Compositional and functional differences in the human gut microbiome correlate with clinical outcome following infection with wild-type Salmonella enterica serovar Typhi.

Insights into disease susceptibility as well as the efficacy of vaccines against typhoid and other enteric pathogens may be informed by better understanding the relationship between the effector immune response and the gut microbiota. In the present study, we characterized the composition (16S rRNA gene profiling) and function (RNA sequencing [RNA-seq]) of the gut microbiota following immunization and subsequent exposure to wild-type Salmonella enterica serovar Typhi in a human challenge model to further investigate the central hypothesis that clinical outcomes may be linked to the gut microbiota. Metatranscriptome analysis of longitudinal stool samples collected from study subjects revealed two stable patterns of gene expression for the human gut microbiota, dominated by transcripts from either Methanobrevibacter or a diverse representation of genera in the Firmicutes phylum. Immunization with one of two live oral attenuated vaccines against S. Typhi had minimal effects on the composition or function of the gut microbiota. It was observed that subjects harboring the methanogen-dominated transcriptome community at baseline displayed a lower risk of developing symptoms of typhoid following challenge with wild-type S. Typhi. Furthermore, genes encoding antioxidant proteins, metal homeostasis and transport proteins, and heat shock proteins were expressed at a higher level at baseline or after challenge with S. Typhi in subjects who did not develop symptoms of typhoid. These data suggest that functional differences relating to redox potential and ion homeostasis in the gut microbiota may impact clinical outcomes following exposure to wild-type S. Typhi.IMPORTANCES. Typhi is a significant cause of systemic febrile morbidity in settings with poor sanitation and limited access to clean water. It has been demonstrated that the human gut microbiota can influence mucosal immune responses, but there is little information available on the impact of the human gut microbiota on clinical outcomes following exposure to enteric pathogens. Here, we describe differences in the composition and function of the gut microbiota in healthy adult volunteers enrolled in a typhoid vaccine trial and report that these differences are associated with host susceptibility to or protection from typhoid after challenge with wild-type S Typhi. Our observations have important implications in interpreting the efficacy of oral attenuated vaccines against enteric pathogens in diverse populations

Impact of Westernized Diet on Gut Microbiota in Children on Leyte Island

10.3389/fmicb.2017.00197Frontiers in Microbiology8FEB19

Preparation and characterization of tetraalkylammonium selenates and selenites

Boxplot of the top 20 taxa across studies not including the Yatsunenko study. The dark horizontal line represents the mean relative abundance and the box represents the bounds of the 25th and 75th percentiles. (PDF 25 kb

Additional file 13: Figure S8. of Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle

Relative variances explained by the PCoA axes from the PCoA analyses A) Relative variances explained by the PCoA axes used in the Additional file 7: Figure S7ABC. B) Relative variances explained by the PCoA axes used in the adjusted sample plot in Additional file 7: Figure S7D, which had its Bacteroides and Prevotella relative abundances removed. (PDF 4 kb

Additional file 9: Figure S5. of Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle

A) Same PCoA plot using the Bray distance metric as in the main paper, except looking at the 3rd and 4th axis, with samples colored by their most prominent taxa. B) Same MDS plot as in A, but with samples colored based on their value for the Prevotella ratio on a spectrum with red indicating no Prevotella and purple no Bacteroides. C) Same PCoA plot with samples colored based on population of origin. D) PCoA plot using the Bray distance metric with the Bacteroides and Prevotella relative abundances taken out. Colored by most prominent taxa in the samples before the removal of Prevotella and Bacteroides. (PDF 47 kb

Additional file 5: of Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle

RDATAand RMD.tar.gz is a zipped file of all the data and R markdown files to reproduce all the analyses done in the article and is the files can be found at : < http://purl.stanford.edu/fs506ff9976 >. (ZIP 11504 kb

Additional file 1: Figure S1. of Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle

PCoA plots using the Bray distance metric with all the samples in the study colored by the origin of the data. (PDF 39 kb

Additional file 11: Figure S3. of Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle

Prevotella distributions within each population. The x-axis represents the sample quantiles and all the samples are plotted on the same graph. The black line represents all the samples scaled together on the x-axis. The green points are from the Native African vs. African American Ou et al. study, the yellow points are from the Russian Urban vs Rural Tyakht et al. study, the pink points are from the Malawi, Venezuela, US Yatsunenko et al. study, the red points are from the Mixed Europe and Asia Arumugam et al. study, the dark blue points are from the European Arumugam et al. study, and the light blue points are from the NIH Human Microbiome Project study. (PDF 16 kb

A prospective study to examine the association of the urinary and fecal microbiota with prostate cancer diagnosis after transrectal biopsy of the prostate using 16sRNA gene analysis.

INTRODUCTION: There is accumulating evidence that variations in the human microbiota may promote disease states including cancer. Our goal was to examine the association between urinary and fecal microbial profiles and the diagnosis of prostate cancer (PC) in patients undergoing transrectal biopsy of the prostate. MATERIALS AND METHODS: We extracted total DNA from urine and fecal samples collected before a prostate biopsy performed for elevated prostatic specific antigen in patients suspected of having PC. We then amplified the extracted DNA and sequenced it using bacterial 16S rRNA gene high-throughput next-generation sequencing platform, and analyzed microbial profiles for taxonomy comparing those patients diagnosed with PC with those who did not receive that diagnosis. RESULTS: We included 30 patients in our analysis (60 samples, one urine and one fecal per patient). The majority of patients with PC (10/14) had similar bacterial communities within their urinary sample profile and clustered separately than patients without cancer (n = 16). Differential analysis of the operational taxonomical units (OTUs) in urine samples revealed decreased abundance of several bacterial species in patients with prostate cancer. Analysis of the bacterial taxonomies of the fecal samples did not reveal any clustering in concordance with benign or malignant prostate biopsies. Patients who had a Gleason score (GS) of 6 (n = 11) were present in both urine bacterial community clusters, but patients with GS 7 or higher (n = 3) did not cluster tightly with non-cancer subjects. CONCLUSIONS: The urinary microbiota of patients with PC tends to cluster separately from those without this disease. Further research is needed to investigate the urinary microbiome potential of serving as a biomarker that could be used to improve the accuracy of pre-biopsy models predicting the presence of PC in post-biopsy tissue examination