The TaxUMAP atlas: Efficient display of large clinical microbiome data reveals ecological competition in protection against bacteremia Journal Article
| Authors: | Schluter, J.; Djukovic, A.; Taylor, B. P.; Yan, J.; Duan, C.; Hussey, G. A.; Liao, C.; Sharma, S.; Fontana, E.; Amoretti, L. A.; Wright, R. J.; Dai, A.; Peled, J. U.; Taur, Y.; Perales, M. A.; Siranosian, B. A.; Bhatt, A. S.; van den Brink, M. R. M.; Pamer, E. G.; Xavier, J. B. |
| Article Title: | The TaxUMAP atlas: Efficient display of large clinical microbiome data reveals ecological competition in protection against bacteremia |
| Abstract: | Longitudinal microbiome data provide valuable insight into disease states and clinical responses, but they are challenging to mine and view collectively. To address these limitations, we present TaxUMAP, a taxonomically informed visualization for displaying microbiome states in large clinical microbiome datasets. We used TaxUMAP to chart a microbiome atlas of 1,870 patients with cancer during therapy-induced perturbations. Bacterial density and diversity were positively associated, but the trend was reversed in liquid stool. Low-diversity states (dominations) remained stable after antibiotic treatment, and diverse communities had a broader range of antimicrobial resistance genes than dominations. When examining microbiome states associated with risk for bacteremia, TaxUMAP revealed that certain Klebsiella species were associated with lower risk for bacteremia localize in a region of the atlas that is depleted in high-risk enterobacteria. This indicated a competitive interaction that was validated experimentally. Thus, TaxUMAP can chart comprehensive longitudinal microbiome datasets, enabling insights into microbiome effects on human health. © 2023 Elsevier Inc. |
| Keywords: | genetics; antiinfective agent; antibiotic resistance; anti-bacterial agents; bacteremia; intestine flora; bacterium; bacteria; microflora; klebsiella; microbiota; taxonomy; enterobacteriaceae; patient data; humans; human; gut microbiome; gastrointestinal microbiome; gut domination |
| Journal Title: | Cell Host & Microbe |
| Volume: | 31 |
| Issue: | 7 |
| ISSN: | 1931-3128 |
| Publisher: | Cell Press |
| Date Published: | 2023-07-12 |
| Start Page: | 1126 |
| End Page: | 1139.e6 |
| Language: | English |
| DOI: | 10.1016/j.chom.2023.05.027 |
| PUBMED: | 37329880 |
| PROVIDER: | scopus |
| PMCID: | PMC10527165 |
| DOI/URL: | |
| Notes: | The MSK Cancer Center Support Grant (P30 CA008748) is acknowledged in the PDF -- Corresponding author is MSK author: Joao Xavier -- Source: Scopus |
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