q2-metnet: QIIME2 package to analyze 16S rRNA data via high-quality metabolic reconstructions of the human gut microbiota.

MOTIVATION: 16S rRNA gene sequencing is the most frequent approach for the characterization of the human gut microbiota. Despite different efforts in the literature, the inference of functional and metabolic interpretations from 16S rRNA gene sequencing data is still a challenging task. High-quality metabolic reconstructions of the human gut microbiota, such as AGORA and AGREDA, constitute a curated resource to improve functional inference from 16S rRNA data, but they are not typically integrated into standard bioinformatics tools. RESULTS: Here, we present q2-metnet, a QIIME2 plugin that enables the contextualization of 16S rRNA gene sequencing data into AGORA and AGREDA. In particular, based on relative abundances of taxa, q2-metnet determines normalized activity scores for the reactions and subsystems involved in the selected metabolic reconstruction. Using these scores, q2-metnet allows the user to conduct differential activity analysis for reactions and subsystems, as well as exploratory analysis using PCA and hierarchical clustering. We apply q2-metnet to a dataset from our group that involves 16S rRNA data from stool samples from lean, allergic to cow's milk, obese and celiac children, and the Belgian Flemish Gut Flora Project cohort, which includes faecal 16S rRNA data from obese and normal-weight adult individuals. In the first case, q2-metnet outperforms existing algorithms in separating different clinical conditions based on predicted pathway abundances and subsystem scores. In the second case, q2-metnet complements competing approaches in predicting functional alterations in the gut microbiota of obese individuals. Overall, q2-metnet constitutes a powerful bioinformatics tool to provide metabolic context to 16S rRNA data from the human gut microbiota. AVAILABILITY: Python code of q2-metnet is available in https://github.com/PlanesLab/q2-metnet and https://figshare.com/articles/dataset/q2-metnet_package/26180446. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities.

MOTIVATION: Simulating gut microbial dynamics is extremely challenging. Several computational tools, notably the widely used BacArena, enable modeling of dynamic changes in the microbial environment. These methods, however, do not comprehensively account for microbe-microbe stimulant or inhibitory effects or for nutrient-microbe inhibitory effects, typically observed in different compounds present in the daily diet. RESULTS: Here, we present BN-BacArena, an extension of BacArena consisting on the incorporation within the native computational framework of a Bayesian network model that accounts for microbe-microbe and nutrient-microbe interactions. Using in vitro experiments, 16S rRNA gene sequencing data and nutritional composition of 55 foods, the output Bayesian network showed 23 significant nutrient-bacteria interactions, suggesting the importance of compounds such as polyols, ascorbic acid, polyphenols and other phytochemicals, and 40 bacteria-bacteria significant relationships. With test data, BN-BacArena demonstrates a statistically significant improvement over BacArena to predict the time-dependent relative abundance of bacterial species involved in the gut microbiota upon different nutritional interventions. As a result, BN-BacArena opens new avenues for the dynamic modeling and simulation of the human gut microbiota metabolism. AVAILABILITY AND IMPLEMENTATION: MATLAB and R code are available in https://github.com/PlanesLab/BN-BacArena.

Zn Biofortification of Dutch Cucumbers with Chemically Modified Spent Coffee Grounds: Zn Enrichment and Nutritional Implications.

Spent coffee grounds (SCGs) are a food waste with a large generation around the world. However, their utilization as a soil organic amendment is difficult due to their phytotoxic effect. In the present work, the impact of agronomic biofortification on Dutch cucumbers was studied by using different chemically modified SCGs, analyzing their effects on Zn content, the release of antioxidant capacity and the production of short-chain fatty acids after in vitro digestion-fermentation. The results indicated variations in the Zn content and chemical composition of cucumbers according to the treatment groups. The functionalized with Zn and activated SCGs were able to increase Zn levels in cucumbers. Meanwhile, the activated hydrochar obtained at 160 °C and the activated and functionalized with Zn SCGs showed the highest Zn supply per serving. Differences in the antioxidant capacity and short-chain fatty acid production were observed between the groups. It is concluded that the growing conditions and the presence of Zn may significantly influence the contribution of these cucumbers to the dietary intake of nutrients and antioxidants, which could have important implications for human health and nutrition.

Biochelates from Spent Coffee Grounds Increases Iron Levels in Dutch Cucumbers but Affects Their Antioxidant Capacity.

Spent coffee grounds (SCG) are a type of food waste and are produced in abundance around the world. However, their utilization as a soil organic amendment is challenging due to their phytotoxic effect. In the present work, the impact of agronomic biofortification on Dutch cucumbers was investigated using different chemically modified SCG and analyzing their effects on iron contents, their capacity for releasing antioxidants, and the production of short-chain fatty acids after in vitro digestion-fermentation. The results indicated variations in the iron contents and chemical compositions of cucumbers according to the treatment groups. Functionalized and activated hydrochar from SCG increased Fe levels in cucumbers. Although activated hydrochar obtained at 160 °C and functionalized with Fe showed the highest iron supply per serving, differences in antioxidant capacity and short-chain fatty acid production were observed between the groups. It is concluded that growing conditions and the presence of iron may significantly influence the contribution of these cucumbers to the dietary intake of nutrients and antioxidants, which could have important implications for human health and nutrition.

Human gut microbiota fermentation of cooked eggplant, garlic, and onion supports distinct microbial communities.

Heating and cooking vegetables not only enhances their palatability but also modifies their chemical structure, which in turn might affect their fermentation by resident gut microbes. Three commonly consumed vegetables that are known to undergo chemical browning, also known as Maillard reaction, during cooking - eggplant, garlic, and onion - were each fried, grilled, or roasted. The cooked vegetables were then subjected to an in vitro digestion-fermentation process aimed to simulate the passage of food through the human oro-gastro-intestinal tract. In the last step, the undigested fractions of these foods were anaerobically fermented by the complex human gut microbiota. We assessed the structure of microbial communities maintained on each cooked vegetable by high-throughput 16S rRNA gene amplicon sequencing, measured the levels of furosine, a chemical marker of the Maillard browning reaction, by HPLC, and determined the antioxidant capacities in all samples with ABTS and FRAP methods. Overall, vegetable type had the largest, statistically significant, effect on the microbiota structure followed by the cooking method. Onion fermentation supported a more beneficial community including an expansion of Bifidobacterium members and inhibition of Enterobacteriaceae. Fermentation of cooked garlic promoted Faecalibacterium growth. Among cooking methods, roasting led to a much higher ratio of beneficial-to-detrimental microbes in comparison with grilling and frying, possibly due to the exclusion of any cooking oil in the cooking process.

Cultivar and Harvest Time of Almonds Affect Their Antioxidant and Nutritional Profile through Gut Microbiota Modifications.

Almonds are a rich source of beneficial compounds for human health. In this work, we assessed the influence of almond cultivars and harvest time on their morphological (length, width and thickness) and nutritional (ash, moisture, proteins) profiles. We also evaluated the impact of an in vitro digestion and fermentation process on almonds' antioxidant and phenolic content, as well as their support of gut microbiota community and functionality, including the production of short-chain fatty acids (SCFAs), lactic and succinic acids. The length, width, and thickness of almonds varied significantly among cultivars, with the latter two parameters also exhibiting significant changes over time. Moisture content decreased with maturity, while protein and ash increased significantly. Total antioxidant capacity released by almonds after digestion and fermentation had different trends depending on the antioxidant capacity method used. The fermentation step contributed more to the antioxidant capacity than the digestion step. Both cultivar and harvest time exerted a significant influence on the concentration of certain phenolic compounds, although the total content remained unaffected. Similarly, fecal microbiota modulation depended on the cultivar and maturity stage, with the Guara cultivar and late maturity showing the largest effects. Cultivar type also exerted a significant impact on the concentration of SCFAs, with the Guara cultivar displaying the highest total SCFAs concentration. Thus, we conclude that cultivar and harvest time are key factors in shaping the morphological and nutritional composition of almonds. In addition, taking into account all the results obtained, the Guara variety has the best nutritional profile.

How Different Are the Influences of Mediterranean and Japanese Diets on the Gut Microbiome?

The gut microbiome is a complex ecosystem, mainly composed of bacteria, that performs essential functions for the host. Its composition is determined by many factors; however, diet has emerged as a key regulator. Both the Mediterranean (MD) and Japanese (JD) diets have been associated with significant health benefits and are therefore considered healthy dietary patterns. Both are plant-based diets and although they have much in common, they also have important differences mainly related to total calorie intake and the consumption of specific foods and beverages. Thus, it has been hypothesized that they exert their beneficial properties through different nutrients and bioactive compounds that interact with gut microbes and induce specific changes on gut metabolic pathways. In this review, we present current data on the effects of the MD and JD on the gut microbiome. Furthermore, we aim to examine whether there are differences or shared effects on the gut microbiome of people who adhere to these dietary patterns.

Evaluation of Tannin-Delivery Approaches for Gut Microbiota Modulation: Comparison of Pectin-Based Microcapsules and Unencapsulated Extracts.

The aim of this study was to investigate the impact of tannins on gut microbiota composition and activity, and to evaluate the use of pectin-microencapsulation of tannins as a potential mode of tannin delivery. Thus, pectin-tannin microcapsules and unencapsulated tannin extracts were in vitro digested and fermented, and polyphenol content, antioxidant capacity, microbiota modulation, and short-chain fatty acid (SCFA) production were analyzed. Pectin microcapsules were not able to release their tannin content, keeping it trapped after the digestive process, and are therefore not recommended for tannin delivery. Unencapsulated tannin extracts were found to exert a positive effect on the human gut microbiota. The digestion step resulted to be a fundamental requirement in order to maximize tannin bioactive effects, especially with regard to condensed tannins, as the antioxidant capacity exerted and the SCFAs produced were greater when tannins were submitted to digestion prior to fermentation. Moreover, tannins interacted differently with the intestinal microbiota depending on whether they underwent prior digestion or not. Polyphenol content and antioxidant capacity correlated with SCFA production and with the abundance of several bacterial taxa.

Total Zn of foods and bioaccesible fractions in the small and large intestine after in vitro digestion and fermentation with fecal material of healthy adults and children: Influence of culinary techniques.

The healthy status of human beings is associated with an appropriate nutritional status in Zn, which must firstly be bioavailable. We measured the total Zn amount and its bioaccesibility in raw foods and after cooking by common culinary techniques. These foods were submitted to an in vitro digestion and fermentation with faecal inocula from healthy adults and children to evaluate Zn bioaccesibility in the small and large intestine. Mean total Zn amount provided by foods was 8.080 µg/g. Zn amount released from food in the small intestine was significantly different among several food groups and lower in raw vegetal foods compared to cooked ones (frying, roasting and grilling; p < 0.05); the same behaviour was found in the large intestine for healthy children. Zn bioaccesibility in the large intestine varied statistically according to the subjects' idiosyncrasies, and was higher in healthy children (p < 0.05) probably due to growth demands and different composition of the colonic microbiota. In healthy adults and children, the bioaccesible fractions were 33.0 ± 20.4 % for the small intestine, 16.4 ± 22.0 and 59.6 ± 29.9% for the large one, and the non-bioaccessible ones 50.6 ± 19.9 and 7.4 ± 9.1%, respectively.

Elucidating the structure of melanoidins derived from biscuits: A preliminary study.

Melanoidins present important physiological activities, but their structure is largely unknown. The objective of the present work was to reveal the physicochemical characteristics of biscuit melanoidins(BM) prepared under high temperature(HT) and low temperature(LT) conditions (150 °C/25 min-100 °C/80 min respectively). BM were characterised and analysed by differential scanning calorimetry, X-ray and FT-IR. Moreover, the antioxidant capacity and the zeta potential were determined. The phenolic content of HT-BM was higher than that of LT-BM (19.5 ± 2.6% vs 7.8 ± 0.3% respectively, p ≤ 0.05) and the antioxidant capacity determined by ABTS/DPPH/FRAP (p ≤ 0.05) was greater. Also, HT-BM presented a 30% increase in crystal structure compared to LT-BM according to X-ray analysis. The magnitude of the negative net charge was significantly higher in HT-BM (-36.8 ± 0.6) than in LT-BM (-16.8 ± 0.1)(p ≤ 0.05). FT-IR analysis confirmed the presence of phenolic and intermediate Maillard reaction compounds bound to the HT-BM structure. In conclusion, the different heating treatments applied to biscuits led to differences in the melanoidin structure.

Comparative Analysis of Traditional Oriental Herbal Fruits as Potential Sources of Polyphenols and Minerals for Nutritional Supplements.

There are a plethora of plant species in India, which have been widely used in vegetable dishes, soups, desserts and herbal medicine. In addition to these traditional uses, today there is the extra possibility of also being able to use these plants in the nutritional supplements industry due to their favorable antioxidant and mineral composition. In this sense, thirteen vegetable species-Chanania lanzan, Ziziphus mauritiana, Nilumbo nucifera, Terminalia catappa, Terminalia arjuna, Terminalia bellirica, Terminalia chebula, Lagenaria siceraria, Luffa aegyptiaca, Praecitrullus fistulosus, Benincasa hispida, Citrullus lanatus var. lanatus and Cucurbita maxima-have been analyzed. In this paper we discuss the distribution of polyphenols and minerals (Na, K, Mg, Ca, Al, P, S, Cr, Mn, Fe, Cu, Zn, Mo, As and Pb) in different seed parts (the rhizome, pericarp, carpel, seed coat and kernel) of the above species and their possible use in the nutritional supplements industry. The concentrations of total polyphenols, flavonoids and minerals ranged from 407 to 3144 mg rutin hydrate/100 g, 24 to 3070 mg quercetin/100 g and 1433 to 7928 mg/100 g, respectively. K, Ca, P and S were abundant in these herbal fruits. In two species of herbal fruits, Terminalia arjuna and Terminalia chebula, only part of the seed structure was suitable for use in nutritional supplements.

Effect of in vitro digestion and fermentation on antioxidant capacity of weight loss foods and Maillard reaction products content.

Cereal snacks and meal replacement shakes are gaining popularity as part of a low-calorie diet. However, some concerns have been risen in relation to their nutrient content and industrial processing. Here we analyzed 74 products, including cereal bars, cereal cakes and meal replacement shakes. We measured furosine and 5-hydroxymethyl-furfural (HMF) due to their relation with industrial processing, mainly thermal treatment, as well as antioxidant capacity after in vitro digestion-fermentation. Most of the products reported a high sugar content, including also large concentrations of HMF and furosine. Small differences were found on antioxidant capacity, although chocolate addition tended to increase the antioxidant power of products. According to our results, antioxidant capacity released after fermentation is higher, which points out to the importance of gut microbes in releasing potentially bioactive compounds. Additionally, we have found alarmingly high concentrations of furosine and HMF, which calls to research into new technologies for food processing to minimize their generation.

Stance4Health Nutritional APP: A Path to Personalized Smart Nutrition.

Access to good nutritional health is one of the principal objectives of current society. Several e-services offer dietary advice. However, multifactorial and more individualized nutritional recommendations should be developed to recommend healthy menus according to the specific user's needs. In this article, we present and validate a personalized nutrition system based on an application (APP) for smart devices with the capacity to offer an adaptable menu to the user. The APP was developed following a structured recommendation generation scheme, where the characteristics of the menus of 20 users were evaluated. Specific menus were generated for each user based on their preferences and nutritional requirements. These menus were evaluated by comparing their nutritional content versus the nutrient composition retrieved from dietary records. The generated menus showed great similarity to those obtained from the user dietary records. Furthermore, the generated menus showed less variability in micronutrient amounts and higher concentrations than the menus from the user records. The macronutrient deviations were also corrected in the generated menus, offering a better adaptation to the users. The presented system is a good tool for the generation of menus that are adapted to the user characteristics and a starting point to nutritional interventions.

Effects of different foods and cooking methods on the gut microbiota: an in vitro approach.

To support personalized diets targeting the gut microbiota, we employed an in vitro digestion-fermentation model and 16S rRNA gene sequencing to analyze the microbiota growing on representative foods of the Mediterranean and Western diets, as well as the influence of cooking methods. Plant- and animal-derived foods had significantly different impacts on the abundances of bacterial taxa. Animal and vegetable fats, fish and dairy products led to increases in many taxa, mainly within the Lachnospiraceae. In particular, fats favored increases in the beneficial bacteria Faecalibacterium, Blautia, and Roseburia. However, butter, as well as gouda cheese and fish, also resulted in the increase of Lachnoclostridium, associated to several diseases. Frying and boiling produced the most distinct effects on the microbiota, with members of the Lachnospiraceae and Ruminococcaceae responding the most to the cooking method employed. Nevertheless, cooking effects were highly individualized and food-dependent, challenging the investigation of their role in personalized diets.

Relationship of Thermal Treatment and Antioxidant Capacity in Cooked Foods.

Most of the foods we eat undergo a cooking process before they are eaten. During such a process, the non-enzymatic browning occurs, which generates compounds such as furosine, 5-hydroxymethylfurfural (HMF) and furfural. These are considered markers of cookedness and can therefore be used as quality indicators. In this work, we study the production of these compounds in different foods (both of plant and animal origin) that are cooked with different techniques. Additionally, we investigate correlations between the production of these markers of cookedness and the antioxidant capacity produced after in vitro digestion and fermentation. We observe that, in general, cereals and vegetables are more thermally damaged. Toasting and frying produce the highest concentrations of Maillard compounds whereas boiling the lowest. Furosine content shows a significant positive correlation with in vitro digestion data in fried foods, and with fermentation in roasted foods. Furfural content shows a significant positive correlation with in vitro digestion results in roasted foods, specifically in the Folin-Ciocalteu method.

Regulación de la respuesta inflamatoria intestinal mediante la ingesta de compuestos de Maillard y su interacción con los receptores RAGE y GPR43 / Regulation of the intestinal inflammatory response through the ingestion of Maillard compounds and their interaction with RAGE and GPR43 receptors

Las señales de daño molecular atraen a los neutrófilos hasta los lugares donde hay infección o inflamación. El receptor acoplado a la proteína G (GPR43) y el receptor para los compuestos avanzados de glicosilación (RAGE) reconocen a ácidos grasos de cadena corta (propionato y butirato) y AGEs (compuestos avanzados de glicosilación) respectivamente, estando ambos receptores abundantemente expresados en los neutrófilos y las células del epitelio intestinal. El papel funcional que juega la activación de estos receptores en la orquestación in vivo de la respuesta inmune no está claro. Nuestro trabajo examina el efecto de la ingesta de AGEs sobre la respuesta inmune, tanto en ratones sanos como en ratones a los que se les indujo una colitis, utilizando ratones transgénicos deficientes en los receptores GPR43 o RAGE. Uno de los principales hallazgos es que tanto el receptor GPR43 como el RAGE son necesarios para el reclutamiento de los neutrófilos en un modelo de inflamación intestinal por lesión de la barrera mucosa. Así mismo hemos comprobado que los AGEs ingeridos con la dieta promueven la aparición de un desequilibrio en el balance inflamatorio a nivel intestinal, dando lugar a un status proinflamatorio. Igualmente hemos demostrado que la carboximetillisina (CML), un tipo de AGE concreto, es capaz de estimular el receptor GPR43 y actuar como un factor quimioatractor de los neutrófilos. Finalmente, hemos ensayado el tratamiento con sRAGE, proteína capaz de captar AGEs libres. Este procedimiento podría ser una terapia prometedora para el tratamiento de la enfermedad inflamatoria intestinal. (AU)

Molecular damage signals attract neutrophils to sites of infection or inflammation. The G-protein coupled receptor (GPR43) and the receptor for advanced glicosilation compounds (RAGE) recognize short-chain fatty acids (propionate and butyrate) and AGEs (advanced glycosylation compounds) respectively, both receptors being abundantly expressed in neutrophils and intestinal epithelial cells. The functional role that activation of these receptors plays in the in vivo orchestration of the immune response is unclear. Our work examines the effect of the ingestion of AGEs on the immune response, both in healthy mice and in mice that were induced to colitis, using transgenic mice deficient in GPR43 or RAGE receptors. One of the main findings is that both the GPR43 receptor and RAGE are necessary for the recruitment of neutrophils in a model of intestinal inflammation due to mucosal barrier injury. We have also verified that the AGEs ingested with the diet promote the appearance of an imbalance in the inflammatory balance at the intestinal level, giving rise to a pro-inflammatory status. We have also show that carboxymethylisine (CML), a specific type of AGE, is capable of stimulating the GPR43 receptor and acting as a neutrophil chemoattraction factor. Finally, we have tested the treatment with sRAGE, a protein capable of capturing free AGEs. This procedure could be a promising therapy for the treatment of inflammatory bowel disease. (AU)

The Role of the Gut Microbiome in Cow's Milk Allergy: A Clinical Approach.

Cow's milk allergy (CMA) is the most prevalent food allergy (FA) in infancy and early childhood and can be present with various clinical phenotypes. The significant increase in FA rates recorded in recent decades has been associated with environmental and lifestyle changes that limit microbial exposure in early life and induce changes in gut microbiome composition. Gut microbiome is a diverse community of microbes that colonize the gastrointestinal tract (GIT) and perform beneficial functions for the host. This complex ecosystem interacts with the immune system and has a pivotal role in the development of oral tolerance to food antigens. Emerging evidence indicates that alterations of the gut microbiome (dysbiosis) in early life cause immune dysregulation and render the host susceptible to immune-mediated diseases later in life. Therefore, the colonization of the gut by "healthy" microbes that occurs in the first years of life determines the lifelong health of the host. Here, we present current data on the possible role of the gut microbiome in the development of CMA. Furthermore, we discuss how gut microbiome modification might be a potential strategy for CMA prevention and treatment.

The Intake of Antioxidant Capacity of Children Depends on Their Health Status.

The gastrointestinal digestion of food and further gut microbial activity render a myriad of different molecules that could be responsible for the biological activities that are classically assigned to their parent compounds. This has been previously shown for some phytochemicals whose antioxidant capacity was either increased or decreased after being metabolized by gut microbes. Whether a global antioxidant capacity that is extracted from food is determined by the gut microbial community structure is still not well described. In the present study, we in vitro digested and fermented 48 different foods that were submitted to different culinary treatments using the stools of lean children, obese children, celiac children and children with an allergy to cow's milk proteins. Their antioxidant capacities were assessed with the DPPH and FRAP assays, and the percentage that each food contributed to their daily antioxidant intake as well as their antioxidant capacity by portion size was inferred. Overall, cereals, fruits and vegetables displayed a higher contribution to their daily antioxidant intake, while tubers, fish and meat exhibited a higher antioxidant capacity by serving size. The food that was fermented in the lean children's and those children that were allergic to cow's milk protein's fecal material, showed a higher antioxidant capacity, which could imply that there is a larger role of the gut microbiota in this area.

Nutritional Habits of Professional Cyclists during Pre-Season.

The first aim of the present study was to assess the dietary intake of professional cyclists during pre-season. The second aim was to assess the dietary habits of this population during a complete season. Fifteen elite male (age: 23.2 ± 5.4 years) and twenty-three elite female (age: 20.1 ± 7.0 years) cyclists volunteered to participate in the study. Dietary nutrient intake during pre-season was assessed using a 72 h dietary recall interview, and a 136-item food frequency questionnaire was used to assess dietary habits during the year. Protein intake exceeded the PRI's recommendation of 0.83 g/kg/day for all cycling groups. Fat exceeded RI recommendations in females in both road (43.3%) and CXO (39.8%) cycling groups, whilst males were found to follow recommendations for fat intake. CHO intake was below recommendations in all groups. Intake of all vitamins exceeded recommendations, with the exception of B9 in female road cyclists (77.8% RDA) and vitamin D in all groups. With regards to mineral intake, consumption exceeded RDA/AI recommendations in all groups except for iodine in male XCO cyclists (61.6%), female road cyclists (61.6%), and female XCO cyclists (58%) and potassium in female road cyclists (74.6%). Males consumed greater amounts of eggs and non-processed foods than females. Road cyclists consumed greater amounts of fish and seafood and had a lower intake of coffee and tea than XCO cyclists. Better knowledge of food guidelines in terms of serving and food variety is important for professional cyclists at may impact health and performance.