README: Sequence Data of Body Site-Specific Microbiota During Pregnancy

Authors: Reet Mändar, Siiri Kõljalg, Jelena Štšepetova
Affiliation: University of Tartu, Estonia
Corresponding Author: Jelena Štšepetova
Email: jelena.stsepetova@ut.ee

1. Dataset Overview
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The dataset comprises a total of 443 samples collected from 105 pregnant women. It contains sequence data derived from clinical materials, obtained through 16S rRNA gene sequencing of DNA extracted from the following sample types: 85 vaginal, 84 cervical, 105 urine, 85 oral, and 84 rectal samples.

All human and DNA samples are stored in the HUMB collection (Human Microbiome Biobank), which is hosted on the website of the Estonian Electronic Microbial Database (EEMB): http://eemb.ut.ee/eng.
The catalogue of the HUMB collection is available at: https://eemb.ut.ee/humb.

2. Data Type and Format
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Data type: Raw 16S rRNA gene sequencing data
Sequencing platform: Illumina
Target region: V3–V4 region of the bacterial 16S rRNA gene
Read type: Paired-end (R1 and R2)
File format: Compressed FASTQ (.fastq.gz)
Each sample consists of two paired-end FASTQ files.

3. Sample Identification
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Sample AC Nr. – number of sample originating from analysis

Sample types included in the dataset:
C – Cervical
M – Mouth (Oral)
R – Rectal
V – Vaginal
U – Urine

R1 (Read 1): the sequence read from the forward end of the DNA fragment.
R2 (Read 2): the sequence read from the reverse end (the other side) of the same fragment.

4. Citation
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Kõljalg, S., Sepp, E., Štšepetova (Shchepetova), J., Süüden, E.-L., Reimand, T., Jaagura, M., Salumets, A., & Mändar, R. (2025). 
Body site-specific micro- and lactobiota in genitourinary infections during pregnancy [Manuscript submitted for publication]. 
Frontiers in Cellular and Infection Microbiology, Section: Extra-intestinal Microbiome. Manuscript ID: 1657715. 
University of Tartu, Estonia.