The core objective of the Food Biosciences Department is to engage in advanced research and technology development in support of the Irish Agri-Food industry sector. Activities fall into three research areas: Food for Health; Cheese Microbiology and Biochemistry and Milk and Product Quality.

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Food Biosciences

Recent Submissions

  • Next-Generation Food Research: Use of Meta-Omic Approaches for Characterizing Microbial Communities Along the Food Chain

    Yap, Min; Ercolini, Danilo; Álvarez-Ordóñez, Avelino; O'Toole, Paul W.; O'Sullivan, Orla; Cotter, Paul D.; Irish Dairy Levy; Science Foundation Ireland; European Commission; SFI/12/RC/2273; et al. (Annual Reviews, 2021-10-22)
    Microorganisms exist along the food chain and impact the quality and safety of foods in both positive and negative ways. Identifying and understanding the behavior of these microbial communities enable the implementation of preventative or corrective measures in public health and food industry settings. Current culture-dependent microbial analyses are time-consuming and target only specific subsets of microbes. However, the greater use of culture-independent meta-omic approaches has the potential to facilitate a thorough characterization of the microbial communities along the food chain. Indeed, these methods have shown potential in contributing to outbreak investigation, ensuring food authenticity, assessing the spread ofantimicrobial resistance, tracking microbial dynamics during fermentation and processing, and uncovering the factors along the food chain that impact food quality and safety. This review examines the community-based approaches, and particularly the application of sequencing-based meta-omics strategies, for characterizing microbial communities along the food chain.
  • Meta-analysis of cheese microbiomes highlights contributions to multiple aspects of quality

    Walsh, Aaron M.; Macori, Guerrino; Kilcawley, Kieran N.; Cotter, Paul D.; Science Foundation Ireland; European Commission; Department of Agriculture, Food and Marine; SFI/12/RC/2273P1; SFI/12/RC/2273P2; 818368; et al. (Springer Science and Business Media LLC, 2020-08-13)
    A detailed understanding of the cheese microbiome is key to the optimization of flavour, appearance, quality and safety. Accordingly, we conducted a high-resolution meta-analysis of cheese microbiomes and corresponding volatilomes. Using 77 new samples from 55 artisanal cheeses from 27 Irish producers combined with 107 publicly available cheese metagenomes, we recovered 328 metagenome-assembled genomes, including 47 putative new species that could influence taste or colour through the secretion of volatiles or biosynthesis of pigments. Additionally, from a subset of samples, we found that differences in the abundances of strains corresponded with levels of volatiles. Genes encoding bacteriocins and other antimicrobials, such as pseudoalterin, were common, potentially contributing to the control of undesirable microorganisms. Although antibiotic-resistance genes were detected, evidence suggested they are not of major concern with respect to dissemination to other microbiomes. Phages, a potential cause of fermentation failure, were abundant and evidence for phage-mediated gene transfer was detected. The anti-phage defence mechanism CRISPR was widespread and analysis thereof, and of anti-CRISPR proteins, revealed a complex interaction between phages and bacteria. Overall, our results provide new and substantial technological and ecological insights into the cheese microbiome that can be applied to further improve cheese production.
  • Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples

    McHugh, Aoife J.; Yap, Min; Crispie, Fiona; Feehily, Conor; Hill, Colin; Cotter, Paul D.; Department of Agriculture, Food and the Marine; Science Foundation Ireland; European Commission; 14/F/883; et al. (Springer Science and Business Media LLC, 2021-02-15)
    Efficient and accurate identification of microorganisms throughout the food chain can potentially allow the identification of sources of contamination and the timely implementation of control measures. High throughput DNA sequencing represents a potential means through which microbial monitoring can be enhanced. While Illumina sequencing platforms are most typically used, newer portable platforms, such as the Oxford Nanopore Technologies (ONT) MinION, offer the potential for rapid analysis of food chain microbiomes. Initial assessment of the ability of rapid MinION-based sequencing to identify microbes within a simple mock metagenomic mixture is performed. Subsequently, we compare the performance of both ONT and Illumina sequencing for environmental monitoring of an active food processing facility. Overall, ONT MinION sequencing provides accurate classification to species level, comparable to Illumina-derived outputs. However, while the MinION-based approach provides a means of easy library preparations and portability, the high concentrations of DNA needed is a limiting factor.
  • Seasonality and Geography Have a Greater Influence than the Use of Chlorine-Based Cleaning Agents on the Microbiota of Bulk Tank Raw Milk

    Yap, Min; Gleeson, David; O’Toole, Paul W.; O'Sullivan, Orla; Cotter, Paul D.; Irish Dairy Levy (American Society for Microbiology, 2021-10-28)
    Cleaning of the production environment is vital to ensure the safety and quality of dairy products. Although cleaning with chlorine-based agents is widely adopted, it has been associated with detrimental effects on milk quality and safety, which has garnered increasing interest in chlorine-free cleaning. However, the influence of these methods on the milk microbiota is not well documented. This study investigated the factors that influence the raw milk microbiota, with a focus on the differences when chlorine-based and chlorine-free cleaning of milking equipment are used. Bulk tank raw milk was sampled during three sampling months (April, August, and November), from farms across Ireland selected to capture the use of different cleaning methods, i.e., exclusively chlorine-based (n = 51) and chlorine-free cleaning (n = 92) and farms that used chlorine-free agents for the bulk tank and chlorine-based cleaning agents for the rest of the equipment (n = 28). Shotgun metagenomic analysis revealed the significant influence of seasonal and geographic factors on the bulk tank milk microbiota, indicated by differences in diversity, taxonomic composition, and functional characteristics. Taxonomic and functional profiles of samples collected in November clustered separately from those of samples collected in other months. In contrast, cleaning methods only accounted for 1% of the variation in the bulk tank milk bacterial community, and samples collected from farms using chlorine-based versus chlorine-free cleaning did not differ significantly, suggesting that the chlorine-free approaches used did not negatively impact microbiological quality. This study shows the value of shotgun metagenomics in advancing our knowledge of the raw milk microbiota.
  • Transcriptional control of central carbon metabolic flux in Bifidobacteria by two functionally similar, yet distinct LacI-type regulators

    Lanigan, Noreen; Kelly, Emer; Arzamasov, Aleksandr A.; Stanton, Catherine; Rodionov, Dmitry A.; van Sinderen, Douwe; Science Foundation Ireland; Department of Agriculture, Food and the Marine; Russian Science Foundation; SFI/12/RC/2273-P1; et al. (Springer Science and Business Media LLC, 2019-11-28)
    Bifdobacteria resident in the gastrointestinal tract (GIT) are subject to constantly changing environmental conditions, which require rapid adjustments in gene expression. Here, we show that two predicted LacI-type transcription factors (TFs), designated AraQ and MalR1, are involved in regulating the central, carbohydrate-associated metabolic pathway (the so-called phosphoketolase pathway or bifd shunt) of the gut commensal Bifdobacterium breve UCC2003. These TFs appear to not only control transcription of genes involved in the bifd shunt and each other, but also seem to commonly and directly afect transcription of other TF-encoding genes, as well as genes related to uptake and metabolism of various carbohydrates. This complex and interactive network of AraQ/MalR1-mediated gene regulation provides previously unknown insights into the governance of carbon metabolism in bifdobacteria.
  • Gamma-aminobutyric acid-producing lactobacilli positively affect metabolism and depressive-like behaviour in a mouse model of metabolic syndrome

    Patterson, E.; Ryan, P. M.; Wiley, N.; Carafa, I.; Sherwin, E.; Moloney, G.; Franciosi, E.; Mandal, R.; Wishart, D. S.; Tuohy, K.; et al. (Springer Science and Business Media LLC, 2019-11-08)
    Metabolic and neuroactive metabolite production represents one of the mechanisms through which the gut microbiota can impact health. One such metabolite, gamma-aminobutyric acid (GABA), can modulate glucose homeostasis and alter behavioural patterns in the host. We previously demonstrated that oral administration of GABA-producing Lactobacillus brevis DPC6108 has the potential to increase levels of circulating insulin in healthy rats. Therefore, the objective of this study was to assess the efcacy of endogenous microbial GABA production in improving metabolic and behavioural outcomes in a mouse model of metabolic dysfunction. Diet-induced obese and metabolically dysfunctional mice received one of two GABA-producing strains, L. brevis DPC6108 or L. brevis DSM32386, daily for 12 weeks. After 8 and 10 weeks of intervention, the behavioural and metabolic profles of the mice were respectively assessed. Intervention with both L. brevis strains attenuated several abnormalities associated with metabolic dysfunction, causing a reduction in the accumulation of mesenteric adipose tissue, increased insulin secretion following glucose challenge, improved plasma cholesterol clearance and reduced despair-like behaviour and basal corticosterone production during the forced swim test. Taken together, this exploratory dataset indicates that intervention with GABA-producing lactobacilli has the potential to improve metabolic and depressive- like behavioural abnormalities associated with metabolic syndrome in mice.
  • Metabolome and microbiome profiling of a stress-sensitive rat model of gut-brain axis dysfunction

    Bassett, Shalome A.; Young, Wayne; Fraser, Karl; Dalziel, Julie E.; Webster, Jim; Ryan, Leigh; Fitzgerald, Patrick; Stanton, Catherine; Dinan, Timothy G.; Cryan, John F.; et al. (Springer Science and Business Media LLC, 2019-10-01)
    Stress negatively impacts gut and brain health. Individual diferences in response to stress have been linked to genetic and environmental factors and more recently, a role for the gut microbiota in the regulation of stress-related changes has been demonstrated. However, the mechanisms by which these factors infuence each other are poorly understood, and there are currently no established robust biomarkers of stress susceptibility. To determine the metabolic and microbial signatures underpinning physiological stress responses, we compared stress-sensitive Wistar Kyoto (WKY) rats to the normoanxious Sprague Dawley (SD) strain. Here we report that acute stress-induced strain-specifc changes in brain lipid metabolites were a prominent feature in WKY rats. The relative abundance of Lactococcus correlated with the relative proportions of many brain lipids. In contrast, plasma lipids were signifcantly elevated in response to stress in SD rats, but not in WKY rats. Supporting these fndings, we found that the greatest diference between the SD and WKY microbiomes were the predicted relative abundance of microbial genes involved in lipid and energy metabolism. Our results provide potential insights for developing novel biomarkers of stress vulnerability, some of which appear genotype specifc.
  • Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome

    Pasolli, Edoardo; De Filippis, Francesca; Mauriello, Italia E.; Cumbo, Fabio; Walsh, Aaron M.; Leech, John; Cotter, Paul D.; Segata, Nicola; Ercolini, Danilo; European Union; et al. (Springer Science and Business Media LLC, 2020-05-25)
    Lactic acid bacteria (LAB) are fundamental in the production of fermented foods and several strains are regarded as probiotics. Large quantities of live LAB are consumed within fermented foods, but it is not yet known to what extent the LAB we ingest become members of the gut microbiome. By analysis of 9445 metagenomes from human samples, we demonstrate that the prevalence and abundance of LAB species in stool samples is generally low and linked to age, lifestyle, and geography, with Streptococcus thermophilus and Lactococcus lactis being most prevalent. Moreover, we identify genome-based differences between food and gut microbes by considering 666 metagenome-assembled genomes (MAGs) newly reconstructed from fermented food microbiomes along with 154,723 human MAGs and 193,078 reference genomes. Our large-scale genome-wide analysis demonstrates that closely related LAB strains occur in both food and gut environments and provides unprecedented evidence that fermented foods can be indeed regarded as a possible source of LAB for the gut microbiome.
  • Whey proteins: targets of oxidation, or mediators of redox protection.

    Giblin, Linda; Yalçın, A Süha; Biçim, Gökhan; Krämer, Anna C; Chen, Zhifei; Callanan, Michael J; Arranz, Elena; Davies, Michael J; European Cooperation in Science and Technology; Novo Nordisk Foundation; et al. (Taylor and Francis, 2019-01-01)
    Bovine whey proteins are highly valued dairy ingredients. This is primarily due to their amino acid content, digestibility, bioactivities and their processing characteristics. One of the reported bioactivities of whey proteins is antioxidant activity. Numerous dietary intervention trials with humans and animals indicate that consumption of whey products can modulate redox biomarkers to reduce oxidative stress. This bioactivity has in part been assigned to whey peptides using a range of biochemical or cellular assays in vitro. Superimposing whey peptide sequences from gastrointestinal samples, with whey peptides proven to be antioxidant in vitro, allows us to propose peptides from whey likely to exhibit antioxidant activity in the diet. However, whey proteins themselves are targets of oxidation during processing particularly when exposed to high thermal loads and/or extensive processing (e.g. infant formula manufacture). Oxidative damage of whey proteins can be selective with regard to the residues that are modified and are associated with the degree of protein unfolding, with α-Lactalbumin more susceptible than β-Lactoglobulin. Such oxidative damage may have adverse effects on human health. This review summarises how whey proteins can modulate cellular redox pathways and conversely how whey proteins can be oxidised during processing. Given the extensive processing steps that whey proteins are often subjected to, we conclude that oxidation during processing is likely to compromise the positive health attributes associated with whey proteins.
  • Metabolic phenotyping of the human microbiome

    Barton, Wiley; O'Sullivan, Orla; Cotter, Paul D.; Science Foundation Ireland; Department of Agriculture, Food and the Marine; SFI/12/RC/2273; 11/PI/1137; 13/SIRG/2160; 16/RC/3835 (F1000 Research, 2019-11-19)
    The human microbiome has been identified as having a key role in health and numerous diseases. Trillions of microbial cells and viral particles comprise the microbiome, each representing modifiable working elements of an intricate bioactive ecosystem. The significance of the human microbiome as it relates to human biology has progressed through culture-dependent (for example, media-based methods) and, more recently, molecular (for example, genetic sequencing and metabolomic analysis) techniques. The latter have become increasingly popular and evolved from being used for taxonomic identification of microbiota to elucidation of functional capacity (sequencing) and metabolic activity (metabolomics). This review summarises key elements of the human microbiome and its metabolic capabilities within the context of health and disease.
  • Actinomyces Produces Defensin-Like Bacteriocins (Actifensins) with a Highly Degenerate Structure and Broad Antimicrobial Activity

    Sugrue, Ivan; O’Connor, Paula M.; Hill, Colin; Stanton, Catherine; Ross, R. Paul; Teagasc Walsh Fellowship Programme; JPI; Science Foundation Ireland; SFI/12/RC/2273 (American Society for Microbiology, 2020-01-29)
    We identified a strain of Actinomyces ruminicola which produces a potent bacteriocin with activity against a broad range of Gram-positive bacteria, many of which are pathogenic to animals and humans. The bacteriocin was purified and found to have a mass of 4,091 ± 1 Da with a sequence of GFGCNLITSNPYQCSNHCKSVGYRGGYCKLRTVCTCY containing three disulfide bridges. Surprisingly, near relatives of actifensin were found to be a series of related eukaryotic defensins displaying greater than 50% identity to the bacteriocin. A pangenomic screen further revealed that production of actifensin-related bacteriocins is a common trait within the genus, with 47 being encoded in 161 genomes. Furthermore, these bacteriocins displayed a remarkable level of diversity with a mean amino acid identity of only 52% between strains/species. This level of redundancy suggests that this new class of bacteriocins may provide a very broad structural basis on which to deliver and design new broad-spectrum antimicrobials for treatment of animal and human infections. IMPORTANCE Bacteriocins (ribosomally produced antimicrobial peptides) are potential alternatives to current antimicrobials given the global challenge of antimicrobial resistance. We identified a novel bacteriocin from Actinomyces ruminicola with no previously characterized antimicrobial activity. Using publicly available genomic data, we found a highly conserved yet divergent family of previously unidentified homologous peptide sequences within the genus Actinomyces with striking similarity to eukaryotic defensins. These actifensins may provide a potent line of antimicrobial defense/offense, and the machinery to produce them could be used for the design of new antimicrobials given the degeneracy that exists naturally in their structure.
  • Naturally Derived Polyphenols Protect Against Corticosterone-Induced Changes in Primary Cortical Neurons

    Donoso, Francisco; Ramírez, Valerie T; Golubeva, Anna V; Moloney, Gerard M; Stanton, Catherine; Dinan, Timothy G; Cryan, John F; Mead Johnson; Cremo; Suntory Wellness; et al. (Oxford University Press (OUP), 2019-12-08)
    Background: Polyphenols are phytochemicals that have been associated with therapeutic effects in stress-related disorders. Indeed, studies suggest that polyphenols exert significant neuroprotection against multiple neuronal injuries, including oxidative stress and neuroinflammation, but the mechanisms are unclear. Evidence indicates that polyphenol neuroprotection may be mediated by activation of Nrf2, a transcription factor associated with antioxidant and cell survival responses. On the other hand, in stress-linked disorders, Fkbp5 is a novel molecular target for treatment because of its capacity to regulate glucocorticoid receptor sensitivity. However, it is not clear the role Fkbp5 plays in polyphenol-mediated stress modulation. In this study, the neuroprotective effects and mechanisms of the naturally derived polyphenols xanthohumol and quercetin against cytotoxicity induced by corticosterone were investigated in primary cortical cells. Methods: Primary cortical cells containing both neurons and astrocytes were pre-incubated with different concentrations of quercetin and xanthohumol to examine the neuroprotective effects of polyphenols on cell viability, morphology, and gene expression following corticosterone insult. Results: Both polyphenols tested prevented the reduction of cell viability and alterations of neuronal/astrocytic numbers due to corticosterone exposure. Basal levels of Bdnf mRNA were also decreased after corticosterone insult; however, this was reversed by both polyphenol treatments. Interestingly, the Nrf2 inhibitor blocked xanthohumol but not quercetin-mediated neuroprotection. In contrast, we found that Fkbp5 expression is exclusively modulated by quercetin. Conclusions: These results suggest that naturally derived polyphenols protect cortical cells against corticosterone-induced cytotoxicity and enhance cell survival via modulation of the Nrf2 pathway and expression of Fkbp5.
  • Seaweed Components as Potential Modulators of the Gut Microbiota

    Shannon, Emer; Conlon, Michael; Hayes, Maria; Teagasc; European Union; 754380 (MDPI AG, 2021-06-23)
    Macroalgae, or seaweeds, are a rich source of components which may exert beneficial effects on the mammalian gut microbiota through the enhancement of bacterial diversity and abundance. An imbalance of gut bacteria has been linked to the development of disorders such as inflammatory bowel disease, immunodeficiency, hypertension, type-2-diabetes, obesity, and cancer. This review outlines current knowledge from in vitro and in vivo studies concerning the potential therapeutic application of seaweed-derived polysaccharides, polyphenols and peptides to modulate the gut microbiota through diet. Polysaccharides such as fucoidan, laminarin, alginate, ulvan and porphyran are unique to seaweeds. Several studies have shown their potential to act as prebiotics and to positively modulate the gut microbiota. Prebiotics enhance bacterial populations and often their production of short chain fatty acids, which are the energy source for gastrointestinal epithelial cells, provide protection against pathogens, influence immunomodulation, and induce apoptosis of colon cancer cells. The oral bioaccessibility and bioavailability of seaweed components is also discussed, including the advantages and limitations of static and dynamic in vitro gastrointestinal models versus ex vivo and in vivo methods. Seaweed bioactives show potential for use in prevention and, in some instances, treatment of human disease. However, it is also necessary to confirm these potential, therapeutic effects in large-scale clinical trials. Where possible, we have cited information concerning these trials.
  • Aquaculture Production of the Brown Seaweeds Laminaria digitata and Macrocystis pyrifera: Applications in Food and Pharmaceuticals

    Purcell-Meyerink, Diane; Packer, Michael A.; Wheeler, Thomas T.; Hayes, Maria; Teagasc; European Union; 754380 (Multidisciplinary Digital Publishing Institute, 2021-02-28)
    Seaweeds have a long history of use as food, as flavouring agents, and find use in traditional folk medicine. Seaweed products range from food, feed, and dietary supplements to pharmaceuticals, and from bioenergy intermediates to materials. At present, 98% of the seaweed required by the seaweed industry is provided by five genera and only ten species. The two brown kelp seaweeds Laminaria digitata, a native Irish species, and Macrocystis pyrifera, a native New Zealand species, are not included in these eleven species, although they have been used as dietary supplements and as animal and fish feed. The properties associated with the polysaccharides and proteins from these two species have resulted in increased interest in them, enabling their use as functional foods. Improvements and optimisations in aquaculture methods and bioproduct extractions are essential to realise the commercial potential of these seaweeds. Recent advances in optimising these processes are outlined in this review, as well as potential future applications of L. digitata and, to a greater extent, M. pyrifera which, to date, has been predominately only wild-harvested. These include bio-refinery processing to produce ingredients for nutricosmetics, functional foods, cosmeceuticals, and bioplastics. Areas that currently limit the commercial potential of these two species are highlighted
  • Evaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome

    Yap, Min; Feehily, Conor; Walsh, Calum J.; Fenelon, Mark; Murphy, Eileen F.; McAuliffe, Fionnuala M.; van Sinderen, Douwe; O’Toole, Paul W.; O’Sullivan, Orla; Cotter, Paul D.; et al. (Springer, 2020-12-10)
    Shotgun metagenomic sequencing is a valuable tool for the taxonomic and functional profiling of microbial communities. However, this approach is challenging in samples, such as milk, where a low microbial abundance, combined with high levels of host DNA, result in inefficient and uneconomical sequencing. Here we evaluate approaches to deplete host DNA or enrich microbial DNA prior to sequencing using three commercially available kits. We compared the percentage of microbial reads obtained from each kit after shotgun metagenomic sequencing. Using bovine and human milk samples, we determined that host depletion with the MolYsis complete5 kit significantly improved microbial sequencing depth compared to other approaches tested. Importantly, no biases were introduced. Additionally, the increased microbial sequencing depth allowed for further characterization of the microbiome through the generation of metagenome-assembled genomes (MAGs). Furthermore, with the use of a mock community, we compared three common classifiers and determined that Kraken2 was the optimal classifier for these samples. This evaluation shows that microbiome analysis can be performed on both bovine and human milk samples at a much greater resolution without the need for more expensive deep-sequencing approaches.
  • Whey for Sarcopenia; Can Whey Peptides, Hydrolysates or Proteins Play a Beneficial Role?

    Gilmartin, Sarah; O’Brien, Nora; Giblin, Linda; Department of Agriculture, Food and the Marine; Science Foundation Ireland; Teagasc Walsh Fellowship Programme; FIRM 15F604-TOMI; 16/RC/3835-VistaMilk (MDPI AG, 2020-06-05)
    As the human body ages, skeletal muscle loses its mass and strength. It is estimated that in 10% of individuals over the age of 60, this muscle frailty has progressed to sarcopenia. Biomarkers of sarcopenia include increases in inflammatory markers and oxidative stress markers and decreases in muscle anabolic markers. Whey is a high-quality, easily digested dairy protein which is widely used in the sports industry. This review explores the evidence that whey protein, hydrolysates or peptides may have beneficial effects on sarcopenic biomarkers in myoblast cell lines, in aged rodents and in human dietary intervention trials with the older consumer. A daily dietary supplementation of 35 g of whey is likely to improve sarcopenic biomarkers in frail or sarcopenia individuals. Whey supplementation, consumed by an older, healthy adult certainly improves muscle mTOR signaling, but exercise appears to have the greatest benefit to older muscle. In vitro cellular assays are central for bioactive and bioavailable peptide identification and to determine their mechanism of action on ageing muscle.
  • The Potential Impact of Probiotics on the Gut Microbiome of Athletes

    Wosinska, Laura; Cotter, Paul D.; O’Sullivan, Orla; Guinane, Caitriona; Science Foundation Ireland; SFI/12/RC/2273 (MDPI AG, 2019-09-21)
    There is accumulating evidence that physical fitness influences the gut microbiome and as a result, promotes health. Indeed, exercise-induced alterations in the gut microbiome can influence health parameters crucial to athletic performance, specifically, immune function, lower susceptibility to infection, inflammatory response and tissue repair. Consequently, maintenance of a healthy gut microbiome is essential for an athlete’s health, training and performance. This review explores the effect of exercise on the microbiome while also investigating the effect of probiotics on various potential consequences associated with over-training in athletes, as well as their associated health benefits.
  • Precision Nutrition and the Microbiome, Part I: Current State of the Science

    Mills, Susan; Stanton, Catherine; Lane, Jonathan; Smith, Graeme; Ross, R. (MDPI AG, 2019-04-24)
    The gut microbiota is a highly complex community which evolves and adapts to its host over a lifetime. It has been described as a virtual organ owing to the myriad of functions it performs, including the production of bioactive metabolites, regulation of immunity, energy homeostasis and protection against pathogens. These activities are dependent on the quantity and quality of the microbiota alongside its metabolic potential, which are dictated by a number of factors, including diet and host genetics. In this regard, the gut microbiome is malleable and varies significantly from host to host. These two features render the gut microbiome a candidate ‘organ’ for the possibility of precision microbiomics—the use of the gut microbiome as a biomarker to predict responsiveness to specific dietary constituents to generate precision diets and interventions for optimal health. With this in mind, this two-part review investigates the current state of the science in terms of the influence of diet and specific dietary components on the gut microbiota and subsequent consequences for health status, along with opportunities to modulate the microbiota for improved health and the potential of the microbiome as a biomarker to predict responsiveness to dietary components. In particular, in Part I, we examine the development of the microbiota from birth and its role in health. We investigate the consequences of poor-quality diet in relation to infection and inflammation and discuss diet-derived microbial metabolites which negatively impact health. We look at the role of diet in shaping the microbiome and the influence of specific dietary components, namely protein, fat and carbohydrates, on gut microbiota composition.
  • Nanoemulsions and acidified milk gels as a strategy for improving stability and antioxidant activity of yarrow phenolic compounds after gastrointestinal digestion

    Villalva, M.; Jaime, L.; Arranz, E.; Zhao, Z.; Corredig, M.; Reglero, G.; Santoyo, S. (Elsevier BV, 2020-04)
    The aim of this study was to improve the stability and antioxidant activity of yarrow phenolic compounds upon an in vitro simulated gastrointestinal digestion. Therefore, two types of caseins-based delivery systems, sodium caseinate stabilized nanoemulsions (NEs) and glucono delta-lactone acidified milk gels (MGs), were formulated containing an ultrasound-assisted yarrow extract (YE) at two concentrations (1 and 2.5 mg/mL). Formulations with 1 mg/mL of YE were chosen based on their higher encapsulation efficiency to perform the in vitro digestion experiments. After digestion, YE-loaded NEs only partially protected phenolic compounds from degradation; meanwhile the phenolic composition of YE including in MGs after digestion was quite similar to undigested YE. Moreover, the antioxidant activity of MGs after digestion was higher than NEs digested samples, which confirms the higher protection of YE phenolic compound by the milk gels systems. This research demonstrated the potential use of acidified MGs as carriers to improve the stability and antioxidant activity of yarrow phenolic compounds. Therefore, these matrices could be employed to develop new dairy products enriched with phenolic compounds.
  • Lactobacillus acidophilus JCM 1132 Strain and Its Mutant with Different Bacteriocin-Producing Behaviour Have Various In Situ Effects on the Gut Microbiota of Healthy Mice

    Wang, Gang; Yu, Yunxia; Garcia-Gutierrez, Enriqueta; Jin, Xing; He, Yufeng; Wang, Linlin; Tian, Peijun; Liu, Zhenmin; Zhao, Jianxin; Zhang, Hao; et al. (MDPI AG, 2019-12-25)
    The production of bacteriocin is considered to be a probiotic trait of lactic acid bacteria (LAB). However, not all strains of LAB harbour bacteriocin genes, even within the same species. Moreover, the effects of bacteriocins on the host gut microbiota and on host physiological indicators are rarely studied. This study evaluated the effects of the bacteriocin-producing Lactobacillus acidophilus strain JCM1132 and its non-producing spontaneous mutant, L. acidophilus CCFM720, on the physiological statuses and gut microbiota of healthy mice. Mice that received the bacteriocin-producing strain JCM1132 exhibited reduced water and food intake. Furthermore, the administration of these strains induced significant changes in the compositional abundance of faecal microbiota at the phylum and genus levels, and some of these changes were more pronounced after one week of withdrawal. The effects of CCFM720 treatment on the gut microbiota seemed to favour the prevention of metabolic diseases to some extent. However, individuals that received JCM1132 treatment exhibited weaker inflammatory responses than those that received CCFM720 treatment. Our results indicate that treatment with bacteriocin-producing or non-producing strains can have different effects on the host. Accordingly, this trait should be considered in the applications of LAB.

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