| Title |
Diversity of the midstream urine microbiome in adults with chronic kidney disease
|
|---|---|
| Published in |
Geriatric Nephrology and Urology, April 2018
|
| DOI | 10.1007/s11255-018-1860-7 |
| Pubmed ID | |
| Authors |
Holly Kramer, Gina Kuffel, Krystal Thomas-White, Alan J. Wolfe, Kavitha Vellanki, David J. Leehey, Vinod K. Bansal, Linda Brubaker, Robert Flanigan, Julia Koval, Anuradha Wadhwa, Michael J. Zilliox |
| Abstract |
To examine the characteristics of the midstream urine microbiome in adults with stage 3-5 non-dialysis-dependent chronic kidney disease (CKD). Patients with non-dialysis-dependent CKD (estimated glomerular filtration rate [eGFR] < 60 ml/min/1.73 m2) and diuretic use were recruited from outpatient nephrology clinics. Midstream voided urine specimens were collected using the clean-catch method. The bacterial composition was determined by sequencing the hypervariable (V4) region of the bacterial 16S ribosomal RNA gene. Extraction negative controls (no urine) were included to assess the contribution of extraneous DNA from possible sources of contamination. Midstream urine microbiome diversity was assessed with the inverse Simpson, Chao and Shannon indices. The diversity measures were further examined by demographic characteristics and by comorbidities. The cohort of 41 women and 36 men with detectable bacterial DNA in their urine samples had a mean age of 71.5 years (standard deviation [SD] 7.9) years (range 60-91 years). The majority were white (68.0%) and a substantial minority were African-American (29.3%) The mean eGFR was 27.2 (SD 13.6) ml/min/1.73 m2. Most men (72.2%) were circumcised and 16.6% reported a remote history of prostate cancer. Many midstream voided urine specimens were dominated (> 50% reads) by the genera Corynebacterium (n = 11), Staphylococcus (n = 9), Streptococcus (n = 7), Lactobacillus (n = 7), Gardnerella (n = 7), Prevotella (n = 4), Escherichia_Shigella (n = 3), and Enterobacteriaceae (n = 2); the rest lacked a dominant genus. The samples had high levels of diversity, as measured by the inverse Simpson [7.24 (95% CI 6.76, 7.81)], Chao [558.24 (95% CI 381.70, 879.35)], and Shannon indices [2.60 (95% CI 2.51, 2.69)]. Diversity measures were generally higher in participants with urgency urinary incontinence and higher estimated glomerular filtration rate (eGFR). After controlling for demographics and diabetes status, microbiome diversity was significantly associated with estimated eGFR (P < 0.05). The midstream voided urine microbiome of older adults with stage 3-5 non-dialysis-dependent CKD is diverse. Greater microbiome diversity is associated with higher eGFR. |
X Demographics
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Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 1 | 100% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 1 | 100% |
Mendeley readers
The data shown below were compiled from readership statistics for 94 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 94 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 14 | 15% |
| Student > Ph. D. Student | 13 | 14% |
| Other | 10 | 11% |
| Student > Master | 10 | 11% |
| Student > Doctoral Student | 7 | 7% |
| Other | 16 | 17% |
| Unknown | 24 | 26% |
| Readers by discipline | Count | As % |
|---|---|---|
| Medicine and Dentistry | 27 | 29% |
| Biochemistry, Genetics and Molecular Biology | 12 | 13% |
| Agricultural and Biological Sciences | 5 | 5% |
| Immunology and Microbiology | 5 | 5% |
| Veterinary Science and Veterinary Medicine | 4 | 4% |
| Other | 12 | 13% |
| Unknown | 29 | 31% |
Attention Score in Context
This research output has an Altmetric Attention Score of 93. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 15 May 2018.
All research outputs
#456,538
of 25,382,440 outputs
Outputs from Geriatric Nephrology and Urology
#8
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Outputs of similar age
#10,384
of 343,384 outputs
Outputs of similar age from Geriatric Nephrology and Urology
#1
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So far Altmetric has tracked 1,493 research outputs from this source. They receive a mean Attention Score of 4.8. This one has done particularly well, scoring higher than 99% of its peers.
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