Gut microbial community structure and complications after kidney transplantation

A pilot study

John R. Lee, Thangamani Muthukumar, Darshana Dadhania, Nora C. Toussaint, Lilan Ling, Eric Pamer, Manikkam Suthanthiran

Research output: Contribution to journalArticle

47 Citations (Scopus)

Abstract

Background. The gut microbiome plays a role in the regulation of the immune system. Methods. We prospectively enrolled 26 kidney transplant recipients and collected serial fecal specimens (N=85) during the first three months of transplantation. We characterized bacterial composition by polymerase chain reaction amplification of the 16S rRNA V4-V5 variable region and deep sequencing using the Illumina MiSeq platform. Results. An increase in the relative abundance of Proteobacteria was observed in the posttransplantation specimens compared to pretransplantation specimens (P=0.04, Wilcoxon signed-rank test). In patients with posttransplant diarrhea, the mean(Tstandard deviation [SD]) Shannon diversity index was lower in those with diarrhea (N=6) than those without diarrhea (N=9) (2.5T0.3 vs. 3.4T0.8; P = 0.02, Wilcoxon rank-sum test). Principal coordinate analysis showed clear separation between the two groups, and linear discriminant analysis effect size (LEfSe) method revealed that Bacteroides, Ruminococcus, Coprococcus, and Dorea were significantly lower in the patients with diarrhea. Principal coordinate analysis also showed clear separation between the acute rejection (AR) group (N=3) and the no AR group (N=23) and the LEfSe method revealed significant differences between the two groups. Fecal abundance of Enterococcus was associated with Enterococcus urinary tract infection (UTI). The median Enterococcus fecal abundance was 24% (range, 8%Y95%) in the three patients with Enterococcus UTI compared to 0% in the 23 patients without Enterococcus UTI (interquartile range, 0.00%Y0.08%) (P=0.005, Wilcoxon rank-sum test). Conclusion. Our pilot study identified significant alterations in the gut microbiota after kidney transplantation. Moreover, distinct microbiota structures were observed in allograft recipients with posttransplant diarrhea, AR, and Enterococcus UTI.

Original languageEnglish
Pages (from-to)697-705
Number of pages9
JournalTransplantation
Volume98
Issue number7
DOIs
Publication statusPublished - 15 Oct 2014
Externally publishedYes

Fingerprint

Enterococcus
Kidney Transplantation
Nonparametric Statistics
Diarrhea
Urinary Tract Infections
Discriminant Analysis
Ruminococcus
High-Throughput Nucleotide Sequencing
Proteobacteria
Bacteroides
Microbiota
Allografts
Immune System
Transplantation
Kidney
Polymerase Chain Reaction

Keywords

  • 16s rRNA deep sequencing
  • Acute rejection
  • Diarrhea
  • Gut microbiota
  • Renal transplantation
  • Urinary tract infection

ASJC Scopus subject areas

  • Transplantation

Cite this

Gut microbial community structure and complications after kidney transplantation : A pilot study. / Lee, John R.; Muthukumar, Thangamani; Dadhania, Darshana; Toussaint, Nora C.; Ling, Lilan; Pamer, Eric; Suthanthiran, Manikkam.

In: Transplantation, Vol. 98, No. 7, 15.10.2014, p. 697-705.

Research output: Contribution to journalArticle

Lee JR, Muthukumar T, Dadhania D, Toussaint NC, Ling L, Pamer E et al. Gut microbial community structure and complications after kidney transplantation: A pilot study. Transplantation. 2014 Oct 15;98(7):697-705. https://doi.org/10.1097/TP.0000000000000370
Lee, John R. ; Muthukumar, Thangamani ; Dadhania, Darshana ; Toussaint, Nora C. ; Ling, Lilan ; Pamer, Eric ; Suthanthiran, Manikkam. / Gut microbial community structure and complications after kidney transplantation : A pilot study. In: Transplantation. 2014 ; Vol. 98, No. 7. pp. 697-705.
@article{ed8fc500c3f342b7a60bcc7193a7ff0c,
title = "Gut microbial community structure and complications after kidney transplantation: A pilot study",
abstract = "Background. The gut microbiome plays a role in the regulation of the immune system. Methods. We prospectively enrolled 26 kidney transplant recipients and collected serial fecal specimens (N=85) during the first three months of transplantation. We characterized bacterial composition by polymerase chain reaction amplification of the 16S rRNA V4-V5 variable region and deep sequencing using the Illumina MiSeq platform. Results. An increase in the relative abundance of Proteobacteria was observed in the posttransplantation specimens compared to pretransplantation specimens (P=0.04, Wilcoxon signed-rank test). In patients with posttransplant diarrhea, the mean(Tstandard deviation [SD]) Shannon diversity index was lower in those with diarrhea (N=6) than those without diarrhea (N=9) (2.5T0.3 vs. 3.4T0.8; P = 0.02, Wilcoxon rank-sum test). Principal coordinate analysis showed clear separation between the two groups, and linear discriminant analysis effect size (LEfSe) method revealed that Bacteroides, Ruminococcus, Coprococcus, and Dorea were significantly lower in the patients with diarrhea. Principal coordinate analysis also showed clear separation between the acute rejection (AR) group (N=3) and the no AR group (N=23) and the LEfSe method revealed significant differences between the two groups. Fecal abundance of Enterococcus was associated with Enterococcus urinary tract infection (UTI). The median Enterococcus fecal abundance was 24{\%} (range, 8{\%}Y95{\%}) in the three patients with Enterococcus UTI compared to 0{\%} in the 23 patients without Enterococcus UTI (interquartile range, 0.00{\%}Y0.08{\%}) (P=0.005, Wilcoxon rank-sum test). Conclusion. Our pilot study identified significant alterations in the gut microbiota after kidney transplantation. Moreover, distinct microbiota structures were observed in allograft recipients with posttransplant diarrhea, AR, and Enterococcus UTI.",
keywords = "16s rRNA deep sequencing, Acute rejection, Diarrhea, Gut microbiota, Renal transplantation, Urinary tract infection",
author = "Lee, {John R.} and Thangamani Muthukumar and Darshana Dadhania and Toussaint, {Nora C.} and Lilan Ling and Eric Pamer and Manikkam Suthanthiran",
year = "2014",
month = "10",
day = "15",
doi = "10.1097/TP.0000000000000370",
language = "English",
volume = "98",
pages = "697--705",
journal = "Transplantation",
issn = "0041-1337",
publisher = "Lippincott Williams and Wilkins",
number = "7",

}

TY - JOUR

T1 - Gut microbial community structure and complications after kidney transplantation

T2 - A pilot study

AU - Lee, John R.

AU - Muthukumar, Thangamani

AU - Dadhania, Darshana

AU - Toussaint, Nora C.

AU - Ling, Lilan

AU - Pamer, Eric

AU - Suthanthiran, Manikkam

PY - 2014/10/15

Y1 - 2014/10/15

N2 - Background. The gut microbiome plays a role in the regulation of the immune system. Methods. We prospectively enrolled 26 kidney transplant recipients and collected serial fecal specimens (N=85) during the first three months of transplantation. We characterized bacterial composition by polymerase chain reaction amplification of the 16S rRNA V4-V5 variable region and deep sequencing using the Illumina MiSeq platform. Results. An increase in the relative abundance of Proteobacteria was observed in the posttransplantation specimens compared to pretransplantation specimens (P=0.04, Wilcoxon signed-rank test). In patients with posttransplant diarrhea, the mean(Tstandard deviation [SD]) Shannon diversity index was lower in those with diarrhea (N=6) than those without diarrhea (N=9) (2.5T0.3 vs. 3.4T0.8; P = 0.02, Wilcoxon rank-sum test). Principal coordinate analysis showed clear separation between the two groups, and linear discriminant analysis effect size (LEfSe) method revealed that Bacteroides, Ruminococcus, Coprococcus, and Dorea were significantly lower in the patients with diarrhea. Principal coordinate analysis also showed clear separation between the acute rejection (AR) group (N=3) and the no AR group (N=23) and the LEfSe method revealed significant differences between the two groups. Fecal abundance of Enterococcus was associated with Enterococcus urinary tract infection (UTI). The median Enterococcus fecal abundance was 24% (range, 8%Y95%) in the three patients with Enterococcus UTI compared to 0% in the 23 patients without Enterococcus UTI (interquartile range, 0.00%Y0.08%) (P=0.005, Wilcoxon rank-sum test). Conclusion. Our pilot study identified significant alterations in the gut microbiota after kidney transplantation. Moreover, distinct microbiota structures were observed in allograft recipients with posttransplant diarrhea, AR, and Enterococcus UTI.

AB - Background. The gut microbiome plays a role in the regulation of the immune system. Methods. We prospectively enrolled 26 kidney transplant recipients and collected serial fecal specimens (N=85) during the first three months of transplantation. We characterized bacterial composition by polymerase chain reaction amplification of the 16S rRNA V4-V5 variable region and deep sequencing using the Illumina MiSeq platform. Results. An increase in the relative abundance of Proteobacteria was observed in the posttransplantation specimens compared to pretransplantation specimens (P=0.04, Wilcoxon signed-rank test). In patients with posttransplant diarrhea, the mean(Tstandard deviation [SD]) Shannon diversity index was lower in those with diarrhea (N=6) than those without diarrhea (N=9) (2.5T0.3 vs. 3.4T0.8; P = 0.02, Wilcoxon rank-sum test). Principal coordinate analysis showed clear separation between the two groups, and linear discriminant analysis effect size (LEfSe) method revealed that Bacteroides, Ruminococcus, Coprococcus, and Dorea were significantly lower in the patients with diarrhea. Principal coordinate analysis also showed clear separation between the acute rejection (AR) group (N=3) and the no AR group (N=23) and the LEfSe method revealed significant differences between the two groups. Fecal abundance of Enterococcus was associated with Enterococcus urinary tract infection (UTI). The median Enterococcus fecal abundance was 24% (range, 8%Y95%) in the three patients with Enterococcus UTI compared to 0% in the 23 patients without Enterococcus UTI (interquartile range, 0.00%Y0.08%) (P=0.005, Wilcoxon rank-sum test). Conclusion. Our pilot study identified significant alterations in the gut microbiota after kidney transplantation. Moreover, distinct microbiota structures were observed in allograft recipients with posttransplant diarrhea, AR, and Enterococcus UTI.

KW - 16s rRNA deep sequencing

KW - Acute rejection

KW - Diarrhea

KW - Gut microbiota

KW - Renal transplantation

KW - Urinary tract infection

UR - http://www.scopus.com/inward/record.url?scp=84921384307&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84921384307&partnerID=8YFLogxK

U2 - 10.1097/TP.0000000000000370

DO - 10.1097/TP.0000000000000370

M3 - Article

VL - 98

SP - 697

EP - 705

JO - Transplantation

JF - Transplantation

SN - 0041-1337

IS - 7

ER -