Application of the next generation sequencing (NGS) method in the study of the microbiota of the female reproductive tract
Katarzyna Biegun, k.biegun@uj.edu.pl, Department of Microbiology, Department of Molecular Medical Microbiology, Jagiellonian University Collegium Medicum
Agnieszka Sroka-Oleksiak, agnieszka.sroka@uj.edu.pl, Department of Microbiology, Department of Molecular Medical Microbiology, Jagiellonian University Collegium Medicum
Wojciech Pabian, mopabian@cyfronet.pl, Clinical Department of Gynecological Endocrinology and Gynecology, Jagiellonian University Collegium Medicumm, Epimedium - infertility clinic in Krakow, Poland
Artur Gurgul, artur.gurgul@urk.edu.pl, Center for Experimental and Innovative Medicine, University of Agriculture
Monika Brzychczy-Włoch, m.brzychczy-wloch@uj.edu.pl, Department of Microbiology, Department of Molecular Medical Microbiology, Jagiellonian University Collegium Medicum
Next-generation sequencing technology has revolutionized the current study of the human microbiome. Ongoing work is aimed at determining the profile of the microbiota in a state of homeostasis as well as searching for markers in the course of various diseases. In the case of the vaginal microbiota, changes in its qualitative and quantitative composition can lead to serious consequences, especially in pregnant women and the developing fetus.
The purpose of this study was to evaluate the usefulness of the NGS method in studying the vaginal microbiota of pregnant women.
The study included a group of 100 patients (Consent of the Bioethics Committee KBET/1072.6120.51.2017). Bacterial DNA was isolated and amplified from collected vaginal swabs, from which a genomic library was prepared for next-generation sequencing in the MiSeq platform (Illumina).
Bacteria belonging to the Firmicutes type (93.02%) were predominant in all samples tested. The remaining bacteria belonged to the Actinobacteria (3.71%), Bacteroidetes (2.35%) and Proteobacteria (0.92%) types. Within the Firmicutes type, the vast majority were bacteria belonging to the genus Lactobacillus (L. gasseri - 37.11% and L. iners - 34.96%). In contrast, bacteria of a potentially pathogenic nature from the genus Streptococcus accounted for only 0.95%.
NGS sequencing makes it possible to analyze the composition of the microbiota, but has not yet been introduced into routine microbial diagnostics due to the lack of standardized protocols for bioinformatics analysis, which, depending on the databases used, can provide different results for species identification.
Funding from NCBR TANGO2/340018/NCBR/2017.