ArticleScience advances2024
Identification of intracellular bacteria from multiple single-cell RNA-seq platforms using CSI-Microbes.
Article in Science advances, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 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
21 citing papers in PubMed.
- scH16S-Seq Maps Klebsiella pneumoniae-Associated Myeloid States and Reveals a CD38-NAD Immunometabolic Axis That Impairs Lysosomal Acidification in Sepsis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Decoding the cancer microbiome: multi-omics, AI, and translational opportunities.Genome biology · 2026Review
- Innovative technologies and future perspectives in tumor microbiomics.Science China. Life sciences · 2026Review
- Intracellular microbial shifts during COVID-19 infection and longitudinal recovery revealed by single-cell RNA sequencing.iScience · 2026Article
- Virus infections and cancers: from mechanisms to therapeutics.Molecular biomedicine · 2026Review
- Sphingomonas paucimobilis-Driven Epithelial-Endothelial Transition in Adenomyosis Pathogenesis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Review
- Decoding Immunotherapy Response in Colorectal Cancer: Translational Insights Beyond MSI.Cancers · 2026Review
- Stenotrophomonas promotes gastrointestinal tumor progression via STING degradation in tumour cells and mitigated immune response.Nature communications · 2026Article
- The intratumoral microbiome in colorectal cancer: origins, microenvironmental interactions, and new horizons in precision medicine.Frontiers in immunology · 2026Review
- MIF-expressing tumor cells mediate immunotherapeutic resistance in esophageal squamous cell carcinoma.Theranostics · 2026Article
- Intratumoral microbiome: a crucial regulating factor in development and progression of colorectal cancer.Molecular biomedicine · 2025Review
- Intratumoral microbiota remodeling of the tumor microenvironment impact solid tumor immunotherapy.Cell death & disease · 2025Review
- HGMT: a database of human gut microbiota for tumors and immunotherapy response.Genome biology · 2025Article
- Fusobacterium nucleatum interacts with cancer-associated fibroblasts to promote colorectal cancer.The EMBO journal · 2025Article
- From lab to life: technological innovations in transforming cancer metastasis detection and therapy.Discover oncology · 2025Review
- Physiologically relevant coculture model for oral microbial-host interactions.International journal of oral science · 2025Article
- Emerging technologies and current challenges in intratumoral microbiota research.Frontiers in cellular and infection microbiology · 2025Review
- An Explainable Graph Neural Framework to Identify Cancer-Associated Intratumoral Microbial Communities.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
18 authors.
Funding
Abstract
The study of the tumor microbiome has been garnering increased attention. We developed a computational pipeline (CSI-Microbes) for identifying microbial reads from single-cell RNA sequencing (scRNA-seq) data and for analyzing differential abundance of taxa. Using a series of controlled experiments and analyses, we performed the first systematic evaluation of the efficacy of recovering microbial unique molecular identifiers by multiple scRNA-seq technologies, which identified the newer 10x chemistries (3' v3 and 5') as the best suited approach. We analyzed patient esophageal and colorectal carcinomas and found that reads from distinct genera tend to co-occur in the same host cells, testifying to possible intracellular polymicrobial interactions. Microbial reads are disproportionately abundant within myeloid cells that up-regulate proinflammatory cytokines like
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What OpenQuestion 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 OpenQuestion graph.