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Iyer A, Soto Martín EC, Cameron GA, Louis P, Duncan SH, Bestwick CS, Russell WR. Gorse (Ulex europeaus) wastes with 5,6-dimethyl benzimidazole supplementation can support growth of vitamin B12 producing commensal gut microbes. PLoS One 2024; 19:e0290052. [PMID: 38422016 PMCID: PMC10903898 DOI: 10.1371/journal.pone.0290052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 12/20/2023] [Indexed: 03/02/2024] Open
Abstract
Many commensal gut microbes are recognized for their potential to synthesize vitamin B12, offering a promising avenue to address deficiencies through probiotic supplementation. While bioinformatics tools aid in predicting B12 biosynthetic potential, empirical validation remains crucial to confirm production, identify cobalamin vitamers, and establish biosynthetic yields. This study investigates vitamin B12 production in three human colonic bacterial species: Anaerobutyricum hallii DSM 3353, Roseburia faecis DSM 16840, and Anaerostipes caccae DSM 14662, along with Propionibacterium freudenreichii DSM 4902 as a positive control. These strains were selected for their potential use as probiotics, based on speculated B12 production from prior bioinformatic analyses. Cultures were grown in M2GSC, chemically defined media (CDM), and Gorse extract medium (GEM). The composition of GEM was similar to CDM, except that the carbon and nitrogen sources were replaced with the protein-depleted liquid waste obtained after subjecting Gorse to a leaf protein extraction process. B12 yields were quantified using liquid chromatography with tandem mass spectrometry. The results suggested that the three butyrate-producing strains could indeed produce B12, although the yields were notably low and were detected only in the cell lysates. Furthermore, B12 production was higher in GEM compared to M2GSC medium. The positive control, P. freudenreichii DSM 4902 produced B12 at concentrations ranging from 7 ng mL-1 to 12 ng mL-1. Univariate-scaled Principal Component Analysis (PCA) of data from previous publications investigating B12 production in P. freudenreichii revealed that B12 yields diminished when the carbon source concentration was ≤30 g L-1. In conclusion, the protein-depleted wastes from the leaf protein extraction process from Gorse can be valorised as a viable substrate for culturing B12-producing colonic gut microbes. Furthermore, this is the first report attesting to the ability of A. hallii, R. faecis, and A. caccae to produce B12. However, these microbes seem unsuitable for industrial applications owing to low B12 yields.
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Affiliation(s)
- Ajay Iyer
- Rowett Institute, University of Aberdeen, Aberdeen, Scotland
| | - Eva C Soto Martín
- Institue of Medical Sciences, University of Aberdeen, Aberdeen, Scotland
| | - Gary A Cameron
- Rowett Institute, University of Aberdeen, Aberdeen, Scotland
| | - Petra Louis
- Rowett Institute, University of Aberdeen, Aberdeen, Scotland
| | - Sylvia H Duncan
- Rowett Institute, University of Aberdeen, Aberdeen, Scotland
| | | | - Wendy R Russell
- Rowett Institute, University of Aberdeen, Aberdeen, Scotland
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Zhang Z, Fan S, Duncan GJ, Morris A, Henderson D, Morrice P, Russell WR, Duncan SH, Neacsu M. Buckwheat ( Fagopyrum esculentum) Hulls Are a Rich Source of Fermentable Dietary Fibre and Bioactive Phytochemicals. Int J Mol Sci 2023; 24:16310. [PMID: 38003497 PMCID: PMC10671810 DOI: 10.3390/ijms242216310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Pseudo-cereals such as buckwheat (Fagopyrum esculentum) are valid candidates to promote diet biodiversity and nutrition security in an era of global climate change. Buckwheat hulls (BHs) are currently an unexplored source of dietary fibre and bioactive phytochemicals. This study assessed the effects of several bioprocessing treatments (using enzymes, yeast, and combinations of both) on BHs' nutrient and phytochemical content, their digestion and metabolism in vitro (using a gastrointestinal digestion model and mixed microbiota from human faeces). The metabolites were measured using targeted LC-MS/MS and GC analysis and 16S rRNA gene sequencing was used to detect the impact on microbiota composition. BHs are rich in insoluble fibre (31.09 ± 0.22% as non-starch polysaccharides), protocatechuic acid (390.71 ± 31.72 mg/kg), and syringaresinol (125.60 ± 6.76 mg/kg). The bioprocessing treatments significantly increased the extractability of gallic acid, vanillic acid, p-hydroxybenzoic acid, syringic acid, vanillin, syringaldehyde, p-coumaric acid, ferulic acid, caffeic acid, and syringaresinol in the alkaline-labile bound form, suggesting the bioaccessibility of these phytochemicals to the colon. Furthermore, one of the treatments, EC_2 treatment, increased significantly the in vitro upper gastrointestinal release of bioactive phytochemicals, especially for protocatechuic acid (p < 0.01). The BH fibre was fermentable, promoting the formation mainly of propionate and, to a lesser extent, butyrate formation. The EM_1 and EC_2 treatments effectively increased the content of insoluble fibre but had no effect on dietary fibre fermentation (p > 0.05). These findings promote the use of buckwheat hulls as a source of dietary fibre and phytochemicals to help meet dietary recommendations and needs.
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Affiliation(s)
- Zhihong Zhang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China;
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK; (S.F.); (G.J.D.); (A.M.); (D.H.); (P.M.); (W.R.R.); (S.H.D.)
| | - Songtao Fan
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK; (S.F.); (G.J.D.); (A.M.); (D.H.); (P.M.); (W.R.R.); (S.H.D.)
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Gary J. Duncan
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK; (S.F.); (G.J.D.); (A.M.); (D.H.); (P.M.); (W.R.R.); (S.H.D.)
| | - Amanda Morris
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK; (S.F.); (G.J.D.); (A.M.); (D.H.); (P.M.); (W.R.R.); (S.H.D.)
| | - Donna Henderson
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK; (S.F.); (G.J.D.); (A.M.); (D.H.); (P.M.); (W.R.R.); (S.H.D.)
| | - Philip Morrice
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK; (S.F.); (G.J.D.); (A.M.); (D.H.); (P.M.); (W.R.R.); (S.H.D.)
| | - Wendy R. Russell
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK; (S.F.); (G.J.D.); (A.M.); (D.H.); (P.M.); (W.R.R.); (S.H.D.)
| | - Sylvia H. Duncan
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK; (S.F.); (G.J.D.); (A.M.); (D.H.); (P.M.); (W.R.R.); (S.H.D.)
| | - Madalina Neacsu
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK; (S.F.); (G.J.D.); (A.M.); (D.H.); (P.M.); (W.R.R.); (S.H.D.)
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Duncan SH, Conti E, Ricci L, Walker AW. Links between Diet, Intestinal Anaerobes, Microbial Metabolites and Health. Biomedicines 2023; 11:biomedicines11051338. [PMID: 37239009 DOI: 10.3390/biomedicines11051338] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
A dense microbial community resides in the human colon, with considerable inter-individual variability in composition, although some species are relatively dominant and widespread in healthy individuals. In disease conditions, there is often a reduction in microbial diversity and perturbations in the composition of the microbiota. Dietary complex carbohydrates that reach the large intestine are important modulators of the composition of the microbiota and their primary metabolic outputs. Specialist gut bacteria may also transform plant phenolics to form a spectrum of products possessing antioxidant and anti-inflammatory activities. Consumption of diets high in animal protein and fat may lead to the formation of potentially deleterious microbial products, including nitroso compounds, hydrogen sulphide, and trimethylamine. Gut anaerobes also form a range of secondary metabolites, including polyketides that may possess antimicrobial activity and thus contribute to microbe-microbe interactions within the colon. The overall metabolic outputs of colonic microbes are derived from an intricate network of microbial metabolic pathways and interactions; however, much still needs to be learnt about the subtleties of these complex networks. In this review we consider the multi-faceted relationships between inter-individual microbiota variation, diet, and health.
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Affiliation(s)
- Sylvia H Duncan
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Elena Conti
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Liviana Ricci
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Alan W Walker
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
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Avelar GM, Dambuza IM, Ricci L, Yuecel R, Mackenzie K, Childers DS, Bain JM, Pradhan A, Larcombe DE, Netea MG, Erwig LP, Brown GD, Duncan SH, Gow NA, Walker AW, Brown AJ. Impact of changes at the Candida albicans cell surface upon immunogenicity and colonisation in the gastrointestinal tract. Cell Surf 2022; 8:100084. [PMID: 36299406 PMCID: PMC9589014 DOI: 10.1016/j.tcsw.2022.100084] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/07/2022]
Abstract
The immunogenicity of Candida albicans cells is influenced by changes in the exposure of microbe-associated molecular patterns (MAMPs) on the fungal cell surface. Previously, the degree of exposure on the C. albicans cell surface of the immunoinflammatory MAMP β-(1,3)-glucan was shown to correlate inversely with colonisation levels in the gastrointestinal (GI) tract. This is important because life-threatening systemic candidiasis in critically ill patients often arises from translocation of C. albicans strains present in the patient's GI tract. Therefore, using a murine model, we have examined the impact of gut-related factors upon β-glucan exposure and colonisation levels in the GI tract. The degree of β-glucan exposure was examined by imaging flow cytometry of C. albicans cells taken directly from GI compartments, and compared with colonisation levels. Fungal β-glucan exposure was lower in the cecum than the small intestine, and fungal burdens were correspondingly higher in the cecum. This inverse correlation did not hold for the large intestine. The gut fermentation acid, lactate, triggers β-glucan masking in vitro, leading to attenuated anti-Candida immune responses. Additional fermentation acids are present in the GI tract, including acetate, propionate, and butyrate. We show that these acids also influence β-glucan exposure on C. albicans cells in vitro and, like lactate, they influence β-glucan exposure via Gpr1/Gpa2-mediated signalling. Significantly, C. albicans gpr1Δ gpa2Δ cells displayed elevated β-glucan exposure in the large intestine and a corresponding decrease in fungal burden, consistent with the idea that Gpr1/Gpa2-mediated β-glucan masking influences colonisation of this GI compartment. Finally, extracts from the murine gut and culture supernatants from the mannan grazing gut anaerobe Bacteroides thetaiotaomicron promote β-glucan exposure at the C. albicans cell surface. Therefore, the local microbiota influences β-glucan exposure levels directly (via mannan grazing) and indirectly (via fermentation acids), whilst β-glucan masking appears to promote C. albicans colonisation of the murine large intestine.
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Affiliation(s)
- Gabriela M. Avelar
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Ivy M. Dambuza
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
- Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Liviana Ricci
- Microbiome, Food Innovation and Food Security Research Theme, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Raif Yuecel
- Iain Fraser Cytometry Centre, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Kevin Mackenzie
- Microscopy & Histology Facility, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Delma S. Childers
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Judith M. Bain
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Arnab Pradhan
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
- Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Daniel E. Larcombe
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
- Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Mihai G. Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
- Department for Immunology & Metabolism, Life and Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany
| | - Lars P. Erwig
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
- Johnson-Johnson Innovation, EMEA Innovation Centre, One Chapel Place, London W1G 0BG, UK
| | - Gordon D. Brown
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
- Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Sylvia H. Duncan
- Microbiome, Food Innovation and Food Security Research Theme, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Neil A.R. Gow
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
- Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Alan W. Walker
- Microbiome, Food Innovation and Food Security Research Theme, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Alistair J.P. Brown
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
- Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
- Corresponding author at: Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK.
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Ricci L, Mackie J, Donachie GE, Chapuis A, Mezerová K, Lenardon MD, Brown AJP, Duncan SH, Walker AW. Human gut bifidobacteria inhibit the growth of the opportunistic fungal pathogen Candida albicans. FEMS Microbiol Ecol 2022; 98:fiac095. [PMID: 36007932 PMCID: PMC9486989 DOI: 10.1093/femsec/fiac095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/29/2022] [Accepted: 08/23/2022] [Indexed: 11/19/2022] Open
Abstract
The human gut microbiota protects the host from invading pathogens and the overgrowth of indigenous opportunistic species via a process called colonization resistance. Here, we investigated the antagonistic activity of human gut bacteria towards Candida albicans, an opportunistic fungal pathogen that can cause severe infections in susceptible individuals. Coculture batch incubations of C. albicans in the presence of faecal microbiota from six healthy individuals revealed varying levels of inhibitory activity against C. albicans. 16S rRNA gene amplicon profiling of these faecal coculture bacterial communities showed that the Bifidobacteriaceae family, and Bifidobacterium adolescentis in particular, were most correlated with antagonistic activity against C. albicans. Follow-up mechanistic studies performed under anaerobic conditions confirmed that culture supernatants of Bifidobacterium species, particularly B. adolescentis, inhibited C. albicans in vitro. Fermentation acids (FA), including acetate and lactate, present in the bifidobacterial supernatants were important contributors to inhibitory activity. However, increasing the pH of both bacterial supernatants and mixtures of FA reduced their anti-Candida effects, indicating a combinatorial effect of prevailing pH and FA. This work, therefore, demonstrates potential mechanisms underpinning gut microbiome-mediated colonization resistance against C. albicans, and identifies particularly inhibitory components such as bifidobacteria and FA as targets for further study.
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Affiliation(s)
- Liviana Ricci
- Rowett Institute, University of Aberdeen, Aberdeen, AB25 2ZD, United Kingdom
- CIBIO - Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, 38123, Italy
| | - Joanna Mackie
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, United Kingdom
| | - Gillian E Donachie
- Rowett Institute, University of Aberdeen, Aberdeen, AB25 2ZD, United Kingdom
| | - Ambre Chapuis
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, United Kingdom
| | - Kristýna Mezerová
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, 77515, Czech Republic
| | - Megan D Lenardon
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, United Kingdom
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Alistair J P Brown
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, United Kingdom
- MRC Centre for Medical Mycology, University of Exeter, Exeter, EX4 4QD, United Kingdom
| | - Sylvia H Duncan
- Rowett Institute, University of Aberdeen, Aberdeen, AB25 2ZD, United Kingdom
| | - Alan W Walker
- Rowett Institute, University of Aberdeen, Aberdeen, AB25 2ZD, United Kingdom
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Molinero N, Conti E, Walker AW, Margolles A, Duncan SH, Delgado S. Survival Strategies and Metabolic Interactions between Ruminococcus gauvreauii and Ruminococcoides bili, Isolated from Human Bile. Microbiol Spectr 2022; 10:e0277621. [PMID: 35863028 PMCID: PMC9431564 DOI: 10.1128/spectrum.02776-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 06/05/2022] [Indexed: 11/26/2022] Open
Abstract
Little is known about the bacteria that reside in the human gallbladder and the mechanisms that allow them to survive within this harsh environment. Here we describe interactions between two strains from a human bile sample, one Ruminococcus gauvreauii (IPLA60001), belonging to the Lachnospiraceae family, and the other, designated as Ruminococcoides bili (IPLA60002T; DSM 110008) most closely related to Ruminococcus bromii within the family Ruminococcaceae. We provide evidence for bile salt resistance and sporulation for these new strains. Both differed markedly in their carbohydrate metabolism. The R. bili strain mainly metabolized resistant starches to form formate, lactate and acetate. R. gauvreauii mainly metabolized sugar alcohols, including inositol and also utilized formate to generate acetate employing the Wood Ljungdahl pathway. Amino acid and vitamin biosynthesis genomic profiles also differed markedly between the two isolates, likely contributing to their synergistic interactions, as revealed by transcriptomic analysis of cocultures. Transcriptome analysis also revealed that R. gauvreauii IPLA60001 is able to grow using the end-products of starch metabolism formed by the R. bili strain such as formate, and potentially other compounds (such as ethanolamine and inositol) possibly provided by the autolytic behavior of R. bili. IMPORTANCE Unique insights into metabolic interaction between two isolates; Ruminococcus gauvreauii IPLA60001 and Ruminococcoides bili IPLA60002, from the human gallbladder, are presented here. The R. bili strain metabolized resistant starches while R. gauvreauii failed to do so but grew well on sugar alcohols. Transcriptomic analysis of cocultures of these strains, provides new data on the physiology and ecology of two bacteria from human bile, with a particular focus on cross-feeding mechanisms. Both biliary strains displayed marked resistance to bile and possess many efflux transporters, potentially involved in bile export. However, they differ markedly in their amino acid catabolism and vitamin synthesis capabilities, a feature that is therefore likely to contribute to the strong synergistic interactions between these strains. This is therefore the first study that provides evidence for syntrophic metabolic cooperation between bacterial strains isolated from human bile.
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Affiliation(s)
- Natalia Molinero
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias (IPLA)-Spanish National Research Council (CSIC), Villaviciosa-Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo-Asturias, Spain
| | - Elena Conti
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, Scotland
| | - Alan W. Walker
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, Scotland
| | - Abelardo Margolles
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias (IPLA)-Spanish National Research Council (CSIC), Villaviciosa-Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo-Asturias, Spain
| | - Sylvia H. Duncan
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, Scotland
| | - Susana Delgado
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias (IPLA)-Spanish National Research Council (CSIC), Villaviciosa-Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo-Asturias, Spain
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Sheridan PO, Louis P, Tsompanidou E, Shaw S, Harmsen HJ, Duncan SH, Flint HJ, Walker AW. Distribution, organization and expression of genes concerned with anaerobic lactate utilization in human intestinal bacteria. Microb Genom 2022; 8. [PMID: 35077342 PMCID: PMC8914356 DOI: 10.1099/mgen.0.000739] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Lactate accumulation in the human gut is linked to a range of deleterious health impacts. However, lactate is consumed and converted to the beneficial short-chain fatty acids butyrate and propionate by indigenous lactate-utilizing bacteria. To better understand the underlying genetic basis for lactate utilization, transcriptomic analyses were performed for two prominent lactate-utilizing species from the human gut, Anaerobutyricum soehngenii and Coprococcus catus, during growth on lactate, hexose sugar or hexose plus lactate. In A. soehngenii L2-7 six genes of the lactate utilization (lct) cluster, including NAD-independent d-lactate dehydrogenase (d-iLDH), were co-ordinately upregulated during growth on equimolar d- and l-lactate (dl-lactate). Upregulated genes included an acyl-CoA dehydrogenase related to butyryl-CoA dehydrogenase, which may play a role in transferring reducing equivalents between reduction of crotonyl-CoA and oxidation of lactate. Genes upregulated in C. catus GD/7 included a six-gene cluster (lap) encoding propionyl CoA-transferase, a putative lactoyl-CoA epimerase, lactoyl-CoA dehydratase and lactate permease, and two unlinked acyl-CoA dehydrogenase genes that are candidates for acryloyl-CoA reductase. A d-iLDH homologue in C. catus is encoded by a separate, partial lct, gene cluster, but not upregulated on lactate. While C. catus converts three mols of dl-lactate via the acrylate pathway to two mols propionate and one mol acetate, some of the acetate can be re-used with additional lactate to produce butyrate. A key regulatory difference is that while glucose partially repressed lct cluster expression in A. soehngenii, there was no repression of lactate-utilization genes by fructose in the non-glucose utilizer C. catus. This suggests that these species could occupy different ecological niches for lactate utilization in the gut, which may be important factors to consider when developing lactate-utilizing bacteria as novel candidate probiotics.
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Affiliation(s)
- Paul O Sheridan
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, AB25 2ZD Aberdeen, UK
| | - Petra Louis
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, AB25 2ZD Aberdeen, UK
| | - Eleni Tsompanidou
- Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Sophie Shaw
- Centre for Genome-Enabled Biology and Medicine, 23 St. Machar Drive, AB24 3RY Aberdeen, UK
| | - Hermie J Harmsen
- Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Sylvia H Duncan
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, AB25 2ZD Aberdeen, UK
| | - Harry J Flint
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, AB25 2ZD Aberdeen, UK
| | - Alan W Walker
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, AB25 2ZD Aberdeen, UK
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Iyer A, Guerrier L, Leveque S, Bestwick CS, Duncan SH, Russell WR. High throughput method development and optimised production of leaf protein concentrates with potential to support the agri-industry. Food Measure 2021. [DOI: 10.1007/s11694-021-01136-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractInvasive plants offer an interesting and unconventional source of protein and the considerable investment made towards their eradication can potentially be salvaged through their revalorisation. To identify viable sources, effective and high-throughput screening methods are required, as well as efficient procedures to isolate these components. Rigorous assessment of low-cost, high-throughput screening assays for total sugar, phenolics and protein was performed, and ninhydrin, Lever and Fast Blue assays were found to be most suitable owing to high reliability scores and false positive errors less than 1%. These assays were used to characterise invasive Scottish plants such as Gorse (Ulex europeans), Broom (Cystisus scoparius) and Fireweed (Chamaenerion angustifolium). Protein extraction (alkali-, heat- and enzyme assisted) were tested on these plants, and further purification (acid and ethanol precipitation, as well as ultrafiltration) procedures were tested on Gorse, based on protein recovery values. Cellulase treatment and ethanol precipitation gave the highest protein recovery (64.0 ± 0.5%) and purity (96.8 ± 0.1%) with Gorse. The amino acid profile of the purified protein revealed high levels of essential amino acids (34.8 ± 0.0%). Comparison of results with preceding literature revealed a strong association between amino acid profiles and overall protein recovery with the extraction method employed. The final purity of the protein concentrates was closely associated to the protein content of the initial plant mass. Leaf protein extraction technology can effectively raise crop harvest indices, revalorise underutilised plants and waste streams.
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Molinero N, Conti E, Sánchez B, Walker AW, Margolles A, Duncan SH, Delgado S. Ruminococcoides bili gen. nov., sp. nov., a bile-resistant bacterium from human bile with autolytic behavior. Int J Syst Evol Microbiol 2021; 71. [PMID: 34398726 DOI: 10.1099/ijsem.0.004960] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strictly anaerobic, resistant starch-degrading, bile-tolerant, autolytic strain, IPLA60002T, belonging to the family Ruminococcaceae, was isolated from a human bile sample of a liver donor without hepatobiliary disease. Cells were Gram-stain-positive cocci, and 16S rRNA gene and whole genome analyses showed that Ruminococcus bromii was the phylogenetically closest related species to the novel strain IPLA60002T, though with average nucleotide identity values below 90 %. Biochemically, the new isolate has metabolic features similar to those described previously for gut R. bromii strains, including the ability to degrade a range of different starches. The new isolate, however, produces lactate and shows distinct resistance to the presence of bile salts. Additionally, the novel bile isolate displays an autolytic phenotype after growing in different media. Strain IPLA60002T is phylogenetically distinct from other species within the genus Ruminococcus. Therefore, we propose on the basis of phylogenetic, genomic and metabolic data that the novel IPLA60002T strain isolated from human bile be given the name Ruminococcoides bili gen. nov., sp. nov., within the new proposed genus Ruminococcoides and the family Ruminococcaceae. Strain IPLA60002T (=DSM 110008T=LMG 31505T) is proposed as the type strain of Ruminococcoides bili.
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Affiliation(s)
- Natalia Molinero
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA)-Consejo Superior de Investigaciones Científicas (CSIC), Villaviciosa-Asturias, Spain
| | - Elena Conti
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, Scotland, AB25 2ZD, UK
| | - Borja Sánchez
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA)-Consejo Superior de Investigaciones Científicas (CSIC), Villaviciosa-Asturias, Spain.,Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo-Asturias, Spain
| | - Alan W Walker
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, Scotland, AB25 2ZD, UK
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA)-Consejo Superior de Investigaciones Científicas (CSIC), Villaviciosa-Asturias, Spain.,Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo-Asturias, Spain
| | - Sylvia H Duncan
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, Scotland, AB25 2ZD, UK
| | - Susana Delgado
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA)-Consejo Superior de Investigaciones Científicas (CSIC), Villaviciosa-Asturias, Spain.,Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo-Asturias, Spain
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Iyer A, Bestwick CS, Duncan SH, Russell WR. Invasive Plants Are a Valuable Alternate Protein Source and Can Contribute to Meeting Climate Change Targets. Front Sustain Food Syst 2021. [DOI: 10.3389/fsufs.2021.575056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Agriculture has come under pressure to meet global food demands, whilst having to meet economic and ecological targets. This has opened newer avenues for investigation in unconventional protein sources. Current agricultural practises manage marginal lands mostly through animal husbandry, which; although effective in land utilisation for food production, largely contributes to global green-house gas (GHG) emissions. Assessing the revalorisation potential of invasive plant species growing on these lands may help encourage their utilisation as an alternate protein source and partially shift the burden from livestock production; the current dominant source of dietary protein, and offer alternate means of income from such lands. Six globally recognised invasive plant species found extensively on marginal lands; Gorse (Ulex europaeus), Vetch (Vicia sativa), Broom (Cytisus scoparius), Fireweed (Chamaenerion angustifolium), Bracken (Pteridium aquilinum), and Buddleia (Buddleja davidii) were collected and characterised to assess their potential as alternate protein sources. Amino acid profiling revealed appreciable levels of essential amino acids totalling 33.05 ± 0.04 41.43 ± 0.05, 33.05 ± 0.11, 32.63 ± 0.04, 48.71 ± 0.02 and 21.48 ± 0.05 mg/g dry plant mass for Gorse, Vetch, Broom Fireweed, Bracken, and Buddleia, respectively. The availability of essential amino acids was limited by protein solubility, and Gorse was found to have the highest soluble protein content. It was also high in bioactive phenolic compounds including cinnamic- phenyl-, pyruvic-, and benzoic acid derivatives. Databases generated using satellite imagery were used to locate the spread of invasive plants. Total biomass was estimated to be roughly 52 Tg with a protein content of 5.2 Tg with a total essential amino acid content of 1.25 Tg (~24%). Globally, Fabaceae was the second most abundant family of invasive plants. Much of the spread was found within marginal lands and shrublands. Analysis of intrinsic agricultural factors revealed economic status as the emergent factor, driven predominantly by land use allocation, with shrublands playing a pivotal role in the model. Diverting resources from invasive plant removal through herbicides and burning to leaf protein extraction may contribute toward sustainable protein, effective land use, and achieving emission targets, while simultaneously maintaining conservation of native plant species.
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11
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Rozman V, Accetto T, Duncan SH, Flint HJ, Vodovnik M. Type IV pili are widespread among non-pathogenic Gram-positive gut bacteria with diverse carbohydrate utilization patterns. Environ Microbiol 2021; 23:1527-1540. [PMID: 33331146 DOI: 10.1111/1462-2920.15362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/15/2020] [Indexed: 12/23/2022]
Abstract
Type IV pili (T4P) are bacterial surface-exposed appendages that have been extensively studied in Gram-negative pathogenic bacteria. Despite recent sequencing efforts, little is known regarding these structures in non-pathogenic anaerobic Gram-positive species, particularly commensals of the mammalian gut. Early studies revealed that T4P in two ruminal Gram-positive species are associated with growth on cellulose, suggesting possible associations of T4P with substrate utilization patterns. In the present study, genome sequences of 118 taxonomically diverse, mainly Gram-positive, bacterial strains isolated from anaerobic (gastrointestinal) environments, have been analysed. The genes likely to be associated with T4P biogenesis were analysed and grouped according to T4P genetic organization. In parallel, consortia of Carbohydrate Active enZYmes (CAZymes) were also analysed and used to predict carbohydrate utilization abilities of selected strains. The predictive power of this approach was additionally confirmed by experimental assessment of substrate-related growth patterns of selected strains. Our analysis revealed that T4P systems with diverse genetic organization are widespread among Gram-positive anaerobic non-pathogenic bacteria isolated from different environments, belonging to two phylogenetically distantly related phyla: Firmicutes and Actinobacteria.
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Affiliation(s)
- Vita Rozman
- Chair of Microbiology and Microbial Biotechnology, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Tomaž Accetto
- Chair of Microbiology and Microbial Biotechnology, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Sylvia H Duncan
- Gut Health Group, Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Harry J Flint
- Gut Health Group, Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Maša Vodovnik
- Chair of Microbiology and Microbial Biotechnology, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
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12
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Chung WSF, Walker AW, Bosscher D, Garcia-Campayo V, Wagner J, Parkhill J, Duncan SH, Flint HJ. Relative abundance of the Prevotella genus within the human gut microbiota of elderly volunteers determines the inter-individual responses to dietary supplementation with wheat bran arabinoxylan-oligosaccharides. BMC Microbiol 2020; 20:283. [PMID: 32928123 PMCID: PMC7490872 DOI: 10.1186/s12866-020-01968-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 09/06/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The human colon is colonised by a dense microbial community whose species composition and metabolism are linked to health and disease. The main energy sources for colonic bacteria are dietary polysaccharides and oligosaccharides. These play a major role in modulating gut microbial composition and metabolism, which in turn can impact on health outcomes. RESULTS We investigated the influence of wheat bran arabinoxylan oligosaccharides (AXOS) and maltodextrin supplements in modulating the composition of the colonic microbiota and metabolites in healthy adults over the age of 60. Male and female volunteers, (n = 21, mean BMI 25.2 ± 0.7 kg/m2) participated in the double-blind, cross over supplement study. Faecal samples were collected for analysis of microbiota, short chain fatty acids levels and calprotectin. Blood samples were collected to measure glucose, cholesterol and triglycerides levels. There was no change in these markers nor in calprotectin levels in response to the supplements. Both supplements were well-tolerated by the volunteers. Microbiota analysis across the whole volunteer cohort revealed a significant increase in the proportional abundance of faecal Bifidobacterium species (P ≤ 0.01) in response to AXOS, but not maltodextrin, supplementation. There was considerable inter-individual variation in the other bacterial taxa that responded, with a clear stratification of volunteers as either Prevotella-plus (n = 8; > 0.1% proportional abundance) or Prevotella-minus (n = 13; ≤0.1% proportional abundance) subjects founded on baseline sample profiles. There was a significant increase in the proportional abundance of both faecal Bifidobacterium (P ≤ 0.01) and Prevotella species (P ≤ 0.01) in Prevotella-plus volunteers during AXOS supplementation, while Prevotella and Bacteroides relative abundances showed an inverse relationship. Proportional abundance of 26 OTUs, including bifidobacteria and Anaerostipes hadrus, differed significantly between baseline samples of Prevotella-plus compared to Prevotella-minus individuals. CONCLUSIONS The wheat bran AXOS supplementation was bifidogenic and resulted in changes in human gut microbiota composition that depended on the initial microbiota profile, specifically the presence or absence of Prevotella spp. as a major component of the microbiota. Our data therefore suggest that initial profiling of individuals through gut microbiota analysis should be considered important when contemplating nutritional interventions that rely on prebiotics. TRIAL REGISTRATION Clinical trial registration number: NCT02693782 . Registered 29 February 2016 - Retrospectively registered, https://clinicaltrials.gov/ct2/show/NCT02693782?term=NCT02693782&rank=1.
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Affiliation(s)
- Wing Sun Faith Chung
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, Scotland AB25 2ZD UK
| | - Alan W. Walker
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, Scotland AB25 2ZD UK
| | - Douwina Bosscher
- Cargill R&D Centre Europe BVBA, Havenstraat 84, B-1800 Vilvoorde, Belgium
| | | | - Josef Wagner
- Pathogen Genomics Group, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES UK
| | - Sylvia H. Duncan
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, Scotland AB25 2ZD UK
| | - Harry J. Flint
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, Scotland AB25 2ZD UK
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13
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Ricci L, Mackie J, Lenardon MD, Jukes C, Hegazy AN, Brown AJ, Duncan SH, Walker AW. Bifidobacterium adolescentis shows potential to strengthen host defence against gastrointestinal infection via inhibition of the opportunistic pathogen Candida albicans and stimulation of human-isolated macrophages killing capacity in vitro. Access Microbiol 2020. [DOI: 10.1099/acmi.ac2020.po0743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human gut microbiota enhances the host’s resistance to enteric pathogens via colonisation resistance, a phenomenon that is driven by multiple mechanisms, such as production of antimicrobial metabolites and activation of host immune responses. However, there is limited information on how individual gut bacterial species, particularly many of the dominant anaerobes, might impact the host’s defence.
This study investigated the potential of specific human gut isolates to bolster the host’s resistance to infection. First, by antagonising the opportunistic fungal pathogen Candida albicans, and secondly, by modulating the killing capacity of human-isolated macrophages in vitro.
Co-culturing C. albicans with faecal microbiota from different healthy individuals revealed varying levels of fungal inhibition. In vitro assays with a panel of representative human gut anaerobes confirmed that culture supernatants from certain bacterial isolates, in particular of Bifidobacterium adolescentis, significantly inhibited C. albicans growth. Mechanistic studies revealed that microbial fermentation acids including acetate and lactate, in combination with the associated decrease in pH, were strong drivers of this inhibitory activity.
In the second in vitro assay, human-isolated macrophages were exposed to bacterial supernatants, and subsequently tested for their capacity to eliminate adherent-invasive Escherichia coli. Among the gut anaerobes tested, B. adolescentis was revealed to exert the strongest immunostimulatory and killing effect when compared to the unstimulated macrophages control.
B. adolescentis is known to be stimulated by dietary consumption of resistant starch andmay therefore represent an attractive target for the development of probiotic and prebiotic interventions tailored to enhancethe host’s natural defences against infection.
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Affiliation(s)
| | - Joanna Mackie
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen,Aberdeen, AB25 2ZD,UK
| | - Megan D. Lenardon
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen,Aberdeen, AB25 2ZD,UK
| | - Caitlin Jukes
- Medical Department, Division of Gastroenterology, Infectiology and Rheumatology, Charite’ ‐Universitätsmedizin Berlin,Berlin,Germany
| | - Ahmed N. Hegazy
- Medical Department, Division of Gastroenterology, Infectiology and Rheumatology, Charite’ ‐Universitätsmedizin Berlin,Berlin,Germany
| | - Alistair J.P. Brown
- MRC Centre for Medical Mycology, University of Exeter,Exeter, EX4 4QD,UK
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen,Aberdeen, AB25 2ZD,UK
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14
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Johnstone AM, Kelly J, Ryan S, Romero-Gonzalez R, McKinnon H, Fyfe C, Naslund E, Lopez-Nicolas R, Bosscher D, Bonnema A, Frontela-Saseta C, Ros-Berruezo G, Horgan G, Ze X, Harrold J, Halford J, Gratz SW, Duncan SH, Shirazi-Beechey S, Flint HJ. Nondigestible Carbohydrates Affect Metabolic Health and Gut Microbiota in Overweight Adults after Weight Loss. J Nutr 2020; 150:1859-1870. [PMID: 32510158 DOI: 10.1093/jn/nxaa124] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/16/2019] [Accepted: 04/09/2020] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The composition of diets consumed following weight loss (WL) can have a significant impact on satiety and metabolic health. OBJECTIVE This study was designed to test the effects of including a nondigestible carbohydrate to achieve weight maintenance (WM) following a period of WL. METHODS Nineteen volunteers [11 females and 8 males, aged 20-62 y; BMI (kg/m2): 27-42] consumed a 3-d maintenance diet (15%:30%:55%), followed by a 21-d WL diet (WL; 30%:30%:40%), followed by 2 randomized 10-d WM diets (20%:30%:50% of energy from protein:fat:carbohydrate) containing either resistant starch type 3 (RS-WM; 22 or 26 g/d for females and males, respectively) or no RS (C-WM) in a within-subject crossover design without washout periods. The primary outcome, WM after WL, was analyzed by body weight. Secondary outcomes of fecal microbiota composition and microbial metabolite concentrations and gut hormones were analyzed in fecal samples and blood plasma, respectively. All outcomes were assessed at the end of each dietary period. RESULTS Body weight was similar after the RS-WM and C-WM diets (90.7 and 90.8 kg, respectively), with no difference in subjectively rated appetite. During the WL diet period plasma ghrelin increased by 36% (P < 0.001), glucose-dependent insulinotropic polypeptide (GIP) decreased by 33% (P < 0.001), and insulin decreased by 46% (P < 0.001), but no significant differences were observed during the RS-WM and C-WM diet periods. Fasting blood glucose was lower after the RS-WM diet (5.59 ± 0.31 mmol/L) than after the C-WM diet [5.75 ± 0.49 mmol/L; P = 0.015; standard error of the difference between the means (SED): 0.09]. Dietary treatments influenced the fecal microbiota composition (R2 = 0.054, P = 0.031) but not diversity. CONCLUSIONS The metabolic benefits, for overweight adults, from WL were maintained through a subsequent WM diet with higher total carbohydrate intake. Inclusion of resistant starch in the WM diet altered gut microbiota composition positively and resulted in lower fasting glucose compared with the control, with no apparent change in appetite. This trial was registered at clinicaltrials.gov as NCT01724411.
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Affiliation(s)
| | - Jennifer Kelly
- Functional and Comparative Genomics, and Psychological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Sheila Ryan
- Functional and Comparative Genomics, and Psychological Sciences, University of Liverpool, Liverpool, United Kingdom
| | | | - Hannah McKinnon
- The Rowett Institute, University of Aberdeen, Foresterhill, United Kingdom
| | - Claire Fyfe
- The Rowett Institute, University of Aberdeen, Foresterhill, United Kingdom
| | | | - Ruben Lopez-Nicolas
- Department of Food Science and Nutrition, Faculty of Veterinary Sciences, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia, Murcia, Spain
| | | | | | - Carmen Frontela-Saseta
- Department of Food Science and Nutrition, Faculty of Veterinary Sciences, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia, Murcia, Spain
| | - Gaspar Ros-Berruezo
- Department of Food Science and Nutrition, Faculty of Veterinary Sciences, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia, Murcia, Spain
| | - Graham Horgan
- Biomathematics and Statistics Scotland, Aberdeen, United Kingdom
| | - Xiaolei Ze
- The Rowett Institute, University of Aberdeen, Foresterhill, United Kingdom
| | - Jo Harrold
- Appetite and Obesity Research Group, Department of Psychological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Jason Halford
- Appetite and Obesity Research Group, Department of Psychological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Silvia W Gratz
- The Rowett Institute, University of Aberdeen, Foresterhill, United Kingdom
| | - Sylvia H Duncan
- The Rowett Institute, University of Aberdeen, Foresterhill, United Kingdom
| | - Soraya Shirazi-Beechey
- Functional and Comparative Genomics, and Psychological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Harry J Flint
- The Rowett Institute, University of Aberdeen, Foresterhill, United Kingdom
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15
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Lopez-Siles M, Aldeguer X, Sabat-Mir M, Serra-Pagès M, Duncan SH, Flint HJ, Garcia-Gil LJ, Martinez-Medina M. Evaluation of bacterial biomarkers to aid in challenging inflammatory bowel diseases diagnostics and subtype classification. World J Gastrointest Pathophysiol 2020; 11:64-77. [PMID: 32435523 PMCID: PMC7226914 DOI: 10.4291/wjgp.v11.i3.64] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/27/2020] [Accepted: 03/30/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The challenges for inflammatory bowel disease (IBD) diagnostics are to discriminate it from gut conditions with similar symptoms such as irritable bowel syndrome (IBS), to distinguish IBD subtypes, to predict disease progression, and to establish the risk to develop colorectal cancer (CRC). Alterations in gut microbiota have been proposed as a source of information to assist in IBD diagnostics. Faecalibacterium prausnitzii (F. prausnitzii), its phylogroups, and Escherichia coli (E. coli) have been reported as potential biomarkers, but their performance in challenging IBD diagnostic situations remains elusive. We hypothesize that bacterial biomarkers based in these species may help to discriminate these conditions of complex diagnostics.
AIM To evaluate the usefulness of indices calculated from the quantification of these species as biomarkers to aid in IBD diagnostics.
METHODS A retrospective study of 131 subjects (31 controls (H); 45 Crohn’s disease (CD), 25 ulcerative colitis (UC), 10 IBS, and 20 CRC patients) was performed to assess the usefulness of bacterial biomarkers in biopsies. Further, the performance of biomarkers in faeces was studied in 29 stool samples (19 CD, 10 UC). Relative abundances of total F. prausnitzii (FP), its phylogroups (PHGI and PHGII), and E. coli (E) quantification were determined by qPCR. Loads were combined to calculate the FP-E index, the PHGI–E index and the PHGII-E index. Biomarkers accuracy to discriminate among conditions was measured by the area under the receiver operating characteristic curve (AUC).
RESULTS In biopsies, FP-E index was good for discriminating IBS from CD (AUC = 0.752) while PHGII-E index was suitable for discriminating IBS from UC (AUC = 0.632). The FP-E index would be the choice to discriminate IBD from CRC, especially from all UC subtypes (AUC ≥ 0.875), regardless of the activity status of the patient. Discrimination between UC patients that had the longest disease duration and those with CRC featured slightly lower AUC values. Concerning differentiation in IBD with shared location, PHGI-E index can establish progression from proctitis and left-sided colitis to ulcerative pancolitis (AUC ≥ 0.800). PHG I-E index analysis in tissue would be the choice to discriminate within IBD subtypes of shared location (AUC ≥ 0.712), while in non-invasive faecal samples FP or PHGI could be good indicators (AUC ≥ 0.833).
CONCLUSION F. prausnitzii phylogroups combined with E. coli offer potential to discriminate between IBD and CRC patients and can assist in IBD subtypes classification, which may help in solving IBD diagnostics challenges.
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Affiliation(s)
- Mireia Lopez-Siles
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona 17003, Spain
| | - Xavier Aldeguer
- Department of Gastroenterology, Hospital Universitari Dr. Josep Trueta, Girona 17007, Spain
| | - Miriam Sabat-Mir
- Department of Gastroenterology, Hospital Santa Caterina, Salt 17190, Spain
| | | | - Sylvia H Duncan
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom
| | - Harry J Flint
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom
| | - L Jesús Garcia-Gil
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona 17003, Spain
| | - Margarita Martinez-Medina
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona 17003, Spain
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16
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Neacsu M, Raikos V, Benavides-Paz Y, Duncan SH, Duncan GJ, Christie JS, Johnstone AM, Russell WR. Sapogenol is a Major Microbial Metabolite in Human Plasma Associated with High Protein Soy-Based Diets: The Relevance for Functional Food Formulations. Foods 2020; 9:E422. [PMID: 32260066 PMCID: PMC7230228 DOI: 10.3390/foods9040422] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 03/26/2020] [Accepted: 03/31/2020] [Indexed: 12/13/2022] Open
Abstract
Legumes are a source of health-promoting macro- and micronutrients, but also contain numerous phytochemicals with useful biological activities, an example of which are saponins. Epidemiological studies suggest that saponins may play a role in protection from cancer and benefit human health by lowering cholesterol. Therefore, they could represent good candidates for specialised functional foods. Following the consumption of a soya-rich high-protein weight-loss diet (SOYA HP WL), the concentrations of Soyasaponin I (SSI) and soyasapogenol B (SSB) were determined in faecal samples from human volunteers (n = 10) and found to be between 1.4 and 17.5 mg per 100 g fresh faecal sample. SSB was the major metabolite identified in volunteers' plasma (n = 10) after consumption of the soya test meal (SOYA MEAL); the postprandial (3 h after meal) plasma concentration for SSB varied between 48.5 ng/mL to 103.2 ng/mL. The metabolism of SSI by the gut microbiota (in vitro) was also confirmed. This study shows that the main systemic metabolites of soyasaponin are absorbed from the gut and that they are bioavailable in plasma predominantly as conjugates of sapogenol. The metabolism and bioavailability of biologically active molecules represent key information necessary for the efficient development of functional foods.
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Affiliation(s)
- Madalina Neacsu
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK; (V.R.); (Y.B.-P.); (S.H.D.); (G.J.D.); (J.S.C.); (A.M.J.); (W.R.R.)
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17
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Kramer T, Kelleher P, van der Meer J, O'Sullivan T, Geertman JMA, Duncan SH, Flint HJ, Louis P. Comparative genetic and physiological characterisation of Pectinatus species reveals shared tolerance to beer-associated stressors but halotolerance specific to pickle-associated strains. Food Microbiol 2020; 90:103462. [PMID: 32336380 DOI: 10.1016/j.fm.2020.103462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 01/09/2020] [Accepted: 02/17/2020] [Indexed: 11/19/2022]
Abstract
Obligate anaerobic bacteria from the genus Pectinatus have been known to cause beer spoilage for over 40 years. Whole genome sequencing was performed on eleven beer spoilage strains (nine Pectinatus frisingensis, one Pectinatus cerevisiiphilus and one Pectinatus haikarae isolate), as well as two pickle spoilage species (Pectinatus brassicae MB591 and Pectinatus sottacetonis MB620) and the tolerance of all species to a range of environmental conditions was tested. Exploration of metabolic pathways for carbohydrates, amino acids and vitamins showed little difference between beer spoilage- and pickle spoilage-associated strains. However, genes for certain carbohydrate- and sulphur-containing amino acid-associated enzymes were only present in the beer spoilage group and genes for specific transporters and regulatory genes were uniquely found in the pickle spoilage group. Transporters for compatible solutes, only present in pickle-associated strains, likely explain their experimentally observed higher halotolerance compared to the beer spoilers. Genes involved in biofilm formation and ATP Binding Cassette (ABC) transporters potentially capable of exporting hop-derived antimicrobial compounds were found in all strains. All species grew in the presence of alcohol up to 5% alcohol by volume (ABV) and hops extract up to 80 ppm of iso-α-acids. Therefore, the species isolated from pickle processes may pose novel hazards in brewing.
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Affiliation(s)
- Timo Kramer
- University of Aberdeen, The Rowett Institute, Foresterhill, AB25 2ZD, Aberdeen, United Kingdom
| | - Philip Kelleher
- APC Microbiome Ireland, Food Science & Technology Building, University College Cork, College Road, Cork, T12 K8AF, Ireland
| | | | - Tadhg O'Sullivan
- Heineken Supply Chain B.V., Burgemeester Smeetsweg 1, 2382 PH, Zoeterwoude, the Netherlands
| | - Jan-Maarten A Geertman
- Heineken Supply Chain B.V., Burgemeester Smeetsweg 1, 2382 PH, Zoeterwoude, the Netherlands
| | - Sylvia H Duncan
- University of Aberdeen, The Rowett Institute, Foresterhill, AB25 2ZD, Aberdeen, United Kingdom
| | - Harry J Flint
- University of Aberdeen, The Rowett Institute, Foresterhill, AB25 2ZD, Aberdeen, United Kingdom
| | - Petra Louis
- University of Aberdeen, The Rowett Institute, Foresterhill, AB25 2ZD, Aberdeen, United Kingdom.
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18
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Chung WSF, Walker AW, Vermeiren J, Sheridan PO, Bosscher D, Garcia-Campayo V, Parkhill J, Flint HJ, Duncan SH. Impact of carbohydrate substrate complexity on the diversity of the human colonic microbiota. FEMS Microbiol Ecol 2019; 95:5124376. [PMID: 30304332 DOI: 10.1093/femsec/fiy201] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 10/08/2018] [Indexed: 12/14/2022] Open
Abstract
The diversity of the colonic microbial community has been linked with health in adults and diet composition is one possible determinant of diversity. We used carefully controlled conditions in vitro to determine how the complexity and multiplicity of growth substrates influence species diversity of the human colonic microbiota. In each experiment, five parallel anaerobic fermenters that received identical faecal inocula were supplied continuously with single carbohydrates (either arabinoxylan-oligosaccharides (AXOS), pectin or inulin) or with a '3-mix' of all three carbohydrates, or with a '6-mix' that additionally contained resistant starch, β-glucan and galactomannan as energy sources. Inulin supported less microbial diversity over the first 6 d than the other two single substrates or the 3- and 6-mixes, showing that substrate complexity is key to influencing microbiota diversity. The communities enriched in these fermenters did not differ greatly at the phylum and family level, but were markedly different at the species level. Certain species were promoted by single substrates, whilst others (such as Bacteroides ovatus, LEfSe P = 0.001) showed significantly greater success with the mixed substrate. The complex polysaccharides such as pectin and arabinoxylan-oligosaccharides promoted greater diversity than simple homopolymers, such as inulin. These findings suggest that dietary strategies intended to achieve health benefits by increasing gut microbiota diversity should employ complex non-digestible substrates and substrate mixtures.
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Affiliation(s)
- Wing Sun Faith Chung
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, Scotland, AB25 2ZD, UK
| | - Alan W Walker
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, Scotland, AB25 2ZD, UK
| | - Joan Vermeiren
- Cargill R&D Centre Europe, BVBA, Havenstraat 84, B-1800 Vilvoorde, Belgium
| | - Paul O Sheridan
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, Scotland, AB25 2ZD, UK
| | - Douwina Bosscher
- Cargill R&D Centre Europe, BVBA, Havenstraat 84, B-1800 Vilvoorde, Belgium
| | | | - Julian Parkhill
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Harry J Flint
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, Scotland, AB25 2ZD, UK
| | - Sylvia H Duncan
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, Scotland, AB25 2ZD, UK
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19
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Laverde Gomez JA, Mukhopadhya I, Duncan SH, Louis P, Shaw S, Collie‐Duguid E, Crost E, Juge N, Flint HJ. Formate cross-feeding and cooperative metabolic interactions revealed by transcriptomics in co-cultures of acetogenic and amylolytic human colonic bacteria. Environ Microbiol 2019; 21:259-271. [PMID: 30362296 PMCID: PMC6378601 DOI: 10.1111/1462-2920.14454] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/14/2018] [Accepted: 10/18/2018] [Indexed: 12/24/2022]
Abstract
Interspecies cross-feeding is a fundamental factor in anaerobic microbial communities. In the human colon, formate is produced by many bacterial species but is normally detected only at low concentrations. Ruminococcus bromii produces formate, ethanol and acetate in approximately equal molar proportions in pure culture on RUM-RS medium with 0.2% Novelose resistant starch (RS3) as energy source. Batch co-culturing on starch with the acetogen Blautia hydrogenotrophica however led to the disappearance of formate and increased levels of acetate, which is proposed to occur through the routing of formate via the Wood Ljungdahl pathway of B. hydrogenotrophica. We investigated these inter-species interactions further using RNAseq to examine gene expression in continuous co-cultures of R. bromii and B. hydrogenotrophica. Transcriptome analysis revealed upregulation of B. hydrogenotrophica genes involved in the Wood-Ljungdahl pathway and of a 10 gene cluster responsible for increased branched chain amino acid fermentation in the co-cultures. Cross-feeding between formate-producing species and acetogens may be a significant factor in short chain fatty acid formation in the colon contributing to high rates of acetate production. Transcriptome analysis also indicated competition for the vitamin thiamine and downregulation of dissimilatory sulfate reduction and key redox proteins in R. bromii in the co-cultures, thus demonstrating the wide-ranging consequences of inter-species interactions in this model system.
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Affiliation(s)
| | | | - Sylvia H. Duncan
- Gut Health GroupThe Rowett Institute, University of AberdeenAberdeenUK
| | - Petra Louis
- Gut Health GroupThe Rowett Institute, University of AberdeenAberdeenUK
| | - Sophie Shaw
- Centre for Genome Enabled Biology and MedicineUniversity of AberdeenOld AberdeenUK
| | - Elaina Collie‐Duguid
- Centre for Genome Enabled Biology and MedicineUniversity of AberdeenOld AberdeenUK
| | - Emmanuelle Crost
- The Gut Health and Food Safety Institute Strategic ProgrammeQuadram Institute BioscienceNorwichUK
| | - Nathalie Juge
- The Gut Health and Food Safety Institute Strategic ProgrammeQuadram Institute BioscienceNorwichUK
| | - Harry J. Flint
- Gut Health GroupThe Rowett Institute, University of AberdeenAberdeenUK
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20
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Lopez-Siles M, Enrich-Capó N, Aldeguer X, Sabat-Mir M, Duncan SH, Garcia-Gil LJ, Martinez-Medina M. Alterations in the Abundance and Co-occurrence of Akkermansia muciniphila and Faecalibacterium prausnitzii in the Colonic Mucosa of Inflammatory Bowel Disease Subjects. Front Cell Infect Microbiol 2018; 8:281. [PMID: 30245977 PMCID: PMC6137959 DOI: 10.3389/fcimb.2018.00281] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 07/25/2018] [Indexed: 12/21/2022] Open
Abstract
Akkermansia muciniphila and Faecalibacterium prausnitzii, cohabitants in the intestinal mucosa, are considered members of a healthy microbiota and reduction of both species occurs in several intestinal disorders, including inflammatory bowel disease. Little is known however about a possible link between the reduction in quantity of these species, and in which circumstances this may occur. This study aims to determine the abundances and co-occurrence of the two species in order to elucidate conditions that may compromise their presence in the gut. Loads of A. muciniphila, total F. prausnitzii and its two phylogroup (16S rRNA gene copies) were determined by quantitative polymerase chain reaction in colonic biopsies from 17 healthy controls (H), 23 patients with ulcerative colitis (UC), 31 patients with Crohn's disease (CD), 3 with irritable bowel syndrome (IBS) and 3 with colorectal cancer (CRC). Data were normalized to total bacterial 16S rRNA gene copies in the same sample. Prevalence, relative abundances and correlation analyses were performed according to type of disease and considering relevant clinical characteristics of patients such as IBD location, age of disease onset, CD behavior, current medication and activity status. Co-occurrence of both species was found in 29% of H, 65% of UC and 29% of CD. Lower levels of total F. prausnitzii and phylogroups were found in subjects with CD, compared with H subjects (P ≤ 0.044). In contrast, no differences were found with the regard to A. muciniphila abundance across different disease states, but CD patients with disease onset below 16 years of age featured a marked depletion of this species. In CD patients, correlation between A. muciniphila and total F. prausnitzii (ρ = 0.362, P = 0.045) was observed, and particularly in those with non-stricturing, non-penetrating disease behavior and under moderate immunosuppressants therapy. Altogether, this study revealed that co-occurrence of both species differs between disease status. In addition, IBD patients featured a reduction of F. prausnitzii but similar loads of A. muciniphila when compared to H subjects, with the exception of those with early onset CD. Depletion of A. muciniphila in this subgroup of subjects suggests that it could be a potential biomarker to assist in pediatric CD diagnosis.
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Affiliation(s)
- Mireia Lopez-Siles
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain
| | - Núria Enrich-Capó
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain
| | - Xavier Aldeguer
- Department of Gastroenterology, Hospital Dr. Josep Trueta, Girona, Spain
| | - Miriam Sabat-Mir
- Department of Gastroenterology, Hospital Santa Caterina, Girona, Spain
| | - Sylvia H Duncan
- Microbiology Group, Rowett Institute of Nutrition and Health, Aberdeen, United Kingdom
| | - L Jesús Garcia-Gil
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain
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21
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Vollmer M, Esders S, Farquharson FM, Neugart S, Duncan SH, Schreiner M, Louis P, Maul R, Rohn S. Mutual Interaction of Phenolic Compounds and Microbiota: Metabolism of Complex Phenolic Apigenin-C- and Kaempferol-O-Derivatives by Human Fecal Samples. J Agric Food Chem 2018; 66:485-497. [PMID: 29236499 DOI: 10.1021/acs.jafc.7b04842] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Human colonic bacteria have an important impact on the biotransformation of flavonoid glycosides and their conversion can result in the formation of bioactive compounds. However, information about the microbial conversion of complex glycosylated flavonoids and the impact on the gut microbiota are still limited. In this study, in vitro fermentations with selected flavonoid O- and C-glycosides and three different fecal samples were performed. As a result, all flavonoid glycosides were metabolized via their aglycones yielding smaller substances. Main metabolites were 3-(4-hydroxyphenyl)propionic acid, 3-phenylpropionic acid, and phenylacetic acid. Differences in the metabolite formation due to different time courses between the donors were determined. Therefore, from all fermentations, the ones with a specific donor were always slower resulting in a lower number of metabolites compared to the others. For example, tiliroside was totally degraded from 0 h (105 ± 13.2 μM) within the first 24 h, while in the fermentations with fecal samples from other donors, tiliroside (107 ± 52.7 μM at 0 h) was not detected after 7 h anymore. In general, fermentation rates of C-glycosides were slower compared to the fermentation rates of O-glycosides. The O-glycoside tiliroside was degraded within 4 h while the gut microbiota converted the C-glycoside vitexin within 13 h. However, significant changes (p < 0.05) in the microbiota composition and short chain fatty acid levels as products of carbohydrate fermentation were not detected between incubations with different phenolic compounds. Therefore, microbiota diversity was not affected and a significant prebiotic effect of phenolic compounds cannot be assigned to flavonoid glycosides in food-relevant concentrations.
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Affiliation(s)
- Maren Vollmer
- Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg , Grindelallee 117, 20146 Hamburg, Germany
| | - Selma Esders
- Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg , Grindelallee 117, 20146 Hamburg, Germany
| | - Freda M Farquharson
- The Rowett Institute, University of Aberdeen , Foresterhill, Aberdeen AB25 2ZD, U.K
| | - Susanne Neugart
- Leibniz Institute of Vegetable and Ornamental Crops , Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Sylvia H Duncan
- The Rowett Institute, University of Aberdeen , Foresterhill, Aberdeen AB25 2ZD, U.K
| | - Monika Schreiner
- Leibniz Institute of Vegetable and Ornamental Crops , Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Petra Louis
- The Rowett Institute, University of Aberdeen , Foresterhill, Aberdeen AB25 2ZD, U.K
| | - Ronald Maul
- Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg , Grindelallee 117, 20146 Hamburg, Germany
| | - Sascha Rohn
- Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg , Grindelallee 117, 20146 Hamburg, Germany
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22
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Mukhopadhya I, Moraïs S, Laverde‐Gomez J, Sheridan PO, Walker AW, Kelly W, Klieve AV, Ouwerkerk D, Duncan SH, Louis P, Koropatkin N, Cockburn D, Kibler R, Cooper PJ, Sandoval C, Crost E, Juge N, Bayer EA, Flint HJ. Sporulation capability and amylosome conservation among diverse human colonic and rumen isolates of the keystone starch-degrader Ruminococcus bromii. Environ Microbiol 2018; 20:324-336. [PMID: 29159997 PMCID: PMC5814915 DOI: 10.1111/1462-2920.14000] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/25/2017] [Accepted: 11/16/2017] [Indexed: 12/16/2022]
Abstract
Ruminococcus bromii is a dominant member of the human colonic microbiota that plays a 'keystone' role in degrading dietary resistant starch. Recent evidence from one strain has uncovered a unique cell surface 'amylosome' complex that organizes starch-degrading enzymes. New genome analysis presented here reveals further features of this complex and shows remarkable conservation of amylosome components between human colonic strains from three different continents and a R. bromii strain from the rumen of Australian cattle. These R. bromii strains encode a narrow spectrum of carbohydrate active enzymes (CAZymes) that reflect extreme specialization in starch utilization. Starch hydrolysis products are taken up mainly as oligosaccharides, with only one strain able to grow on glucose. The human strains, but not the rumen strain, also possess transporters that allow growth on galactose and fructose. R. bromii strains possess a full complement of sporulation and spore germination genes and we demonstrate the ability to form spores that survive exposure to air. Spore formation is likely to be a critical factor in the ecology of this nutritionally highly specialized bacterium, which was previously regarded as 'non-sporing', helping to explain its widespread occurrence in the gut microbiota through the ability to transmit between hosts.
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Affiliation(s)
| | - Sarah Moraïs
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovotIsrael
- Present address:
Faculty of Natural Sciences, Ben‐Gurion University of the NegevBeer‐Sheva 8499000Israel
| | | | - Paul O. Sheridan
- Microbiology GroupThe Rowett Institute, University of AberdeenAberdeenUK
| | - Alan W. Walker
- Microbiology GroupThe Rowett Institute, University of AberdeenAberdeenUK
| | - William Kelly
- AgResearch Limited, Grasslands Research Centre, Palmerston North 4442New Zealand
| | - Athol V. Klieve
- School of Agriculture and Food SciencesThe University of QueenslandQLDSt Lucia, Australia
- Queensland Alliance for Agriculture and Food InnovationThe University of QueenslandQLDSt Lucia, Australia
| | - Diane Ouwerkerk
- Queensland Alliance for Agriculture and Food InnovationThe University of QueenslandQLDSt Lucia, Australia
- Department of Agriculture and FisheriesAgri‐Science QueenslandBrisbaneQLDAustralia
| | - Sylvia H. Duncan
- Microbiology GroupThe Rowett Institute, University of AberdeenAberdeenUK
| | - Petra Louis
- Microbiology GroupThe Rowett Institute, University of AberdeenAberdeenUK
| | - Nicole Koropatkin
- Department of Microbiology and ImmunologyUniversity of Michigan Medical SchoolAnn ArborMIUSA
| | - Darrell Cockburn
- Department of Microbiology and ImmunologyUniversity of Michigan Medical SchoolAnn ArborMIUSA
| | - Ryan Kibler
- Department of Microbiology and ImmunologyUniversity of Michigan Medical SchoolAnn ArborMIUSA
| | - Philip J. Cooper
- Hospital Cantonal “Padre Alberto Buffoni”, Avenida 3 de Julio y Victor VillegasQuinindeEsmeraldas ProvinceEcuador
| | - Carlos Sandoval
- Hospital Cantonal “Padre Alberto Buffoni”, Avenida 3 de Julio y Victor VillegasQuinindeEsmeraldas ProvinceEcuador
| | - Emmanuelle Crost
- The Gut Health and Food Safety Institute Strategic Programme, Institute of Food ResearchNorwichUK
| | - Nathalie Juge
- The Gut Health and Food Safety Institute Strategic Programme, Institute of Food ResearchNorwichUK
| | - Edward A. Bayer
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovotIsrael
| | - Harry J. Flint
- Microbiology GroupThe Rowett Institute, University of AberdeenAberdeenUK
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23
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Reichardt N, Vollmer M, Holtrop G, Farquharson FM, Wefers D, Bunzel M, Duncan SH, Drew JE, Williams LM, Milligan G, Preston T, Morrison D, Flint HJ, Louis P. Specific substrate-driven changes in human faecal microbiota composition contrast with functional redundancy in short-chain fatty acid production. ISME J 2017; 12:610-622. [PMID: 29192904 PMCID: PMC5776475 DOI: 10.1038/ismej.2017.196] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 10/03/2017] [Accepted: 10/09/2017] [Indexed: 01/04/2023]
Abstract
The diet provides carbohydrates that are non-digestible in the upper gut and are major carbon and energy sources for the microbial community in the lower intestine, supporting a complex metabolic network. Fermentation produces the short-chain fatty acids (SCFAs) acetate, propionate and butyrate, which have health-promoting effects for the human host. Here we investigated microbial community changes and SCFA production during in vitro batch incubations of 15 different non-digestible carbohydrates, at two initial pH values with faecal microbiota from three different human donors. To investigate temporal stability and reproducibility, a further experiment was performed 1 year later with four of the carbohydrates. The lower pH (5.5) led to higher butyrate and the higher pH (6.5) to more propionate production. The strongest propionigenic effect was found with rhamnose, followed by galactomannans, whereas fructans and several α- and β-glucans led to higher butyrate production. 16S ribosomal RNA gene-based quantitative PCR analysis of 22 different microbial groups together with 454 sequencing revealed significant stimulation of specific bacteria in response to particular carbohydrates. Some changes were ascribed to metabolite cross-feeding, for example, utilisation by Eubacterium hallii of 1,2-propanediol produced from fermentation of rhamnose by Blautia spp. Despite marked inter-individual differences in microbiota composition, SCFA production was surprisingly reproducible for different carbohydrates, indicating a level of functional redundancy. Interestingly, butyrate formation was influenced not only by the overall % butyrate-producing bacteria in the community but also by the initial pH, consistent with a pH-dependent shift in the stoichiometry of butyrate production.
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Affiliation(s)
- Nicole Reichardt
- The Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, UK.,Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Maren Vollmer
- The Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - Grietje Holtrop
- Biomathematics and Statistics Scotland, Foresterhill, Aberdeen, UK
| | | | - Daniel Wefers
- Department of Food Chemistry and Phytochemistry, Karlsruhe Institute of Technology (KIT), Adenauerring 20A, Karlsruhe, Germany
| | - Mirko Bunzel
- Department of Food Chemistry and Phytochemistry, Karlsruhe Institute of Technology (KIT), Adenauerring 20A, Karlsruhe, Germany
| | - Sylvia H Duncan
- The Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - Janice E Drew
- The Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - Lynda M Williams
- The Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - Graeme Milligan
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Thomas Preston
- Scottish Universities Environmental Research Centre, University of Glasgow, Rankine Avenue, East Kilbride, UK
| | - Douglas Morrison
- Scottish Universities Environmental Research Centre, University of Glasgow, Rankine Avenue, East Kilbride, UK
| | - Harry J Flint
- The Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - Petra Louis
- The Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, UK
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24
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Hegazy AN, West NR, Stubbington MJ, Wendt E, Suijker KI, Datsi A, This S, Danne C, Campion S, Duncan SH, Owens BM, Uhlig HH, McMichael A, Bergthaler A, Teichmann SA, Keshav S, Powrie F. Circulating and Tissue-Resident CD4 + T Cells With Reactivity to Intestinal Microbiota Are Abundant in Healthy Individuals and Function Is Altered During Inflammation. Gastroenterology 2017; 153:1320-1337.e16. [PMID: 28782508 PMCID: PMC5687320 DOI: 10.1053/j.gastro.2017.07.047] [Citation(s) in RCA: 210] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 07/21/2017] [Accepted: 07/25/2017] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Interactions between commensal microbes and the immune system are tightly regulated and maintain intestinal homeostasis, but little is known about these interactions in humans. We investigated responses of human CD4+ T cells to the intestinal microbiota. We measured the abundance of T cells in circulation and intestinal tissues that respond to intestinal microbes and determined their clonal diversity. We also assessed their functional phenotypes and effects on intestinal resident cell populations, and studied alterations in microbe-reactive T cells in patients with chronic intestinal inflammation. METHODS We collected samples of peripheral blood mononuclear cells and intestinal tissues from healthy individuals (controls, n = 13-30) and patients with inflammatory bowel diseases (n = 119; 59 with ulcerative colitis and 60 with Crohn's disease). We used 2 independent assays (CD154 detection and carboxy-fluorescein succinimidyl ester dilution assays) and 9 intestinal bacterial species (Escherichia coli, Lactobacillus acidophilus, Bifidobacterium animalis subsp lactis, Faecalibacterium prausnitzii, Bacteroides vulgatus, Roseburia intestinalis, Ruminococcus obeum, Salmonella typhimurium, and Clostridium difficile) to quantify, expand, and characterize microbe-reactive CD4+ T cells. We sequenced T-cell receptor Vβ genes in expanded microbe-reactive T-cell lines to determine their clonal diversity. We examined the effects of microbe-reactive CD4+ T cells on intestinal stromal and epithelial cell lines. Cytokines, chemokines, and gene expression patterns were measured by flow cytometry and quantitative polymerase chain reaction. RESULTS Circulating and gut-resident CD4+ T cells from controls responded to bacteria at frequencies of 40-4000 per million for each bacterial species tested. Microbiota-reactive CD4+ T cells were mainly of a memory phenotype, present in peripheral blood mononuclear cells and intestinal tissue, and had a diverse T-cell receptor Vβ repertoire. These cells were functionally heterogeneous, produced barrier-protective cytokines, and stimulated intestinal stromal and epithelial cells via interleukin 17A, interferon gamma, and tumor necrosis factor. In patients with inflammatory bowel diseases, microbiota-reactive CD4+ T cells were reduced in the blood compared with intestine; T-cell responses that we detected had an increased frequency of interleukin 17A production compared with responses of T cells from blood or intestinal tissues of controls. CONCLUSIONS In an analysis of peripheral blood mononuclear cells and intestinal tissues from patients with inflammatory bowel diseases vs controls, we found that reactivity to intestinal bacteria is a normal property of the human CD4+ T-cell repertoire, and does not necessarily indicate disrupted interactions between immune cells and the commensal microbiota. T-cell responses to commensals might support intestinal homeostasis, by producing barrier-protective cytokines and providing a large pool of T cells that react to pathogens.
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Affiliation(s)
- Ahmed N. Hegazy
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, John Radcliffe Hospital, University of Oxford, United Kingdom,Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, United Kingdom
| | - Nathaniel R. West
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, John Radcliffe Hospital, University of Oxford, United Kingdom,Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, United Kingdom
| | - Michael J.T. Stubbington
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, United Kingdom,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Emily Wendt
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, John Radcliffe Hospital, University of Oxford, United Kingdom
| | - Kim I.M. Suijker
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, United Kingdom
| | - Angeliki Datsi
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, John Radcliffe Hospital, University of Oxford, United Kingdom
| | - Sebastien This
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, John Radcliffe Hospital, University of Oxford, United Kingdom
| | - Camille Danne
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, United Kingdom
| | - Suzanne Campion
- Nuffield Department of Medicine Research Building, University of Oxford, Oxford, United Kingdom
| | - Sylvia H. Duncan
- Microbial Ecology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Benjamin M.J. Owens
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, John Radcliffe Hospital, University of Oxford, United Kingdom
| | - Holm H. Uhlig
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, John Radcliffe Hospital, University of Oxford, United Kingdom,Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Andrew McMichael
- Nuffield Department of Medicine Research Building, University of Oxford, Oxford, United Kingdom
| | | | - Andreas Bergthaler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sarah A. Teichmann
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, United Kingdom,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Satish Keshav
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, John Radcliffe Hospital, University of Oxford, United Kingdom
| | - Fiona Powrie
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, John Radcliffe Hospital, University of Oxford, United Kingdom; Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, United Kingdom.
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25
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Chung WSF, Meijerink M, Zeuner B, Holck J, Louis P, Meyer AS, Wells JM, Flint HJ, Duncan SH. Prebiotic potential of pectin and pectic oligosaccharides to promote anti-inflammatory commensal bacteria in the human colon. FEMS Microbiol Ecol 2017; 93:4331632. [DOI: 10.1093/femsec/fix127] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 09/29/2017] [Indexed: 01/16/2023] Open
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26
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Vollmer M, Schröter D, Esders S, Neugart S, Farquharson FM, Duncan SH, Schreiner M, Louis P, Maul R, Rohn S. Chlorogenic acid versus amaranth's caffeoylisocitric acid – Gut microbial degradation of caffeic acid derivatives. Food Res Int 2017; 100:375-384. [DOI: 10.1016/j.foodres.2017.06.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 06/02/2017] [Accepted: 06/02/2017] [Indexed: 10/19/2022]
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27
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Hatziioanou D, Gherghisan-Filip C, Saalbach G, Horn N, Wegmann U, Duncan SH, Flint HJ, Mayer MJ, Narbad A. Discovery of a novel lantibiotic nisin O from Blautia obeum A2-162, isolated from the human gastrointestinal tract. Microbiology (Reading) 2017; 163:1292-1305. [PMID: 28857034 DOI: 10.1099/mic.0.000515] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A novel lanC-like sequence was identified from the dominant human gut bacterium Blautia obeum strain A2-162. This sequence was extended to reveal a putative lantibiotic operon with biosynthetic and transport genes, two sets of regulatory genes, immunity genes, three identical copies of a nisin-like lanA gene with an unusual leader peptide, and a fourth putative lanA gene. Comparison with other nisin clusters showed that the closest relationship was to nisin U. B. obeum A2-162 demonstrated antimicrobial activity against Clostridium perfringens when grown on solid medium in the presence of trypsin. Fusions of predicted nsoA structural sequences with the nisin A leader were expressed in Lactococcus lactis containing the nisin A operon without nisA. Expression of the nisA leader sequence fused to the predicted structural nsoA1 produced a growth defect in L. lactis that was dependent upon the presence of biosynthetic genes, but failed to produce antimicrobial activity. Insertion of the nso cluster into L. lactis MG1614 gave an increased immunity to nisin A, but this was not replicated by the expression of nsoI. Nisin A induction of L. lactis containing the nso cluster and nisRK genes allowed detection of the NsoA1 pre-peptide by Western hybridization. When this heterologous producer was grown with nisin induction on solid medium, antimicrobial activity was demonstrated in the presence of trypsin against C. perfringens, Clostridium difficile and L. lactis. This research adds to evidence that lantibiotic production may be an important trait of gut bacteria and could lead to the development of novel treatments for intestinal diseases.
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Affiliation(s)
- Diane Hatziioanou
- Gut Health and Food Safety Institute Strategic Programme, Quadram Institute Bioscience, Colney, Norwich, NR4 7UA, UK
| | - Cristina Gherghisan-Filip
- Gut Health and Food Safety Institute Strategic Programme, Quadram Institute Bioscience, Colney, Norwich, NR4 7UA, UK
| | | | - Nikki Horn
- Gut Health and Food Safety Institute Strategic Programme, Quadram Institute Bioscience, Colney, Norwich, NR4 7UA, UK
| | - Udo Wegmann
- Gut Health and Food Safety Institute Strategic Programme, Quadram Institute Bioscience, Colney, Norwich, NR4 7UA, UK
| | - Sylvia H Duncan
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - Harry J Flint
- Gut Health Group, Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - Melinda J Mayer
- Gut Health and Food Safety Institute Strategic Programme, Quadram Institute Bioscience, Colney, Norwich, NR4 7UA, UK
| | - Arjan Narbad
- Gut Health and Food Safety Institute Strategic Programme, Quadram Institute Bioscience, Colney, Norwich, NR4 7UA, UK
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Flint HJ, Duncan SH, Louis P. The impact of nutrition on intestinal bacterial communities. Curr Opin Microbiol 2017; 38:59-65. [DOI: 10.1016/j.mib.2017.04.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/02/2017] [Accepted: 04/12/2017] [Indexed: 12/16/2022]
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Lopez-Siles M, Duncan SH, Garcia-Gil LJ, Martinez-Medina M. Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics. ISME J 2017; 11:841-852. [PMID: 28045459 PMCID: PMC5364359 DOI: 10.1038/ismej.2016.176] [Citation(s) in RCA: 403] [Impact Index Per Article: 57.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 10/15/2016] [Accepted: 11/10/2016] [Indexed: 12/13/2022]
Abstract
There is an increasing interest in Faecalibacterium prausnitzii, one of the most abundant bacterial species found in the gut, given its potentially important role in promoting gut health. Although some studies have phenotypically characterized strains of this species, it remains a challenge to determine which factors have a key role in maintaining the abundance of this bacterium in the gut. Besides, phylogenetic analysis has shown that at least two different F. prausnitzii phylogroups can be found within this species and their distribution is different between healthy subjects and patients with gut disorders. It also remains unknown whether or not there are other phylogroups within this species, and also if other Faecalibacterium species exist. Finally, many studies have shown that F. prausnitzii abundance is reduced in different intestinal disorders. It has been proposed that F. prausnitzii monitoring may therefore serve as biomarker to assist in gut diseases diagnostics. In this mini-review, we aim to serve as an overview of F. prausnitzii phylogeny, ecophysiology and diversity. In addition, strategies to modulate the abundance of F. prausnitzii in the gut as well as its application as a biomarker for diagnostics and prognostics of gut diseases are discussed. This species may be a useful potential biomarker to assist in ulcerative colitis and Crohn's disease discrimination.
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Affiliation(s)
- Mireia Lopez-Siles
- Laboratori de Microbiologia Molecular, Departament de Biologia, Universitat de Girona, Girona, Spain
| | - Sylvia H Duncan
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - L Jesús Garcia-Gil
- Laboratori de Microbiologia Molecular, Departament de Biologia, Universitat de Girona, Girona, Spain
- Laboratori de Microbiologia Molecular, Departament de Biologia, Universitat de Girona, Carrer de Maria Aurèlia Capmany, 40, E-17003, Girona, Spain. E-mail:
| | - Margarita Martinez-Medina
- Laboratori de Microbiologia Molecular, Departament de Biologia, Universitat de Girona, Girona, Spain
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Neacsu M, McMonagle J, Fletcher RJ, Hulshof T, Duncan SH, Scobbie L, Duncan GJ, Cantlay L, Horgan G, de Roos B, Duthie GG, Russell WR. Availability and dose response of phytophenols from a wheat bran rich cereal product in healthy human volunteers. Mol Nutr Food Res 2017; 61. [PMID: 27356494 DOI: 10.1002/mnfr.201600202] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 04/18/2016] [Accepted: 04/19/2016] [Indexed: 12/11/2022]
Abstract
SCOPE Phytophenols present in cereals are metabolised to compounds that could be partly responsible for the reduced risk of chronic diseases and all-cause mortality associated with fibre-rich diets. The bioavailability, form and in vivo concentrations of these metabolites require to be established. MATERIALS AND METHODS Eight healthy volunteers consumed a test meal containing a recommended dose (40 g) and high dose (120 g) of ready-to-eat wheat bran cereal and the systemic and colonic metabolites determined quantitatively by LC-MS. CONCLUSION Analysis of the systemic metabolomes demonstrated that a wide range of phytophenols were absorbed/excreted (43 metabolites) within 5 h of consumption. These included 16 of the 21 major parent compounds identified in the intervention product and several of these were also found to be significantly increased in the colon. Not all of the metabolites were increased with the higher dose, suggesting some limitation in absorption due to intrinsic factors and/or the food matrix. Many compounds identified (e.g. ferulic acid and major metabolites) exhibit anti-inflammatory activity and impact on redox pathways. The combination of postprandial absorption and delivery to the colon, as well as hepatic recycling of the metabolites at these concentrations, is likely to be beneficial to both systemic and gut health.
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Affiliation(s)
- Madalina Neacsu
- Natural Products Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Jolene McMonagle
- Kellogg Europe Trading Limited, Lakeshore Drive, County Dublin, Ireland
| | - Reg J Fletcher
- Kellogg Europe Trading Limited, Lakeshore Drive, County Dublin, Ireland
| | - Toine Hulshof
- Kellogg Europe Trading Limited, Lakeshore Drive, County Dublin, Ireland
| | - Sylvia H Duncan
- Microbial Ecology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Lorraine Scobbie
- Natural Products Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Gary J Duncan
- Scientific Services, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Louise Cantlay
- Scientific Services, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | | | - Baukje de Roos
- Metabolic Health, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Garry G Duthie
- Natural Products Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Wendy R Russell
- Natural Products Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
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Moraïs S, Cockburn DW, Ben-David Y, Koropatkin NM, Martens EC, Duncan SH, Flint HJ, Mizrahi I, Bayer EA. Lysozyme activity of theRuminococcus champanellensiscellulosome. Environ Microbiol 2016; 18:5112-5122. [DOI: 10.1111/1462-2920.13501] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 08/16/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Sarah Moraïs
- Biomolecular Sciences Department; The Weizmann Institute of Science; Rehovot Israel
| | - Darrell W. Cockburn
- Department of Microbiology and Immunology; University of Michigan Medical School; Ann Arbor MI 48109 USA
| | - Yonit Ben-David
- Biomolecular Sciences Department; The Weizmann Institute of Science; Rehovot Israel
| | - Nicole M. Koropatkin
- Department of Microbiology and Immunology; University of Michigan Medical School; Ann Arbor MI 48109 USA
| | - Eric C. Martens
- Department of Microbiology and Immunology; University of Michigan Medical School; Ann Arbor MI 48109 USA
| | - Sylvia H. Duncan
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen; Aberdeen UK
| | - Harry J. Flint
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen; Aberdeen UK
| | - Itzhak Mizrahi
- The Department of Life Sciences & the National Institute for Biotechnology in the Negev; Ben-Gurion University of the Negev; Beer-Sheva 84105 Israel
| | - Edward A. Bayer
- Biomolecular Sciences Department; The Weizmann Institute of Science; Rehovot Israel
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Duncan SH, Russell WR, Quartieri A, Rossi M, Parkhill J, Walker AW, Flint HJ. Wheat bran promotes enrichment within the human colonic microbiota of butyrate-producing bacteria that release ferulic acid. Environ Microbiol 2016; 18:2214-25. [PMID: 26636660 PMCID: PMC4949515 DOI: 10.1111/1462-2920.13158] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 11/09/2015] [Accepted: 11/27/2015] [Indexed: 01/02/2023]
Abstract
Cereal fibres such as wheat bran are considered to offer human health benefits via their impact on the intestinal microbiota. We show here by 16S rRNA gene-based community analysis that providing amylase-pretreated wheat bran as the sole added energy source to human intestinal microbial communities in anaerobic fermentors leads to the selective and progressive enrichment of a small number of bacterial species. In particular, OTUs corresponding to uncultured Lachnospiraceae (Firmicutes) related to Eubacterium xylanophilum and Butyrivibrio spp. were strongly enriched (by five to 160 fold) over 48 h in four independent experiments performed with different faecal inocula, while nine other Firmicutes OTUs showed > 5-fold enrichment in at least one experiment. Ferulic acid was released from the wheat bran during degradation but was rapidly converted to phenylpropionic acid derivatives via hydrogenation, demethylation and dehydroxylation to give metabolites that are detected in human faecal samples. Pure culture work using bacterial isolates related to the enriched OTUs, including several butyrate-producers, demonstrated that the strains caused substrate weight loss and released ferulic acid, but with limited further conversion. We conclude that breakdown of wheat bran involves specialist primary degraders while the conversion of released ferulic acid is likely to involve a multi-species pathway.
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Affiliation(s)
- Sylvia H Duncan
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Wendy R Russell
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Andrea Quartieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Maddalena Rossi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Julian Parkhill
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Alan W Walker
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Harry J Flint
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
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Sheridan PO, Duncan SH, Walker AW, Scott KP, Louis P, Flint HJ. Objections to the proposed reclassification of Eubacterium rectale as Agathobacter rectalis. Int J Syst Evol Microbiol 2016; 66:2106. [PMID: 26916277 DOI: 10.1099/ijsem.0.000969] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Paul O Sheridan
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen,Aberdeen,UK
| | - Sylvia H Duncan
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen,Aberdeen,UK
| | - Alan W Walker
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen,Aberdeen,UK
| | - Karen P Scott
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen,Aberdeen,UK
| | - Petra Louis
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen,Aberdeen,UK
| | - Harry J Flint
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen,Aberdeen,UK
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O Sheridan P, Martin JC, Lawley TD, Browne HP, Harris HMB, Bernalier-Donadille A, Duncan SH, O'Toole PW, P Scott K, J Flint H. Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes. Microb Genom 2016; 2:e000043. [PMID: 28348841 PMCID: PMC5320581 DOI: 10.1099/mgen.0.000043] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 12/11/2015] [Indexed: 12/25/2022] Open
Abstract
Firmicutes and Bacteroidetes are the predominant bacterial phyla colonizing the healthy human large intestine. Whilst both ferment dietary fibre, genes responsible for this important activity have been analysed only in the Bacteroidetes, with very little known about the Firmicutes. This work investigates the carbohydrate-active enzymes (CAZymes) in a group of Firmicutes, Roseburia spp. and Eubacterium rectale, which play an important role in producing butyrate from dietary carbohydrates and in health maintenance. Genome sequences of 11 strains representing E. rectale and four Roseburia spp. were analysed for carbohydrate-active genes. Following assembly into a pan-genome, core, variable and unique genes were identified. The 1840 CAZyme genes identified in the pan-genome were assigned to 538 orthologous groups, of which only 26 were present in all strains, indicating considerable inter-strain variability. This analysis was used to categorize the 11 strains into four carbohydrate utilization ecotypes (CUEs), which were shown to correspond to utilization of different carbohydrates for growth. Many glycoside hydrolase genes were found linked to genes encoding oligosaccharide transporters and regulatory elements in the genomes of Roseburia spp. and E. rectale, forming distinct polysaccharide utilization loci (PULs). Whilst PULs are also a common feature in Bacteroidetes, key differences were noted in these Firmicutes, including the absence of close homologues of Bacteroides polysaccharide utilization genes, hence we refer to Gram-positive PULs (gpPULs). Most CAZyme genes in the Roseburia/E. rectale group are organized into gpPULs. Variation in gpPULs can explain the high degree of nutritional specialization at the species level within this group.
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Affiliation(s)
- Paul O Sheridan
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
| | - Jennifer C Martin
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
| | | | | | - Hugh M B Harris
- 3 Department of Microbiology & Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Annick Bernalier-Donadille
- 4 Unité de Microbiologie INRA, Centre de Recherche de Clermont-Ferrand/Theix, 63122 Saint Genès Champanelle, France
| | - Sylvia H Duncan
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
| | - Paul W O'Toole
- 3 Department of Microbiology & Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Karen P Scott
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
| | - Harry J Flint
- 1 Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen AB21 9SB, UK
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35
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Moraïs S, Ben David Y, Bensoussan L, Duncan SH, Koropatkin NM, Martens EC, Flint HJ, Bayer EA. Enzymatic profiling of cellulosomal enzymes from the human gut bacterium, Ruminococcus champanellensis, reveals a fine-tuned system for cohesin-dockerin recognition. Environ Microbiol 2016; 18:542-56. [PMID: 26347002 DOI: 10.1111/1462-2920.13047] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/02/2015] [Accepted: 09/02/2015] [Indexed: 12/16/2023]
Abstract
Ruminococcus champanellensis is considered a keystone species in the human gut that degrades microcrystalline cellulose efficiently and contains the genetic elements necessary for cellulosome production. The basic elements of its cellulosome architecture, mainly cohesin and dockerin modules from scaffoldins and enzyme-borne dockerins, have been characterized recently. In this study, we cloned, expressed and characterized all of the glycoside hydrolases that contain a dockerin module. Among the 25 enzymes, 10 cellulases, 4 xylanases, 3 mannanases, 2 xyloglucanases, 2 arabinofuranosidases, 2 arabinanases and one β-glucanase were assessed for their comparative enzymatic activity on their respective substrates. The dockerin specificities of the enzymes were examined by ELISA, and 80 positives out of 525 possible interactions were detected. Our analysis reveals a fine-tuned system for cohesin-dockerin specificity and the importance of diversity among the cohesin-dockerin sequences. Our results imply that cohesin-dockerin pairs are not necessarily assembled at random among the same specificity types, as generally believed for other cellulosome-producing bacteria, but reveal a more organized cellulosome architecture. Moreover, our results highlight the importance of the cellulosome paradigm for cellulose and hemicellulose degradation by R. champanellensis in the human gut.
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Affiliation(s)
- Sarah Moraïs
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Yonit Ben David
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Lizi Bensoussan
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Sylvia H Duncan
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Harry J Flint
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Edward A Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
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Chung WSF, Walker AW, Louis P, Parkhill J, Vermeiren J, Bosscher D, Duncan SH, Flint HJ. Modulation of the human gut microbiota by dietary fibres occurs at the species level. BMC Biol 2016; 14:3. [PMID: 26754945 PMCID: PMC4709873 DOI: 10.1186/s12915-015-0224-3] [Citation(s) in RCA: 235] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 12/23/2015] [Indexed: 01/08/2023] Open
Abstract
Background Dietary intake of specific non-digestible carbohydrates (including prebiotics) is increasingly seen as a highly effective approach for manipulating the composition and activities of the human gut microbiota to benefit health. Nevertheless, surprisingly little is known about the global response of the microbial community to particular carbohydrates. Recent in vivo dietary studies have demonstrated that the species composition of the human faecal microbiota is influenced by dietary intake. There is now potential to gain insights into the mechanisms involved by using in vitro systems that produce highly controlled conditions of pH and substrate supply. Results We supplied two alternative non-digestible polysaccharides as energy sources to three different human gut microbial communities in anaerobic, pH-controlled continuous-flow fermentors. Community analysis showed that supply of apple pectin or inulin resulted in the highly specific enrichment of particular bacterial operational taxonomic units (OTUs; based on 16S rRNA gene sequences). Of the eight most abundant Bacteroides OTUs detected, two were promoted specifically by inulin and six by pectin. Among the Firmicutes, Eubacterium eligens in particular was strongly promoted by pectin, while several species were stimulated by inulin. Responses were influenced by pH, which was stepped up, and down, between 5.5, 6.0, 6.4 and 6.9 in parallel vessels within each experiment. In particular, several experiments involving downshifts to pH 5.5 resulted in Faecalibacterium prausnitzii replacing Bacteroides spp. as the dominant sequences observed. Community diversity was greater in the pectin-fed than in the inulin-fed fermentors, presumably reflecting the differing complexity of the two substrates. Conclusions We have shown that particular non-digestible dietary carbohydrates have enormous potential for modifying the gut microbiota, but these modifications occur at the level of individual strains and species and are not easily predicted a priori. Furthermore, the gut environment, especially pH, plays a key role in determining the outcome of interspecies competition. This makes it crucial to put greater effort into identifying the range of bacteria that may be stimulated by a given prebiotic approach. Both for reasons of efficacy and of safety, the development of prebiotics intended to benefit human health has to take account of the highly individual species profiles that may result. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0224-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wing Sun Faith Chung
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Greenburn Road, Bucksburn, Aberdeen, Scotland, AB21 9SB, UK
| | - Alan W Walker
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Greenburn Road, Bucksburn, Aberdeen, Scotland, AB21 9SB, UK.,Pathogen Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Petra Louis
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Greenburn Road, Bucksburn, Aberdeen, Scotland, AB21 9SB, UK
| | - Julian Parkhill
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | | | | | - Sylvia H Duncan
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Greenburn Road, Bucksburn, Aberdeen, Scotland, AB21 9SB, UK
| | - Harry J Flint
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Greenburn Road, Bucksburn, Aberdeen, Scotland, AB21 9SB, UK.
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37
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Rossi O, van Berkel LA, Chain F, Tanweer Khan M, Taverne N, Sokol H, Duncan SH, Flint HJ, Harmsen HJM, Langella P, Samsom JN, Wells JM. Faecalibacterium prausnitzii A2-165 has a high capacity to induce IL-10 in human and murine dendritic cells and modulates T cell responses. Sci Rep 2016; 6:18507. [PMID: 26725514 PMCID: PMC4698756 DOI: 10.1038/srep18507] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 10/06/2015] [Indexed: 02/06/2023] Open
Abstract
Faecalibacterium prausnitzii strain A2-165 was previously reported to have anti-inflammatory properties and prevent colitis in a TNBS model. We compared the immunomodulatory properties of strain A2-165 to four different F. prausnitzii isolates and eight abundant intestinal commensals using human dendritic cells (DCs) and mouse BMDCs in vitro. Principal component analysis revealed that the cytokine response to F. prausnitzii A2-165 is distinct from the other strains in eliciting high amounts of IL-10 secretion. The mouse DNBS model of relapsing IBD was used to compare the protective effects of F. prausnitzii A2-165 and Clostridium hathewayi, a low secretor of IL-10, on the Th1-driven inflammatory response to DNBS; attenuation of disease parameters was only observed with F. prausnitzii. In an in vivo mouse model of nasal tolerance to ovalbumin, F. prausnitzii A2-165 enhanced ovalbumin-specific T cell proliferation and reduced the proportion of IFN-γ(+) T cells in CLNs. Similarly, in vitro F. prausnitzii A2-165 stimulated BMDCs increased ovalbumin-specific T cell proliferation and reduced the number of IFN-γ(+) T cells. These mechanisms may contribute to the anti-inflammatory effects of F. prausnitzii in colitis and support the notion that this abundant bacterium might contribute to immune homeostasis in the intestine via its anti-inflammatory properties.
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Affiliation(s)
- Oriana Rossi
- Host-Microbe Interactomics Group, University of Wageningen, 6708 WD, The Netherlands
| | - Lisette A van Berkel
- Department of Pediatrics, Erasmus Medical Center - Sophia Children's Hospital, 3015 CE, Rotterdam, The Netherlands
| | - Florian Chain
- Commensal and Probiotics-Host Interactions Laboratory, UMR 1319 Micalis, INRA, 78352, Jouy-en-Josas, France.,UMR 1319 Micalis, AgroparisTech, 78352, Jouy-en-Josas, France
| | - M Tanweer Khan
- Department of Medical Microbiology, University Medical Center Groningen, 9700 RB, Groningen, The Netherlands
| | - Nico Taverne
- Host-Microbe Interactomics Group, University of Wageningen, 6708 WD, The Netherlands
| | - Harry Sokol
- Commensal and Probiotics-Host Interactions Laboratory, UMR 1319 Micalis, INRA, 78352, Jouy-en-Josas, France.,UMR 1319 Micalis, AgroparisTech, 78352, Jouy-en-Josas, France.,Department of Gastroenterology and Nutrition, Hôpital SaintAntoine and UPMC University of Paris, 75012, Paris, France.,Equipe AVENIR Gut Microbiota and Immunity, INSERM U1057/UMR CNRS 7203, Université Pierre et Marie Curie 6, 75005, Paris, France
| | - Sylvia H Duncan
- Microbial Ecology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, AB21 9SB, Aberdeen, United Kingdom
| | - Harry J Flint
- Microbial Ecology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, AB21 9SB, Aberdeen, United Kingdom
| | - Hermie J M Harmsen
- Department of Medical Microbiology, University Medical Center Groningen, 9700 RB, Groningen, The Netherlands
| | - Philippe Langella
- Commensal and Probiotics-Host Interactions Laboratory, UMR 1319 Micalis, INRA, 78352, Jouy-en-Josas, France.,UMR 1319 Micalis, AgroparisTech, 78352, Jouy-en-Josas, France
| | - Janneke N Samsom
- Department of Pediatrics, Erasmus Medical Center - Sophia Children's Hospital, 3015 CE, Rotterdam, The Netherlands
| | - Jerry M Wells
- Host-Microbe Interactomics Group, University of Wageningen, 6708 WD, The Netherlands
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Rios-Covian D, Gueimonde M, Duncan SH, Flint HJ, de los Reyes-Gavilan CG. Enhanced butyrate formation by cross-feeding betweenFaecalibacterium prausnitziiandBifidobacterium adolescentis. FEMS Microbiol Lett 2015; 362:fnv176. [DOI: 10.1093/femsle/fnv176] [Citation(s) in RCA: 175] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2015] [Indexed: 02/06/2023] Open
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Ben David Y, Dassa B, Borovok I, Lamed R, Koropatkin NM, Martens EC, White BA, Bernalier-Donadille A, Duncan SH, Flint HJ, Bayer EA, Moraïs S. Ruminococcal cellulosome systems from rumen to human. Environ Microbiol 2015; 17:3407-26. [PMID: 25845888 DOI: 10.1111/1462-2920.12868] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 03/24/2015] [Accepted: 03/31/2015] [Indexed: 01/19/2023]
Abstract
A cellulolytic fiber-degrading bacterium, Ruminococcus champanellensis, was isolated from human faecal samples, and its genome was recently sequenced. Bioinformatic analysis of the R. champanellensis genome revealed numerous cohesin and dockerin modules, the basic elements of the cellulosome, and manual sequencing of partially sequenced genomic segments revealed two large tandem scaffoldin-coding genes that form part of a gene cluster. Representative R. champanellensis dockerins were tested against putative cohesins, and the results revealed three different cohesin-dockerin binding profiles which implied two major types of cellulosome architectures: (i) an intricate cell-bound system and (ii) a simplistic cell-free system composed of a single cohesin-containing scaffoldin. The cell-bound system can adopt various enzymatic architectures, ranging from a single enzyme to a large enzymatic complex comprising up to 11 enzymes. The variety of cellulosomal components together with adaptor proteins may infer a very tight regulation of its components. The cellulosome system of the human gut bacterium R. champanellensis closely resembles that of the bovine rumen bacterium Ruminococcus flavefaciens. The two species contain orthologous gene clusters comprising fundamental components of cellulosome architecture. Since R. champanellensis is the only human colonic bacterium known to degrade crystalline cellulose, it may thus represent a keystone species in the human gut.
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Affiliation(s)
- Yonit Ben David
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Bareket Dassa
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Bryan A White
- Department of Animal Sciences and Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | | | - Sylvia H Duncan
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Harry J Flint
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Edward A Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Sarah Moraïs
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
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Rossi O, Khan MT, Schwarzer M, Hudcovic T, Srutkova D, Duncan SH, Stolte EH, Kozakova H, Flint HJ, Samsom JN, Harmsen HJM, Wells JM. Faecalibacterium prausnitzii Strain HTF-F and Its Extracellular Polymeric Matrix Attenuate Clinical Parameters in DSS-Induced Colitis. PLoS One 2015; 10:e0123013. [PMID: 25910186 PMCID: PMC4409148 DOI: 10.1371/journal.pone.0123013] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 02/26/2015] [Indexed: 12/11/2022] Open
Abstract
A decrease in the abundance and biodiversity of intestinal bacteria within the Firmicutes phylum has been associated with inflammatory bowel disease (IBD). In particular, the anti-inflammatory bacterium Faecalibacterium prausnitzii, member of the Firmicutes phylum and one of the most abundant species in healthy human colon, is underrepresented in the microbiota of IBD patients. The aim of this study was to investigate the immunomodulatory properties of F. prausnitzii strain A2-165, the biofilm forming strain HTF-F and the extracellular polymeric matrix (EPM) isolated from strain HTF-F. For this purpose, the immunomodulatory properties of the F. prausnitzii strains and the EPM were studied in vitro using human monocyte-derived dendritic cells. Then, the capacity of the F. prausnitzii strains and the EPM of HTF-F to suppress inflammation was assessed in vivo in the mouse dextran sodium sulphate (DSS) colitis model. The F. prausnitzii strains and the EPM had anti-inflammatory effects on the clinical parameters measured in the DSS model but with different efficacy. The immunomodulatory effects of the EPM were mediated through the TLR2-dependent modulation of IL-12 and IL-10 cytokine production in antigen presenting cells, suggesting that it contributes to the anti-inflammatory potency of F. prausnitzii HTF-F. The results show that F. prausnitzii HTF-F and its EPM may have a therapeutic use in IBD.
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Affiliation(s)
- Oriana Rossi
- Host-Microbe Interactomics Group, Animal Science Department, University of Wageningen, Wageningen, The Netherlands
| | - M. Tanweer Khan
- Department of Cell Biology, section Membrane Cell Biology, University Medical Center Groningen, Groningen, The Netherlands
| | - Martin Schwarzer
- Institute of Microbiology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Tomas Hudcovic
- Institute of Microbiology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Dagmar Srutkova
- Institute of Microbiology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Sylvia H. Duncan
- Microbial Ecology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Ellen H. Stolte
- Host-Microbe Interactomics Group, Animal Science Department, University of Wageningen, Wageningen, The Netherlands
| | - Hana Kozakova
- Institute of Microbiology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Harry J. Flint
- Microbial Ecology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Janneke N. Samsom
- Department of Pediatrics, Division of Gastroenterology and Nutrition, Erasmus Medical Center—Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Hermie J. M. Harmsen
- Department of Cell Biology, section Membrane Cell Biology, University Medical Center Groningen, Groningen, The Netherlands
| | - Jerry M. Wells
- Host-Microbe Interactomics Group, Animal Science Department, University of Wageningen, Wageningen, The Netherlands
- * E-mail:
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Kettle H, Louis P, Holtrop G, Duncan SH, Flint HJ. Modelling the emergent dynamics and major metabolites of the human colonic microbiota. Environ Microbiol 2014; 17:1615-30. [PMID: 25142831 DOI: 10.1111/1462-2920.12599] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 08/14/2014] [Indexed: 02/06/2023]
Abstract
We present here a first attempt at modelling microbial dynamics in the human colon incorporating both uncertainty and adaptation. This is based on the development of a Monod-equation based, differential equation model, which produces computer simulations of the population dynamics and major metabolites of microbial communities from the human colon. To reduce the complexity of the system, we divide the bacterial community into 10 bacterial functional groups (BFGs) each distinguished by its substrate preferences, metabolic pathways and its preferred pH range. The model simulates the growth of a large number of bacterial strains and incorporates variation in microbiota composition between people, while also allowing succession and enabling adaptation to environmental changes. The model is shown to reproduce many of the observed changes in major phylogenetic groups and key metabolites such as butyrate, acetate and propionate in response to a one unit pH shift in experimental continuous flow fermentors inoculated with human faecal microbiota. Nevertheless, it should be regarded as a learning tool to be updated as our knowledge of bacterial groups and their interactions expands. Given the difficulty of accessing the colon, modelling can play an extremely important role in interpreting experimental data and predicting the consequences of dietary modulation.
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Affiliation(s)
- Helen Kettle
- Biomathematics and Statistics Scotland, Kings Buildings, Edinburgh, EH9 3JZ, UK
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Reichardt N, Duncan SH, Young P, Belenguer A, McWilliam Leitch C, Scott KP, Flint HJ, Louis P. Erratum: Phylogenetic distribution of three pathways for propionate production within the human gut microbiota. ISME J 2014. [DOI: 10.1038/ismej.2014.48] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Lopez-Siles M, Martinez-Medina M, Busquets D, Sabat-Mir M, Duncan SH, Flint HJ, Aldeguer X, Garcia-Gil LJ. Mucosa-associated Faecalibacterium prausnitzii and Escherichia coli co-abundance can distinguish Irritable Bowel Syndrome and Inflammatory Bowel Disease phenotypes. Int J Med Microbiol 2014; 304:464-75. [PMID: 24713205 DOI: 10.1016/j.ijmm.2014.02.009] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 10/31/2013] [Accepted: 02/09/2014] [Indexed: 12/19/2022] Open
Affiliation(s)
- Mireia Lopez-Siles
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain
| | | | - David Busquets
- Departament de Gastroenterologia, Hospital Dr. Josep Trueta, Girona, Spain
| | - Miriam Sabat-Mir
- Departament de Gastroenterologia, Hospital Santa Caterina, Salt, Girona, Spain
| | - Sylvia H Duncan
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Harry J Flint
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Xavier Aldeguer
- Departament de Gastroenterologia, Hospital Dr. Josep Trueta, Girona, Spain
| | - L Jesús Garcia-Gil
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain.
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Salonen A, Lahti L, Salojärvi J, Holtrop G, Korpela K, Duncan SH, Date P, Farquharson F, Johnstone AM, Lobley GE, Louis P, Flint HJ, de Vos WM. Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men. ISME J 2014; 8:2218-30. [PMID: 24763370 DOI: 10.1038/ismej.2014.63] [Citation(s) in RCA: 419] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 02/01/2014] [Accepted: 03/12/2014] [Indexed: 02/07/2023]
Abstract
There is growing interest in understanding how diet affects the intestinal microbiota, including its possible associations with systemic diseases such as metabolic syndrome. Here we report a comprehensive and deep microbiota analysis of 14 obese males consuming fully controlled diets supplemented with resistant starch (RS) or non-starch polysaccharides (NSPs) and a weight-loss (WL) diet. We analyzed the composition, diversity and dynamics of the fecal microbiota on each dietary regime by phylogenetic microarray and quantitative PCR (qPCR) analysis. In addition, we analyzed fecal short chain fatty acids (SCFAs) as a proxy of colonic fermentation, and indices of insulin sensitivity from blood samples. The diet explained around 10% of the total variance in microbiota composition, which was substantially less than the inter-individual variance. Yet, each of the study diets induced clear and distinct changes in the microbiota. Multiple Ruminococcaceae phylotypes increased on the RS diet, whereas mostly Lachnospiraceae phylotypes increased on the NSP diet. Bifidobacteria decreased significantly on the WL diet. The RS diet decreased the diversity of the microbiota significantly. The total 16S ribosomal RNA gene signal estimated by qPCR correlated positively with the three major SCFAs, while the amount of propionate specifically correlated with the Bacteroidetes. The dietary responsiveness of the individual's microbiota varied substantially and associated inversely with its diversity, suggesting that individuals can be stratified into responders and non-responders based on the features of their intestinal microbiota.
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Affiliation(s)
- Anne Salonen
- Immunobiology Research Program, Department of Bacteriology and Immunology, Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Leo Lahti
- 1] Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands [2] Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Jarkko Salojärvi
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | | | - Katri Korpela
- Immunobiology Research Program, Department of Bacteriology and Immunology, Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Sylvia H Duncan
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Priya Date
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Freda Farquharson
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | | | - Gerald E Lobley
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Petra Louis
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Harry J Flint
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Willem M de Vos
- 1] Immunobiology Research Program, Department of Bacteriology and Immunology, Haartman Institute, University of Helsinki, Helsinki, Finland [2] Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands [3] Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
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Pettit LJ, Browne HP, Yu L, Smits WK, Fagan RP, Barquist L, Martin MJ, Goulding D, Duncan SH, Flint HJ, Dougan G, Choudhary JS, Lawley TD. Functional genomics reveals that Clostridium difficile Spo0A coordinates sporulation, virulence and metabolism. BMC Genomics 2014; 15:160. [PMID: 24568651 PMCID: PMC4028888 DOI: 10.1186/1471-2164-15-160] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 02/14/2014] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Clostridium difficile is an anaerobic, Gram-positive bacterium that can reside as a commensal within the intestinal microbiota of healthy individuals or cause life-threatening antibiotic-associated diarrhea in immunocompromised hosts. C. difficile can also form highly resistant spores that are excreted facilitating host-to-host transmission. The C. difficile spo0A gene encodes a highly conserved transcriptional regulator of sporulation that is required for relapsing disease and transmission in mice. RESULTS Here we describe a genome-wide approach using a combined transcriptomic and proteomic analysis to identify Spo0A regulated genes. Our results validate Spo0A as a positive regulator of putative and novel sporulation genes as well as components of the mature spore proteome. We also show that Spo0A regulates a number of virulence-associated factors such as flagella and metabolic pathways including glucose fermentation leading to butyrate production. CONCLUSIONS The C. difficile spo0A gene is a global transcriptional regulator that controls diverse sporulation, virulence and metabolic phenotypes coordinating pathogen adaptation to a wide range of host interactions. Additionally, the rich breadth of functional data allowed us to significantly update the annotation of the C. difficile 630 reference genome which will facilitate basic and applied research on this emerging pathogen.
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Kennedy NA, Walker AW, Berry SH, Duncan SH, Farquarson FM, Louis P, Thomson JM, Satsangi J, Flint HJ, Parkhill J, Lees CW, Hold GL. The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing. PLoS One 2014; 9:e88982. [PMID: 24586470 PMCID: PMC3933346 DOI: 10.1371/journal.pone.0088982] [Citation(s) in RCA: 185] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 01/13/2014] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION Determining bacterial community structure in fecal samples through DNA sequencing is an important facet of intestinal health research. The impact of different commercially available DNA extraction kits upon bacterial community structures has received relatively little attention. The aim of this study was to analyze bacterial communities in volunteer and inflammatory bowel disease (IBD) patient fecal samples extracted using widely used DNA extraction kits in established gastrointestinal research laboratories. METHODS Fecal samples from two healthy volunteers (H3 and H4) and two relapsing IBD patients (I1 and I2) were investigated. DNA extraction was undertaken using MoBio Powersoil and MP Biomedicals FastDNA SPIN Kit for Soil DNA extraction kits. PCR amplification for pyrosequencing of bacterial 16S rRNA genes was performed in both laboratories on all samples. Hierarchical clustering of sequencing data was done using the Yue and Clayton similarity coefficient. RESULTS DNA extracted using the FastDNA kit and the MoBio kit gave median DNA concentrations of 475 (interquartile range 228-561) and 22 (IQR 9-36) ng/µL respectively (p<0.0001). Hierarchical clustering of sequence data by Yue and Clayton coefficient revealed four clusters. Samples from individuals H3 and I2 clustered by patient; however, samples from patient I1 extracted with the MoBio kit clustered with samples from patient H4 rather than the other I1 samples. Linear modelling on relative abundance of common bacterial families revealed significant differences between kits; samples extracted with MoBio Powersoil showed significantly increased Bacteroidaceae, Ruminococcaceae and Porphyromonadaceae, and lower Enterobacteriaceae, Lachnospiraceae, Clostridiaceae, and Erysipelotrichaceae (p<0.05). CONCLUSION This study demonstrates significant differences in DNA yield and bacterial DNA composition when comparing DNA extracted from the same fecal sample with different extraction kits. This highlights the importance of ensuring that samples in a study are prepared with the same method, and the need for caution when cross-comparing studies that use different methods.
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Affiliation(s)
- Nicholas A. Kennedy
- Gastrointestinal Unit, Centre for Genomic and Experimental Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Alan W. Walker
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Susan H. Berry
- Gastrointestinal Research Group, Division of Applied Medicine, Aberdeen University, Aberdeen, United Kingdom
| | - Sylvia H. Duncan
- Rowett Institute of Nutrition and Health, Aberdeen University, Aberdeen, United Kingdom
| | - Freda M. Farquarson
- Rowett Institute of Nutrition and Health, Aberdeen University, Aberdeen, United Kingdom
| | - Petra Louis
- Rowett Institute of Nutrition and Health, Aberdeen University, Aberdeen, United Kingdom
| | - John M. Thomson
- Department of Digestive Disorders, Aberdeen Royal Infirmary, Foresterhill, Aberdeen, United Kingdom
| | - Jack Satsangi
- Gastrointestinal Unit, Centre for Genomic and Experimental Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Harry J. Flint
- Rowett Institute of Nutrition and Health, Aberdeen University, Aberdeen, United Kingdom
| | - Julian Parkhill
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Charlie W. Lees
- Gastrointestinal Unit, Centre for Genomic and Experimental Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Georgina L. Hold
- Gastrointestinal Research Group, Division of Applied Medicine, Aberdeen University, Aberdeen, United Kingdom
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Hatziioanou D, Mayer MJ, Duncan SH, Flint HJ, Narbad A. A representative of the dominant human colonic Firmicutes, Roseburia faecis M72/1, forms a novel bacteriocin-like substance. Anaerobe 2013; 23:5-8. [DOI: 10.1016/j.anaerobe.2013.07.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 07/18/2013] [Accepted: 07/22/2013] [Indexed: 11/29/2022]
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Scott KP, Martin JC, Duncan SH, Flint HJ. Prebiotic stimulation of human colonic butyrate-producing bacteria and bifidobacteria, in vitro. FEMS Microbiol Ecol 2013; 87:30-40. [PMID: 23909466 DOI: 10.1111/1574-6941.12186] [Citation(s) in RCA: 282] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/23/2013] [Accepted: 07/29/2013] [Indexed: 01/27/2023] Open
Abstract
Dietary macronutrients affect the composition of the gut microbiota, and prebiotics are used to improve and maintain a healthy gut. The impact of prebiotics on dominant gut bacteria other than bifidobacteria, however, is under-researched. Here, we report carbohydrate utilisation patterns for representative butyrate-producing anaerobes, belonging to the Gram-positive Firmicutes families Lachnospiraceae and Ruminococcaceae, by comparison with selected Bacteroides and Bifidobacterium species. Growth assessments using anaerobic Hungate tubes and a new rapid microtitre plate assay were generally in good agreement. The Bacteroides strains tested showed some growth on basal medium with no added carbohydrates, utilising peptides in the growth medium. The butyrate-producing strains exhibited different growth profiles on the substrates, which included starch, inulin, fructooligosaccharides (FOS), galactooligosaccharides (GOS) and xylooligosaccharides (XOS). Eleven were able to grow on short-chain FOS, but this number decreased as the chain length of the fructan substrates increased. Long-chain inulin was utilised by Roseburia inulinivorans, but by none of the Bifidobacterium species examined here. XOS was a more selective growth substrate than FOS, with only six of the 11 Firmicutes strains able to use XOS for growth. These results illustrate the selectivity of different prebiotics and help to explain why some are butyrogenic.
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Affiliation(s)
- Karen P Scott
- Microbial Ecology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Bucksburn, Aberdeen, UK
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Wegmann U, Louis P, Goesmann A, Henrissat B, Duncan SH, Flint HJ. Complete genome of a new Firmicutes species belonging to the dominant human colonic microbiota ('Ruminococcus bicirculans') reveals two chromosomes and a selective capacity to utilize plant glucans. Environ Microbiol 2013; 16:2879-90. [PMID: 23919528 DOI: 10.1111/1462-2920.12217] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 06/28/2013] [Accepted: 07/14/2013] [Indexed: 01/22/2023]
Abstract
The recently isolated bacterial strain 80/3 represents one of the most abundant 16S rRNA phylotypes detected in the healthy human large intestine and belongs to the Ruminococcaceae family of Firmicutes. The completed genome sequence reported here is the first for a member of this important family of bacteria from the human colon. The genome comprises two large chromosomes of 2.24 and 0.73 Mbp, leading us to propose the name Ruminococcus bicirculans for this new species. Analysis of the carbohydrate active enzyme complement suggests an ability to utilize certain hemicelluloses, especially β-glucans and xyloglucan, for growth that was confirmed experimentally. The enzymatic machinery enabling the degradation of cellulose and xylan by related cellulolytic ruminococci is however lacking in this species. While the genome indicated the capacity to synthesize purines, pyrimidines and all 20 amino acids, only genes for the synthesis of nicotinate, NAD+, NADP+ and coenzyme A were detected among the essential vitamins and co-factors, resulting in multiple growth requirements. In vivo, these growth factors must be supplied from the diet, host or other gut microorganisms. Other features of ecological interest include two type IV pilins, multiple extracytoplasmic function-sigma factors, a urease and a bile salt hydrolase.
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Affiliation(s)
- Udo Wegmann
- Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA, UK
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