Root-associated bacterial communities and root metabolite composition are linked to nitrogen use efficiency in sorghum.

The development of cereal crops with high nitrogen use efficiency (NUE) is a priority for worldwide agriculture. In addition to conventional plant breeding and genetic engineering, the use of the plant microbiome offers another approach to improving crop NUE. To gain insight into the bacterial communities associated with sorghum lines that differ in NUE, a field experiment was designed comparing 24 diverse lines under sufficient and deficient nitrogen (N).

Increased signal-to-noise ratios within experimental field trials by regressing spatially distributed soil properties as principal components.

Environmental variability poses a major challenge to any field study. Researchers attempt to mitigate this challenge through replication. Thus, the ability to detect experimental signals is determined by the degree of replication and the amount of environmental variation, noise, within the experimental system.

Feature selection and causal analysis for microbiome studies in the presence of confounding using standardization.

Background: Microbiome studies have uncovered associations between microbes and human, animal, and plant health outcomes. This has led to an interest in developing microbial interventions for treatment of disease and optimization of crop yields which requires identification of microbiome features that impact the outcome in the population of interest. That task is challenging because of the high dimensionality of microbiome data and the confounding that results from the complex and dynamic interactions among host, environment, and microbiome.

Microbial Community Field Surveys Reveal Abundant Population in Sorghum Rhizosphere Composed of Many Closely Related Phylotypes.

While the root-associated microbiome is typically less diverse than the surrounding soil due to both plant selection and microbial competition for plant derived resources, it typically retains considerable complexity, harboring many hundreds of distinct bacterial species. Here, we report a time-dependent deviation from this trend in the rhizospheres of field grown sorghum. In this study, 16S rRNA amplicon sequencing was used to determine the impact of nitrogen fertilization on the development of the root-associated microbiomes of 10 sorghum genotypes grown in eastern Nebraska.

Metabolomics of sorghum roots during nitrogen stress reveals compromised metabolic capacity for salicylic acid biosynthesis.

Sorghum ( [L.] Moench) is the fifth most productive cereal crop worldwide with some hybrids having high biomass yield traits making it promising for sustainable, economical biofuel production. To maximize biofuel feedstock yields, a more complete understanding of metabolic responses to low nitrogen (N) will be useful for incorporation in crop improvement efforts.

Data Processing for GC-MS- and LC-MS-Based Untargeted Metabolomics.

Gas chromatography and liquid chromatography coupled to mass spectrometry are used extensively in untargeted metabolomics, which involves the profiling of small metabolites in biological samples. The complex raw dataset produced from untargeted metabolomics requires proper processing before it can be statistically analyzed and interpreted. This chapter describes a high-throughput data processing workflow routinely used in our laboratory, including feature detection and alignment, data reduction, and spectral-matching-based annotation.

High-throughput quantitative analysis of phytohormones in sorghum leaf and root tissue by ultra-performance liquid chromatography-mass spectrometry.

Plant development, growth, and adaptation to stress are regulated by phytohormones, which can influence physiology even at low concentrations. Phytohormones are chemically grouped according to both structure and function as auxins, cytokinins, abscisic acid, jasmonates, salicylates, gibberellins, and brassinosteroids, among others. This chemical diversity and requirement for highly sensitive detection in complex matrices create unique challenges for comprehensive phytohormone analysis.

Shifts in microbial communities in soil, rhizosphere and roots of two major crop systems under elevated CO and O.

Rising atmospheric concentrations of CO and O are key features of global environmental change. To investigate changes in the belowground bacterial community composition in response to elevated CO and O (eCO and eO) the endosphere, rhizosphere and soil were sampled from soybeans under eCO and maize under eO. The maize rhizosphere and endosphere α-diversity was higher than soybean, which may be due to a high relative abundance of Rhizobiales.

Linking dietary patterns with gut microbial composition and function.

Emerging insights have implicated the gut microbiota as an important factor in the maintenance of human health. Although nutrition research has focused on how direct interactions between dietary components and host systems influence human health, it is becoming increasingly important to consider nutrient effects on the gut microbiome for a more complete picture. Understanding nutrient-host-microbiome interactions promises to reveal novel mechanisms of disease etiology and progression, offers new disease prevention strategies and therapeutic possibilities, and may mandate alternative criteria to evaluate the safety of food ingredients.

Dietary supplementation with rice bran or navy bean alters gut bacterial metabolism in colorectal cancer survivors.

Scope: Heat-stabilized rice bran (SRB) and cooked navy bean powder (NBP) contain a variety of phytochemicals that are fermented by colonic microbiota and may influence intestinal health. Dietary interventions with these foods should be explored for modulating colorectal cancer risk.

Methods And Results: A randomized-controlled pilot clinical trial investigated the effects of eating SRB (30 g/day) or cooked navy bean powder (35 g/day) on gut microbiota and metabolites (NCT01929122).

Ovariectomy results in differential shifts in gut microbiota in low versus high aerobic capacity rats.

The increased risk for cardiometabolic disease with the onset of menopause is widely studied and likely precipitated by the decline in endogenous estradiol (E2), yet the precise mechanisms are unknown. The gut microbiome is involved in estrogen metabolism and has been linked to metabolic disease, suggesting its potential involvement in the postmenopausal phenotype. Furthermore, menopause-associated risk factors, as well as gut ecology, are altered with exercise.

Pilot dietary intervention with heat-stabilized rice bran modulates stool microbiota and metabolites in healthy adults.

Heat-stabilized rice bran (SRB) has been shown to regulate blood lipids and glucose, modulate gut mucosal immunity and inhibit colorectal cancer in animal and human studies. However, SRB's effects on gut microbial composition and metabolism and the resulting implications for health remain largely unknown. A pilot, randomized-controlled trial was developed to investigate the effects of eating 30 g/day SRB on the stool microbiome and metabolome.

Cancer-promoting effects of microbial dysbiosis.

Humans depend on our commensal bacteria for nutritive, immune-modulating, and metabolic contributions to maintenance of health. However, this commensal community exists in careful balance that, if disrupted, enters dysbiosis; this has been shown to contribute to the pathogenesis of colon, gastric, esophageal, pancreatic, laryngeal, breast, and gallbladder carcinomas. This development is closely tied to host inflammation, which causes and is aggravated by microbial dysbiosis and increases vulnerability to pathogens.

Stool microbiome and metabolome differences between colorectal cancer patients and healthy adults.

In this study we used stool profiling to identify intestinal bacteria and metabolites that are differentially represented in humans with colorectal cancer (CRC) compared to healthy controls to identify how microbial functions may influence CRC development. Stool samples were collected from healthy adults (n = 10) and colorectal cancer patients (n = 11) prior to colon resection surgery at the University of Colorado Health-Poudre Valley Hospital in Fort Collins, CO. The V4 region of the 16s rRNA gene was pyrosequenced and both short chain fatty acids and global stool metabolites were extracted and analyzed utilizing Gas Chromatography-Mass Spectrometry (GC-MS).