ArticleGenome research2023
Simultaneous profiling of host expression and microbial abundance by spatial metatranscriptome sequencing.
Article in Genome research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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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.
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Who cites it
12 citing papers in PubMed, 18 citations in OpenAlex.
- Living Microbial Drugs.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Review
- Analysis of unmapped RNA-seq data from cancer spatial transcriptome toward characterizing cancer microbiome.Scientific reports · 2026Article
- Spatial transcriptomics maps host-gut microbiome biogeography at high resolution.Nature microbiology · 2026Article
- Novel Approaches for Investigating Host Responses to HIV Infection in Ex Vivo Human Genital Tissues.American journal of reproductive immunology (New York, N.Y. : 1989) · 2026Review
- Genotype-Environment-Driven Dysbiosis in the Skin Microbiome of Ichthyosis.The Journal of investigative dermatology · 2026Article
- Spatial architecture of development and disease.Nature reviews. Genetics · 2026Review
- Microbial Omics.Progress in molecular and subcellular biology · 2026Review
- SMTdb: A Comprehensive Spatial Meta-Transcriptome Resource in Cancer.Molecular biology and evolution · 2025Article
- The new microbiome on the block: challenges and opportunities of using human tumor sequencing data to study microbes.Nature methods · 2025Review
- Optimizing mouse metatranscriptome profiling by selective removal of redundant nucleic acid sequences.mSystems · 2025Article
- Spatial transcriptomics identifies novel Pseudomonas aeruginosa virulence factors.Cell genomics · 2025Article
- Spatial methods for microbiome-host interactions.Nature biotechnology · 2024Article
Corrections and comments
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Authors and funding
12 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We developed an analysis pipeline that can extract microbial sequences from spatial transcriptomic (ST) data and assign taxonomic labels, generating a spatial microbial abundance matrix in addition to the default host expression matrix, enabling simultaneous analysis of host expression and microbial distribution. We called the pipeline spatial metatranscriptome (SMT) and applied it on both human and murine intestinal sections and validated the spatial microbial abundance information with alternative assays. Biological insights were gained from these novel data that showed host-microbe interaction at various spatial scales. Finally, we tested experimental modification that can increase microbial capture while preserving host spatial expression quality and, by use of positive controls, quantitatively showed the capture efficiency and recall of our methods. This proof-of-concept work shows the feasibility of SMT analysis and paves the way for further experimental optimization and application.
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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.