gould TJ, Gesquiere LR, Barreiro LB, Alberts SC, Blekhman R, Gilbert JA, Tung J, Mukherjee S, Archie EA. Universal gut microbial relationships in the gut microbiome of wild baboons. eLife. 2023 May;12:e83152.

Published In

eLife

DOI

EISSN

2050-084X

ISSN

2050-084X

Publication Date

May 2023

Volume

12

Start / End Page

e83152

Related Subject Headings

  • RNA, Ribosomal, 16S
  • Papio
  • Microbiota
  • Humans
  • Gastrointestinal Microbiome
  • Bacteria
  • Animals
  • 42 Health sciences
  • 32 Biomedical and clinical sciences
  • 31 Biological sciences