The impact of urine collection method on canine urinary microbiota detection: a cross-sectional study.
The impact of urine collection method on canine urinary microbiota detection: a cross-sectional study.
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DOI：
10.1186/s12866-023-02815-y
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发表时间：
2023-04-13
期刊：
影响因子：
4.2
通讯作者：
Furrow, Eva
中科院分区：
文献类型：
--
作者：
Coffey, Emily L.;Gomez, Andres M.;Ericsson, Aaron C.;Burton, Erin N.;Granick, Jennifer L.;Lulich, Jody P.;Furrow, Eva
泌尿道内有独特的微生物群落，在泌尿生殖系统健康和疾病中起着重要作用。狗自然患有与人类相同的几种泌尿系统疾病（例如，尿路感染、肿瘤形成、尿石症），并且代表了用于研究尿微生物群在各种疾病状态中的作用的有价值的转化模型。尿液采集技术是尿液微生物群研究设计的关键组成部分。然而，收集方法对犬尿液微生物群表征的影响仍然未知。因此，本研究的目的是确定尿液采集技术是否会改变犬尿液样本中检出的微生物种群。通过膀胱穿刺术和中段排尿采集无症状犬的尿液。从每份样本中分离微生物DNA，并提交细菌16 S rRNA基因V4区的扩增子测序，然后进行分析，以比较尿液采集技术之间的微生物多样性和组成。与膀胱穿刺术尿液相比，通过中段排尿收集的样本显示出显著更高的序列读数计数（P = .036）和观察到的丰富度（P = .0024）。Bray Curtis和Unweighted UniFrac的β多样性测量结果显示，不同采集方法的微生物组成存在明显差异（分别为P = .0050，R2 = 0.06和P = .010，R2 = 0.07）。七个分类群被确定为组之间的差异丰富。巴氏杆菌科，嗜血杆菌，Friedmanniella，链球菌的两个变种，梭杆菌在排尿中过度代表，而更丰富的伯克霍尔德氏菌-Caballeronia-副伯克霍尔德氏菌特征膀胱穿刺样本。在最小序列深度的五个阈值下进行分析，并使用三种数据标准化策略来验证结果;无论最小读取计数要求或标准化方法如何，α和β多样性的模式保持一致。通过膀胱穿刺收集的犬尿液样本中的微生物组成与通过中段排尿收集的样本不同。未来的研究人员在设计犬尿微生物群研究时，应根据感兴趣的生物学问题选择单一的尿液收集方法。此外，作者建议在解释未使用相同尿液采集方法的研究结果时应谨慎。在线版本包含补充材料，可通过10.1186/s12866-023-02815-y获得。
The urinary tract harbors unique microbial communities that play important roles in urogenital health and disease. Dogs naturally suffer from several of the same urological disorders as humans (e.g., urinary tract infections, neoplasia, urolithiasis) and represent a valuable translational model for studying the role of urinary microbiota in various disease states. Urine collection technique represents a critical component of urinary microbiota research study design. However, the impact of collection method on the characterization of the canine urinary microbiota remains unknown. Therefore, the objective of this study was to determine whether urine collection technique alters the microbial populations detected in canine urine samples. Urine was collected from asymptomatic dogs by both cystocentesis and midstream voiding. Microbial DNA was isolated from each sample and submitted for amplicon sequencing of the V4 region of the bacterial 16 S rRNA gene, followed by analyses to compare microbial diversity and composition between urine collection techniques. Samples collected via midstream voiding exhibited significantly higher sequence read counts (P = .036) and observed richness (P = .0024) than cystocentesis urine. Bray Curtis and Unweighted UniFrac measures of beta diversity showed distinct differences in microbial composition by collection method (P = .0050, R2 = 0.06 and P = .010, R2 = 0.07, respectively). Seven taxa were identified as differentially abundant between groups. Pasteurellaceae, Haemophilus, Friedmanniella, two variants of Streptococcus, and Fusobacterium were over-represented in voided urine, while a greater abundance of Burkholderia-Caballeronia-Paraburkholderia characterized cystocentesis samples. Analyses were performed at five thresholds for minimum sequence depth and using three data normalization strategies to validate results; patterns of alpha and beta diversity remained consistent regardless of minimum read count requirements or normalization method. Microbial composition differs in canine urine samples collected via cystocentesis as compared to those collected via midstream voiding. Future researchers should select a single urine collection method based on the biological question of interest when designing canine urinary microbiota studies. Additionally, the authors suggest caution when interpreting results across studies that did not utilize identical urine collection methods. The online version contains supplementary material available at 10.1186/s12866-023-02815-y.
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影响因子：
15.5
作者：
Cuscó A;Belanger JM;Gershony L;Islas-Trejo A;Levy K;Medrano JF;Sánchez A;Oberbauer AM;Francino O
通讯作者：
Francino O
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Hrbacek J;Morais D;Cermak P;Hanacek V;Zachoval R
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影响因子：
4.7
作者：
García-Fonticoba R;Ferrer L;Francino O;Cuscó A
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影响因子：
3.5
作者：
Estrada-de Los Santos P;Palmer M;Chávez-Ramírez B;Beukes C;Steenkamp ET;Briscoe L;Khan N;Maluk M;Lafos M;Humm E;Arrabit M;Crook M;Gross E;Simon MF;Dos Reis Junior FB;Whitman WB;Shapiro N;Poole PS;Hirsch AM;Venter SN;James EK
通讯作者：
James EK
影响因子：
48
作者：
Callahan BJ;McMurdie PJ;Rosen MJ;Han AW;Johnson AJ;Holmes SP
通讯作者：
Holmes SP