Fig 1. T-RFLP-based comparison of the vaginal and uterine microbiomes of healthy cows postpartum.

PCR amplicons of the 16S rRNA were obtained from DNA samples using primers 6-FAM-labeled 27F and 1052R and digested with MspI restriction enzyme. Fluorescently labeled terminal restriction fragments (TRFs) were resolved in an ABI 3730xl genetic analyzer (Applied Biosystems). GeneScan Liz 600 size standard was used for fragment sizing using GeneMapper v4.0 (Applied Biosystems). Operational Taxonomic Units (OTUs) were assigned in T-Align from TRFs representing at least 0.5% of the total signal and consistently found in duplicated samples. A) Heat map representing community profiles obtained from postpartum vaginal (N = 47) and uterine (N = 47) samples. The profile of each sample (rows) is populated by OTUs of varying lengths (columns). The relative abundance of the OTUs in a given profile is indicated by the colour key on the top where black and red represent the lowest and highest values and the midpoint (yellow) was set as the 95 percentile. The heat map was produced in Excel 2010 using the conditional formatting function and subsequently imported as image into CorelDraw X4. B) Distribution of OTUs in the reproductive tract of healthy cows postpartum. Black, vagina; Red, uterus. The regions marked on top show the contribution of OTUs to the total number of observed OTUS. i, 50%; m, 40%; s, 10%. C) Network showing high frequency OTUs (green circles) present in both vaginal (black triangles) and uterine (red circles) samples. OTUs and samples are connected through edges. The size of the green circles represents the OTU frequency among sampled animals. Samples with higher number of connections are displayed closer to the OTUs. D) Ordination of samples by non-metric multidimensional scaling (nMDS) based on the Bray-Curtis resemblance of the samples. Vaginal and uterine samples are represented by black triangles and red circles, respectively.