ArticleNature biotechnology2023
Contamination source modeling with SCRuB improves cancer phenotype prediction from microbiome data.
Article in Nature biotechnology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
51 citing papers in PubMed, 69 citations in OpenAlex.
- Gut Colonization With Vancomycin-Resistant Enterococcus Shapes the Gut Microbiome in the Intensive Care Unit.The Journal of infectious diseases · 2025Trial
- Gut microbial community and host intestinal gene expression with combined fish oil and soluble corn fiber compared with corn oil and maltodextrin: A randomized crossover trial in healthy older individuals.The American journal of clinical nutrition · 2025Trial
- A phase 2 randomized, placebo-controlled trial of inulin for the prevention of gut pathogen colonization and infection among patients admitted to the intensive care unit for sepsis.Critical care (London, England) · 2025Trial
- Spatial Heterogeneity of Intratumoral Microbiota and Its Roles in Tumor-Microbiota Interactions and Therapeutic Implications.Pathogens (Basel, Switzerland) · 2026Review
- Microbiome-Driven Carcinogenesis and Circulating Microbial Signals in Genitourinary Cancers.Cancer science · 2026Review
- The gastric ecosystem: assessing resident microbiome vs. transient microorganisms in obesity and following bariatric interventions.NPJ biofilms and microbiomes · 2026Review
- Identify contaminants with decontam on the QIIME 2 Framework.Microbiology resource announcements · 2026Article
- The microbiome across the prostate disease continuum: from health and BPH to prostatitis/CPPS and cancer.Oncogene · 2026Review
- Potential of Clinical Care-Collected Gut Biopsies for Advancing Personalised Medicine in Inflammatory Bowel Disease.United European gastroenterology journal · 2026Review
- CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomic data.Nature communications · 2026Article
- Lung microbiota analysis in early-stage lung adenocarcinoma.Microbiology spectrum · 2026Article
- A generalizable cross-continent prediction of esophageal squamous cell carcinoma using the oral microbiome.Communications medicine · 2026Article
- Associations of epidemiologic risk factors with Fusobacterium nucleatum and bacterial alpha diversity in the colorectal tumor-associated microbiota.Cancer causes & control : CCC · 2026Article
- Planning and Analyzing a Low-Biomass Microbiome Study: A Data Analysis Perspective.The Journal of infectious diseases · 2026Review
- Mitigation and detection of putative microbial contaminant reads from long-read metagenomic datasets.Microbial genomics · 2026Article
- Microbiome analysis of 940 lung cancers in never-smokers reveals lack of clinically relevant associations.Nature communications · 2025Article
- Environmental and maternal imprints on infant gut metabolic development.Cell host & microbe · 2025Article
- From dysbiosis to mechanisms: Why cervicovaginal microbiome-HPV studies must catch up with biology.PLoS pathogens · 2025Article
- Acute Respiratory Infections (ARIs): Current Etiological Perspectives and Advances in Viral Metagenomics-A Review.Viruses · 2025Review
- Microbial signals in primary and metastatic brain tumors.Nature medicine · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
14 authors at 7 institutions in 2 countries.
Funding
Abstract
Sequencing-based approaches for the analysis of microbial communities are susceptible to contamination, which could mask biological signals or generate artifactual ones. Methods for in silico decontamination using controls are routinely used, but do not make optimal use of information shared across samples and cannot handle taxa that only partially originate in contamination or leakage of biological material into controls. Here we present Source tracking for Contamination Removal in microBiomes (SCRuB), a probabilistic in silico decontamination method that incorporates shared information across multiple samples and controls to precisely identify and remove contamination. We validate the accuracy of SCRuB in multiple data-driven simulations and experiments, including induced contamination, and demonstrate that it outperforms state-of-the-art methods by an average of 15-20 times. We showcase the robustness of SCRuB across multiple ecosystems, data types and sequencing depths. Demonstrating its applicability to microbiome research, SCRuB facilitates improved predictions of host phenotypes, most notably the prediction of treatment response in melanoma patients using decontaminated tumor microbiome data.
Indexed as
Identifiers
What Socratic holds
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 Socratic graph.