Innovation in sequencing techniques has enabled the identification of microbiome in low biomass sites. In this study, we sought to investigate the utility of 16S rRNA deep sequencing of whole blood in kidney transplant recipients and to assess a link between the gut microbiota and the blood microbiota. We recruited 63 kidney transplant recipients who provided 163 whole blood specimens over the first 140 days after transplantation. We profiled the blood microbiome using 16S rRNA gene sequencing of the V4-V5 hypervariable region and additionally evaluated the gut microbiota in a subset of kidney transplant recipients who had gut bacteria detected in the blood. We generated a median of 19,959 sequences per blood specimen and found that most whole blood microbiome profiles consisted of mitochondrial DNA. While we did not identify classically pathogenic bacteria in the blood such as Escherichia, Klebsiella, and Enterococcus, we identified 25 gut bacterial taxa at very low levels in the blood of 22 kidney transplant recipients. For 9 of these kidney transplant recipients the same bacterial taxa detected in the blood were also identified in the gut microbiota. Our study is one of the first to show the detection of gut bacterial DNA in the blood of kidney transplant patients.

DMD and JRL hold patent US-2020-0048713-A1 titled, Methods of Detecting Cell-Free DNA in Biological Samples, licensed to Eurofins Viracor. FS has stock in BioNTech. DMD participated in industry sponsored studies sponsored by AlloVir Inc., CSL Behring, and Memo Therapeutics AG and served as a consultant for CareDx. JRL received research support under an investigator-initiated research grant from BioFire Diagnostics, LLC.; JRL received an honorarium for a talk from Astellas and travel support from Calliditas; JRL was on the board of directors for the Chinese American Medical Society and was on the executive committee for the New York Society of Nephrology.

This manuscript was funded, in part, by National Institute of Health grant R21 AI 173849 (J.R.L.), National Institute of Health grant R01 DK 139249 (J.R.L.), and National Institutes of Health grant R01 AI 184528 (J.R.L.). F. S. is supported by research fellowship funding from the German Research Foundation (DFG, project number 539291308).

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The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

The Weill Cornell Institutional Review Board approved this protocol, and all subjects provided written informed consent.

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I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).

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I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.

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Sequencing data that support the findings of this study will be made available in the database of Genotypes and Phenotypes (dbGaP) phs004121.v1 upon publication.