Analysis of microbial sequences in plasma cell-free DNA for early-onset breast cancer patients and healthy females
Open accessAbstract
BACKGROUND: Cell-free circulating DNA (cfDNA) is becoming a useful biopsy for noninvasive diagnosis of diseases. Microbial sequences in plasma cfDNA may provide important information to improve prognosis and treatment. We have developed a stringent method to identify microbial species via microbial cfDNA in the blood plasma of early-onset breast cancer (EOBC) patients and healthy females. Empirically, microbe-originated sequence reads were identified by mapping non-human PE reads in cfDNA libraries to microbial databases. Those mapped concordantly to unique microbial species were assembled into contigs, which were subsequently aligned to the same databases. Microbial species uniquely aligned were identified and compared across all individuals on MCRPM (Microbial CfDNA Reads Per Million quality PE reads) basis. RESULTS: The predominant microbial cfDNAs in all plasma samples examined are originated from bacteria and these bacteria were limited to only a few genera. Among those, Acinetobacter johnsonii XBB1 and low levels of Mycobacterium spp. were commonly found in all healthy females, but also present in an EOBC patient. Compared to those in healthy counterparts, bacterial species in EOBC patients are more diverse and more likely to present at high levels. Among these three EOBC patients tested, a patient who has record high titer (2,724 MCRPM) of Pseudomonas mendocina together with 8.82 MCRPM of Pannonibacter phragmitetus has passed away; another patient infected by multiple Sphingomonas species remains alive; while the third patient who has similar microbial species (Acinetobacter johnsonii XBB1) commonly seen in normal controls is having a normal life. CONCLUSIONS: Our preliminary data on the profiles of microbial cfDNA sequences suggested that it may have some prognostic value in cancer patients. Validation in larger number of patients is warranted.
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Blood-based microbial DNA can be clinically informative in cancer, including cancers with blood-barrier or lymphatic disruptions.
“There is mounting evidence that blood-based microbial DNA (hereafter “mbDNA”) can be clinically informative in cancer39–44, including those featuring blood-barrier or lymphatic disruptions (e.g. COAD)39”
From RETRACTED ARTICLE: Microbiome analyses of blood and tissues suggest cancer diagnostic approach (2020) · cites this paper as [44]
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RETRACTED ARTICLE: Microbiome analyses of blood and tissues suggest cancer diagnostic approach
Poore, G. D., Kopylova, E., Zhu, Q., Carpenter, C., Fraraccio, S., Wandro, S., Kosciolek, T., Janssen, S., Metcalf, J., Song, S. J., et al. (2020) · Nature · doi:10.1038/s41586-020-2095-1 · Cited by 989 · see citing works
RetractedSaid, S., & Ibrahim, W. (2025) · Cancer Management and Research · doi:10.2147/cmar.s405590 · Cited by 25 · see citing works
- Authors
- Huang, Y.-F., Chen, Y.-J., Fan, T.-C., Chang, N.-C., Chen, Y.-J., Midha, M. K., Chen, T.-H., Yang, H.-H., Wang, Y.-T., Yu, A. L., & Chiu, K.-P.
- Affiliations
- Genomics Research Center, Academia Sinica (TW)
- Chang Gung University (TW)
- National Taiwan University (TW)
- Corresponding author
- Chiu, Kuo-Ping
- Venue
- BMC Medical Genomics
- Published
- 2018-02
- Volume
- 11
- Issue
- S1
- Pages
- 16-16
- ISSN
- 1755-8794 (ISSN-L)
- PMC
- PMC5836824
- OpenAlex
- W2786496513
- Cited by
- 72
- References
- 29
- Citations by year
- 2026: 7 · 2025: 12 · 2024: 10 · 2023: 13 · 2022: 7 · 2021: 5 · 2020: 14 · 2019: 3 · 2018: 1
- FWCI
- 1.89
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- BMC Medical Genomics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Funders
- Academia Sinica
- Genomics Research Center, Academia Sinica
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- microbial cell-free DNA, early-onset breast cancer, plasma cfDNA, microbial identification, Acinetobacter johnsonii, Pseudomonas mendocina, Pannonibacter phragmitetus, Sphingomonas, Mycobacterium, bacterial diversity, prognostic factors
- MeSH terms
- Cell-Free Nucleic Acids, Adult, Breast Neoplasms, DNA, Bacterial, Female, Humans, Prognosis, Biomarkers, Case-Control Studies, Age of Onset
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