ISSN Print 2500–1094
ISSN Online 2542–1204
BIOMEDICAL JOURNAL OF PIROGOV UNIVERSITY (MOSCOW, RUSSIA)
ORIGINAL RESEARCH
Semen microbiota: cluster analysis of real-time PCR data
About authors
1 Ural State Medical University, Yekaterinburg, Russia
2 Medical Center “Garmonia”, Yekaterinburg, Russia
3 Yeltsin Ural Federal University, Yekaterinburg, Russia
4 Krasovskii Institute of Mathematics and Mechanics, Yekaterinburg, Russia
5 Ivanovo State Medical Academy, Ivanovo, Russia
Correspondence should be addressed: Еkaterina S. Voroshilina
Furmanova, 30, Yekaterinburg, 620142; moc.liamg@anilihsorov
About paper
Compliance with ethical standards: the study was approved by the Ethics Committee of Ural State Medical University, Federal State Budget Educational Institution of Higher Education under the Ministry of Health of the Russian Federation (Protocol № 7 of September 20, 2019). All patients signed the informed written consent to participation in the study.
Acknowledgments: the authors would like to thank VN Khayutin, director of "Garmonia" Medical Center, for allowing them to conduct the study in the clinic's laboratory department.
Author contribution: Voroshilina ES — organization of the study, data analysis, article authoring; Zornikov DL — data analysis, article authoring; Ivanov AV — statistical processing, data analysis, article authoring; Pochernikov DG — patients’ clinical profile, clinical data collection, data analysis, article authoring; Panacheva EA — literature review, data analysis, conducting PCR tests, article authoring.
Received: 2020-09-21
Accepted: 2020-10-09
Published online: 2020-10-28
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Fig. 1. Results of cluster analysis of semen microbiota analyzed by means of qPCR (n = 350). The ordinate shows the values of the features in the centroid. Diagrams of the predominant groups of microorganisms are highlighted using red rectangles. Cluster 1 (n = 172; Fig. A) is characterized by the predominance of obligate anaerobes, cluster 2 (n = 78; Fig. B) is characterized by the predominance of Lactobacillus spp., cluster 3 (n = 62; Fig. C) is characterized by the predominance of gram-positive facultative anaerobes, cluster 4 (n = 38; Fig. D) is characterized by the predominance of Enterobacteriaceae spp. / Enterococcus spp.
Fig. 1. Results of cluster analysis of semen microbiota analyzed by means of qPCR (n = 350). The ordinate shows the values of the features in the centroid. Diagrams of the predominant groups of microorganisms are highlighted using red rectangles. Cluster 1 (n = 172; Fig. A) is characterized by the predominance of obligate anaerobes, cluster 2 (n = 78; Fig. B) is characterized by the predominance of lactobacilli, cluster 3 (n = 62; Fig. C) is characterized by the predominance of gram-positive facultative anaerobes, cluster 4 (n = 38; Fig. D) is characterized by the predominance of Enterobacteria / Enterococci
Fig. 2. Results of the cluster stability analysis 1 (A), 2 (B), 3 (C), 4 (D). The grey marker on the graphs shows cluster stability index on a random subsample, the red marker shows the median of the stability indices, calculated for 1000 random subsamples of the ƒ volume, the blue marker shows the cluster stability index on a set of the ƒ volume
Table 1. Detection rate for individual MO groups present in quantities exceeding the threshold value (n = 634)*
Note: * — for Ureaplasma urealyticum, Ureaplasma parvum, Mycoplasma hominis threshold is > 0, for the other MO groups threshold is ≥ 103 GE/ml.
Table 2. Clustering quality values
