<p>The Food Processing and Postharvest Handling Innovation Lab (FPIL) project seeks to reduce food loss and link up consumers with food-to-food fortified instant products that are enriched with micronutrient sources that target vitamin A, zinc, and iron deficiencies. These are mostly maize-based products, but may be combined with other cereals, such as sorghum, and pseudocereals, such as amaranth. The general goal of this thesis study was to facilitate the adoption of extrusion technology to process instant flours, assess the acceptance and willingness to pay (WTP) for these products, and to assess the health impacts of the products on gut health. A low-cost, single-screw extruder was used that was developed at Purdue, and has been placed in different locations in Africa country study sites. The first study aimed to optimize process conditions of a low-cost single-screw extruder, currently done at 35% feed moisture, for African small- to medium-scale entrepreneurs to produce good quality and low-cost pregelatinized instant pearl millet porridge flours and other whole grains by relating feed moisture (27, 29, 31, 33, and 35%) to extrusion energy, drying time and physicochemical properties. We found that we could lower the feed moisture to 27% and still attain good pasting profiles of the porridges, reduce drying time, have better expansion of the extrudates, obtain increased <i>L</i>* color values of the flours, and with a higher extrusion energy but lower drying time. In conclusion, the single screw extruder can be efficiently operated at 27% feed moisture compared to the currently used 35% feed moisture and obtain instant flours with desired quality. It is not known whether higher extrudate energy consumption may be offset by the lower drying time representing lower drying energy. In the second study, we investigated extrusion enhance <i>in vitro</i> fecal fermentation of maize bran, which has been characterized by a poor gut microbiota fermentation property due to its highly crosslinked and densely branched arabinoxylan chemical structure, making it poorly available to the gut microbiota. We hypothesized that this dense cell wall matrix can be opened for better fermentation by applying extrusion. Test conditions of a twin-screw extruder at Purdue were low (200 RPM) and high (400 RPM) shear rates applied to a maize meal and bran mixture (60:40) at different feed moisture conditions (20, 25, 30%). <i>In vitro</i> fermentation of test materials was conducted on stool samples from three donors. Extrusion increased total short chain fatty acids and produced individualized donor effects on the gut microbiota. Some extruder test condition effects were observed on certain bacteria. For example, extrusion at 30% feed moisture and 400 RPM tended to increase genera of <i>Subdoligranulum</i> and <i>Eubacterium hallii</i> and <i>Ruminococcus</i> <i>torques</i> groups in Donor 1 compared to non-extruded bran. There was also a trend of increase in <i>Subdoligranulum</i> and <i>Blautia</i> in extruded compared to non-extruded bran in Donor 2. In Donor 3, <i>Lachnospiraceae NK4A136</i> group was increased at 20 and 25% feed moistures at 200 RPM and 30% feed moisture at 400 RPM compared to non-extruded bran. In the final study, we investigated the acceptance and WTP for instant fortified flours using the Becker-DeGroot-Marschak mechanism when consumers are incrementally given nutrition information and demonstration how to reconstitute instant flours. This study was conducted in Eldoret, Kenya. Participants preferred the fortified thick porridge higher in maize content than fortified thin porridge prepared from the same blend. Contrarily, thin porridge made from fortified flour with higher sorghum content was ranked more highly than for the corresponding thick porridge. Participants were willing to pay more for instant fortified products higher in sorghum when given product name and nutrient composition, even without a practical demonstration of how to reconstitute the flours. For the instant product higher in maize, consumers needed demonstration of how to reconstitute the instant flour for them pay a higher premium. These findings suggest that food-to-food fortified instant porridge flours have the potential to be adopted and can be used as a vehicle to deliver micronutrients to these populations and that extrusion somewhat enhances fermentation of whole grain fibers by the gut microbiome.</p>

<p>Consumption of soy foods has been shown to provide beneficial health outcomes such as reduction of menopause symptoms, reduced risk of breast cancer and prostate cancer, improved cardiovascular health, and improved bone health. The mechanism hypothesized to be driving these outcomes is the conversion of the soy isoflavone daidzein into the metabolite equol by bacteria in the gut microbiome. Equol is an exclusively microbially produced metabolite with a high binding affinity to mammalian estrogen receptors. Not all humans harbor equol-producing microbes in their gut, and less than half of the population can be classified as equol producers. To date, soy feeding research published suffers from confounding factors that make assessing the causal impact of equol production in health difficult due to: (i) large interpersonal variation of the human microbiome and human genomes and that (ii) all lab-raised rodent models harboring natural microbiomes are highly efficient equol producers. In this study, we sought to establish a gnotobiotic mouse model harboring synthetic bacterial communities with divergent equol-producing capacities by designing two communities: the Equol(-) community and Equol(+) community. The Equol(-) community was designed to include ten bacterial strains commonly found within a human microbiome without equol-producing capacity<em>.</em> To create the Equol(+) community, the equol-producing bacteria <em>Adlercreutzia equolifaciens</em> was added to the Equol(-) community<em>.</em> Female and male germ-free C57BL/6 mice were colonized with either the Equol(-) or Equol(+) community for 4 weeks. Daidzein was administered by dietary supplementation (1.5% wt/wt daidzein) in a semi-purified diet containing fermentable fiber starting two weeks prior to bacterial colonization. As expected, equol was detected in the serum of mice colonized with the Equol(+) community, but not detectable in those colonized with the Equol(-) community. There were no sex differences detected in equol production. 16S rRNA gene sequencing of mouse cecal content revealed that ~50-80% of the strains from each community colonized within the mice at detectable levels. Strain-specific qPCR improved the detection of strains not observed consistently through 16S rRNA gene sequencing. Our results demonstrated that this model is reliable in producing the expected equol producing and non-equol producing phenotypes when colonized with the Equol(+) and Equol(-) communities, respectively. This model system can be utilized in a broad range of future studies to conclusively determine the causal impact of endogenous equol production in many areas, such as cardiometabolic health and bone health.</p>

Microbiome plays an important role in human health. The analysis of association between microbiome and clinical outcome has become an active direction in biostatistics research. Testing the microbiome effect on clinical phenotypes directly using operational taxonomic unit abundance data is a challenging problem due to the high dimensionality, non-normality and phylogenetic structure of the data. Most of the studies only focus on describing the change of microbe population that occur in patients who have the specific clinical condition. Instead, a statistical strategy utilizing distance-based or similarity-based non-parametric testing, in which a distance or similarity measure is defined between any two microbiome samples, is developed to assess association between microbiome composition and outcomes of interest. Despite the improvements, this test is still not easily interpretable and not able to adjust for potential covariates. A novel approach, kernel-based semi-parametric regression framework, is applied in evaluating the association while controlling the covariates. The framework utilizes a kernel function which is a measure of similarity between samples' microbiome compositions and characterizes the relationship between the microbiome and the outcome of interest. This kernel-based regression model, however, cannot be applied in longitudinal studies since it could not model the correlation between the repeated measurements. We proposed microbiome association exact tests (MAETs) in linear mixed model can deal with longitudinal microbiome data. MAETs can test not only the effect of overall microbiome but also the effect from specific cluster of the OTUs while controlling for others by introducing more random effects in the model. The current methods for multiple variance component testing are based on either asymptotic distribution or parametric bootstrap which require large sample size or high computational cost. The exact (R)LRT tests, an computational efficient and powerful testing methodology, was derived by Crainiceanu. Since the exact (R)LRT can only be used in testing one variance component, we proposed an approach that combines the recent development of exact (R)LRT and a strategy for simplifying linear mixed model with multiple variance components to a single case. The Monte Carlo simulation studies present correctly controlled type I error and provided superior power in testing association between microbiome and outcomes in longitudinal studies. Finally, the MAETs were applied to longitudinal pulmonary microbiome datasets to demonstrate that microbiome composition is associated with lung function and immunological outcomes. We also successfully found two interesting genera Prevotella and Veillonella which are associated with forced vital capacity.

<p>  </p> <p>Plant roots form an intimate relationship with a diversity of soil microorganisms. Some soil-borne microbes cause harmful diseases on crops, but others promote plant growth and enhance host resilience against stressors. Beneficial bacteria have a high potential as a strategy for sustainable agricultural management, many of which have been recognized and commercialized for improving crop growth. Unfortunately, field inoculants of beneficial bacteria often give inconsistent results due to various environmental factors hindering their beneficial properties. Improving crop production utilizing beneficial bacteria requires two approaches: 1) breeding for crops with the enhanced association for beneficial bacteria and 2) improving formulation methods for producing more potent microbial products. To contribute to these goals, we address three critical questions utilizing the tomato root microbiome as a model system. First, we asked how beneficial root-associated bacteria could be efficiently identified. We developed a strategy to select beneficial bacteria from a novel collection of 183 bacterial endophytes isolated from roots of two field-grown tomato species. The results suggest that isolates with similar traits impact plant growth at the same levels, regardless of their taxonomic classification or host origin. Next, we asked whether host genetics contribute to the root microbiome assembly and response to beneficial microbes. An assessment of the root microbiome profile and plant binary interaction experiments suggested the role of host genetics in influencing root recruitment and response to beneficial bacteria. Subsequently, we asked whether root-associated bacteria induce physiological changes in root tissues in the host. We identified two isolates from our bacterial endophyte collection that significantly promoted the growth of tomato genotype H7996 (<em>Solanum lycopersicum</em>). Plant-binary interaction experiments suggested a significant increase of cell wall lignification in the root vasculature starting 96-hour post-inoculation with beneficial bacteria. Additional studies are needed to uncover a possible correlation between the induced vasculature lignification and the growth-promoting effects of the two isolates on H7996. Altogether, our findings highlight the multi-faceted role of root-associated bacteria in promoting plant growth and support the development of crop improvement strategies in optimizing host association with soil bacteria.</p>