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

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  • Whole genome sequence analysis; an improved technology that identifies underlying genotypic differences between closely related Listeria monocytogenes strains

    Fox, Edward M.; Casey, Aidan; Jordan, Kieran; Coffey, Aidan; Gahan, Cormac G.M.; McAuliffe, Olivia (Elsevier, 2017-07-08)
    As the new technology of whole genome sequencing (WGS) has been shown to have greater discriminatory power in differentiating strains than the much-used pulsed-field gel electrophoresis (PFGE), there is currently a transition from using PFGE to WGS for disease outbreak investigation. Therefore, there is a need for comparison of bacterial isolates using both PFGE and WGS. In this study, two pairs of L. monocytogenes strains with geographically diverse sources of isolation but which had indistinguishable or closely related PFGE profiles, were subjected to WGS analysis. Comparative analysis of their genomes showed that one pair of strains which had closely related PFGE profiles in fact differed significantly from one another in terms of their antibiotic and heavy metal stress resistance determinants, and mobile genetic elements. Therefore, this research demonstrated the ability of WGS analysis to differentiate very closely related strains and that WGS analysis represents the most effective tool available for subtyping L. monocytogenes isolates.
  • Early Salmonella Typhimurium infection in pigs disrupts Microbiome composition and functionality principally at the ileum mucosa

    Argüello, Héctor; Estellé, Jordi; Zaldívar-López, Sara; Jiménez-Marín, Ángeles; Carvajal, Ana; López-Bascón, Mª Asunción; Crispie, Fiona; O’Sullivan, Orla; Cotter, Paul D.; Priego-Capote, Feliciano; et al. (Springer Nature, 2018-05-17)
    Salmonella is a major foodborne pathogen which successfully infects animal species for human consumption such as swine. The pathogen has a battery of virulence factors which it uses to colonise and persist within the host. The host microbiota may play a role in resistance to, and may also be indirectly responsible from some of the consequences of, Salmonella infection. To investigate this, we used 16S rRNA metagenomic sequencing to determine the changes in the gut microbiota of pigs in response to infection by Salmonella Typhimurium at three locations: ileum mucosa, ileum content and faeces. Early infection (2 days post-infection) impacted on the microbiome diversity at the mucosa, reflected in a decrease in representatives of the generally regarded as desirable genera (i.e., Bifidobacterium and Lactobacillus). Severe damage in the epithelium of the ileum mucosa correlated with an increase in synergistic (with respect to Salmonella infection; Akkermansia) or opportunistically pathogenic bacteria (Citrobacter) and a depletion in anaerobic bacteria (Clostridium spp., Ruminococcus, or Dialliser). Predictive functional analysis, together with metabolomic analysis revealed changes in glucose and lipid metabolism in infected pigs. The observed changes in commensal healthy microbiota, including the growth of synergistic or potentially pathogenic bacteria and depletion of beneficial or competing bacteria, could contribute to the pathogen’s ability to colonize the gut successfully. The findings from this study could be used to form the basis for further research aimed at creating intervention strategies to mitigate the effects of Salmonella infection.
  • Mining Milk for Factors which Increase the Adherence of Bifidobacterium longum subsp. infantis to Intestinal Cells

    Quinn, Erinn M.; Slattery, Helen; Thompson, Aoife P.; Kilcoyne, Michelle; Joshi, Lokesh; Hickey, Rita M.; Teagasc Walsh Fellowship Programme (MDPI, 2018-12-03)
    Bifidobacteria play a vital role in human nutrition and health by shaping and maintaining the gut ecosystem. In order to exert a beneficial effect, a sufficient population of bifidobacteria must colonise the host. In this study, we developed a miniaturised high-throughput in vitro assay for assessing the colonising ability of bacterial strains in human cells. We also investigated a variety of components isolated from different milk sources for their ability to increase the adherence of Bifidobacterium longum subsp. infantis ATCC 15697, a common member of the gastrointestinal microbiota of breastfed infants, to HT-29 cells. Both conventional and miniaturised colonisation assays were employed to examine the effect of 13 different milk-derived powders on bacterial adherence, including positive controls which had previously resulted in increased bifidobacterial adherence (human milk oligosaccharides and a combination of 3′- and 6′-sialylactose) to intestinal cells. Immunoglobulin G enriched from bovine whey and goat milk oligosaccharides resulted in increased adhesion (3.3- and 8.3-fold, respectively) of B. infantis to the intestinal cells and the miniaturised and conventional assays were found to yield comparable and reproducible results. This study highlights the potential of certain milk components to favourably modulate adhesion of bifidobacteria to human intestinal cells.
  • Collective unconscious: How gut microbes shape human behavior

    Dinan, Timothy G.; Stilling, Roman M.; Stanton, Catherine; Cryan, John F.; Science Foundation Ireland; Health Research Board; European Union; SFI/12/RC/2273; HRA_POR/2011/23; HRA_POR/2012/32; et al. (Elsevier, 2015-03-03)
    The human gut harbors a dynamic and complex microbial ecosystem, consisting of approximately 1 kg of bacteria in the average adult, approximately the weight of the human brain. The evolutionary formation of a complex gut microbiota in mammals has played an important role in enabling brain development and perhaps sophisticated social interaction. Genes within the human gut microbiota, termed the microbiome, significantly outnumber human genes in the body, and are capable of producing a myriad of neuroactive compounds. Gut microbes are part of the unconscious system regulating behavior. Recent investigations indicate that these microbes majorly impact on cognitive function and fundamental behavior patterns, such as social interaction and stress management. In the absence of microbes, underlying neurochemistry is profoundly altered. Studies of gut microbes may play an important role in advancing understanding of disorders of cognitive functioning and social interaction, such as autism.
  • Food for thought: The role of nutrition in the microbiota-gut–brain axis

    Oriach, Clara Seira; Robertson, Ruairi C.; Stanton, Catherine; Cryan, John F.; Dinan, Timothy G.; Science Foundation Ireland; Health Research Board of Ireland; Sea Change Strategy, NutraMara programme; Department of Agriculture, Food and the Marine; SFI/12/RC/2273; et al. (Elsevier, 2016-01-21)
    Recent research has provided strong evidence for the role of the commensal gut microbiota in brain function and behaviour. Many potential pathways are involved in this bidirectional communication between the gut microbiota and the brain such as immune mechanisms, the vagus nerve and microbial neurometabolite production. Dysbiosis of gut microbial function has been associated with behavioural and neurophysical deficits, therefore research focused on developing novel therapeutic strategies to treat psychiatric disorders by targeting the gut microbiota is rapidly growing. Numerous factors can influence the gut microbiota composition such as health status, mode of birth delivery and genetics, but diet is considered among the most crucial factors impacting on the human gut microbiota from infancy to old age. Thus, dietary interventions may have the potential to modulate psychiatric symptoms associated with gut–brain axis dysfunction. Further clinical and in vivo studies are needed to better understand the mechanisms underlying the link between nutrition, gut microbiota and control of behaviour and mental health.
  • Understanding and Exploiting Phage–Host Interactions

    Stone, Edel; Campbell, Katrina; Grant, Irene; McAuliffe, Olivia; Teagasc Walsh Fellowship Programme; Teagasc; 2016034; 0027 (MDPI, 2019-06-18)
    Initially described a century ago by William Twort and Felix d’Herelle, bacteriophages are bacterial viruses found ubiquitously in nature, located wherever their host cells are present. Translated literally, bacteriophage (phage) means ‘bacteria eater’. Phages interact and infect specific bacteria while not affecting other bacteria or cell lines of other organisms. Due to the specificity of these phage–host interactions, the relationship between phages and their host cells has been the topic of much research. The advances in phage biology research have led to the exploitation of these phage–host interactions and the application of phages in the agricultural and food industry. Phages may provide an alternative to the use of antibiotics, as it is well known that the emergence of antibiotic-resistant bacterial infections has become an epidemic in clinical settings. In agriculture, pre-harvest and/or post-harvest application of phages to crops may prevent the colonisation of bacteria that are detrimental to plant or human health. In addition, the abundance of data generated from genome sequencing has allowed the development of phage-derived bacterial detection systems of foodborne pathogens. This review aims to outline the specific interactions between phages and their host and how these interactions may be exploited and applied in the food industry.
  • Bovine mastitis is a polymicrobial disease requiring a polydiagnostic approach

    Angeliki, Angelopoulou; Holohan, Ross; Rea, Mary C.; Warda, Alicja K.; Hill, Colin; Ross, R Paul; Science Foundation Ireland; SFI/12/RC/2273 (Elsevier, 2019-08-07)
    Bovine mastitis, an inflammation of the udder, is associated with increases in milk somatic cell count usually resulting from bacterial infection. We analysed 50 mastitic milk samples via cultivation, 16S rRNA sequencing and a combination of the two (culturomics) to define the complete microbial content of the milk. Most samples contained over 10,000 cfu mL-1 total bacterial counts including isolates that were haemolysin positive (n = 36). Among colonies isolated from blood agar plates, Streptococcus uberis was dominant (11/50) followed by Streptococcus dysgalactiae (6/50), Pseudomonas (6/50), Enterococcus faecalis (6/50), Escherichia coli (6/50), Staphylococcus argenteus (4/50), Bacillus (4/50) and Staphylococcus aureus (2/50). 16S rRNA profiling revealed that amplicons were dominated by Rhodococcus, Staphylococcus, Streptococcus and Pseudomonas. A higher inter-sample diversity was noted in the 16S rRNA readouts, which was not always reflected in the plating results. The combination of the two methods highlights the polymicrobial complexity of bovine mastitis.
  • Manipulation of gut microbiota blunts the ventilatory response to hypercapnia in adult rats

    O'Connor, Karen M.; Lucking, Eric F.; Golubeva, Anna V.; Strain, Conall R.; Fouhy, Fiona; Cenit, María C.; Dhaliwal, Pardeep; Bastiaanssen, Thomaz F.S.; Burns, David P.; Stanton, Catherine; et al. (Elsevier, 2019-03-18)
    Background: It is increasingly evident that perturbations to the diversity and composition of the gut microbiota have significant consequences for the regulation of integrative physiological systems. There is growing interest in the potential contribution of microbiota-gut-brain signalling to cardiorespiratory control in health and disease. Methods: In adult male rats, we sought to determine the cardiorespiratory effects of manipulation of the gut microbiota following a 4-week administration of a cocktail of antibiotics. We subsequently explored the effects of administration of faecal microbiota from pooled control (vehicle) rat faeces, given by gavage to vehicle- and antibiotic-treated rats. Findings: Antibiotic intervention depressed the ventilatory response to hypercapnic stress in conscious animals, owing to a reduction in the respiratory frequency response to carbon dioxide. Baseline frequency, respiratory timing variability, and the expression of apnoeas and sighs were normal. Microbiota-depleted rats had decreased systolic blood pressure. Faecal microbiota transfer to vehicle- and antibiotic-treated animals also disrupted the gut microbiota composition, associated with depressed ventilatory responsiveness to hypercapnia. Chronic antibiotic intervention or faecal microbiota transfer both caused significant disruptions to brainstem monoamine neurochemistry, with increased homovanillic acid:dopamine ratio indicative of increased dopamine turnover, which correlated with the abundance of several bacteria of six different phyla. Interpretation: Chronic antibiotic administration and faecal microbiota transfer disrupt gut microbiota, brainstem monoamine concentrations and the ventilatory response to hypercapnia. We suggest that aberrant microbiota-gut-brain axis signalling has a modulatory influence on respiratory behaviour during hypercapnic stress.
  • Bovine milk oligosaccharides as anti-adhesives against the respiratory tract pathogen Streptococcus pneumoniae

    Ryan, Joseph Thomas; Slattery, Helen; Hickey, Rita M.; Marotta, Mariarosaria; Enterprise Ireland; CC20080001 (Elsevier, 2018-02-20)
    Streptococcus pneumoniae is a Gram-positive pathogen, which is regularly found in the upper respiratory tract of healthy individuals. Increased numbers of S. pneumoniae have been observed colonising the upper respiratory tract of children affected by respiratory tract infections. Galβ1-4GlcNAcβ1-3Gal has been previously identified as one of the receptors involved in the adherence and translocation of S. pneumoniae. As this structure is similar to the milk oligosaccharide lacto-N-neoTetraose, many studies have investigated if free milk oligosaccharides can inhibit the adhesion of S. pneumoniae to epithelial cells of the respiratory tract. Here, we demonstrate that bovine oligosaccharides, which were extracted from demineralised whey, using a combination of membrane filtration and chromatography, were capable of reducing S. pneumoniae adhesion to pharynx and lung cells in vitro when tested at physiological concentrations. This study strengthens the potential use of bovine derived milk oligosaccharides as functional ingredients to reduce the incidence of infectious diseases.
  • Brans of the roller-milled barley fractions rich in polyphenols and health-promoting lipophilic molecules

    Gangopadhyay, Nirupama; Harrison, Sabine M; Brunton, Nigel P; Hidalgo-Ruiz, José L; Gallagher, Eimear; Rai, Dilip K; Department of Agriculture, Food and the Marine; 11/SF/317 (Elsevier, 2018-09-01)
    Three different roller-milled fractions namely bran, middlings, and flour of five commonly grown Irish barley varieties were investigated for the presence of β-glucan, polyphenols, and health-promoting lipophilic molecules. β-glucan was predominantly located in barley middlings. Polyphenols, as indicated by total phenolic content and the antioxidant activities, were abundant in the outermost bran fractions of barley. Similarly the health-promoting lipophilic molecules including phytosterols, unsaturated fatty acids, and tocols were most abundant in the barley bran fraction. However, the distribution of individual polyphenols and lipophilic compounds varied within the grain; for example ferulic acid and procyainidin C were not detected in flour fraction. Principal component analysis (PCA) clearly indicated a higher distribution of most bioactive molecules in bran as compared to middlings and flour fractions. The PCA also established possible correlations between the five barley varieties and their fractions based on their clustering in the plot.
  • Exploitation of SPR to Investigate the Importance of Glycan Chains in the Interaction between Lactoferrin and Bacteria

    O'Riordan, Noelle; Kilcoyne, Michelle; Joshi, Lokesh; Hickey, Rita M.; Teagasc Walsh Fellowship Programme (MDPI, 2017-06-27)
    Bovine lactoferrin (LF) has been shown to prevent adhesion to and invasion of mammalian cell lines by pathogenic bacteria, with evidence for direct bacterial binding by the milk glycoprotein. However, the glycosylation pattern of LF changes over the lactation cycle. In this study, we aim to investigate the effect that this variation has on the milk glycoprotein’s ability to interact with pathogens. Surface plasmon resonance technology was employed to compare the binding of LF from colostrum (early lactation) and mature milk (late lactation) to a panel of pathogenic bacteria (Staphylococcus aureus, Escherichia coli, Cronobacter sakazakii, Streptococcus pneumoniae, Pseudomonas aeruginosa, Listeria monocytogenes and Salmonella typhimurium). Novel interactions with LF were identified for C. sakazakii, S. pneumoniae and P. aeruginosa with the highest binding ability observed for mature milk LF in all cases, with the exception of S. typhimurium. The difference in bacterial binding observed may be as a result of the varying glycosylation profiles. This work demonstrates the potential of LF as a functional food ingredient to prevent bacterial infection
  • Characterization of protein hydrolysates from blue whiting (Micromesistius poutassou) and their application in beverage fortification

    Egerton, Sian; Culloty, Sarah; Whooley, Jason; Stanton, Catherine; Ross, R. Paul; Irish Research Council; Biomarine Ingredients Ireland Ltd.; The APC Microbiome Institute; EPSPG/2015/57; SFI/12/RC/2273 (Elsevier, 2017-10-21)
    Enzymatic hydrolysis of fish proteins has been employed as a principle method for converting under-utilised fish into valuable products for the pharmaceutical and health food industries. In this study, six commercial enzymes were tested for their ability to make fish protein hydrolysate powders from whole blue whiting. The chemical and functional properties of these powders were compared. The powders all had high solubility (>80%) across a wide pH range in water and their solubility improved further within a vitamin-tea beverage matrix (>85%). Varying degrees of anti-oxidant activities were recorded for the powders using three model systems (DPPH, ferrous chelating and reducing power). This study demonstrates that commercial enzymes are useful for the extraction and alteration of fish protein from a low value source to produce highly digestible, low molecular weight peptide powders that could be used as a fortifying health ingredient, especially in beverages.
  • Preparation and characterization of lotus seed starch-fatty acid complexes formed by microfluidization

    Chen, Bingyan; Guo, Zebin; Miao, Song; Zeng, Shaoxiao; Jia, Xiangze; Zhang, Yi; Zheng, Baodong; National Natural Science Foundation of China; Scientific and Technological Innovation Team Support Plan of Institution of Higher Learning in Fujian Province; Construction Projects of Top University; et al. (Elsevier, 2018-05-22)
    Using dynamic high pressure microfluidization, we prepared starch-lipid complexes from lotus seed starch (LS) and six saturated fatty acids (FAs) of different carbon chain length and analyzed their semi-crystalline structure and digestibility. Iodine blue value analysis showed the highest complex index (86.3%) was observed between LS and octanoic acid (C8). X-ray diffraction analysis showed crystal structure changed from V6II to V6I type with decreasing FA chain length. Small angle x-ray scattering and differential scanning calorimetry analyses confirmed the presence of a strong V6I-type mass fractal structure with a Bragg distance of 12.3 nm in LS-C8, which can be considered to be a type-II complex with high melting temperature (Tp = 123.98 °C). Scanning electron microscopy results showed the complexes had more spherocrystals with decreasing FA chain length. Compared to other FAs, C8 significantly reduced the LS susceptibility to digestive enzymes, increased slowly digestion starch content (26.06%) and decreased digestion rate (3.59 × 10−2).
  • Food for thought: The role of nutrition in the microbiota-gut–brain axis

    Oriach, Clara Seira; Robertson, Ruairi C; Stanton, Catherine; Cryan, John F.; Dinan, Timothy G.; Science Foundation Ireland; Health Research Board of Ireland; Sea Change Strategy NutraMara programme; SMART FOOD project; Department of Agriculture, Food and the Marine; et al. (Elsevier, 2016-01-21)
    Recent research has provided strong evidence for the role of the commensal gut microbiota in brain function and behaviour. Many potential pathways are involved in this bidirectional communication between the gut microbiota and the brain such as immune mechanisms, the vagus nerve and microbial neurometabolite production. Dysbiosis of gut microbial function has been associated with behavioural and neurophysical deficits, therefore research focused on developing novel therapeutic strategies to treat psychiatric disorders by targeting the gut microbiota is rapidly growing. Numerous factors can influence the gut microbiota composition such as health status, mode of birth delivery and genetics, but diet is considered among the most crucial factors impacting on the human gut microbiota from infancy to old age. Thus, dietary interventions may have the potential to modulate psychiatric symptoms associated with gut–brain axis dysfunction. Further clinical and in vivo studies are needed to better understand the mechanisms underlying the link between nutrition, gut microbiota and control of behaviour and mental health.
  • Beneficial modulation of the gut microbiota

    Cotter, Paul D. (Elsevier, 2016-03-29)
    As the scientific community continues to develop an ever-greater understanding of the composition and function of the human gut microbiota, and the role of specific microbial populations in health and disease, attention has turned to the tools that are at our disposal with respect to altering these microbes in a beneficial way. The options available include the use of diet, probiotics/prebiotics, antimicrobials and, potentially, exercise. Here, our recent investigations of the relationship between protein, bacteriocin producing probiotics and exercise and the gut microbiota and, in turn, health will be described.
  • The gut microbiota and the liver. Pathophysiological and clinical implications

    Quigley, Eamonn M.; Stanton, Catherine; Murphy, Eileen F. (Elsevier, 2012-11-23)
    This article reviews the microbiota in the pathogenesis of liver disease and its complications and the therapeutic impact of modulating the microbiota
  • Bacterial conjugated linoleic acid production and their applications

    Yang, Bo; Gao, He; Stanton, Catherine; Ross, R Paul; Zhang, Hao; Chen, Yong Q.; Chen, Haiqin; Chen, Wei; National Natural Science Foundation of China; National Natural Science Foundation of Jiangsu Province; et al. (Elsevier, 2017-09-07)
    Conjugated linoleic acid (CLA) has been shown to exert various potential physiological properties including anti-carcinogenic, anti-obesity, anti-cardiovascular and anti-diabetic activities, and consequently has been considered as a promising food supplement. Bacterial biosynthesis of CLA is an attractive approach for commercial production due to its high isomer-selectivity and convenient purification process. Many bacterial species have been reported to convert free linoleic acid (LA) to CLA, hitherto only the precise CLA-producing mechanisms in Propionibacterium acnes and Lactobacillus plantarum have been illustrated completely, prompting the development of recombinant technology used in CLA production. The purpose of the article is to review the bacterial CLA producers as well as the recent progress on describing the mechanism of microbial CLA-production. Furthermore, the advances and potential in the heterologous expression of CLA genetic determinants will be presented.
  • Hydrolysis of Ks1- and L-casein-derived peptides with a broad specifcity aminopeptidase and proline specific aminopeptidases from Lactococcus lactis subsp. cremoris AM2

    Bouchier, Paul J.; Fitzgerald, Richard J.; O'Cuinn, Gerard; Forbairt; IRish Dairy LEvy; European Union; AIR2-CT94-1560 (Wiley, 1999-03-29)
    Aminopeptidase hydrolysis of αs1- and β-casein-derived synthetic peptides containing non-consecutive and consecutive proline residues was characterised. Aminopeptidase P (Pep P) (EC 3.4.11.9) or post-proline dipeptidyl aminopeptidase (PPDA) (EC 3.4.14.5) along with lysine-paranitroanilide hydrolase (KpNA-H) (EC 3.4.11.1) activities are required in the degradation of peptides containing non-consecutive proline residues. However, both Pep P and PPDA along with KpNA-H are required for hydrolysis of peptides containing consecutive proline residues. The results demonstrate the mechanism by which combinations of purified general and proline specific aminopeptidases from Lactococcus lactis subsp. cremoris AM2 hydrolyse peptides containing proline residues.
  • Maternal omega-3 fatty acids regulate offspring obesity through persistent modulation of gut microbiota

    Robertson, Ruairi C; Kaliannan, Kanakaraju; Strain, Conall R.; Ross, R Paul; Stanton, Catherine; Kang, Jing X.; Science Foundation Ireland; Health Research Board; NutraMara programme; SMART FOOD project; et al. (BMC, 2018-05-24)
    Background: The early-life gut microbiota plays a critical role in host metabolism in later life. However, little is known about how the fatty acid profile of the maternal diet during gestation and lactation influences the development of the offspring gut microbiota and subsequent metabolic health outcomes. Results: Here, using a unique transgenic model, we report that maternal endogenous n-3 polyunsaturated fatty acid (PUFA) production during gestation or lactation significantly reduces weight gain and markers of metabolic disruption in male murine offspring fed a high-fat diet. However, maternal fatty acid status appeared to have no significant effect on weight gain in female offspring. The metabolic phenotypes in male offspring appeared to be mediated by comprehensive restructuring of gut microbiota composition. Reduced maternal n-3 PUFA exposure led to significantly depleted Epsilonproteobacteria, Bacteroides, and Akkermansia and higher relative abundance of Clostridia. Interestingly, offspring metabolism and microbiota composition were more profoundly influenced by the maternal fatty acid profile during lactation than in utero. Furthermore, the maternal fatty acid profile appeared to have a long-lasting effect on offspring microbiota composition and function that persisted into adulthood after life-long high-fat diet feeding. Conclusions: Our data provide novel evidence that weight gain and metabolic dysfunction in adulthood is mediated by maternal fatty acid status through long-lasting restructuring of the gut microbiota. These results have important implications for understanding the interaction between modern Western diets, metabolic health, and the intestinal microbiome.
  • Cholestasis induced by bile duct ligation promotes changes in the intestinal microbiome in mice.

    Cabrera-Rubio, Raul; Patterson, Angela M; Cotter, Paul D.; Beraza, Naiara; Biotechnology and Biological Sciences Research Council; BB/J004529/1; BBS/E/F/00044509; BB/R012490/1; BBS/E/F/000PR10355; BB/CCG1860/1 (Nature, 2019-08-23)
    Increasing evidence point to the relevance of intestinal disfunction and changes in the microbiome composition during chronic liver disease. More specifically, recent studies have highlighted that cholestatic diseases associate with a reduction in the microbiome diversity in patients. Still, the dynamics of the changes in the microbiome composition observed, as well as their implication in contributing to the pathogenesis of this disease remain largely undefined. Hence, experimental mouse models resembling the human pathogenesis are crucial to move forward our understanding on the mechanisms underpinning cholestatic disease and to enable the development of effective therapeutics. Our results show that the bile duct ligation (BDL) experimental model of cholestasis leads to rapid and significant changes in the microbiome diversity, with more than 100 OTUs being significantly different in faecal samples obtained from WT mice at 3 days and 7 days after BDL when compared to control animals. Changes in the microbial composition in mice after BDL included the enrichment of Akkermansia, Prevotella, Bacteroides and unclassified Ruminococcaceae in parallel with a drastic reduction of the presence of Faecalibacterium prausnitzii. In conclusion, our results support that bile duct ligation induces changes in the microbiome that partly resemble the gut microbial changes observed during human cholestatic disease.

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