Longitudinal analysis reveals transition barriers between dominant ecological states in the gut microbiome
| Autor: | Roie Levy, Jennifer C. Lovejoy, Tomasz Wilmanski, John C. Earls, Nathan D. Price, Ohad Manor, Sean M. Gibbons, Andrew T. Magis, Leroy Hood, Gilbert S. Omenn |
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| Rok vydání: | 2020 |
| Předmět: |
Adult
Male Genus Prevotella Prevotella multiomic microbiome Genus Bacteroides Cohort Studies Feces state transition Bacteroides Humans Longitudinal Studies Microbiome Relative species abundance Phylogeny Aged Multidisciplinary Bacteria biology Ecology Systems Biology Middle Aged Biological Sciences biology.organism_classification Gut microbiome Gastrointestinal Microbiome Molecular physiology Female |
| Zdroj: | Proceedings of the National Academy of Sciences of the United States of America |
| ISSN: | 1091-6490 0027-8424 |
| DOI: | 10.1073/pnas.1922498117 |
| Popis: | Significance Deep molecular phenotyping of individuals provides the opportunity for biological insight into host physiology. As the human microbiome is increasingly being recognized as an important determinant of host health, understanding the host–microbiome relationship in a multiomics context may pave the way forward for targeted interventions. In this study, we analyze gut microbial composition of 101 individuals over the course of a year, alongside clinical markers and serum metabolomics. We establish association between specific gut compositional states and host health biomarkers (e.g., of inflammation). Finally, we provide evidence for an apparent transition barrier between these compositional states. A deeper understanding of microbiome dynamics and the associated variation in host phenotypes furthers our ability to engineer effective interventions that optimize wellness. The Pioneer 100 Wellness Project involved quantitatively profiling 108 participants’ molecular physiology over time, including genomes, gut microbiomes, blood metabolomes, blood proteomes, clinical chemistries, and data from wearable devices. Here, we present a longitudinal analysis focused specifically around the Pioneer 100 gut microbiomes. We distinguished a subpopulation of individuals with reduced gut diversity, elevated relative abundance of the genus Prevotella, and reduced levels of the genus Bacteroides. We found that the relative abundances of Bacteroides and Prevotella were significantly correlated with certain serum metabolites, including omega-6 fatty acids. Primary dimensions in distance-based redundancy analysis of clinical chemistries explained 18.5% of the variance in bacterial community composition, and revealed a Bacteroides/Prevotella dichotomy aligned with inflammation and dietary markers. Finally, longitudinal analysis of gut microbiome dynamics within individuals showed that direct transitions between Bacteroides-dominated and Prevotella-dominated communities were rare, suggesting the presence of a barrier between these states. One implication is that interventions seeking to transition between Bacteroides- and Prevotella-dominated communities will need to identify permissible paths through ecological state-space that circumvent this apparent barrier. |
| Databáze: | OpenAIRE |
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