Blood, Gut, and Oral Microbiome in Kidney Transplant Recipients

Introduction

Disturbances of normal gut microbiome (dysbiosis) may be important in the pathogenesis of chronic kidney disease (CKD).[1] Although complications after kidney transplantation, such as infection and rejection episodes, remain major challenges, few studies have evaluated the human gut microbiome in kidney transplant recipients (KTRs). Changes in gut microbiome composition pre- and posttransplant in KTRs were observed, specifically a decrease in diversity associated with an increase in the relative abundance of Proteobacteria, particularly in members of the Enterobacteriaceae family.[23] Besides, it has been demonstrated that the gut microbiota can also influence tacrolimus dosage, and that immunosuppressive therapy may impact on the gut microbiome.[45] Moreover, oral bacteriome were found to be altered in KTRs, with an overgrowth of potentially opportunistic pathogens.[26] Different studies have shown the existence of a blood microbiome in healthy patients and in patients with noninfectious diseases.[7891011] Recently, a study has shown that blood microbiome in CKD patients harbors a lower diversity and different taxonomic profiles in comparison to healthy controls.[10] Even if it could be expected that blood microbiome also exists in KTR patients, no information is currently available on the blood microbiome of KTRs, nor its comparison with gut or oral microbiome.

The presence of dysbiosis in KTR may impact on the type and concentration of uremic toxins, systemic inflammation, and the appearance of infections.[12] In fact, previous studies suggested that a specific microbiota profile could be associated with adverse events after kidney transplantation, specifically rejection events and infectious complications (diarrhea and urinary tract infections).[2313141516]

Given the high impact that dysbiosis may have in KTR outcomes, we evelauated the blood microbiome in KTR and its relationship with the gut and the oral microbiome, 3 months after kidney transplantation.

Materials and Methods

Results

CKD etiologies of KTR included autosomal dominant polycystic kidney disease (two patients), IgA nephropathy, obstructive uropathy, focal segmental glomerulosclerosis, and lupus nephritis (one each). Induction therapy included the use of basiliximab in five patients and of antithymocyte globulin in one patient. All patients were under maintenance therapy with prednisone, tacrolimus, and mycophenolate mofetil. Five months after transplant, one patient suffered a cerebrovascular event and mycophenolate was shifted to everolimus. The general clinical characterization of KTR and the infection events are presented in Table 1 and Supplementary Table 1, respectively. All patients presented stable renal function and no rejection episodes up to 2 years after kidney transplantation.

Gut, oral, and blood microbiome were analyzed in these patients. A total of 409 OTUs were detected among samples; the following details were observed for the samples’ OTUs, which are given as median (range): oral samples with 115 (106–128) OTUs, gut samples with 88 (59–105) OTUs, and blood samples with 50 (42–82) OTUs. The rarefaction curve analysis demonstrated the sufficiency of our read coverage to capture sample diversity [

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Figure 1

Relative abundance of bacterial taxa at the phylum level in kidney transplant recipients. Taxa are identified by name in the plot for abundance >1%. Taxa are merged into the “Other” category only if they exist in any sample with abundance greater than 0.01%. Taxa are merged into the “Multi-affiliation” category when they can correspond to two or more different taxa

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Moreover, each patient presented between three and seven different OTUs sharing the three monitored sites. It was found that 3.7% (15 OTUs) of the total OTUs were shared among the gut, oral, and blood samples within the same patient in at least one of the patients. These OTUs were classified mainly as Proteobacteria and Firmicutes, but single representative OTUs among Actinobacteria, Bacteroidetes, and Fusobacteria were also reported [Figure 2]. Among the set of 15 shared OTUs, four OTUs (1%) were present in multiple patients, which were the OTUs classified as Streptococcus (two OTUs), Pseudomonas, and multi-affiliated Enterobacteriaceae (possibly Escherichia or Enterobacter). Lactobacillus was also found to be shared among multiple samples within some patients, but the OTU was proven to be different among the tested samples, that is, saliva, blood, and feces.

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Figure 2

Shared taxa among the gut, oral, and blood samples in kidney transplant recipients. A set of 15 shared OTUs found in the six kidney transplant recipients studied belong to the following represented phyla, with the respective number of OTUs per phyla or family (when higher than 1) given in parentheses. OTU taxonomy (family and respective genus) found in the three habitats of multiple patients are represented in bold. OTU = operational taxonomic unit

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Discussion

We describe the blood microbiome of KTRs and clearly show distinct microbiome profiles among the gut, oral, and blood samples. A small percentage of phylotypes were found to be shared among these different human habitats, unraveling a possible mobile microbiome in stable KTR patients. Interestingly, these phylotypes included possible KTR pathogens such as Pseudomonas, Streptococcus, and classified Enterobacteriaceae. As previously reported, the gut microbiome was dominated by Bacteroidetes and Firmicutes phyla.[1213] Moreover, Fricke et al.[2] showed that the most significant changes in the human microbiome between pre- and posttransplant occurred immediately after transplantation (1 month), justifying the evaluation of KTRs 3 months after kidney transplantation, as conducted in this study. In the oral microbiome, the dominant phyla were Proteobacteria, Bacteroidetes, Fusobacteria, and Firmicutes. This composition disagrees with other studies that evaluated oral swabs in KTRs[2] and dental plaque or saliva in healthy controls,[2122] where Firmicutes, especially Streptococcus, were the most prevalent genus. More similarities were found when we analyzed the most prevalent families in the oral microbiome of the patients: Campylobacteraceae, Fusobacteriaceae, Neisseriaceae, Pasteurellaceae, Porphyromonadaceae, Prevotellaceae, Streptococcaceae. Nonetheless, other studies also reported slightly different microbiome profiles with lower levels of Firmicutes and a higher proportion of Proteobacteria and Bacteroidetes among solid-organ transplant recipients and Barrett’s esophagus patients.[623] Fricke et al.[2] reported the blood samples rarely harbored microbial components in transplant recipients. However, presently, multiple studies describe and acknowledge the presence of a distinct blood microbiome in healthy and disease-affected individuals[7811] and even report the detection of viable bacteria.[9]

Our study revealed Proteobacteria, Firmicutes, and Actinobacteria phyla as the dominant phyla in the blood microbiome profile of the KTRs. This is in line with another study that showed higher abundance of Enterobacteriaceae and Pseudomonadaceae families in the blood microbiome of nondiabetic CKD patients in comparison to healthy controls.[10]

Interestingly, a small group of shared OTUs among different human-associated environments (oral, blood, and gut) was reported in this study. Previously, 219 OTUs shared between the urine and gut samples, 193 OTUs shared between the oral and gut samples, and 16 OTUs shared between the urine and oral samples were reported.[2] The present study reports for the first time a shared, and maybe mobile, microbiome in samples collected from three different body sites (gut, blood, and oral). This finding suggests the presence of a systemic microbiome, comprising particular bacteria or bacterial DNA, which could be found in different body habitats and/or are associated with mobility throughout the human body. The full consequence of this phenomenon is still unknown, but it is possibly associated with systemic infections or colonization, and may have an impact in the microbiome, systemic inflammation, and patient blood management. Also, whatever the nature (living bacteria or bacterial DNA) of the taxa found in these three microbiomes, it may represent an interesting source of inflammation or infection risk biomarkers for KTR.

In conclusion, KTRs present a specific blood microbiome profile, different from the gut and oral habitats, but with a low proportion of phylotypes shared among different habitats that can represent a shared microbiome in KTRs and/or an interesting source of biomarkers. The clinical relevance of this observation should be further explored.