Alpha-diversity and microbial community structure of the male urinary microbiota depend on urine sampling method.
Alpha-diversity and microbial community structure of the male urinary microbiota depend on urine sampling method.
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DOI：
10.1038/s41598-021-03292-x
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发表时间：
2021-12-09
影响因子：
4.6
通讯作者：
Zachoval R
中科院分区：
文献类型：
--
作者：
Hrbacek J;Morais D;Cermak P;Hanacek V;Zachoval R
迄今为止发表的尿液微生物群研究方法存在相当大的差异，包括任何生物医学分析的基石：样本收集。本研究的目的是比较男性首次收集的排尿（FCU）、中段排尿（MSU）和无菌导尿的尿液微生物群，并确定最合适的尿液采样方法。49例接受内镜泌尿外科手术的男性（平均年龄71.3岁）入组研究。每个人都贡献了三个样本：首尿（FCU），中段尿（MSU）和导尿管尿样。对样本进行下一代测序（NGS，n = 35）和扩增定量尿培养（EQUC，n = 31）。使用NGS，拟杆菌门，厚壁菌门和变形菌门是我们人群中最丰富的门。最丰富的属（按相对丰度顺序）包括：普雷沃菌属、韦荣氏球菌属、链球菌属、卟啉单胞菌属、弯曲杆菌属、假单胞菌属、葡萄球菌属、Ezakiella、埃希氏菌属和小杆菌属。105个样品中有82个是由一个单一的属。FCU、MSU和导尿管尿液样本在五个α多样性指标中的三个指标（ANOVA，p < 0.05）中存在显著差异：操作分类单位的估计数量、Chao 1和基于丰度的覆盖率估计值。使用PIME方法（微生物组评价的流行区间）进行β多样性比较，根据采样模式对尿液样本进行聚类。EQUC在30/31（97%）FCU和27/31（87%）MSU样本中检出可培养细菌。只有4/31（13%）的导尿管尿液样本显示细菌生长。在无菌条件下经尿道导尿获得的尿样似乎与自发排尿的尿样不同。更准确反映膀胱微生物群无尿道污染的附加值是否超过尿道导管插入的侵入性仍有待确定。
Considerable variation exists in the methodology of urinary microbiota studies published so far including the cornerstone of any biomedical analysis: sample collection. The aim of this study was to compare the urinary microbiota of first-catch voided urine (FCU), mid-stream voided urine (MSU) and aseptically catheterised urine in men and define the most suitable urine sampling method. Forty-nine men (mean age 71.3 years) undergoing endoscopic urological procedures were enrolled in the study. Each of them contributed three samples: first-catch urine (FCU), mid-stream urine (MSU) and a catheterised urine sample. The samples were subjected to next-generation sequencing (NGS, n = 35) and expanded quantitative urine culture (EQUC, n = 31). Using NGS, Bacteroidetes, Firmicutes, and Proteobacteria were the most abundant phyla in our population. The most abundant genera (in order of relative abundance) included: Prevotella, Veillonella, Streptococcus, Porphyromonas, Campylobacter, Pseudomonas, Staphylococcus, Ezakiella, Escherichia and Dialister. Eighty-two of 105 samples were dominated by a single genus. FCU, MSU and catheterised urine samples differed significantly in three of five alpha-diversity measures (ANOVA, p < 0.05): estimated number of operational taxonomic units, Chao1 and abundance-based coverage estimators. Beta-diversity comparisons using the PIME method (Prevalence Interval for Microbiome Evaluation) resulted in clustering of urine samples according to the mode of sampling. EQUC detected cultivable bacteria in 30/31 (97%) FCU and 27/31 (87%) MSU samples. Only 4/31 (13%) of catheterised urine samples showed bacterial growth. Urine samples obtained by transurethral catheterisation under aseptic conditions seem to differ from spontaneously voided urine samples. Whether the added value of a more exact reflection of the bladder microbiota free from urethral contamination outweighs the invasiveness of urethral catheterisation remains to be determined.
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