Selective decontamination of the digestive tract (SDD) is aimed at elimination of potential pathogenic microorganisms. In this study, the effect of SDD on gut microbiota was evaluated in a large homogenous group of elective colorectal cancer surgery patients. Rectal swabs were taken from 118 patients undergoing colorectal surgery. These patients were randomly assigned to receive perioperative SDD or to the control group (no SDD). Rectal swabs were taken prior to surgery, 3 days after commencing administration of SDD. Gut microbial profiles were obtained with the IS-pro technique, a standardized microbiota profiling assay applicable in clinical routine. Differences in abundance for different taxonomical groups and diversity between the groups were assessed. Unsupervised and supervised classification techniques were used to assess microbial signatures, differentiating between the SDD group and the control group. Patients in the SDD group had different gut microbial signatures than in the control group, also in phyla that are not a target for SDD. Escherichia coli, Sutterella spp., Faecalibacterium prausnitzii, and Streptococcus spp. were the species that differed the most between the two groups. The SDD group showed clustering into two subgroups. In one subgroup, a decrease in Proteobacteria was observed, whereas the other subgroup showed a shift in Proteobacteria species. This study shows that SDD not only decreases colonization of the gastrointestinal tract with potential pathogenic Gram-negative microorganisms, but also reduces the abundance of normal colonizers of our gastrointestinal system and leads to a shift in total microbiota composition.

Background Genital infections burden and frequency of detrimental, non-Lactobacillus dominated vaginal microbiota (VMB) are high in sub-Saharan Africa. In countries such as Tanzania these challenges overlap with, and possibly contribute to, maternal complications. Objectives This study reported on prevalence of common, and often curable, Chlamydia trachomatis (CT), Neisseria gonorrhea (NG), Trichomonas vaginalis (TV), Mycoplasma genitalium (MG), human papillomavirus (HPV) infections, and on VMB composition among pregnant and post-delivery women in Pemba Island, Tanzania. Methods Vaginal swabs were collected at two timepoints during pregnancy and once after delivery by Pemba Biobank. Molecular assays were used to detect HPV, CT, NG, TV, and MG in samples from 438 individual women. IS-pro kit was used to characterize the VMB in a subset of women (n=90) based on 16S-23S rDNA interspacer region length. VMB were defined based on dominant species. Shannon diversity index, for number (richness) and relative abundance of species, was calculated and Mann-Whitney test used for analysis. Results In samples from 20.5% of the women, at least one pathogen was detected. Infection with HPV was the most prevalent (10.3%), followed by TV (7.1%), CT (4.6%), MG (2.1%), and NG (0%). The most common VMB were Lactobacillus-dominant during pregnancy (77% at first, and 81% at second timepoint), and non-Lactobacillus-dominant (73.9%) postdelivery. The Shannon diversity was lower during pregnancy than postdelivery (p=0.03). A decrease in VMB richness (p=0.02) was observed during pregnancy. Klebsiella species and Streptococcus anginosus were the most common microorganisms with pathogenic potential (pathobionts) at all timepoints. A high abundance of pathobionts was seen in women with non-Lactobacillus-dominant VMB. At second timepoint during pregnancy, 67% of the women carrying a genital pathogen had Lactobacillus iners-dominant VMB. Conclusion This study contributes knowledge on VMB composition and its changes during pregnancy and post-delivery, as well as simultaneous presence of pathobionts and genital pathogens.

Background 16S rRNA gene sequencing is currently the most common way of determining the composition of microbiota. This technique has enabled many new discoveries to be made regarding the relevance of microbiota to the health and disease of the host. However, compared to other diagnostic techniques, 16S rRNA gene sequencing is fairly costly and labor intensive, leaving room for other techniques to improve on these aspects. Results The current study aimed to compare the output of 16S rRNA gene sequencing to the output of the quick IS-pro analysis, using vaginal swab samples from 297 women of reproductive age. 16S rRNA gene sequencing and IS-pro analyses yielded very similar vaginal microbiome profiles, with a median Pearson's R-2 of 0.97, indicating a high level of similarity between both techniques. Conclusions We conclude that the results of 16S rRNA gene sequencing and IS-pro are highly comparable and that both can be used to accurately determine the vaginal microbiota composition, with the IS-pro analysis having the benefit of rapidity.

The authors of the above article would like to apologise for errors in Figure 3 of their article. An old version of the figure file image was uploaded by the authors, with sub-sections A, B, C and D rearranged. The correct version of Figure 3 is included overpage. The electronic version of this article has been updated at https://doi.org/10.1093/humrep/dez065. The authors would liketo assure readers that this does not affect any content of the article. (Figure Presented).

The authors of the above article would like to apologise for errors in Figure 3 of their article. An old version of the figure file image was uploaded by the authors, with sub-sections A, B, C and D rearranged. The correct version of Figure 3 is included overpage. The electronic version of this article has been updated at https://doi.org/10.1093/humrep/dez065. The authors would liketo assure readers that this does not affect any content of the article. (Figure Presented).