Evidence map›Paper›PMID 38396294›Full record

ArticleOncogene2024

Robustness of cancer microbiome signals over a broad range of methodological variation.

Gregory D Sepich-Poore, Daniel McDonald, Evguenia Kopylova, Caitlin Guccione, Qiyun Zhu, George Austin, Carolina Carpenter, Serena Fraraccio, Stephen Wandro, Tomasz Kosciolek and 11 more

Erratum issuedAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Oncogene, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 57 papers.

0numbers the graph read from it
0cells of the map it votes in
57citing 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

57 citing papers in PubMed.

  1. Review
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  4. Article
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  6. Article
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  8. Article
  9. Review
  10. Harnessing the microbiome for cancer therapy.Nature reviews. Microbiology · 2026
    Review
  11. Article
  12. Review
  13. Article
  14. Review
  15. Review
  16. Article
  17. IntratumoralScience advances · 2026
    Article
  18. Article
  19. Review
  20. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

21 authors.

Gregory D Sepich-Poore *Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0002-3443-3715
Daniel McDonald *Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Evguenia Kopylova *Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Caitlin Guccione *Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Qiyun ZhuDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
George AustinDepartment of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA.
Carolina CarpenterCenter for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
Serena FraraccioCenter for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
Stephen WandroCenter for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
Tomasz KosciolekDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Stefan JanssenDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Jessica L MetcalfDepartment of Animal Sciences, Colorado State University, Fort Collins, CO, USA.
Se Jin SongDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Jad KanbarDepartment of Medicine, University of California San Diego, La Jolla, CA, USA.
Sandrine Miller-MontgomeryDepartment of Bioengineering, University of California San Diego, La Jolla, CA, USA.
Robert HeatonDepartment of Psychiatry, University of California San Diego, La Jolla, CA, USA.
Rana MckayMoores Cancer Center, University of California San Diego Health, La Jolla, CA, USA.ORCID 0000-0002-0581-7963
Sandip Pravin PatelCenter for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
Austin D SwaffordCenter for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
Tal KoremProgram for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.ORCID 0000-0002-0609-0858
Rob KnightDepartment of Bioengineering, University of California San Diego, La Jolla, CA, USA. rknight@ucsd.edu.ORCID 0000-0002-0975-9019

Funding

Training in Biomedical Informatics at Columbia UniversityT15LM007079 · NLM · COLUMBIA UNIV NEW YORK MORNINGSIDE · PI NOEMIE ELHADAD, GEORGE M HRIPCSAK · 1992 to 2026
$28.9M
Mapping host-microbe-metabolite interactions in 3D to find diet-derived enhancers of immunityDP1AT010885 · NCCIH · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI KNIGHT, ROB · 2019 to 2023
$5.5M
Advanced Development of Informatics Technologies for Cancer Research and Management (U24 Clinical Trial Optional)U24CA248454 · NCI · NORTHERN ARIZONA UNIVERSITY · PI CAPORASO, JAMES GREGORY · 2020 to 2024
$3.7M
NCCIH NIH HHS DP1 AT010885NCI NIH HHS U24 CA248454NLM NIH HHS T15 LM007079
6 · The paper itself

Abstract

In 2020, we identified cancer-specific microbial signals in The Cancer Genome Atlas (TCGA) [1]. Multiple peer-reviewed papers independently verified or extended our findings [2-12]. Given this impact, we carefully considered concerns by Gihawi et al. [13] that batch correction and database contamination with host sequences artificially created the appearance of cancer type-specific microbiomes. (1) We tested batch correction by comparing raw and Voom-SNM-corrected data per-batch, finding predictive equivalence and significantly similar features. We found consistent results with a modern microbiome-specific method (ConQuR [14]), and when restricting to taxa found in an independent, highly-decontaminated cohort. (2) Using Conterminator [15], we found low levels of human contamination in our original databases (~1% of genomes). We demonstrated that the increased detection of human reads in Gihawi et al. [13] was due to using a newer human genome reference. (3) We developed Exhaustive, a method twice as sensitive as Conterminator, to clean RefSeq. We comprehensively host-deplete TCGA with many human (pan)genome references. We repeated all analyses with this and the Gihawi et al. [13] pipeline, and found cancer type-specific microbiomes. These extensive re-analyses and updated methods validate our original conclusion that cancer type-specific microbial signatures exist in TCGA, and show they are robust to methodology.

Indexed as

MicrobiotaNeoplasmsHumans

Identifiers

PMID38396294
PMCPMC10997506

What OpenQuestion holds

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Registered trials

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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.