AIMS:To examine the associations between ultra-processed food (UPF) intake, glycemic control, cardiovascular risk factors, and gut microbiome in adults with type 1 diabetes (T1D). METHODS:In 253 adults with T1D, diet was assessed using the EPIC food-frequency questionnaire, and UPFs classified according to NOVA. Evaluations included lipid profile, HbA1c, and continuous glucose monitoring metrics. In a subgroup (n = 103), gut microbiota composition/function was analyzed using shotgun metagenomic sequencing and beta-diversity assessed by PERMANOVA. Associations were examined using multivariable regression models adjusted for age and Mediterranean diet adherence. RESULTS:Mean UPF intake was 15.5 % of total food intake. Higher UPF intake was independently associated with higher triglycerides (β per 20 g/1000 kcal = 3.62 mg/dL; 95 %CI 1.16-6.08) and lower HDL-cholesterol (β =  - 0.98 mg/dL; 95 %CI - 1.72 to - 0.24). Sugar/artificially sweetened beverages were positively associated with triglycerides and animal-based UPFs inversely associated with HDL cholesterol. In participants on multiple daily injections or open-loop systems, ready-to-eat mixed dishes were positively associated with HbA1c. Microbiome beta-diversity significantly differed according to UPF intake. Triglycerides positively associated with microbial pathways (ketogluconate, tetrapyrrole, and acetate metabolism). CONCLUSION:Higher UPF intake was associated with atherogenic dyslipidemia, poorer glycemic control in selected groups, and gut microbiome alterations in adults with T1D. The study was registered at ClinicalTrials.gov with the identifier NCT05936242.

Thanks to the standard microbiology protocols of isolation and culturing, hundreds of strains have been isolated from fermented foods throughout the last decades, and phenotypic traits linked with pro-technological properties and health claims have been investigated. However, culture-independent metagenomic analyses have revealed an unexpected microbial diversity in foods fermented spontaneously or by undefined starter cultures. Here, we report the most groundbreaking advancements in the understanding of fermented foods ecology by presenting case studies where metagenomics has been applied, contributing to identifying novel species in silico or to deciphering the microbiome structure associated with spontaneous fermentations. We also highlight the potential of metagenomics in supporting the identification of potential probiotics and discuss the future ahead, particularly focusing on the integration of multi-omics approaches.

N-Acylethanolamines (NAEs) are bioactive lipid mediators involved in the regulation of appetite, inflammation, and gut-brain signaling. This study investigated the metabolic fate of dietary NAEs following the consumption of two test meals with differing NAE contents in subjects with ileostomy and evaluated their effects on gastrointestinal hormones, glycaemia, and appetite regulation. An acute, double-blind, randomized, crossover postprandial study was conducted in ileostomy patients who consumed either a high-NAE meal (HNM) or a low-NAE meal (LNM) on two separate occasions. Ileal fluid and plasma samples were collected over an 8-hour postprandial period for analysis of NAEs and endocannabinoids (ECs). Baseline ileal microbiota composition was assessed. At the end of the 8-hour period, participants completed a buffet meal test to evaluate ad libitum energy intake. Dietary NAEs were significantly recovered in ileal fluids after HNM intake, with concentrations approximately 3-fold higher than those after LNM, suggesting partial digestion and release from the food matrix. No significant differences in postprandial plasma NAE concentrations were observed between meals. HNM consumption led to higher postprandial levels of plasma insulin, C-peptide, and glucose-dependent insulinotropic polypeptide, despite no differences in glycemic response or subsequent ad libitum energy intake. Metagenomic analysis identified clusters of ileal microbial taxa associated with circulating lipid profiles, suggesting a role of the small intestinal microbiota in the metabolism of NAEs and ECs. Dietary NAEs reach the small intestine at active concentrations and may influence local signaling via GPR119, with microbiota composition influencing their release from food.

Legumes represent a valuable and vegetable source of proteins and fiber with a very low environmental footprint production, therefore, both dietary guidelines and international agencies suggest increasing their production and consumption. Despite their favorable nutritional composition, they also naturally contain antinutritional factors such as phytic acid, that limit the absorption of micronutrients. This, coupled with the lower bioavailability of proteins as compared with meat, diminishes the biological and economic value of legumes. However, recent studies have shed a light on the power of fermentation to improve the protein profile of pulse and neutralize antinutritional compounds. In this review, we explore the benefits of legumes fermentation in depth, focusing on the role of microorganisms in enhancing the nutritional and sensory enhancement of legumes. Furthermore, we describe the properties and the microorganisms involved in the production of several craft-based fermented legumes typically consumed by non-Westernized populations, particularly delving into their effects on the gut microbiome and on the human health.

Gut microbiota may contribute to the adiposity-associated disease risk, but human studies reported inconsistent associations of adiposity with gut microbiota composition. We examined associations of body mass index (BMI) with alpha diversity and relative microbial abundance at the phylum and genus taxonomic levels (based on 16S rRNA amplicon sequencing or metagenomics) among 7415 adults from eight European observational studies in a joint federated analysis of harmonized data using DataSHIELD. Higher BMI (per 5 kg/m2) was associated with lower alpha diversity (β: -0.05; 95% CI: -0.07, -0.03) and, on the phylum level, positively associated with Proteobacteria, but neither with Firmicutes nor Bacteroidetes nor their ratio, where high between-study heterogeneity was observed. On the genus level, BMI was inversely associated with the relative abundance of Faecalibacterium of the Firmicutes phylum (β: -0.11; 95% CI: -0.14, -0.07) but positively with the odds of detection of Dorea, Streptococcus, and Clostridium (all three Firmicutes) as well as Collinsella (Actinobacteria). This federated analysis of multiple studies found lower alpha diversity, alongside depleted Faecalibacterium, as well as higher odds of detection of Dorea, Streptococcus, Clostridium, and Collinsella with higher adiposity. By combining data from diverse study populations using harmonized data and statistical methods, our analysis partly overcomes sources of heterogeneity that may explain previously observed inconsistencies.

The healthy vaginal microbiota is typically dominated by Lactobacillus species, while the dominance of different taxa often signals dysbiosis. Vaginal probiotics offer a promising therapeutic avenue to restore microbial balance and prevent recurrent infections. Using probiogenomics, this study investigated 19 novel strains belonging to four Lactobacillus species (Lactobacillus crispatus, Lactobacillus gasseri, Lactobacillus paragasseri, Limosilactobacillus fermentum) isolated from the vaginal environment of fertile and menopausal women. Through genomic screening and comparative genomics, we identified complementary roles between these species in activities crucial to women’s health. Our results indicate that vaginal Lactobacillus strains are genomically adapted to this niche, promoting persistence and pathogen-fighting. Furthermore, we demonstrated the potential ability of vaginal lactobacilli to survive the gastrointestinal transit and to explicate beneficial activities at the intestinal level, suggestion the possibility to be used through oral supplementation when topical application is not feasible. Although we confirmed L. crispatus as the most specialized to the vaginal niche, L. gasseri showed equivalent and complementary genetic traits, highlighting its previously underestimated role. L. paragasseri showed an interesting dichotomy, with beneficial traits alongside potentially unfavorable ones, while Lm. fermentum of vaginal origin may potentially have a role in the gut-vagina axis. In conclusion, our results strongly support the development of multispecies and multistrain probiotic blends, as the combined metabolic cooperation of vaginal lactobacilli may offer greater efficacy for vaginal health compared to single-strain supplements.

Targeted dietary strategies and supplements represent a promising approach for the treatment of cognitive problems. Multi-omic approaches may facilitate and accelerate the discovery of new psychobiotic strains and their applications. In this work, we applied metagenomics and comparative genomics to guide the isolation and screening of novel psychobiotic strains from fermented foods. Metagenomes of 1185 fermented food were screened, revealing the occurrence of genes coding for the biosynthesis of neuroactive molecules, supporting the isolation of 73 novel Lactic Acid Bacteria (LAB) strains. Comparative genomic analysis highlighted species-specific patterns, identifying Levilactobacillus brevis, Lactiplantibacillus plantarum, Limosilactobacillus fermentum as potential psychobiotics. In vitro functional screening for the production of neuroactive metabolites confirmed four strains, Lactiplantibacillus plantarum TUCC00000144, Limosilactobacillus fermentum TUCC00000777, Levilactobacillus brevis TO10, Lentilactobacillus diolivorans B92, as the most promising candidates for the development of dietary supplements or innovative fermented food products aimed at supporting mental health.

Meat processing environments harbor complex microbial ecosystems that may be transferred to the final product, thus influencing product quality and safety. Several factors may affect microbiome composition, such as seasonality and sanitation procedures. In this study, we carried out a metagenomic analysis over two seasons across four beef processing facilities, following beef carcasses from farm-to-fork. The pre-maturation environment was dominated by Corynebacterium xerosis and Acinetobacter johnsonii in summer, and by Bifidobacterium pseudolongum and Cutibacterium acnes in winter, whereas meat maturation environments were colonized by a specialized lactic acid bacterial community. The long-term maturation stage was led by Carnobacterium divergens and Carnobacterium maltaromaticum, whereas Pseudolactococcus carnosus and Pseudolactococcus paracarnosus prevailed during the retail stage. The environmental microbiome exhibited broad metabolic potential, in contrast to the specialized, low-diversity profiles of mature meat. Routine sanitation practices did not fully remove detectable microbial DNA signatures from environmental surfaces and were associated with shifts in taxonomic and functional profiles, including a greater representation of biofilm-associated genes. We also identified a diverse phage community, and statistical modeling revealed strong negative predictive associations with Listeria monocytogenes, Salmonella enterica, and Staphylococcus aureus. Collectively, our findings demonstrate that the beef processing microbiome is shaped by the interaction of multiple ecological forces. Understanding these interactions provides a comprehensive framework for ecology-based strategies to improve meat quality, safety, and shelf-life.

The term Next Generation Probiotics (NGPs) refers to microbial strains positively impacting on human health, but do not belong to common probiotic species (e.g., lactic acid bacteria, LAB). We characterized genomically and phenotypically 14 strains isolated from the gut microbiome of healthy individuals, to evaluate their ability to produce urolithins, equol and short-chain fatty acids (SCFA). The 4 most promising strains (namely Bacteroides uniformis A4, Bacteroides thetaiotaomicron A14, unclassified Bacteroidaceae A26 and unclassified Lachnospiraceae A49) were used for the production of a synbiotic formulation, containing the strains and the precursors of health-promoting molecules. This dietary supplement was administered for 2 weeks to a continuous mucosal-Simulator of the Human Intestinal Microbial Ecosystem (mSHIME) model inoculated with a faecal sample from a low fiber-consuming donor. We performed Shotgun Metagenome Sequencing on a total of 204 samples collected from lumen and mucosa compartments, and determined the concentration of SCFA, equol and urolithin. Our results highlighted that the potential NGP strains contained in the supplement persisted in the gut ecosystem during 2 weeks of washout (Wilcoxon’s rank sum test, p-value < 0.05). In addition, the treatment led to an enrichment in beneficial taxa and to an increase in the production of SCFAs (p-value < 0.05). This study demonstrated that feeding the gut microbiota with NGPs and dietary prebiotics can modulate both the gut microbiome and metabolome, suggesting a potential beneficial impact on human health. However, further in vivo studies are needed to confirm these results.

The microbial organisms living in food and food systems have a key role in food processing, quality, safety, and even in human health promotion. This review aims to summarize recent advancements in the characterization of novel species from metagenomics data, with a focus on their relevance for food microbiology. We discuss the generation of metagenome-assembled genomes, a crucial step that facilitates comparative genomic analyses and development of databases for taxonomic profiling and functional potential characterization. We also highlight how these approaches enable new applications in food science and examine the broader implications of these findings to better understand the interactions between food and human health. Finally, we present key challenges that need to be addressed to fully characterize the hidden diversity of food microbiomes and to exploit their potential for innovation in food science and health-related applications.

We selected ingredients with a high content of bioactive components typical of the Mediterranean diet (MD) and designed an MD-based food. Its effect on human gut microbiota, microbiome, and metabolome was explored in comparison to placebo by feeding a Twin Mucosal Simulator of the Human Intestinal Microbial Ecosystem (Twin M-SHIME). The fecal donor used for the inoculation of the Twin M-SHIME was chosen within a cohort of individuals showing low adherence to MD. The administration of MD-based food increased the abundance of numerous taxa, almost all having the potential to exert beneficial activities. The reshaping of the microbiota reflected on microbiome changes: genes responsible for colanic acid biosynthesis (implicated in healthy aging) and carbohydrate metabolism increased, whereas genes involved in l-valine pathway decreased. MD-based food temporarily increased short-chain fatty acid (SCFA) synthesis, reflecting the increase of genes responsible for butyrate synthesis and fiber degradation. MD-based food modulated the synthesis of volatile organic compounds (VOCs), mainly esters derived from medium- and long-chain fatty acids and polyunsaturated fatty acids.

The consumption of water of low microbiological quality can be detrimental and may cause significant health issues. Thus, amplicon sequencing can be an advantageous method to observe bacterial diversity in water. This study aimed to understand the complex bacterial communities present in natural mineral water packaged in 20 L returnable containers through amplicon sequencing. A high bacterial diversity was found in natural mineral water. Forty-eight bacterial genera were most abundant in the natural mineral water of different brands analyzed. These genera included Blastomonas, Brevundimonas, Gemmata, Methylobacterium, Mycobacterium, Nevskia, Nocardioides, Phenylobacterium, Pimelobacter, Ramlibacter, Rhodobacter, Sphingomonas, and Xenophilus. Also, a high bacterial diversity was found between the mineral waters brands tested in this study. Storage conditions were also shown to affect bacterial composition. Several genera known to contain pathogenic and opportunistic pathogenic species that may impact consumers' health were detected in the water samples examined.

Grana Padano (GP), Trentingrana (TG), and Parmigiano Reggiano (PR) are among the finest Italian Protected Designation of Origin (PDO) cheeses. GP, TG, and PR undergo extensive proteolysis during ripening, where the microbiome metabolizes amino acids, producing flavour and bioactive molecules. We explored the microbiome, volatilome, and metaproteome of PDO GP (n = 42), TG (n = 18), and PR (n = 60). Findings revealed diverse microbial communities enriched in proteolytic microbes, associated with cheese-specific processing technology. Correlations between lactic acid bacteria strains and specific volatile compounds were identified in PR. Importantly, we identified genes involved in the production of neuroactive molecules, suggesting potential connections between cheeses consumption and mental health, along with genes related to bacteriocin biosynthesis, possibly enhancing cheese safety, shelf life, and process sustainability. This study provides novel insights into the functional attributes of long-ripened cheeses microbiome, highlighting their potential as sources of psychobiotics and bioprotective strains.

Postbiotics, defined as "preparations of inanimate microorganisms and/or their components that confer a health benefit to the host," are emerging as a new frontier in nutritional and clinical research. This review aims to summarize the current scientific literature on postbiotics administration, comparing the evidence associated with the use of live or inactivated forms of microorganisms. The administration of a probiotic or postbiotic should not be considered as mutually exclusive, but rather as interdependent approaches, that can be chosen based on the specific microorganism, the target population and its specific needs. In addition, we highlighted the potential of 'omics approaches as an efficient tool for the screening of microbial strains to identify postbiotic genetic traits. Finally, we discussed the issues that still limit the broad diffusion of postbiotic products on the market. Indeed, we highlighted that there is certainly an urgent need for greater clarity and a specific regulation to encourage research and development in the postbiotic sector.

Poultry production chain comprises a complex network involving various stages from rearing to the final distribution of poultry products. This study explores the intricate dynamics within this chain, using shotgun metagenomics, particularly focusing on taxonomic and functional composition of the microbiome, antibiotic resistance and virulence potential. Moreover, the study of the impact of different packaging and storage conditions provides insights into how diverse packaging strategies and storage temperature can impact the shelf-life of chicken meat.Microbiome mapping in poultry processing facility revealed the dominance of Brochothrix thermosphacta, Pseudomonas fragi and Psychrobacter immobilis on poultry-based products and industrial surfaces. Indeed, surfaces of equipment and tools have a significant impact on the microbial composition of the final food products. Furthermore, the study of the microbiome dynamics in chicken meat stored in different packaging (air, modified atmosphere, under vacuum) and temperatures (0, 4 and 10 °C) revealed temperature-dependent microbiota shifts in chicken meat, highlighting specific spoilage organisms (SSOs) in the different packaging methods.Additionally, our results showed that poultry-based products and industrial surfaces belonging to carcasses processing area hosted elevated levels of Antibiotic Resistance Genes, mainly associated with resistance to aminoglycosides, β-lactams, MLSPs (which includes macrolides, lincosamides, streptogramins and pleuromutilins) amphenicols and tetracyclines classes and several Virulence-associated genes related to adherence, biofilm, effector delivery system, motility, nutritional/metabolic factors and regulation. Finally, our findings underscored a notably mobile resistome, showing multiple AR class correlated with mobile elements. This poses a considerable risk, emphasizing the urgent need for proactive measures in addressing potential antibiotic resistance genes dissemination in the poultry chain.

Antimicrobial resistance (AMR) is an escalating global health problem, endangering human, animal, and environmental health. In animal farming, the widespread use of antimicrobials is recognized one of the major drivers of AMR. Therefore, this review provides a meta-analysis of 37 studies published between 2014 and 2024, comparing the prevalence of antimicrobial resistance genes (ARGs) in antibiotic-free (ABF) versus conventional animal farming (CONV) systems. The statistical analysis revealed that CONV farms exhibited a higher likelihood of harboring ARGs, with a pooled odds ratio of 2.38 (95 % CI: 2.00-2.83) in the fixed-effects model and 3.21 (95 % CI: 1.68-6.13) in the random-effects model. Significant heterogeneity was observed (I2 = 82.8 %, p < 0.0001), highlighting the variations across the study designs. However, ARGs were still detected in 97 % of ABF farms, suggesting that antibiotic reduction alone may not be enough to control AMR in animal farming. These findings underscore the complex nature of AMR, influenced by environmental contamination, microbial interactions, human practices, and ecological pressures such as climate change. Future strategies should adopt a holistic One Health approach to effectively mitigate AMR risks across sectors and safeguard public and planetary health.

Food production systems may act as transmission routes for antimicrobial-resistant (AMR) bacteria and AMR genes (AMRGs) to humans. However, the food resistome remains poorly characterized. Here 1,780 raw-material (milk, brine, fresh meat and so on), end-product (cheese, fish, meat products and vegetables) and surface (processing, cooling, smoking, ripening and packing rooms) samples from 113 food processing facilities were subjected to whole-metagenome sequencing. Assembly-free analyses demonstrated that >70% of all known AMRGs, including many predicted to confer resistance to critically important antibiotics, circulate throughout food production chains, with those conferring resistance to tetracyclines, β-lactams, aminoglycosides and macrolides being the most abundant overall. An assembly-based analysis highlighted that bacteria from the ESKAPEE group, together with Staphylococcus equorum and Acinetobacter johnsonii, were the main AMRG carriers. Further evaluation demonstrated that ~40% of the AMRGs were associated with mobile genetic elements, mainly plasmids. These findings will help guide the appropriate use of biocides and other antimicrobials in food production settings when designing efficient antimicrobial stewardship policies.

Coffee silverskin, the outer layer of the green coffee bean, represents a major by-product of the coffee industry derived from the roasting process. In recent years the development of sustainable and circular strategies to manage and valorise organic wastes and by-products has become increasingly relevant and the potential of coffee silverskin in food industry, cosmetics, and bioconversion applications is gaining attention. In the present work we addressed the valorisation of coffee silverskin through insect bioconversion using the larvae of the black soldier fly Hermetia illucens, one of the most promising bioconversion agents among insects. These larvae grow on a huge variety of organic substrates due to their outstanding adaptability, that is conferred by the plasticity of the midgut physiology and associated microbiota. Our results demonstrate that black soldier fly larvae were able to grow and develop on coffee silverskin. The larvae reduced this by-product by 25% and a high protein insect biomass (i.e. 56 g per 100 g of dry matter) was obtained. Interestingly, 25% of the hemicellulose fraction of coffee silverskin was degraded by the larvae. In addition, the larval gut microbiota, which plays a key role in larvae digestion adaptability and bioconversion, was shaped by growing the larvae on coffee silverskin and bacterial taxa involved in complex polysaccharide degradation were selected. In conclusion, black soldier fly larvae may represent (1) a valuable tool for the development of new and sustainable strategies for coffee silverskin bioconversion and valorisation, and (2) an effective bioincubator for the selection and isolation of microbial strains with peculiar degrading capacity.

BACKGROUND AND AIMS:The Mediterranean diet (MD) has been associated with better glycaemic control in children with type 1 diabetes mellitus (T1DM) and favourable microbiome profiles in healthy individuals. However, it remains unclear whether MD adherence is associated with glycaemic control via microbiome. This study examined the relationships among MD adherence, gut microbiome, and glycaemic control in adults with T1DM and assessed the microbiome's ability to predict clinical and dietary outcomes. METHODS AND RESULTS:In a cross-sectional study of 253 adults with T1DM, dietary intake was assessed using the EPIC food frequency questionnaire, and MD adherence was measured using the rMED score. Participants were stratified by adherence level (low, medium, high). Glycaemic control was evaluated using HbA1c and CGM metrics. Shotgun metagenomic sequencing of stool samples (n = 103) assessed the gut microbiome. Statistical analyses included ANOVA, PERMANOVA, LEfSe, and machine learning modeling. Higher MD adherence was associated with lower HbA1c levels (7.1 % vs 7.7 %; p < 0.001), greater time in range (67.0 % vs 59.4 %; p-trend = 0.03), and higher HDL cholesterol (1.62 vs 1.39 mmol/L; p = 0.01). High MD adherence was linked to a greater abundance of bacterial species such as Faecalibacterium prausnitzii. Both high MD adherence and lower HbA1c were associated with distinct microbiome functional pathways. Microbiome-based machine learning models predicted dietary patterns and clinical metrics. CONCLUSIONS:In adults with T1DM, greater MD adherence is associated with better glycaemic control and a favourable gut microbiome. Specific microbial pathways may underlie these associations. Integrating diet and microbiome data supports personalized care. The study was registered at ClinicalTrials.gov with the identifier NCT05936242.