Diversity of the midstream urine microbiome in adults with chronic kidney disease.
Diversity of the midstream urine microbiome in adults with chronic kidney disease.
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DOI：
10.1007/s11255-018-1860-7
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发表时间：
2018-06
影响因子：
2
通讯作者：
Zilliox MJ
中科院分区：
文献类型：
--
作者：
Kramer H;Kuffel G;Thomas-White K;Wolfe AJ;Vellanki K;Leehey DJ;Bansal VK;Brubaker L;Flanigan R;Koval J;Wadhwa A;Zilliox MJ
研究3-5期非透析依赖性慢性肾病（CKD）成人中游尿液微生物组的特征。非透析依赖性CKD（估计肾小球滤过率[eGFR] < 60 ml/min/1.73 m2）和使用利尿剂的患者从门诊肾脏病诊所招募。采用净捕法采集中游空尿标本。通过对细菌16S核糖体RNA基因的高变区（V4）测序来确定细菌的组成。纳入提取阴性对照（无尿），以评估来自可能污染源的外来DNA的贡献。采用逆Simpson、Chao和Shannon指数评价中游尿液微生物组多样性。通过人口统计学特征和合并症进一步检查了多样性措施。尿液样本中检测到细菌DNA的41名女性和36名男性的平均年龄为71.5岁（标准差[SD] 7.9）岁（范围60-91岁）。大多数是白人（68.0%），少数是非裔美国人（29.3%），平均eGFR为27.2 (SD 13.6) ml/min/1.73 m2。大多数男性（72.2%）行包皮环切术，16.6%报告有前列腺癌的早期病史。许多中游尿液标本以棒状杆菌属（n = 11）、葡萄球菌属（n = 9）、链球菌属（n = 7）、乳酸杆菌属（n = 7）、加德纳菌属（n = 7）、普雷沃氏菌属（n = 4）、埃希氏志贺氏菌属（n = 3）和肠杆菌科（n = 2）为主（bbb50 % reads）；其余的缺乏一个优势属。通过逆Simpson指数[7.24 (95% CI 6.76, 7.81)]、Chao指数[558.24 (95% CI 381.70, 879.35)]和Shannon指数[2.60 (95% CI 2.51, 2.69)]测量，样本具有高水平的多样性。在急迫性尿失禁和肾小球滤过率（eGFR）较高的参与者中，多样性指标通常较高。在控制人口统计学和糖尿病状况后，微生物组多样性与估计的eGFR显著相关（P < 0.05）。3-5期非透析依赖型CKD老年人中游空尿微生物组是多种多样的。较高的微生物组多样性与较高的eGFR相关。
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.
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影响因子：
5.7
作者：
Lewis DA;Brown R;Williams J;White P;Jacobson SK;Marchesi JR;Drake MJ
通讯作者：
Drake MJ
影响因子：
7.4
作者：
Fouts DE;Pieper R;Szpakowski S;Pohl H;Knoblach S;Suh MJ;Huang ST;Ljungberg I;Sprague BM;Lucas SK;Torralba M;Nelson KE;Groah SL
通讯作者：
Groah SL
影响因子：
7.2
作者：
Abernethy, Melinda G.;Rosenfeld, Amy;Kenton, Kimberly
通讯作者：
Kenton, Kimberly
影响因子：
30.3
作者：
Gevers D;Kugathasan S;Denson LA;Vázquez-Baeza Y;Van Treuren W;Ren B;Schwager E;Knights D;Song SJ;Yassour M;Morgan XC;Kostic AD;Luo C;González A;McDonald D;Haberman Y;Walters T;Baker S;Rosh J;Stephens M;Heyman M;Markowitz J;Baldassano R;Griffiths A;Sylvester F;Mack D;Kim S;Crandall W;Hyams J;Huttenhower C;Knight R;Xavier RJ
通讯作者：
Xavier RJ
影响因子：
3.7
作者：
Nienhouse V;Gao X;Dong Q;Nelson DE;Toh E;McKinley K;Schreckenberger P;Shibata N;Fok CS;Mueller ER;Brubaker L;Wolfe AJ;Radek KA
通讯作者：
Radek KA