Mary Wilson
Well-known member
January 22, 2025
DOI: 10.1016/j.cell.2024.12.017
Richard J. Abdill[SUP]1,7[/SUP] ∙ Samantha P. Graham[SUP]2,7[/SUP] ∙ Vincent Rubinetti[SUP]3,4[/SUP]∙ Mansooreh Ahmadian[SUP]5[/SUP] ∙ Parker Hicks[SUP]3[/SUP] ∙ Ashwin Chetty[SUP]1[/SUP] ∙ Daniel McDonald[SUP]6[/SUP] ∙ Pamela Ferretti[SUP]1[/SUP] ∙ Elizabeth Gibbons[SUP]1[/SUP] ∙ Marco Rossi[SUP]1[/SUP] ∙ Arjun Krishnan[SUP]3,5[/SUP] ∙ Frank W. Albert[SUP]2[/SUP] ∙ Casey S. Greene[SUP]3,4[/SUP] ∙ Sean Davis[SUP]3,4[/SUP] ∙ Ran Blekhman[SUP]1,8[/SUP]
Highlights
•
168,000 public 16S gut microbiome samples processed and integrated at microbiomap.org
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Microbiome composition and diversity differ widely between world regions
•
Technical factors like amplicon choice associate with compositional differences
•
Classifiers trained on compendium data can infer world regions from composition
Summary
The factors shaping human microbiome variation are a major focus of biomedical research. While other fields have used large sequencing compendia to extract insights requiring otherwise impractical sample sizes, the microbiome field has lacked a comparably sized resource for the 16S rRNA gene amplicon sequencing commonly used to quantify microbiome composition. To address this gap, we processed 168,464 publicly available human gut microbiome samples with a uniform pipeline. We use this compendium to evaluate geographic and technical effects on microbiome variation. We find that regions such as Central and Southern Asia differ significantly from the more thoroughly characterized microbiomes of Europe and Northern America and that composition alone can be used to predict a sample’s region of origin. We also find strong associations between microbiome variation and technical factors such as primers and DNA extraction. We anticipate this growing work, the Human Microbiome Compendium, will enable advanced applied and methodological research.
https://www.cell.com/cell/fulltext/S0092-8674(24)01430-2
DOI: 10.1016/j.cell.2024.12.017
Richard J. Abdill[SUP]1,7[/SUP] ∙ Samantha P. Graham[SUP]2,7[/SUP] ∙ Vincent Rubinetti[SUP]3,4[/SUP]∙ Mansooreh Ahmadian[SUP]5[/SUP] ∙ Parker Hicks[SUP]3[/SUP] ∙ Ashwin Chetty[SUP]1[/SUP] ∙ Daniel McDonald[SUP]6[/SUP] ∙ Pamela Ferretti[SUP]1[/SUP] ∙ Elizabeth Gibbons[SUP]1[/SUP] ∙ Marco Rossi[SUP]1[/SUP] ∙ Arjun Krishnan[SUP]3,5[/SUP] ∙ Frank W. Albert[SUP]2[/SUP] ∙ Casey S. Greene[SUP]3,4[/SUP] ∙ Sean Davis[SUP]3,4[/SUP] ∙ Ran Blekhman[SUP]1,8[/SUP]
Highlights
•
168,000 public 16S gut microbiome samples processed and integrated at microbiomap.org
•
Microbiome composition and diversity differ widely between world regions
•
Technical factors like amplicon choice associate with compositional differences
•
Classifiers trained on compendium data can infer world regions from composition
Summary
The factors shaping human microbiome variation are a major focus of biomedical research. While other fields have used large sequencing compendia to extract insights requiring otherwise impractical sample sizes, the microbiome field has lacked a comparably sized resource for the 16S rRNA gene amplicon sequencing commonly used to quantify microbiome composition. To address this gap, we processed 168,464 publicly available human gut microbiome samples with a uniform pipeline. We use this compendium to evaluate geographic and technical effects on microbiome variation. We find that regions such as Central and Southern Asia differ significantly from the more thoroughly characterized microbiomes of Europe and Northern America and that composition alone can be used to predict a sample’s region of origin. We also find strong associations between microbiome variation and technical factors such as primers and DNA extraction. We anticipate this growing work, the Human Microbiome Compendium, will enable advanced applied and methodological research.
https://www.cell.com/cell/fulltext/S0092-8674(24)01430-2