Community diversity is associated with intra-species genetic diversity and gene loss in the human gut microbiome
- Département de sciences biologiques, Université de Montréal, Canada
- Computational and Systems Biology, University of California, Los Angeles, United States
- Bioinformatics and Systems Biology Program, University of California, San Diego, United States
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, United States
- McGill Genome Centre, McGill University, Canada
- Quebec Centre for Biodiversity Science, Canada
- McGill Centre for Microbiome Research, Canada
- Department of Microbiology and Immunology, McGill University, Canada
- Department of Human Genetics, University of California, Los Angeles, United States
Figures
Figure 1
Diversity begets diversity (DBD) and ecological controls (EC) hypotheses illustrated.
Hypothetical microbial communities are illustrated as gray circles containing assemblages of microbial species, shown in different colors. 'DBD' means that the focal species is more likely to …
Figure 2 with 2 supplements
Positive association between community diversity and within-species polymorphism in cross-sectional Human Microbiome Project (HMP) samples.
(A) Scatter plots showing the relationship between community Shannon diversity and within-species polymorphism rate (estimated at synonymous sites) in the nine most prevalent species in HMP. (B) …
Figure 2—figure supplement 1
Results of generalized additive models predicting within-species polymorphism rate (at synonymous sites) as a function of community diversity at higher taxonomic levels (Human Microbiome Project [HMP] data).
(A1–E1) The predictor is Shannon diversity. (A2–E2) The predictor is richness. Adjusted R-squared (R2) and Chi-squared p-values corresponding to the predictor are displayed in each panel …
Figure 2—figure supplement 2
Results of generalized additive models predicting within-species polymorphism rate (at nonsynonymous sites) in a focal species as a function of community diversity at higher taxonomic levels (Human Microbiome Project [HMP] data).
(A1–E1) The predictor is Shannon diversity. (A2–E2) The predictor is richness. Adjusted R-squared (R2) and Chi-squared p-values corresponding to the predictor are displayed in each panel …
Figure 3 with 1 supplement
Associations between community diversity and strain number in cross-sectional Human Microbiome Project (HMP) samples.
(A) Scatter plots showing the relationship between Shannon diversity and the inferred number of strains within each of the nine most prevalent species in HMP. (B) Scatter plots showing the …
Figure 3—figure supplement 1
Results of generalized linear mixed models predicting strain count in a focal species as a function of community diversity at higher taxonomic levels (Human Microbiome Project [HMP] data).
Strain number in a focal species is positively correlated with Shannon (A1–E1) whereas its correlation with richness remains negative (A2–E2) through all taxonomic levels. The Y-axis is the …
Figure 4
Positive association between community diversity and gene loss in Human Microbiome Project (HMP) time series.
(A) Scatter plots showing the relationship between Shannon diversity at time point 1 (tp1) and gene loss between tp1 and tp2 within each of the nine most prevalent species in HMP. (B) Scatter plots …
Figure 5 with 1 supplement
Community diversity is associated with increases in focal species polymorphism over short time lags and net gene loss in dense gut microbiome time series.
(A) Results of a generalized additive model (GAM) predicting polymorphism change in a focal species as a function of the interaction between Shannon diversity at the first time point and the time …
Figure 5—figure supplement 1
Results of a generalized additive model (GAM) predicting polymorphism change in a focal species as a function of the interaction between Shannon diversity at the first time point and the time lag (days) between two time points in the Poyet time series.
The response (Y-axis) was log-transformed in the Gaussian GAM. Several different time lags are shown to illustrate the inversion of the relationship around a lag time of 150 days. See Supplementary …
Additional files
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Supplementary file 1
Supplementary tables a–i.
- https://cdn.elifesciences.org/articles/78530/elife-78530-supp1-v2.docx
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Supplementary file 2
R syntax and statistics of all generalized models.
- https://cdn.elifesciences.org/articles/78530/elife-78530-supp2-v2.docx
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MDAR checklist
- https://cdn.elifesciences.org/articles/78530/elife-78530-mdarchecklist1-v2.docx
