Application of multi-omic features clustering and pathway enrichment to clarify the impact of vitamin B2 supplementation on broiler caeca microbiome.

Background: The results of omic methodologies are often reported as separate datasets. In this study we applied for the first time multi-omic features clustering and pathway enrichment to clarify the biological impact of vitamin B2 supplementation on broiler caeca microbiome. Methods: The caeca contents of broilers fed +50 and +100 mg/kg vitamin B2 were analyzed by shotgun metagenomic and metabolomic. Latent variables extracted from NMR spectra, as well as taxonomic and functional features profiled from metagenomes, were integrated to characterize the effect of vitamin B2 in modulating caeca microbiome. A pathway-based network was obtained by mapping the observed input genes and compounds, highlighting connected strands of metabolic ways through pathway-enrichment analysis. Results: At day 14, the taxonomic, functional and metabolomic features in the caeca of tested broilers showed some degree of separation between control and treated groups, becoming fully clear at 28 days and persisting up to 42 days. In the caeca of birds belonging to the control group Alistipes spp. was the signature species, while the signature species in the caeca of broilers fed +50 and +100 mg/kg vitamin B2 were Bacteroides fragilis and Lactobacillus crispatus, Lactobacillus reuteri, Ruminococcus torques, Subdoligranum spp., respectively. The pathway enrichment analysis highlighted that the specific biochemical pathways enhanced by the supplementations of vitamin B2 were N-Formyl-L-aspartate amidohydrolase, producing Aspartate and Formate; L-Alanine:2-oxoglutarate amino transferase, supporting the conversion of L-Alanine and 2-Oxoglutarate in Pyruvate and L-Glutamate; 1D-myo-inositol 1/4 phosphate phosphohydrolase, converting Inositol 1/4-phosphate and water in myo-Inositol and Orthophosphate. The results of this study demonstrated that the caeca of birds fed +50 and + 100 mg/kg were those characterized by taxonomic groups more beneficial to the host and with a higher concentration of myo-inositol, formic acid, amino acids and pyruvate involved in glycolysis and amino acid biosynthesis. Conclusion: In this study we demonstrated how to perform multi-omic features integration to describe the biochemical mechanisms enhanced by the supplementation of different concentrations of vitamin B2 in the poultry diet. The relationship between vitamin B2 supplementation and myo-inositol production was highlighted in our study for the first time.

K-Clique Multiomics Framework: A Novel Protocol to Decipher the Role of Gut Microbiota Communities in Nutritional Intervention Trials.

The availability of omics data providing information from different layers of complex biological processes that link nutrition to human health would benefit from the development of integrated approaches combining holistically individual omics data, including those associated with the microbiota that impacts the metabolisation and bioavailability of food components. Microbiota must be considered as a set of populations of interconnected consortia, with compensatory capacities to adapt to different nutritional intake. To study the consortium nature of the microbiome, we must rely on specially designed data analysis tools. The purpose of this work is to propose the construction of a general correlation network-based explorative tool, suitable for nutritional clinical trials, by integrating omics data from faecal microbial taxa, stool metabolome (1H NMR spectra) and GC-MS for stool volatilome. The presented approach exploits a descriptive paradigm necessary for a true multiomics integration of data, which is a powerful tool to investigate the complex physiological effects of nutritional interventions.

The NMR added value to the green foodomics perspective: Advances by machine learning to the holistic view on food and nutrition.

Food is a complex matter, literally. From production to functionalization, from nutritional quality engineering to predicting effects on health, the interest in finding an efficient physicochemical characterization of food has boomed in recent years. The sheer complexity of characterizing food and its interaction with the human organism has however made the use of data driven approaches in modeling a necessity. High-throughput techniques, such as nuclear magnetic resonance (NMR) spectroscopy, are well suited for omics data production and, coupled with machine learning, are paving a promising way of modeling food-human interaction. The foodomics approach sets the framework for omic data integration in food studies, in which NMR experiments play a key role. NMR data can be used to assess nutritional qualities of food, helping the design of functional and sustainable sources of nutrients; detect biomarkers of intake and study how they impact the metabolism of different individuals; study the kinetics of compounds in foods or their by-products to detect pathological conditions; and improve the efficiency of in silico models of the metabolic network.

Effects of Vitamin B2 Supplementation in Broilers Microbiota and Metabolome.

The study of the microbiome in broiler chickens holds great promise for the development of strategies for health maintenance and performance improvement. Nutritional strategies aimed at modulating the microbiota-host relationship can improve chickens' immunological status and metabolic fitness. Here, we present the results of a pilot trial aimed at analyzing the effects of a nutritional strategy involving vitamin B2 supplementation on the ileum, caeca and litter microbiota of Ross 308 broilers, as well as on the metabolic profile of the caecal content. Three groups of chickens were administered control diets and diets supplemented with two different dosages of vitamin B2. Ileum, caeca, and litter samples were obtained from subgroups of birds at three time points along the productive cycle. Sequencing of the 16S rRNA V3-V4 region and NMR metabolomics were used to explore microbiota composition and the concentration of metabolites of interest, including short-chain fatty acids. Vitamin B2 supplementation significantly modulated caeca microbiota, with the highest dosage being more effective in increasing the abundance of health-promoting bacterial groups, including Bifidobacterium, resulting in boosted production of butyrate, a well-known health-promoting metabolite, in the caeca environment.

Olive oil by-product as functional ingredient in bakery products. Influence of processing and evaluation of biological effects.

Nowadays, the strong demand for adequate nutrition is accompanied by concern about environmental pollution and there is a considerable emphasis on the recovery and recycling of food by-products and wastes. In this study, we focused on the exploitation of olive pomace as functional ingredient in biscuits and bread. Standard and enriched bakery products were made using different flours and fermentation protocols. After characterization, they were in vitro digested and used for supplementation of intestinal cells (Caco-2), which underwent exogenous inflammation. The enrichment caused a significant increase in the phenolic content in all products, particularly in the sourdough fermented ones. Sourdough fermentation also increased tocol concentration. The increased concentration of bioactive molecules did not reflect the anti-inflammatory effect, which was modulated by the baking procedure. Conventionally fermented bread enriched with 4% pomace and sourdough fermented, not-enriched bread had the greatest anti-inflammatory effect, significantly reducing IL-8 secretion in Caco-2 cells. The cell metabolome was modified only after supplementation with sourdough fermented bread enriched with 4% pomace, probably due to the high concentration of tocopherol that acted synergistically with polyphenols. Our data highlight that changes in chemical composition cannot predict changes in functionality. It is conceivable that matrices (including enrichment) and processing differently modulated bioactive bioaccessibility, and consequently functionality.

Olive oil industry by-products. Effects of a polyphenol-rich extract on the metabolome and response to inflammation in cultured intestinal cell.

Over the past years, researchers and food manufacturers have become increasingly interested in olive polyphenols due to the recognition of their biological properties and probable role in the prevention of various diseases such as inflammatory bowel disease. Olive pomace, one of the main by-products of olive oil production, is a potential low-cost, phenol-rich ingredient for the formulation of functional food. In this study, the aqueous extract of olive pomace was characterized and used to supplement human intestinal cell in culture (Caco-2). The effect on the cell metabolome and the anti-inflammatory potential were then evaluated. Modification in the metabolome induced by supplementation clearly evidenced a metabolic shift toward a "glucose saving/accumulation" strategy that could have a role in maintaining anorexigenic hormone secretion and could explain the reported appetite-suppressing effect of the administration of polyphenol-rich food. In both basal and inflamed condition, supplementation significantly reduced the secretion of the main pro-inflammatory cytokine, IL-8. Thus, our data confirm the therapeutic potential of polyphenols, and specifically of olive pomace in intestinal bowel diseases. Although intervention studies are needed to confirm the clinical significance of our findings, the herein reported results pave the road for exploitation of olive pomace in the formulation of new, value-added foods. In addition, the application of a foodomics approach allowed observing a not hypothesized modulation of glucose metabolism.