ArticleCell host & microbe2023
The TaxUMAP atlas: Efficient display of large clinical microbiome data reveals ecological competition in protection against bacteremia.
Article in Cell host & microbe, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 21 citations in OpenAlex.
- A retrospectively registered pilot randomized controlled trial of postbiotic administration during antibiotic treatment increases microbiome diversity and enriches health-associated taxa.Infection and immunity · 2026Trial
- Article
- Toward a Dual-Axis Model of Microbiome Modulation in Cancer Immunotherapy: Pathobiont Elimination and Functional Ecosystem Restoration.Cellular and molecular bioengineering · 2026Article
- Antibiotic-induced gut microbiome dysbiosis: risks and strategies for mitigation.The EMBO journal · 2026Review
- Metabiosis underlies a microbiota permissive to Pseudomonadota and increases the risk of gut-borne bloodstream infection.bioRxiv : the preprint server for biology · 2026Article
- Interactive visualization of metric distortion in nonlinear data embeddings using the distortions package.Briefings in bioinformatics · 2026Article
- DynaBiome: interpretable unsupervised learning of gut microbiome dysbiosis via temporal deep models.BMC bioinformatics · 2026Article
- Sugar ABC transporter repertoires predict ecological dynamics in gut microbiome communities.Research square · 2026Article
- Klebsiella ARO112 promotes microbiota recovery, pathobiont clearance and prevents inflammation in IBD mice.Nature communications · 2025Article
- Leveraging strain competition to address antimicrobial resistance with microbiota therapies.Gut microbes · 2025Review
- Ecological management of the microbiota in patients with cancer.Nature reviews. Clinical oncology · 2025Review
- Suppression of gut colonization by multidrug-resistant Escherichia coli clinical isolates through cooperative niche exclusion.Nature communications · 2025Article
- Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations.Nature microbiology · 2025Article
- Klebsiella oxytoca facilitates microbiome recovery via antibiotic degradation and restores colonization resistance in a diet-dependent manner.Nature communications · 2025Article
- A comparativeFrontiers in microbiology · 2025Article
- Targeting the immuno-inflammatory-microbial network: a key strategy for sepsis treatment.Frontiers in immunology · 2025Review
- Klebsiella oxytoca inhibits Salmonella infection through multiple microbiota-context-dependent mechanisms.Nature microbiology · 2024Article
- Microbiota and metabolic adaptation shapebioRxiv : the preprint server for biology · 2024Article
- Immune-Related Colitis Is Associated with Fecal Microbial Dysbiosis and Can Be Mitigated by Fecal Microbiota Transplantation.Cancer immunology research · 2024Article
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Authors and funding
20 authors at 6 institutions in 1 country.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.