Evidence map›Paper›PMID 41576946›Full record

ArticleCell genomics2026

Microbial single-cell omics in situ.

Xihong Lan, Qiaoxing Liang, Jinhua He, Jiayi Wu, Xiaoying Zhang, Fei Li, Lili Li, Guoping Zhao, Ruidong Guo, Huijue Jia

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell genomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Xihong LanSchool of Life Sciences, Fudan University, Shanghai 200433, China; State Key Laboratory of Genetics and Development of Complex Phenotypes, Fudan University, Shanghai 200433, China; Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou 511458, China; Central Laboratory of Panyu Central Hospital, The Affiliated Panyu Central Hospital of Guangzhou Medical University, Guangzhou 511400, China.
Qiaoxing LiangSchool of Life Sciences, Fudan University, Shanghai 200433, China; State Key Laboratory of Genetics and Development of Complex Phenotypes, Fudan University, Shanghai 200433, China; Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou 511458, China.
Jinhua HeCentral Laboratory of Panyu Central Hospital, The Affiliated Panyu Central Hospital of Guangzhou Medical University, Guangzhou 511400, China.
Jiayi WuGreater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou 511458, China.
Xiaoying ZhangCentral Laboratory of Panyu Central Hospital, The Affiliated Panyu Central Hospital of Guangzhou Medical University, Guangzhou 511400, China.
Fei LiSchool of Life Sciences, Fudan University, Shanghai 200433, China; State Key Laboratory of Genetics and Development of Complex Phenotypes, Fudan University, Shanghai 200433, China; Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou 511458, China.
Lili LiGreater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou 511458, China.
Guoping ZhaoSchool of Life Sciences, Fudan University, Shanghai 200433, China; State Key Laboratory of Genetics and Development of Complex Phenotypes, Fudan University, Shanghai 200433, China; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
Ruidong GuoSchool of Life Sciences, Fudan University, Shanghai 200433, China.
Huijue JiaSchool of Life Sciences, Fudan University, Shanghai 200433, China; State Key Laboratory of Genetics and Development of Complex Phenotypes, Fudan University, Shanghai 200433, China; Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou 511458, China; Zhejiang University, Hangzhou, China. Electronic address: huijue_jia@fudan.edu.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Metagenomics has enabled the understanding of the microbial composition and functional potential in various environments. Using laser-induced forward transfer (LIFT) technology, we report high-quality microbial single-cell genomes or transcriptomes in complex samples such as mouse gut, human saliva, and tumor sections. Bacterial cells in close proximity to each other or to host cells could be directly analyzed using this single-cell approach. Bacterial cells in mice or human samples could be fluorescently labeled for single-cell visualization before collection. The high-quality single-cell transcriptome results allow us to delineate cell-fate commitment in Bacillus sporulation and preliminarily characterize gene expression from Bacteroides in a colorectal cancer sample. The method is scalable and precise and empowers insights about microbial populations and single-cell interactions with the host.

Indexed as

Single-Cell AnalysisAnimalsBacillusBacteroidesColorectal NeoplasmsHumansMiceMultiomicsSalivaSingle-Cell Gene Expression AnalysisTranscriptomecolorectal cancerhost-associated microbiomein situ microscopylaser-induced forward transferLIFTmicrobial nicotine metabolismmicrobial single-cell genomesmicrobial single-cell transcriptomeRaman spectrometryscRNAsporulation

Identifiers

PMID41576946
PMCPMC13069861

What OpenQuestion holds

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Registered trials

None linked

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.