Abstract
The aim of this study aimed to examine the existence of a bacterial metagenome in the bone marrow of patients with acute myeloid leukemia (AML). We re-examined whole-genome sequencing data from the bone marrow samples of seven patients with AML, four of whom were remitted after treatment, for metagenomic analysis. After the removal of human reads, unmapped reads were used to profile the species-level composition. We used the metagenomic binning approach to confirm whether the identified taxon was a complete genome of known or novel strains. We observed a unique and novel microbial signature in which Carnobacterium maltaromaticum was the most abundant species in five patients with AML or remission. The complete genome of C. maltaromaticum “BMAML_KR01,” which was observed in all samples, was 100% complete with 8.5% contamination and closely clustered with C. maltaromaticum strains DSM20730 and SF668 based on single nucleotide polymorphism variations. We identified five unique proteins that could contribute to cancer progression and 104 virulent factor proteins in the BMAML_KR01 genome. To our knowledge, this is the first report of a new strain of C. maltaromaticum in patients with AML. The presence of C. maltaromaticum and its new strain in patients indicates an urgent need to validate the existence of this bacterium and evaluate its pathophysiological role.
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Data availability
The raw sequence data used in this study can be found in a public repository: the Clinical & Omics Data Archive (CODA) at the Korea National Institute of Health (accession number R000111; (https://coda.nih.go.kr/, accessed on September 30, 2022). In addition, we have recovered complete genome data of C. maltaromaticum that is publicly available through the NCBI BioProject (accession: PRJNA896709).
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Acknowledgements
We are grateful for the computing resources provided by the Global Science Experimental Data Hub Center (GSDC) Project and the Korea Research Environment Open NETwork (KREONET) of the Korea Institute of Science and Technology Information (KISTI).
Funding
This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korean government (MSIT) (No. 2023R1A2C2006416).
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SR contributed to the methodology, formal analysis, visualization, and writing the original draft of the study. YK and SSY contributed to the resources and review/editing of the manuscript. SYW and KSA contributed to the methodology and investigation. HLK contributed to the resources, data curation, investigation, and review/editing of the manuscript. HNK contributed to the conceptualization, supervision, and review/editing of the manuscript.
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The bone marrow samples used in this study were collected from patients who provided informed consent, and the study was approved by the Seoul National University Hospital Institutional Review Board (IRB No. H-1103-004-353). All study procedures, including data collection and analyses, were performed following the ethical standards of the Helsinki Declaration.
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Supplementary Table S1. Basic characteristics of study patients. Supplementary Table S2: Abundance, completeness and contamination of each bin identified in this study. Supplementary Table S3: NCBI accession number of 21 genomes of Carnobacterium maltaromaticum used in this study including number of CDS and the isolation source. Supplementary Table S4: Number of SNPs observed in 21 genomes of Carnobacterium maltaromaticum used in this study. Supplementary Table S5: Number of virulent factor genes observed in BMAML_KR01 genome. Supplementary Figure S1. Circular representation of the pan-genome of all the Carnobacterium maltaromaticum genomes used in this study. C. maltaromaticum LMA28 was used as the reference genome and the inner most circle (dark brown) represents the pan-genome. The white gaps in the circle of each Carnobacterium maltaromaticum genome represents genome variations.
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Raza, S., Koh, Y., Yoon, SS. et al. Identification of novel Carnobacterium maltaromaticum strains in bone marrow samples of patients with acute myeloid leukemia using a metagenomic binning approach. Int Microbiol 26, 1033–1040 (2023). https://doi.org/10.1007/s10123-023-00360-2
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DOI: https://doi.org/10.1007/s10123-023-00360-2