Enrichment of yoghurts with additional bacterial strains holds the potential to improve the nutritional value of the product. By incorporating an adjunct strain in combination with the starter culture, 183 enriched yogurts were produced, covering 19 species from 9 different genera. Interestingly, this enrichment substantially increased the total number of metabolites produced. Moreover, the set of newly produced metabolites alone was sufficient for a clear cluster-separation of yoghurts enriched with adjunct strains from the same genus. Furthermore, 35 metabolites known to be aroma compounds or associated with beneficial health effects were identified by targeted metabolomics. Determination of the relative concentration of these metabolites revealed that a set of enriched yoghurts produced high concentrations of DL-indole-3-lactic acid, 3-phenyllactic acid, short-chain fatty acids, amino acids and the neurotransmitter gamma-aminobutyric acid, particularly in yoghurts enriched with Lactobacillus, Propionibacterium, or Acidipropionibacterium strains, having the potential to further improve the health benefits associated with consumption of yoghurt. This study is the first in which a comprehensive series of enriched yoghurts were produced by adding an adjunct strain, followed by a metabolic profiling using three different platforms (LC-MS, GC-MS, and GC-MS volatiles), allowing the identification of a wide variety of different compounds.

Background:Psychobiotics are microorganisms that modulate brain function via the gut-brain axis and are increasingly studied for their cognitive benefits. Lactobacillus and Bifidobacterium species, widely present in fermented foods, are considered safe and may influence cognition by modulating neuroinflammation, neurotransmitters, and gut barrier integrity. This systematic review examined the effects of foods fermented with these species on cognitive performance in healthy adults and individuals with mild cognitive impairment. Methods:We conducted the systematic review following EFSA guidelines, Cochrane methodology, and a PROSPERO protocol, using CADIMA for study selection and data extraction. PubMed, Scopus, and Cochrane Library were searched (1 January 1970-31 August 2023) for human intervention and observational studies assessing cognitive outcomes after ingestion of foods fermented with Lactobacillus or Bifidobacterium. Eligible populations included healthy adults and individuals with mild cognitive impairment; studies involving disease were excluded. Screening, data extraction, and bias assessment followed Muka et al.'s 24-step guide using ROBINS and Cochrane/CADIMA frameworks. Evidence was synthesized narratively, while a non-systematic component examined food characteristics, potential mechanisms, and factors affecting bioavailability of bioactive constituents. Results:We included 21 studies (8 interventional, 13 observational). The majority of studies reported benefits, particularly in episodic memory, executive functions, and global cognition, but evidence was limited by inadequate controls, small sample sizes, short interventions, inconsistent domain assessment, and incomplete food characterization. Observational studies had larger populations and longer follow-ups but were limited by exposure assessment and depth of cognitive testing. Conclusion:Consumption of foods fermented with Lactobacillus and/or Bifidobacterium species may offer promising cognitive benefits. However, following EFSA's guidance on the substantiation of health claims, the current evidence is "neither convincing nor sufficient" to establish a causal relationship. Well-designed studies with thorough product characterization are needed to substantiate effects and support potential health claims. Systematic review registration:This study was registered at the Open Science Framework (10.17605/OSF.IO/Z6GRW).

Yogurt is a fermented dairy product widely recognized for its nutritional value and potential health benefits, particularly due to its high content of calcium, phosphorus, vitamins, and other bioactive compounds. Its purported role in promoting bone health has attracted increasing attention, especially among adults at risk of osteoporosis. However, the specific impact of yogurt consumption on bone health remains controversial, as current evidence is limited and often inconclusive. This systematic review and meta-analysis sought to evaluate the exclusive effects of yogurt consumption on bone health in adults with and without osteoporosis. Employing rigorous inclusion and exclusion criteria and standardized methodologies, the study reviewed data from both observational and clinical studies to assess the effect of yogurt consumption on bone mineral density (BMD), fracture risk, and other bone health markers. In addition, yogurt characteristics were documented in accordance with EFSA guidelines, the possible bioactive components listed, and their potential mechanism of action in relation to bone health discussed. Studies fitting the inclusion and exclusion criteria (n = 12) were all observational, limiting the ability to infer causality. The meta-analysis of cohort studies (n = 6) found no significant association between yogurt consumption and hip fracture risk (HR = 1.01, 95% CI: 0.96-1.07), while the observed positive effect on BMD was minimal and clinically irrelevant (SMD = 0.009). Although some studies reported modest improvements in BMD and bone biomarkers, the overall evidence remains inconclusive, hindered by the heterogeneity in study designs and inconsistent yogurt intake. In conclusion, current evidence does not support a significant role of yogurt consumption in preventing fractures or improving BMD in adults. Well-designed randomized controlled studies are needed to clarify its effects, particularly in adults at risk of or with osteoporosis or osteopenia. In conclusion, the effectiveness of yogurt as a primary strategy for enhancing bone health is not fully substantiated by current data, though its inclusion within a balanced diet may still offer benefits for bone health. Systematic review registration:https://osf.io/, 10.17605/OSF.IO/ES2PM.

Worldwide, fermented foods (FF) are recognized as healthy and safe. Despite the rapid increase of research papers, there is a lack of systematic evaluation of the health benefits and risks of FF. The COST Action CA20128 “Promoting innovation of fermented foods” (PIMENTO) aims to provide a comprehensive assessment on the available evidence by compiling a set of 16 reviews. Seven reviews will cover clinical and biological endpoints associated with major health indicators across several organ systems, including the cardiovascular, gastrointestinal, neurological, immune, and skeletal systems. Nine reviews will address broader biological questions associated with FF including bioactive compounds and vitamin production, nutrient bioavailability and bioaccessibility, the role of FF in healthy diets and personalized nutrition, food safety, regulatory practices, and finally, the health properties of novel and ethnic FF. For each outcome assessed in the reviews, an innovative approach will be adopted based on EFSA’s published guidance for health claim submissions. In particular, each review will be composed of three parts: (1) a systematic review of available human studies; (2) a non-systematic review of the mechanism of action related to the clinical endpoints measured by the human studies identified in part 1; and (3) a non-systematic review of the characterization of the FF investigated in the human studies identified in part 1. The evidence and research gaps derived from the reviews will be summarized and published in the form of a strategic road map that will pave the way for future research on FF.

Indole derivatives are microbial metabolites of the tryptophan pathway involved in gut immune homeostasis. They bind to the aryl hydrocarbon receptor (AhR), thereby modulating development of intestinal group 3 innate lymphoid cells (ILC3) and subsequent interleukin-22 production. In mice, indole derivatives of the maternal microbiota can reach the milk and drive early postnatal ILC3 development. Apart from the gut microbiota, lactic acid bacteria (LAB) also produce indole compounds during milk fermentation. Using germ-free mice, the aim of our study was to test if maternal intake of a dairy product enriched in AhR-activating indoles produced by fermentation could boost maturation of the intestinal innate immune system in the offspring. A set of 631 LAB strains were genetically screened for their potential to produce indole compounds. Among these, 125 strains were tested in combination with standard strains to produce yoghurts that were screened for their ability to activate AhR in vitro using the HepG2-AhR-Luc cell line. The most active yoghurt and a control yoghurt were formulated as pellets and fed to germ-free dams during pregnancy and lactation. Analysis of the offspring on postnatal day 14 using flow cytometry revealed an increase in the frequency of small intestinal lamina propria NKp46 +ILC3 s in the pups born to dams that had consumed the purified diet containing an AhR-active yoghurt (AhrY-diet) compared to control yoghurt (ConY-diet). Selection of LABs based on their ability to produce a fermented dairy able to activate AhR appears to be an effective approach to produce a yoghurt with immunomodulatory properties. IMPORTANCE:Key progresses in the sequencing and functional annotation of microbial organisms have revolutionized research in the fields of human metabolism and food biotechnology. In particular, the gut microbiome is now recognized as an important mediator of the impact of nutrition on human metabolism. Annotated genomes of a large number of bacteria are now available worldwide, which selectively transform food through fermentation to produce specific bioactive compounds with the potential to modulate human health. A previous research has demonstrated that the maternal microbiota shapes the neonatal immune system. Similarly, this report shows that lactic acid bacteria can be selected to produce fermented food that can also modulate postnatal intestinal immunity.

Unraveling bacterial gene function drives progress in various areas, such as food production, pharmacology, and ecology. While omics technologies capture high-dimensional phenotypic data, linking them to genomic data is challenging, leaving 40-60% of bacterial genes undescribed. To address this bottleneck, we introduce Scoary2, an ultra-fast microbial genome-wide association studies (mGWAS) software. With its data exploration app and improved performance, Scoary2 is the first tool to enable the study of large phenotypic datasets using mGWAS. As proof of concept, we explore the metabolome of yogurts, each produced with a different Propionibacterium reichii strain and discover two genes affecting carnitine metabolism.

Genomic screening of bacteria is common practice to select strains with desired properties. However, 40-60% of all bacterial genes are still unknown, making capturing the phenotype an important part of the selection process. While omics-technologies collect high-dimensional phenotypic data, it remains challenging to link this information to genomic data to elucidate the impact of specific genes on phenotype. To this end, we present Scoary2, an ultra-fast software for microbial genome-wide association studies (mGWAS), enabling integrative data exploration. As proof of concept, we explore the metabolome of 44 yogurts with different strains of Propionibacterium freudenreichii , discovering two genes affecting carnitine metabolism.

Huge numbers of bacteria live in the human gut. We know those bacteria are important to our health, so we need to treat them well. We wanted to know whether it was possible to design new yogurts that can introduce special bacteria into the gut, to improve our well-being. We studied hundreds of types of bacteria isolated from cheese and yogurt and found that 24 of these bacterial species can perform most of the important bacterial functions that happen in the human gut. Therefore, there is exciting potential for designing new, gut-healthy yogurts.

Impact of herbage proportion, breed, average days in lactation (ADiL), and season on bulk milk composition of 12 dairy farms were investigated over a year using a mixed effect model approach. A 10%-points higher proportion of herbage led to higher contents of omega 3 (n-3) fatty acids (FAs), conjugated linoleic acids (CLA), vaccenic acid, and branched chain FAs (+0.08, +0.08, +0.19, +0.05 g 100 g(-1) fat, respectively). Breed influenced n-3 FAs and CLA (+0.31, +0.17 g 100 g(-1) fat, respectively), k-casein, lipoprotein lipase, beta-lactoglobulin, total whey protein, fatty acid synthase, and glycoprotein-2, resulting in +0.96,-0.019,-0.83,-1.12, +0.009, and +0.01 g 100 g(-1) measured proteins, respectively, in Brown Swiss milk. ADiL influenced lactoferrin and crude protein; season affected all FAs and proteins examined. The identification of these quantitative relationships allow predictions that provide new insights for the production, processing and commercialisation of grassland-based dairy products. (C) (http://creativecommons.org/licenses/by/4.0/).

The diversity of the human microbiome is positively associated with human health. However, this diversity is endangered by Westernized dietary patterns that are characterized by a decreased nutrient variety. Diversity might potentially be improved by promoting dietary patterns rich in microbial strains. Various collections of bacterial cultures resulting from a century of dairy research are readily available worldwide, and could be exploited to contribute towards this end. We have conducted a functional in silico analysis of the metagenome of 24 strains, each representing one of the species in a bacterial culture collection composed of 626 sequenced strains, and compared the pathways potentially covered by this metagenome to the intestinal metagenome of four healthy, although overweight, humans. Remarkably, the pan-genome of the 24 strains covers 89% of the human gut microbiome’s annotated enzymatic reactions. Furthermore, the dairy microbial collection covers biological pathways, such as methylglyoxal degradation, sulfate reduction, γ-aminobutyric (GABA) acid degradation and salicylate degradation, which are differently covered among the four subjects and are involved in a range of cardiometabolic, intestinal, and neurological disorders. We conclude that microbial culture collections derived from dairy research have the genomic potential to complement and restore functional redundancy in human microbiomes.

Geranylgeranyl diphosphate (GGPP), a prenyl diphosphate synthesized by GGPP synthase (GGPS), represents a metabolic hub for the synthesis of key isoprenoids, such as chlorophylls, tocopherols, phylloquinone, gibberellins, and carotenoids. Protein-protein interactions and the amphipathic nature of GGPP suggest metabolite channeling and/or competition for GGPP among enzymes that function in independent branches of the isoprenoid pathway. To investigate substrate conversion efficiency between the plastid-localized GGPS isoform GGPS11 and phytoene synthase (PSY), the first enzyme of the carotenoid pathway, we used recombinant enzymes and determined their in vitro properties. Efficient phytoene biosynthesis via PSY strictly depended on simultaneous GGPP supply via GGPS11. In contrast, PSY could not access freely diffusible GGPP or time-displaced GGPP supply via GGPS11, presumably due to liposomal sequestration. To optimize phytoene biosynthesis, we applied a synthetic biology approach and constructed a chimeric GGPS11-PSY metabolon (PYGG). PYGG converted GGPP to phytoene almost quantitatively in vitro and did not show the GGPP leakage typical of the individual enzymes. PYGG expression in Arabidopsis resulted in orange-colored cotyledons, which are not observed if PSY or GGPS11 are overexpressed individually. This suggests insufficient GGPP substrate availability for chlorophyll biosynthesis achieved through GGPP flux redirection to carotenogenesis. Similarly, carotenoid levels in PYGG-expressing callus exceeded that in PSY- or GGPS11-overexpression lines. The PYGG chimeric protein may assist in provitamin A biofortification of edible plant parts. Moreover, other GGPS fusions may be used to redirect metabolic flux into the synthesis of other isoprenoids of nutritional and industrial interest.

Une alimentation basee principalement sur l’herbe peut engen-drer une augmentation de la teneur du lait en acides gras po-lyinsatures (Bisig et al. 2008; Wyss et al. 2011). Par conse-quent, ce lait peut avoir de potentiels effets benefiques pour la sante del’homme. Comme pour les acides gras, le lait contient egalement des proteines ayant une action benefique pour la sante comme par exemple la lactoferrine (Adlerova et al. 2008). Jusque a pre-sent, l’influence du regime alimentaire des vaches laitieres sur la composition proteique du lait n’a ete que peu ou pas etudiee. Cette etude a donc pour objectif d’analyser l’impact des diffe-rentes strategies d’alimentation sur la composition en acides gras et en proteines du lait de vache.