Explore the vast range of titles available.

Prebiotic fibers, polyphenols and other molecular components of food crops significantly affect the composition and function of the human gut microbiome and human health. The abundance of these, frequently uncharacterized, microbiome-active components vary within individual crop species. Here, we employ high throughput in vitro fermentations of pre-digested grain using a human microbiome to identify segregating genetic loci in a food crop, sorghum, that alter the composition and function of human gut microbes. Evaluating grain produced by 294 sorghum recombinant inbreds identifies 10 loci in the sorghum genome associated with variation in the abundance of microbial taxa and/or microbial metabolites. Two loci co-localize with sorghum genes regulating the biosynthesis of condensed tannins. We validate that condensed tannins stimulate the growth of microbes associated with these two loci. Our work illustrates the potential for genetic analysis to systematically discover and characterize molecular components of food crops that influence the human gut microbiome. Diet affects the human gut microbiome, but studies linking crop genetics to seed traits that influence the human gut microbiome are lacking. Here, the authors develop an in vitro microbiome screening method and reveal the association between sorghum genes regulating condensed tannin biosynthesis and human gut microbiome.

Swine are a major reservoir of an array of zoonotic Salmonella enterica subsp. enterica lineage I serovars including Derby, Typhimurium, and 4,[5],12:i:- (a.k.a. Monophasic Typhimurium). In this study, we assessed the gastrointestinal (GI) microbiome composition of pigs in different intestinal compartments and the feces following infection with specific zoonotic serovars of S. enterica ( S . Derby, S . Monophasic, and S. Typhimurium). 16S rRNA based microbiome analysis was performed to assess for GI microbiome changes in terms of diversity (alpha and beta), community structure and volatility, and specific taxa alterations across GI biogeography (small and large intestine, feces) and days post-infection (DPI) 2, 4, and 28; these results were compared to disease phenotypes measured as histopathological changes. As previously reported, only S . Monophasic and S. Typhimurium induced morphological alterations that marked an inflammatory milieu restricted to the large intestine in this experimental model. S. Typhimurium alone induced significant changes at the alpha- (Simpson’s and Shannon’s indexes) and beta-diversity levels, specifically at the peak of inflammation in the large intestine and feces. Increased community dispersion and volatility in colonic apex and fecal microbiomes were also noted for S. Typhimurium. All three Salmonella serovars altered community structure as measured by co-occurrence networks; this was most prominent at DPI 2 and 4 in colonic apex samples. At the genus taxonomic level, a diverse array of putative short-chain fatty acid (SCFA) producing bacteria were altered and often decreased during the peak of inflammation at DPI 2 and 4 within colonic apex and fecal samples. Among all putative SCFA producing bacteria, Prevotella showed a broad pattern of negative correlation with disease scores at the peak of inflammation. In addition, Prevotella 9 was found to be significantly reduced in all Salmonella infected groups compared to the control at DPI 4 in the colonic apex. In conclusion, this work further elucidates that distinct swine-related zoonotic serovars of S. enterica can induce both shared (high resilience) and unique (altered resistance) alterations in gut microbiome biogeography, which helps inform future investigations of dietary modifications aimed at increasing colonization resistance against Salmonella through GI microbiome alterations.

Common beans, which contain diverse bioactive molecules, have not been systematically studied for their variation in how they affect the human gut microbiome. We measured taxonomic shifts and metabolite production of three human gut microbiomes cultured with 299 common bean cultivars under conditions that mimic the nutrient availability of the human colon. Common bean population structure (landrace and market class) had significant effects on microbiota diversity, composition, and metabolite production. Genome-wide association analysis identified seven multiple effect loci (MEL) where genetic variation in the common bean genome affected the microbiome. One MEL on chromosome Pv 05 had impacts on the abundance of several Lachnospiraceae and Ruminococcaceae . Molecular complementation experiments suggested that variation in the biosynthesis of saponins at this MEL was the mechanism driving the variability in microbiota composition and function. This study provides innovative understanding of how genetics of common beans affects the human gut microbiome and potentially human health. Population genomic analyses identify multiple effect loci in the common bean genome that influence seed components and metabolites that consequently affect the human gut microbiome.

A sanitary challenge was carried out to induce suboptimal herd health while investigating the effect of amino acids supplementation on piglet responses. Weaned piglets of high sanitary status (6.33 ± 0.91 kg of BW) were distributed in a 2 × 2 factorial arrangement into two similar facilities with contrasting sanitary conditions and two different diets. Our results suggest that increased Trp, Thr, and Met dietary supplementation could support the immune systems of piglets under a sanitary challenge. In this manner, AA+ supplementation improved the performance and metabolism of piglets under mixed management and poor sanitary conditions. No major temporal microbiome changes were associated with differences in performance regardless of sanitary conditions or diets. Since piglets often become mixed in multiple-site production systems and facility hygiene is also often neglected, this study suggests that increased Trp, Thr, and Met (AA+) dietary supplementation could contribute to mitigating the side effects of these harmful risk factors in modern pig farms.

Nutrition has a significant impact on the gastrointestinal (GI) microbiome, which can influence pig metabolism, nutrient absorption, biomolecule synthesis, and bioavailability (including bile acids and short-chain fatty acids), as well as colonization resistance to GI pathogens and overall disease tolerance through immune maturation and regulation. The aim of this study was to assess the impact of functional amino acid supplementation on the fecal microbiome of pigs allocated into GOOD vs. POOR sanitary conditions (SC) over time, using 16S rRNA data. A total of 120 female growing pigs were randomly assigned in a 2 × 2 factorial arrangement (n = 30/treatment), consisting of two sanitary conditions (GOOD vs. POOR) and two diets [control (CN; 100% NRC, 2012) vs. supplemented with AA (Trp, Thr, and Met+Cys: Lys ratios increased to 20% higher than CN)]. Pigs were allocated to the GOOD SC group and were sham-inoculated, and the barn was kept clean, whereas pigs housed under POOR SC were challenged with Salmonella Typhimurium, in addition to the spreading fecal material from a commercial farm undergoing poor growth performance. Fecal samples were collected at day post-challenge (DPC) 0, 10, and 21, and extracted DNA was sequenced for 16S rRNA data analysis. Although alpha-diversity analysis revealed minor, statistically significant changes between groups, beta-diversity analysis demonstrated a significant separation between communities based on sanitary conditions at DPC 21. Accordingly, the most important taxa differentiating the two groups were the enrichment of the following taxa in the POOR group at DPC 21: Clostridium sensu stricto 1 , Dorea , Intestinibacter , Lactobacillus , Romboutsia , Ruminococcus torques , Subdoligranulum , Terrisporobacter , and Turicibacter . Network and correlation structural analysis further revealed a sub-structuring of the data, with positive correlations forming in the POOR SC group: Sub-cluster 1 ( Romboutsia , Turicibacter , Clostridium sensu stricto 1 , Terrisporobacter , and Intestinibacter ) and Sub-cluster 2 ( Dorea , Subdoligranulum , Ruminococcus torques , Blautia , Holdemanella , and Solobacterium ). In conclusion, temporal changes in the fecal swine microbiome of growing pigs reflected the S. Typhimurium challenge and poor sanitary status despite a dietary surplus of functional amino acids.

Celiac disease and nonceliac gluten sensitivity are provoked by the consumption of gluten from wheat, barley, rye, and related grains. Affected individuals are advised to adhere to gluten-free diets. Recently, gluten-free foods have become a marketing trend with gluten-free options both in packaged foods and in restaurants and food service establishments. Pasta is one of the primary gluten-containing foods in diets in North America and Europe. Gluten-free pasta formulations are commercially available. In restaurants, multiple pasta dishes are often prepared simultaneously in large pots with multiple compartments and shared cooking water. The objective of this study was to determine whether gluten transfer occurs between traditional and gluten-free pasta when cooked simultaneously in the same water. Pasta was boiled in a commercial, four-compartment, 20-qt (18.9-L) cooking pot containing three batches of traditional penne pasta and one batch of gluten-free penne pasta. The amount of pasta (dry weight) was either 52 g (recommended serving size) or 140 g (typical restaurant portion). Five consecutive batches of pasta were boiled, and cooking water and gluten-free pasta were sampled at completion of cooking. Water and gluten-free pasta samples were tested for gluten with the Neogen Veratox for Gliadin enzyme-linked immunosorbent assay kit. Gluten concentrations were low (<20 ppm) in both water and gluten-free pasta samples through five 52-g batches. Gluten concentrations in the 52-g gluten-free pasta samples slowly increased through five batches but were never >20 ppm. During cooking of the 140-g gluten-free pasta samples, the gluten concentrations in the cooking water increased with each batch to >50 and >80 ppm after the fourth and fifth batches, respectively. The gluten concentrations in the 140-g gluten-free pasta samples approached 20 ppm by the fourth batch and reached nearly 40 ppm after the fifth batch. Although gluten transfer does not occur at a high rate, gluten-free pasta should be prepared in a separate cooking vessel in restaurant and food service establishments.

The composition and function of the human gut microbiome are associated with many aspects of human health and disease and are shaped by diet. Staple grains, which comprise a significant percentage of calories consumed by humans, consist of few elite hybrid lines that have been artificially selected for crop yield and resilience traits. A quantitative genetics approach was employed to identify and characterize novel plant traits that impact human nutrition mediated by the gut microbiome in a diverse population of sorghum. This work demonstrates genetic diversity in sorghum can explain variation in bacteria from the microbiomes of eight human subjects tested in vitro. In a genome-wide analysis, we identified loci in sorghum associated with gut microbes of two human subjects. Genome-wide mapping of various biochemical and agronomic traits in sorghum revealed seed traits likely causal for the microbiome associations. An identified locus on chromosome four encompasses the tan1 gene known to regulate condensed tannin accumulation in sorghum, which has been shown to have a tremendous impact on gut microbes. In a separate project, we examined the effects of genetic variation in a bulk nutritional trait (seed protein composition) using near-isogenic lines of maize popcorn with wildtype or quality protein popcorn mutations which lead to seed protein composition with higher levels of essential amino acids: lysine and tryptophan. Detailed analyses of the differential effects of popcorn vs quality protein popcorn on the gut bacteria resulted in the enrichment of butyrate-producing bacteria coupled with an increase in butyrate production associated with human health which can be attributed to a microbial enzymatic pathway for the conversion of lysine and fructoselysine to butyrate. Cumulatively, this work demonstrates that plant seed composition, driven by genetics, within two distinct species of grain crops has significant effects on gut microbes, particularly on microbial taxa considered to be beneficial. Further targeted breeding approaches to improve these nutritional traits can enhance a plant’s ability to enrich beneficial bacteria and metabolites ultimately improving human health.

Substantial functional metabolic diversity exists within species of cultivated grain crops that directly or indirectly provide more than half of all calories consumed by humans around the globe. While such diversity is the molecular currency used for improving agronomic traits, diversity is poorly characterized for its effects on human nutrition and utilization by gut microbes. Moreover, we know little about agronomic traits’ potential tradeoffs and pleiotropic effects on human nutritional traits. Here, we applied a quantitative genetics approach using a meta-analysis and parallel genome-wide association studies of Sorghum bicolor traits describing changes in the composition and function of human gut microbe communities, and any of 200 sorghum seed and agronomic traits across a diverse sorghum population to identify associated genetic variants. A total of 15 multiple-effect loci (MEL) were initially found where different alleles in the sorghum genome produced changes in seed that affected the abundance of multiple bacterial taxa across 2 human microbiomes in automated in vitro fermentations. Next, parallel genome-wide studies conducted for seed, biochemical, and agronomic traits in the same population identified significant associations within the boundaries of 13/15 MEL for microbiome traits. In several instances, the colocalization of variation affecting gut microbiome and agronomic traits provided hypotheses for causal mechanisms through which variation could affect both agronomic traits and human gut microbes. This work demonstrates that genetic factors affecting agronomic traits in sorghum seed can also drive significant effects on human gut microbes, particularly bacterial taxa considered beneficial. Understanding these pleiotropic relationships will inform future strategies for crop improvement toward yield, sustainability, and human health.

Plant resistance to heat stress can be modelled by variation attributable to the genotype, environment, the rhizosphere microbiome, and their interactions. Using this Genotype × Environment × Rhizosphere Microbiome (GERMs) model, we studied three cereal genotypes: two inbred maize lines with contrasting heat sensitivity, and a sorghum inbred that displayed moderate heat tolerance. Plants were grown under optimal and heat stressed conditions across two soil treatments. We developed a systems-level metatranscriptomics approach to examine both plant and microbial transcriptomic profiles and integrated them with microbiome compositional data and plant phenotypes. We compared our strategy to amplicon profiling and found that our metatranscriptomic strategy offers greater functional and taxonomic resolution, allowing us to characterize active microbial pathways and analyze them jointly with plant gene expression profiles within a single system. We show that the microbiome functional profile is driven by host genotype and environmental factors and can enhance plant resilience. Our analyses identified plant genes and microbial pathways consistently associated with heat tolerance and key host-microbe interactions. Specifically, we identified D-amino acid metabolism as a plausible mechanism underlying a synergistic response to heat stress. These results demonstrate that the rhizosphere microbiome is not a passive component but an active participant in plant responses to abiotic stress. This work offers a new perspective on cereal adaptation to high temperatures and underscores the utility of the GERMs framework for dissecting functional relationships among plant genotype, environment, and the rhizosphere microbiome.