Background & aims: The human gut microbiota plays a key role in health. Factors shaping its composition and diversity have been widely studied during infancy and adulthood, but far less in adolescence, despite this being a key developmental stage. We examined the potential associations between the gut microbiota of adolescents and 82 variables measured from pregnancy to adolescence. Methods: In this cross-sectional study, stool samples were collected from 366 adolescents (age range: 13-16 years) from two INMA cohorts (Spain), while a range of variables, including diet, lifestyle, sociodemographic factors, health status, antibiotic use, vaccination, COVID-19, anthropometrics, and pubertal development, were collected from pregnancy to adolescence. The gut microbiota was characterized using 16S rRNA gene sequencing and assessed using α- and β-diversity indices and abundances of individual taxa. Associations were evaluated using linear models and permutational multivariate analysis of variance (PERMANOVA). Results: Vegetable intake during pregnancy was positively associated with α-diversity, as well as with general composition and the abundance of four genera (inversely with Dialister , Lachnoclostridium and Agathobacter , and positively with Phascolarctobacterium ). Legume intake was also inversely associated with Desulfovibrionaceae and Sutterella . During adolescence, cereal and pasta intake was positively associated with α-diversity, as well as with general composition and inversely associated with Bacteroides , whereas fish and seafood intake was inversely associated with α-diversity. Relevant non-dietary variables measured during pregnancy and at birth, such as biological sex, parental social class, and maternal education, and during adolescence, such as antibiotic use, body mass index, and pubertal status, were also associated with general composition of the gut microbiota and different taxa in either direction. Conclusions: Diet during pregnancy and adolescence, together with some anthropometric, clinical, and biological factors, appeared to play an important role in shaping the composition and diversity of the gut microbiota in this population of adolescents.

Despite their relevance, studies of the long-term stability of the gut microbiome are rare due to the difficulty in following the same individual through long periods of time, particularly during childhood and adolescence. Here, we have been able to analyze microbiome stability throughout a 3-year period in toddlers, adolescents, and adults of the same population, at the levels of taxonomic composition and functional profile. Our analyses show that stability is lower at taxonomical than at functional level in all three age groups, indicating the existence of functional redundancy through time. Considering the entire period of sampling, toddlers were significantly more unstable than the other two groups at the level of taxonomic composition. However, local analyses revealed that low stability for both composition and function was restricted to the time period between 20 and 24 months of age, whereas after this point stability levels in toddlers were similar to those of adolescents and adults. Although the microbiome stabilized at around two years of age in terms of large-scale, rapid changes in diversity, composition, and functional profile, further changes did occur both before and after adolescence. Therefore, adolescence remains a transitional period, in which the abundances of some taxa and functions still differ from adult levels. These include, among others, Bifidobacterium, Streptococcus, Bacteroides fragilis and several members of the Lachnospiraceae, as well as various functions related to energy metabolism. Overall, our results pinpoint the two-years mark as a point of significant stabilization for the gut microbiome, without precluding the further occurrence of important changes in the relative abundance of specific taxa and gene functions both before and after adolescence.

The Sahara Desert and the Sahel region in North Africa contribute approximately 50-70% of global atmospheric dust emissions. Microorganisms can attach to dust particles and be dispersed into exogenous environments, being subsequently deposited by gravitational sedimentation (dry deposition) or through aqueous precipitation (wet deposition) also known as muddy rain. In the present work, five muddy rain samples were collected in Granada (Spain) during different episodes in 2021-2022. The SEM-EDX study demonstrated a high content of fine clay particles which may facilitate the atmospheric transport of microorganisms. The colonization of strategic microsites and the formation of mineral aggregates might be possible mineral-bacteria interactions. According to metagenomic analysis, Pseudomonadota (64%), Bacteroidota (13%), and Bacillota (6%) were the main phyla. At the genus level, extremophiles, plant-beneficial bacteria, and others involved in soil biogeochemical cycles have been described. Fourteen cultivable microorganisms were isolated and identified by means of 16S rRNA sequencing. Members of the phyla Pseudomonadota, Bacillota, Actinomycetota and Bacteroidota have been found. Among the isolates, Stenotrophomonas rhizophila and Brevundimonas bullata potentially exert beneficial effects at the ecosystem level. In general, muddy rain facilitates the transport and dispersal of microorganisms from different environments, with a potential positive influence on soils and vegetation in terrestrial ecosystems.

Faced with the challenge of reducing food waste, transforming discarded fruit into functional ingredients useful for the food industry is a valuable solution. Ingredients from fruit such as persimmons, which are rich in indigestible carbohydrates and bioactive compounds with antiradical capacity, could positively impact on the health of certain population groups due to their potential prebiotic effect. This study aimed to select the most suitable drying conditions and milling intensity for obtaining powdered persimmon ingredients with a prebiotic-like effects observed in vitro for postmenopausal women, and to evaluate this effect by considering the stimulation of health-promoting bacterial growth and short-chain fatty acids (SCFAs) production. First, the effect of the drying method (hot air drying at 60 and 70 °C, and freeze-drying) and grinding intensity on antiradical capacity, particle size, and the release of bioactive antiradical components into the intestinal lumen after an in vitro gastrointestinal digestion was determined. Next, the effect of these conditions on the microbiota composition of postmenopausal women was preliminary assessed in a batch colonic fermentation experiment for 24 h. The results showed that the ingredient dried with air at 70 °C had the highest phenol and flavonoid content, suffered the least degradation during in vitro gastrointestinal digestion and promoted the differential growth of fiber-degrader genera. Consequently, this was the ingredient selected as the most suitable. Lastly, the impact of this ingredient on the microbiota composition of 4 postmenopausal women has been evaluated in a long-term study using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®) coupled to high throughput sequencing. The growth stimulation of health-associated bacteria, such as Akkermansia muciniphila, Faecalibacterium prausnitzii or Phascolarctobacterium faecium, and the promotion of beneficial metabolic pathways, such as the sugar uptake-specific phosphotransferase system, sugar metabolism and propionate and isobutyrate production, were detected along 14 days of persimmon powder supplementation. A holistic framework for promoting human health while advancing environmental sustainability is represented by the combination of sustainable by-product valorization and microbiota-targeted functional food development.

While a proportion of the microbiota plays a beneficial role, there is no conclusive evidence that the entire microbiome is mutualistic. Here, we have studied the intestinal microbiota of three healthy age groups from the Valencian Region (Spain). We have periodically obtained stool samples to determine the 16S rRNA gene amplicons, metagenomes, and metatranscriptomes, and we have observed that the microbiota’s stability differs with age, being less stable in infants. Regarding analyses of the conserved microbiota across the three age groups throughout the study period, shared genera account for about 60%. In addition, we identified a core of microbial taxa present in all individuals, which could represent mutualistic symbionts. Finally, in a previous study, we detected that tryptophan and indole production by intestinal bacteria decreases substantially with host age. Metagenomics and metatranscriptomics analyses show that tryptophanase mRNA synthesis in the genus Akkermansia is approximately 10 times lower in adults and the elderly than in children, consistent with this enzyme’s low levels or absence in these groups. Consequently, this supports the hypothesis that an uncoupling might occur between some microbiota taxa and the human host at older ages.

This study aimed to evaluate the gut microbiota and mycobiota composition, depending on the Mediterranean diet (MD) adherence, using metataxonomics. Combining metagenomics and metatranscriptomics, we also investigate the gene expression level in the bacterial community. Two groups of healthy subjects greatly differing in adherence were selected. Significant differences in microbiota composition were observed between individuals with high adherence (HAMD; mean 10.5 +/- 0.9 points) and low adherence (LAMD; 5.23 +/- 83 points). Notably, the olive oil, vegetable, and fruit consumption presented an important discriminant power between groups. Saccharomyces, Penicillium, and Candida were the most abundant genera. Mycobiota richness was higher in LAMD than in HAMD. Aspergillus was identified as a biomarker for LAMD, whereas Yarrowia, a potential probiotic, was a biomarker for HAMD. Metatranscriptomics indicated that Bacillota was the most metabolically active phylum in the gut microbiota. The low-abundant genus, Methanobrevibacter, showed high transcriptional activity, contributing to the crucial methanogenesis process. Gene expression analyses further highlighted functional differences. Overall, HAMD microbiota presented increased metabolic activity, protein synthesis, and cellular mobility. Overexpression of flagellin and urease genes may enhance immune response in HAMD. Further metatranscriptomic studies are necessary to deepen our understanding of intestinal microbiota transcriptional programs and their interactions with the diet and human health.

INTRODUCTION:The potential involvement of pathogens in the development of atherosclerosis has been studied for decades. Some previous studies have successfully identified the presence of pathogens in the atheromatous plaque. However, many of these determinations are aimed at detecting the presence of a particular species. The use of omics technologies allows for the analysis of the complete microbial profile of a given sample. In the specific case of atheromatous plaque, the study of the bacterial load composition would help to clarify the possible relationship between infection and atherosclerosis and identify whether there is a bacterial profile associated with unstable plaques and, therefore, with the consequent risk of ischemic events. METHODOLOGY:We analyzed cross-sectional fragments of carotid atheromatous plaque (N=57) and serum (N=54) from patients with recent neurological symptoms and asymptomatic patients (control group). Nucleic acids were extracted from the samples by enzymatic digestion and homogenization, with additional treatment with type I collagenase in the case of plaques. Bacterial ribosomal RNA (16S-rRNA gene) was amplified and subjected to massive sequencing using the Illumina® Miseq platform. The bioinformatic analysis, to identify the taxonomic composition, and biostatistical analysis, to determine the significant taxa, of the 16S-rRNA was performed in the R environment. As contamination control, bacterial species ratios ≥10 with respect to negative controls were considered significant. RESULTS:The presence of bacterial 16S-rRNA was very low in both types of samples. The bacterial composition in terms of α diversity and β diversity differed between plaque and serum; however, we did not observe significant differences between samples from symptomatic and asymptomatic patients. The most abundant phylum and genus in plaque were Firmicutes and Staphylococcus, respectively. For Staphylococcus, we found 100% similarity homology of the 16S-rRNA with 3 species (S. epidermidis, S. caprae, and S. capitis). In serum, the most abundant phyla were Firmicutes and Proteobacteria, with Streptococcus being the dominant genus, for which we found 100% homology of the 16S-rRNA with 20 species of oral streptococci. CONCLUSIONS:We have successfully applied massive sequencing techniques to determine the presence and relative abundance of bacterial species in atheromatous plaques and serum of patients undergoing carotid endarterectomy. We have not observed significant differences between symptomatic and asymptomatic patients regarding the main genera, so we cannot establish a direct connection between bacterial composition and atheromatous plaque vulnerability. However, a possible association between atherosclerosis and the presence of staphylococci and streptococci in plaque and serum, respectively, cannot be ruled out.

Introducción La posible implicación de patógenos en el desarrollo de la aterosclerosis se ha estudiado durante décadas. Algunos estudios previos han logrado identificar la presencia de patógenos en la placa de ateroma. Sin embargo, muchas de estas determinaciones, se basan en técnicas estándar, son dirigidas y están encaminadas a detectar la presencia de una especie en particular. El empleo de tecnologías ómicas permite analizar el perfil microbiano completo de una determinada muestra. En el caso concreto de la placa de ateroma, el estudio de la composición carga bacteriana, ayudaría a esclarecer la posible relación entre infección y aterosclerosis e identificar si existe un perfil bacteriano asociado con placas inestables y, por lo tanto, con el consecuente riesgo de eventos isquémicos. Metodología Analizamos fragmentos transversales de placa de ateroma carotídeo (N=57) y suero (N=54) de los pacientes con sintomatología neurológica reciente y asintomáticos (grupo control). Se extrajeron los ácidos nucleicos de las muestras mediante digestión enzimática y homogeneización, previo tratamiento adicional con colagenasa tipo I en el caso de las placas. Se amplificó el RNA ribosomal bacteriano (gen 16S-rRNA) y se sometió a secuenciación masiva mediante a plataforma Illumina® Miseq. El análisis bioinformático, para identificar la composición taxónomica, y bioestadístico, para determinar los taxones significativos, del 16S-rRNA se realizó en el entorno R. Como control de contaminación se consideraron significativas ratios de especies bacterianas ≥10 respecto a controles negativos. Resultados La presencia de 16S-rRNA bacteriano fue muy baja en ambos tipos de muestra. La composición bacteriana en términos de diversidad α y diversidad β difirió entre placa y suero; sin embargo, no observamos diferencias significativas entre muestras de los pacientes sintomáticos y asintomáticos. El filo y género más abundante en placa fueron, respectivamente, Firmicutes y Staphylococcus. Para Staphylococcus encontramos homología con el 100% de similitud del 16S-rRNA con 3 especies (S. epidermidis, S. caprae y S. capitis). En suero, los filos más abundantes fueron, Firmicutes y Proteobacteria, siendo Streptococcus el género dominante, para el que encontramos 100% de homología del 16S-rRNA con 20 especies de estreptococos orales. Conclusiones Hemos aplicado con éxito técnicas de secuenciación masiva para determinar la presencia y abundancia relativa de especies bacterianas en placas de ateroma y suero de los pacientes sometidos a endarterectomía carotídea. No hemos observado diferencias significativas entre los pacientes sintomáticos y asintomáticos en cuanto a los principales géneros, por lo que no podemos establecer una conexión directa entre la composición bacteriana y la vulnerabilidad de la placa de ateroma. Sin embargo, no se descarta una posible asociación entre la aterosclerosis y la presencia de estafilococos y estreptococos en placa y suero, respectivamente.

The human gut microbiota plays a critical role in maintaining health and homeostasis. Kefir, a traditional fermented beverage, is recognized for its health benefits, yet the underlying mechanisms remain incompletely understood. This study aimed to investigate the microbial composition, functional profiles, viability, and immunomodulatory properties of 11 commercial kefir beverages compared to 4 pharmaceutical probiotic formulations. Samples were analyzed both before and after in vitro gastrointestinal digestion, and their effects on intestinal immune signaling pathways, including Aryl Hydrocarbon Receptor (AhR), Toll-like Receptor 4 (TLR4), and Toll-like Receptor 9 (TLR9), were assessed. Our findings revealed high variability in kefir microbiomes, with significant differences in bacterial and fungal communities across samples. A negative correlation was found between fungal diversity, bacterial diversity, and immune receptor responses, suggesting that microbe-microbe interactions play a key role in kefir's immunomodulatory potential. Differences between kefirs and pharmaceutical probiotics, particularly in TLR9 modulation, highlight the distinct immunoregulatory effects of kefir. Future research should focus on strain-specific contributions, bioactive metabolites, long-term health effects of kefir consumption and synergic outcomes derived from milk matrix-microbial elements interactions. This study provides a foundation for further exploration into the therapeutic potential of fermented foods in promoting immune balance and gut homeostasis.

Studies on the human virome based on the application of metagenomic approaches involve overcoming a series of challenges and limitations inherent not only to the biological features of viruses, but also to methodological pitfalls which different approaches have tried to minimize. These approaches fall into two main categories: bulk-metagenomes and virus-like particle (VLP) enrichment. In order to address issues associated with commonly used experimental procedures to assess the degree of reliability, representativeness, and reproducibility, we designed a comparative analysis applied to three experimental protocols, one based on bulk-metagenomes and two based on VLP enrichment. These protocols were applied to stool samples from 10 adult participants, including two replicas per protocol and subject. We evaluated the performances of the three methods, not only through the analysis of the resulting composition, abundance, and diversity of the virome via taxonomical classification and type of molecule (DNA versus RNA, single stranded vs. double stranded), but also according to how the a priori identical replicas differed from each other according to the extraction methods used. Our results highlight the strengths and weaknesses of each approach, offering valuable insights and tailored recommendations for drawing reliable conclusions based on specific research goals.

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.

Although gut dysbiosis is associated with cow’s milk allergy (CMA), causality remains uncertain. This study aimed to identify specific bacterial signatures that influence the development and outcome of the disease. We also investigated the effect of hypoallergenic formula (HF) consumption on the gut microbiome of milk-allergic children. 16S rRNA amplicon sequencing was applied to characterize the gut microbiome of 32 milk-allergic children aged 5–12 years and 36 age-matched healthy controls. We showed that the gut microbiome of children with CMA differed significantly from that of healthy children, regardless of whether they consumed cow’s milk. Compared to that of healthy cow’s milk consumers, it was depleted in Bifidobacterium, Coprococcus catus, Monoglobus, and Lachnospiraceae GCA-900066575, while being enriched in Oscillibacter valericigenes, Negativibacillus massiliensis, and three genera of the Ruminococcaceae family. Of these, only the Ruminococcaceae taxa were also enriched in healthy children not consuming cow’s milk. Furthermore, the gut microbiome of children who developed tolerance and had received an HF was similar to that of healthy children, whereas that of children who had not received an HF was significantly different. Our results demonstrate that specific gut microbiome signatures are associated with CMA, which differ from those of dietary milk elimination. Moreover, HF consumption affects the gut microbiome of children who develop tolerance.

The presence of components of nutritional interest makes fresh almond bagasse an interesting by-product for obtaining functional ingredients. Stabilization through a dehydration process is an interesting option for its integral use, ensuring its conservation and management. Subsequently, it can be turned into powder, facilitating its use as an ingredient. The aim of this paper was to determine the effects of hot air drying at 60 and 70 °C and lyophilization on the release of phenolic components and antiradical capacity in in vitro gastrointestinal digestion and colonic fermentation, as well as on growing microbiota composition by applying high throughput sequencing. The novelty of this study lies in this holistic approach; considering both technological and physiological aspects related to gastrointestinal digestion and colonic fermentation will provide the best conditions for functional foods. The results obtained showed that lyophilization provides a powder with a total phenol content and antiradical capacity higher than hot air drying. Furthermore, in dehydrated samples, both in vitro digestion and colonic fermentation revealed a phenol content and anti-radical capacity superior to those existing in undigested products. In addition, after colonic fermentation, beneficial bacteria species have been identified. Obtaining powders from almond bagasse is presented as an interesting opportunity for the valorization of this by-product.

Western diet, high in fats and sugars and low in greens, contributes to dysbiosis of the gut microbiota, which can lead to a variety of chronic diseases related with inflammation. Supplementation with bioactive compounds can help to maintain a healthy eubiotic state. Thus, we performed a 4-weeks nutritional intervention on healthy volunteers to investigate whether a blend of natural tannin extracts could induce healthy changes in the microbial intestinal ecosystem. Changes in the composition and functionality of the microbiota could be observed from the first two weeks onward. 16S rRNA amplicon next-generation sequencing (NGS) revealed a significant increase in microbial diversity at the end of the intervention, as well as trends toward increases in the relative abundances of several beneficial taxa, such as Ruminococcus bicirculans, Faecalibacterium prausnitzii, Lachnospiraceae UCG 010, Lachnospiraceae NK4A136, Bacteroides thetaiotaomicron and B. uniformis. Remarkably, some of the identified taxa were also identified as responsible for an increase in the production of short-chain fatty acids (SCFAs), microbial metabolites that contribute to the modulation of the immune system and have various other anti-inflammatory functions in the gut. Taken together, these results suggest that the tannin supplementation could exert a prebiotic effect by selectively stimulating the growth and the activity of bacteria that are advantageous for the host.

While the intestinal microbiome seems a major driver of persistent immune defects in people with HIV (PWH), little is known about its fungal component, the mycobiome. We assessed the inter-kingdom mycobiome-bacteriome interactions, the impact of diet, and the association with the innate and adaptive immunity in PWH on antiretroviral therapy. We included 24 PWH individuals and 12 healthy controls. We sequenced the Internal Transcribed Spacer 2 amplicons, determined amplicon sequence variants, measured biomarkers of the innate and adaptive immunity in blood and relations with diet. Compared to healthy controls, PWH subjects exhibited a distinct and richer mycobiome and an enrichment for Debaryomyces hansenii, Candida albicans, and Candida parapsilosis. In PWH, Candida and Pichia species were strongly correlated with several bacterial genera, including Faecalibacterium genus. Regarding the links between the mycobiome and systemic immunology, we found a positive correlation between Candida species and the levels of proinflammatory cytokines (sTNF-R2 and IL-17), interleukin 22 (a cytokine implicated in the regulation of mucosal immunity), and CD8+ T cell counts. This suggests an important role of the yeasts in systemic innate and adaptive immune responses. Finally, we identified inter-kingdom interactions implicated in fiber degradation, short-chain fatty acid production, and lipid metabolism, and an effect of vegetable and fiber intake on the mycobiome. Therefore, despite the great differences in abundance and diversity between the bacterial and fungal communities of the gut, we defined the changes associated with HIV, determined several different inter-kingdom associations, and found links between the mycobiome, nutrient metabolism, and systemic immunity.

Aims: Children with HIV exhibit chronic inflammation and immune dysfunction despite antiretroviral therapy (ART). Strategies targeting persistent inflammation are needed to improve health in people living with HIV. The gut microbiota likely interacts with the immune system, but the clinical implications of modulating the dysbiosis by nutritional supplementation are unclear. Methods: Pilot, double-blind, randomized placebo-controlled trial in which 24 HIV-infected on ART were randomized to supplementation with a daily mixture of symbiotics, omega-3/6 fatty acids and amino acids, or placebo four weeks, in combination with ART. We analyzed inflammatory markers and T-cell activation changes and their correlations with shifts in fecal microbiota. Results: Twenty-four HIV-infected children were recruited and randomized to receive a symbiotic nutritional supplement or placebo. Mean age was 12 ± 3.9 years, 62.5% were female. All were on ART and had HIV RNA < 50/mL. We did not detect changes in inflammatory (IL-6, IL-7, IP-10), microbial translocation (sCD14), mucosal integrity markers (IFABP, zonulin) or the kynurenine to tryptophan ratio, or changes in markers of the adaptive immune response in relation to the intervention. However, we found correlations between several key bacteria and the assessed inflammatory and immunological parameters, supporting a role of the microbiota in immune modulation in children with HIV. Conclusions: In this exploratory study, a four-week nutritional supplementation had no significant effects in terms of decreasing inflammation, microbial translocation, or T-cell activation in HIV-infected children. However, the correlations found support the interaction between gut microbiota and the immune system.

Abstract Background Dietary interventions are likely tools for modulation of the gut microbiota but the large inter-individual variability in gut microbiota composition leads to different host responsiveness and the impact of a particular food cannot be assessed. In contrast, in vitro fermentation models allow characterization of the fecal microbiota when fermenting a large number of different foods. Furthermore, cooking methods also directly influence the effects of food on gut microbiota composition. The aim of this study was to investigate the gut microbiota growing on representative foods of the Mediterranean and Western diets as well as the influence of cooking methods using in vitro fermentations. Results We performed in vitro digestions and fermentations of 55 foods, raw or cooked using up to 5 cooking methods, for a total of 159 combinations, employing fecal material from three healthy adults as inoculum. The composition of the bacterial communities was determined by sequencing the 16S rRNA gene. Foods derived from plants or animals had significantly different impacts on the abundances of bacterial taxa. Animal and vegetable fats, fish and dairy products led to the greatest shifts in microbial composition. Specifically, an increase in the beneficial bacteria Faecalibacterium, Blautia and Roseburia was identified in animal and vegetable fats. However, butter, dairy products and fish also resulted in higher abundances of Lachnoclostridium, which has been associated to several diseases. With respect to cooking methods, only frying and roasting had strong and common effects across all food categories. In general, fried foods showed more differences than other cooking methods, and Ruminococcus was particularly responsive to the cooking method employed. Conclusions Despite substantial differences in baseline microbiota composition, some shared effects were detected across the three analyzed individuals, such as the substantial impact of high-fat foods on the abundance of health-relevant bacteria. Cooking methods effects on the gut microbiota resulted to be highly individualized and food-dependent, making them challenging to investigate and integrate into personalized diet. Further characterization of the responses of the fermentative microbiota to food-cooking method combinations will enable the refinement of dietary interventions aimed at gut microbiota modulation, paving the way towards personalized nutrition.

Aims:Vaccine response is poor among children living with HIV. The gut microbiota has been identified as a potential target to improve vaccine immunogenicity, but data are scarce in the context of HIV infection.Methods:Pilot, double-blind, randomized placebo-controlled trial in which 24 HIV-infected children were randomized to receive a mixture of symbiotics, omega-3/6 fatty acids, and amino acids or placebo for 4 weeks, each in combination with ART, and were then immunized against influenza. Vaccine response and safety of the nutritional supplementation were the primary outcomes.Results:Eighteen HIV-infected children completed the follow-up period (mean age 11.5 ± 4.14 years, 61% female). The nutritional supplement was safe but did not enhance the response to the influenza vaccine. A 4-fold rise in antibody titers was obtained in only 37.5% of participants in the intervention arm vs. 40% in the placebo. No immunological or inflammatory predictors of vaccine response were identified.Conclusions:In this exploratory study, a 4-week course of symbiotics did not increase influenza vaccine immunogenicity in HIV-infected children. Larger studies are warranted to address the potential of modulating the microbiome in children living with HIV.

Understanding how diet and gut microbiota interact in the context of human health is a key question in personalized nutrition. Genome-scale metabolic networks and constraint-based modeling approaches are promising to systematically address this complex problem. However, when applied to nutritional questions, a major issue in existing reconstructions is the limited information about compounds in the diet that are metabolized by the gut microbiota. Here, we present AGREDA, an extended reconstruction of diet metabolism in the human gut microbiota. AGREDA adds the degradation pathways of 209 compounds present in the human diet, mainly phenolic compounds, a family of metabolites highly relevant for human health and nutrition. We show that AGREDA outperforms existing reconstructions in predicting diet-specific output metabolites from the gut microbiota. Using 16S rRNA gene sequencing data of faecal samples from Spanish children representing different clinical conditions, we illustrate the potential of AGREDA to establish relevant metabolic interactions between diet and gut microbiota.

Food and food bioactive components are major drivers of modulation of the human gut microbiota. Tannin extracts consist of a mix of bioactive compounds, which are already exploited in the food industry for their chemical and sensorial properties. The aim of our study was to explore the viability of associations between tannin wood extracts of different origin and food as gut microbiota modulators. 16S rRNA amplicon next-generation sequencing (NGS) was used to test the effects on the gut microbiota of tannin extracts from quebracho, chestnut, and tara associated with commercial food products with different composition in macronutrients. The different tannin-enriched and non-enriched foods were submitted to in vitro digestion and fermentation by the gut microbiota of healthy subjects. The profile of the short chain fatty acids (SCFAs) produced by the microbiota was also investigated. The presence of tannin extracts in food promoted an increase of the relative abundance of the genus Akkermansia, recognized as a marker of a healthy gut, and of various members of the Lachnospiraceae and Ruminococcaceae families, involved in SCFA production. The enrichment of foods with tannin extracts had a booster effect on the production of SCFAs, without altering the profile given by the foods alone. These preliminary results suggest a positive modulation of the gut microbiota with potential benefits for human health through the enrichment of foods with tannin extracts.