Browsing by Author "Bagheri, Sahar"

Now showing 1 - 2 of 2
  • Thumbnail Image
    ItemOpen Access
    Improved Resolution of Prevotella Species, Strains and Genes Reveals TheirDiversity and Virulence Potential in the Female Genital Tract
    (2021-01-29) Bagheri, Sahar; Sycuro, Laura K; Poissant, Jocelyn; Devinney, Rebekah; Lynch, Tarah; Geuking, Markus B
    Bacteria belonging to the genus Prevotella inhabit numerous human body sites, including the female genital tract. Although Prevotella species commonly, and often benignly colonize the vagina, their increased abundance is associated with the dysbiotic condition bacterial vaginosis (BV). Prevotella isolates are also routinely cultured from women experiencing upper genital tract infection and the genus has repeatedly been associated with preterm birth, but the ascending species and mechanisms involved are poorly understood. I developed a new bioinformatics tool that enabled me to ask, for the first time, whether genital Prevotella species encode the Type IX Secretion System, a feature that could contribute to their niche adaptation and virulence (Chapter II). The other objective of my thesis was to better define the phylogenetic breadth and genomic heterogeneity of Prevotella species that colonize the female genital tract. I sought to advance our understanding of how Prevotella impacts human pregnancy by: 1) Identifying the most prevalent and abundant Prevotella species in the lower vs. upper female genital tract; and 2) Performing the first comparative genomics study of the two most common vaginal Prevotella species, P. bivia and P. amnii, which have both been associated with preterm birth. I undertook these analyses using a multidisciplinary approach that included a systematic literature review (Chapter III), pangenome analysis (Chapter III), and a bioinformatics meta-analysis of 19 published microbiome datasets (Chapter IV). My research showed that genital Prevotella populations are much more diverse than previously appreciated, although relatively few genital Prevotella species were consistently detected in high abundance across cohorts. The correlated distribution of Prevotella species prevalence in the lower and upper genital tract suggests they may translocate via broadly conserved or passive mechanisms.The two most prevalent and closely related genital tract Prevotella species are genomically and functionally heterogeneous. Their distinct evolutionary history, driven by horizontal gene transfer and genome reduction, reflects both acquisition and loss of genes involved in evasion, adaptation, and niche partitioning. By expanding our understanding of genital Prevotella species diversity, and establishing parameters for their sensitive and specific detection, this work lays the foundation for future studies that will define the predictive and causal roles these enigmatic bacteria play in reproductive health.
  • Thumbnail Image
    ItemOpen Access
    Noninvasive sampling of the small intestinal chyme for microbiome, metabolome and antimicrobial resistance genes in dogs, a proof of concept
    (2023-12-16) Menard, Julie; Bagheri, Sahar; Menon, Sharanya; Yu, Y. T.; Goodman, Laura B.
    Abstract Background The gastrointestinal microbiome and metabolome vary greatly throughout the different segments of the gastrointestinal tract, however current knowledge of gastrointestinal microbiome and metabolome in health and disease is limited to fecal samples due to ease of sampling. The engineered Small Intestinal MicroBiome Aspiration (SIMBA™) capsule allows specific sampling of the small intestine in humans. We aimed to determine whether administration of SIMBA™ capsules to healthy beagle dogs could reliably and safely sample the small intestinal microbiome and metabolome when compared to their fecal microbiome and metabolome. Results Eleven beagle dogs were used for the study. Median transit time of capsules was 29.93 h (range: 23.83–77.88). Alpha diversity, as measured by the Simpson diversity, was significantly different (P = 0.048). Shannon diversity was not different (P = 0.114). Beta diversity results showed a significant difference between capsule and fecal samples regarding Bray–Curtis, weighted and unweighted unifrac (P = 0.002) and ANOSIM distance metric s (R = 0.59, P = 0.002). In addition to observing a statistically significant difference in the microbial composition of capsules and feces, distinct variation in the metabolite profiles was seen between the sample types. Heat map analysis showed 16 compounds that were significantly different between the 2 sampling modes (adj-P value ranged between 0.004 and 0.036) with 10 metabolites more abundant in the capsule than in the feces and 6 metabolites more abundant in the feces compared to the capsules. Conclusions The engineered Small Intestinal MicroBiome Aspiration (SIMBA™) capsule was easy and safe to administer to dogs. Microbiome and metabolome analysis from the capsule samples were significantly different than that of the fecal samples and were like previously published small intestinal microbiome and metabolome composition. Graphical abstract