Periodic Reporting for period 1 - NUTROME (Mining food for nutraceuticals for beneficial microbiome modulation)
Reporting period: 2023-06-01 to 2025-05-31
The human gut microbiome is recognized as an essential element in human health and disruption of the homeostasis between the host and gut microbiome has been associated with the development of various diseases. Diet plays a major role in modulating the gut microbiome, but understanding the exact relationship and its effect on health remains a key challenge in microbiome research. NUTROME aimed to develop nutraceuticals (food components with health benefits) based on key dietary components of the Mediterranean diet that are capable of modulating alterations (or dysbiosis) of the human gut microbiome of the elderly. This group of population was chosen because of the role of gut microbiota in aging-related health decline. Alterations in the gut microbiota in the elderly are characterized by a low-diversity gut microbiome that is linked to an intensified inflammatory state, which increases the risk of frailty and mortality. Since the elderly in developed countries is increasing very rapidly, the investigation of modulators for microbiota restoration as a therapeutic strategy for age-related dysbiosis is of great interest.
NUTROME project focused on three types of key food ingredients: essential oils from aromatic plants and spices, (poly)phenols from berries and bovine milk lactoferrin with different iron-saturation levels. Bioactive components found in essential oils have a wide range of bioactive properties, including antimicrobial, anti-inflammatory, anticancer, and antioxidant activities. The health beneficial properties of berry-derived (poly)phenols have been previously described including antioxidant, anti-inflammatory, antihypertensive, and antihyperglycemic activities. Lactoferrin is considered a high-value ingredient because of its iron-binding, anti-inflammatory, antimicrobial, immunomodulatory and antioxidant properties. These key food ingredients were extracted, purified and characterised to establish the profile of bioactive compounds obtained and their bioactive properties. Clove and thyme essential oils were prepared with good extraction yield resulting in extracts with strong antioxidant and antimicrobial properties. (Poly)phenol fractions from diverse berries were extracted and fractionation techniques were applied to obtain fractions rich on different types of (poly)phenol, including phenolic acids, proanthocyanidins, anthocyanins and flavonols. These extracts displayed also high antioxidant activity and intermediate antimicrobial properties. Lastly, lactoferrin with different iron saturation levels was prepared with the aim of assessing the impact of iron saturation level on the bioactive properties of lactoferrin.
After obtaining the bioactive compound extracts, a new form of presenting them by nanoencapsulation was developed to improve stability and bioactivity on the target site and microbial population of interest in the gut. These new formulations were based on oil-in-water nanoemulsions made by high-pressure homogenisation that were optimised and characterised.
Understanding how key dietary components and gut microbiome interact required insight of the taxonomic and functional composition and relevant ecological dynamics of the microbiome by cutting-edge microbiome manipulations and multi-omics approach. In a first stage, the impact of the bioactive compounds was studied using a simple gut bacterial community. This consortium was composed by seven gut bacterial species associated with healthy ageing namely Alistipes putredinis, Barnesiella intestinihominis, Coprococcus catus, Dorea longicatena, Agathobacter rectalis, Faecalibacterium prausnitzii, and Roseburia hominis. The consortium was used as a reductionist model to study the impact of bioactive compounds on the structure and function of microbial communities in a controlled experimental setting. This model was included as a preliminary screening to reduce the number of variables to be tested with the whole gut microbiome and thus to make the artificial colon studies more targeted and time/cost efficient.
The impact of selected key food ingredients was then tested in an in vitro colon model of the whole gut microbiome from elderly donors. “Healthy” and “frail” elderly donors were selected from a subset of a well-phenotyped cohort of subjects who live in community or long-stay residential care, and whose gut microbiota conformed to the typical clustering patterns correlated to health or frailty in the cohort. Equal numbers of male and female subjects were enrolled to include the sex variable in the analysis of the results. The human gut microbiome model was simulated in a single-stage continuous fermentation system mimicking the human colon in the absence or presence of bioactive compounds. The influence of key food ingredients on the gut microbiota composition was assessed by high-throughput sequencing of the 16S rRNA gene and biostatistical analyses. Bioinformatics analyses revealed the significant impact of some of the bioactive compounds, including clove extract, iron-saturated lactoferrin and blueberry extract, on the composition of the gut microbiome of elderly donors.
After obtaining the bioactive compound extracts, a new form of presenting them by nanoencapsulation was developed to improve stability and bioactivity on the target site and microbial population of interest in the gut. These new formulations were based on oil-in-water nanoemulsions made by high-pressure homogenisation that were optimised and characterised.
Understanding how key dietary components and gut microbiome interact required insight of the taxonomic and functional composition and relevant ecological dynamics of the microbiome by cutting-edge microbiome manipulations and multi-omics approach. In a first stage, the impact of the bioactive compounds was studied using a simple gut bacterial community. This consortium was composed by seven gut bacterial species associated with healthy ageing namely Alistipes putredinis, Barnesiella intestinihominis, Coprococcus catus, Dorea longicatena, Agathobacter rectalis, Faecalibacterium prausnitzii, and Roseburia hominis. The consortium was used as a reductionist model to study the impact of bioactive compounds on the structure and function of microbial communities in a controlled experimental setting. This model was included as a preliminary screening to reduce the number of variables to be tested with the whole gut microbiome and thus to make the artificial colon studies more targeted and time/cost efficient.
The impact of selected key food ingredients was then tested in an in vitro colon model of the whole gut microbiome from elderly donors. “Healthy” and “frail” elderly donors were selected from a subset of a well-phenotyped cohort of subjects who live in community or long-stay residential care, and whose gut microbiota conformed to the typical clustering patterns correlated to health or frailty in the cohort. Equal numbers of male and female subjects were enrolled to include the sex variable in the analysis of the results. The human gut microbiome model was simulated in a single-stage continuous fermentation system mimicking the human colon in the absence or presence of bioactive compounds. The influence of key food ingredients on the gut microbiota composition was assessed by high-throughput sequencing of the 16S rRNA gene and biostatistical analyses. Bioinformatics analyses revealed the significant impact of some of the bioactive compounds, including clove extract, iron-saturated lactoferrin and blueberry extract, on the composition of the gut microbiome of elderly donors.
Therefore, NUTROME has contributed to the scientific community’s understanding of the influence of certain food components and ingredients on the human gut microbiome. These may help in the advance on strategies to boost potential modulators through diet and supplementation for the elderly to improve their health status by slowing the onset of age-related health loss and/or ameliorating symptomology. However, further research is required to evaluate the stability and bioactivity of the key food ingredients under simulated grastrointestinal conditions, to assess the impact of bioactive compounds on the function of the microbiome in terms of metabolisation of bioactive compounds with potential synthesis of derivatives with other bioactive properties and to study the mechanistic function of bioactive compounds in cellular models and in vivo models.