Evidence map›Paper›PMID 41714823›Full record

ReviewNature cancer2026

Setting higher standards for reports of microbial species in human cancers.

Steven L Salzberg, Minghao Chia, Alfred Tay, Noel F C C de Miranda, Vincent Smit, Jelle Wesseling, Rafael Irizarry, Barry Marshall, Eske Willerslev, Jacques Neefjes and 1 more

Abstract readReview
In one paragraph

Review in Nature cancer, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Review
  2. Article
  3. Review
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

11 authors.

Steven L Salzberg *Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA. steven.salzberg@gmail.com.
Minghao Chia *Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.ORCID http://orcid.org/0000-0001-6473-9881
Alfred TayMarshall Centre, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia.ORCID http://orcid.org/0000-0001-9705-4010
Noel F C C de MirandaDepartment of Pathology, Leiden University Medical Center, Leiden, the Netherlands.ORCID http://orcid.org/0000-0001-6122-1024
Vincent SmitDepartment of Pathology, Leiden University Medical Center, Leiden, the Netherlands.
Jelle WesselingDepartment of Pathology, Leiden University Medical Center, Leiden, the Netherlands.ORCID http://orcid.org/0000-0002-8940-2676
Rafael IrizarryDepartment of Data Science, Dana Faber Cancer Institute, Boston, MA, USA.
Barry MarshallMarshall Centre, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia.
Eske WillerslevCentre for Ancient Environmental Genomics and The Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0002-7081-6748
Jacques NeefjesDepartment of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands. j.j.c.neefjes@lumc.nl.ORCID http://orcid.org/0000-0001-6763-2211
Niranjan NagarajanGenome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore. nagarajann@a-star.edu.sg.ORCID http://orcid.org/0000-0003-0850-5604

Funding

Computational Methods for Microbial and Microbiome Sequence AnalysisR35GM130151 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI Steven L. Salzberg · 2019 to 2026
$2.9M
MOH | National Medical Research Council (NMRC) OFYIRG21nov-0024National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore) NRFI09-0015NIGMS NIH HHS R35 GM130151U.S. Department of Health & Human Services | National Institutes of Health (NIH) R35-GM130151
6 · The paper itself

Abstract

The presence of microbiota in human tumors has been reported widely based on bioinformatic analyses of DNA sequencing datasets; however, the source of microbial sequences in atypical anatomical sites is challenging to validate, as these could derive from sampling, storage, handling and processing of samples, similar to what has been described in studies of ancient DNA. Contamination of microbial reference genomes can also be a source of microbial signals, causing misclassification of human reads. Here, we overview the required quality controls and validation approaches and summarize optimal practices to improve the rigor and standards of tumor microbiome studies.

Indexed as

MicrobiotaNeoplasmsComputational BiologyHumansQuality ControlSequence Analysis, DNA

Identifiers

PMID41714823
PMCPMC13180263

What OpenQuestion holds

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Read underepoch 390

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.