Isoflavones are found almost exclusively in soybeans and soy products. They have been extensively studied for improving health. Better understanding isoflavones bioavailability is also essential compared to their metabolism. Two aspects of isoflavone bioavailability were investigated in this project;Golden Syrian hamsters were investigated to attempt validating this model as relevant to humans for isoflavones bioavailability and their cholesterol lowering effect. Differences between sex (females>males) and isoflavone (genistein>daidzein), similar patterns of urinary excretion between females and women and clustering of animals as high excreters/low degraders and low excreters/high degraders for daidzein and genistein were features shared with humans that may validate hamsters as a model to study isoflavones bioavailability. Cecal but not fecal in vitro daidzein and genistein degradation rates were correlated with urinary excretion levels. Finally, high daidzein, genistein and total isoflavone urinary excretion was associated with lower levels of total cholesterol compared to low excretion;To identify human fecal bacterial species influencing isoflavone disappearance, polymerase chain reaction and denaturing gradient gel electrophoresis allowed qualitative and significantly quantitative profiling of fecal microbial profiles based on each strain's 16S DNA. When comparing gut microbial profiles to in vitro fecal isoflavones disappearance, 7 bands of interest were identified when focusing on intra-individual variability of fecal glycitein degradation over a one month interval. Screening of 33 subjects gave 5 bands of greater intensity in the 4 highest compared to the 4 lowest glycitein degraders, 5 bands for genistein and no bands for daidzein. Sequencing and identification of microorganisms using Basic Local Alignment Search Tool gave matches to Bacteroides, Prevotella and Clostridium species. These strains were investigated using a fecal suspension matrix where nutrient availability was rich (attempting to mimic rapid gut transit time and low degradation rate) or poor (long gut transit time; high degradation rate). Species increasing significantly isoflavones disappearance in both media were B. acidifaciens, T. forsythensis, P. pallens, B. uniformis, E. ramulus and C. orbiscindens. These species were hypothesized to be present all individuals with greater proportions of these strains in high versus low degraders, as reflected by DGGE analysis.