Are gut bacterial relationships shared across baboons?

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Ecological relationships between bacteria mediate the services that gut microbiomes provide to their hosts. Understanding the overall direction and strength of these relationships is essential for learning how ecology affects microbiome assembly, dynamics, and host health. But whether bacterial relationships are shared across hosts or personalized to individuals is debated.

Researchers applied a robust multinomial logistic-normal modeling framework to time-series data comprising 5,534 samples from 56 baboons over 13 years. They inferred thousands of bacterial abundance correlations within individual baboons and tested how universal those correlations were. They also compared the patterns with two human datasets.

Most bacterial correlations were weak, negative, and universal across hosts; shared correlation patterns dominated host-specific correlations by almost twofold. Taxon pairs whose correlation signs differed between hosts—positive in some and negative in others—always had weak correlations within hosts. Baboons with the most similar bacterial correlation patterns also had similar microbiome taxonomic compositions and tended to be genetic relatives.

Universality in baboons was similar to that in human infants and stronger than in one dataset of human adults. Bacterial families with universal correlations in human infants were often universal in baboons too. The researchers say their work provides new tools for analyzing the universality of bacterial associations across hosts, with implications for microbiome personalization, community assembly and stability, and the design of microbiome interventions to improve host health.