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Cook R, Telatin A, Hsieh SY, Newberry F, Tariq MA, Baker DJ, Carding SR, Adriaenssens EM. Nanopore and Illumina sequencing reveal different viral populations from human gut samples. Microb Genom 2024; 10. [PMID: 38683195 DOI: 10.1099/mgen.0.001236] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024] Open
Abstract
The advent of viral metagenomics, or viromics, has improved our knowledge and understanding of global viral diversity. High-throughput sequencing technologies enable explorations of the ecological roles, contributions to host metabolism, and the influence of viruses in various environments, including the human intestinal microbiome. However, bacterial metagenomic studies frequently have the advantage. The adoption of advanced technologies like long-read sequencing has the potential to be transformative in refining viromics and metagenomics. Here, we examined the effectiveness of long-read and hybrid sequencing by comparing Illumina short-read and Oxford Nanopore Technology (ONT) long-read sequencing technologies and different assembly strategies on recovering viral genomes from human faecal samples. Our findings showed that if a single sequencing technology is to be chosen for virome analysis, Illumina is preferable due to its superior ability to recover fully resolved viral genomes and minimise erroneous genomes. While ONT assemblies were effective in recovering viral diversity, the challenges related to input requirements and the necessity for amplification made it less ideal as a standalone solution. However, using a combined, hybrid approach enabled a more authentic representation of viral diversity to be obtained within samples.
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Affiliation(s)
- Ryan Cook
- Quadram Institute Bioscience, Norwich, NR4 7UQ, UK
| | | | | | - Fiona Newberry
- Department of Biosciences, Nottingham Trent University, Nottingham, NG11 8NS, UK
| | - Mohammad A Tariq
- Faculty of Health and Life Sciences, University of Northumbria, Newcastle upon Tyne, NE1 8ST, UK
| | - Dave J Baker
- Quadram Institute Bioscience, Norwich, NR4 7UQ, UK
| | - Simon R Carding
- Quadram Institute Bioscience, Norwich, NR4 7UQ, UK
- Norwich Medical School, University of East Anglia, Norwich, NR4 7TJ, UK
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2
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Fonseca S, Carvalho AL, Miquel-Clopés A, Jones EJ, Juodeikis R, Stentz R, Carding SR. Corrigendum: Extracellular vesicles produced by the human gut commensal bacterium Bacteroides thetaiotaomicron elicit anti-inflammatory responses from innate immune cells. Front Microbiol 2024; 14:1353539. [PMID: 38235433 PMCID: PMC10794089 DOI: 10.3389/fmicb.2023.1353539] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
[This corrects the article DOI: 10.3389/fmicb.2022.1050271.].
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Affiliation(s)
- Sonia Fonseca
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Ana L. Carvalho
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, United Kingdom
- Department of Women's and Children's Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | | | - Emily J. Jones
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Rokas Juodeikis
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Régis Stentz
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Simon R. Carding
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
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3
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Juodeikis R, Martins C, Saalbach G, Richardson J, Koev T, Baker DJ, Defernez M, Warren M, Carding SR. Differential temporal release and lipoprotein loading in B. thetaiotaomicron bacterial extracellular vesicles. J Extracell Vesicles 2024; 13:e12406. [PMID: 38240185 PMCID: PMC10797578 DOI: 10.1002/jev2.12406] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/24/2023] [Accepted: 01/01/2024] [Indexed: 01/22/2024] Open
Abstract
Bacterial extracellular vesicles (BEVs) contribute to stress responses, quorum sensing, biofilm formation and interspecies and interkingdom communication. However, the factors that regulate their release and heterogeneity are not well understood. We set out to investigate these factors in the common gut commensal Bacteroides thetaiotaomicron by studying BEV release throughout their growth cycle. Utilising a range of methods, we demonstrate that vesicles released at different stages of growth have significantly different composition, with early vesicles enriched in specifically released outer membrane vesicles (OMVs) containing a larger proportion of lipoproteins, while late phase BEVs primarily contain lytic vesicles with enrichment of cytoplasmic proteins. Furthermore, we demonstrate that lipoproteins containing a negatively charged signal peptide are preferentially incorporated in OMVs. We use this observation to predict all Bacteroides thetaiotaomicron OMV enriched lipoproteins and analyse their function. Overall, our findings highlight the need to understand media composition and BEV release dynamics prior to functional characterisation and define the theoretical functional capacity of Bacteroides thetaiotaomicron OMVs.
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Affiliation(s)
- Rokas Juodeikis
- Food, Microbiome, and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
| | | | | | | | - Trey Koev
- Food, Microbiome, and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
- School of PharmacyUniversity of East AngliaNorwichUK
| | - Dave J. Baker
- Food, Microbiome, and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
| | - Marianne Defernez
- Food, Microbiome, and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
| | - Martin Warren
- Food, Microbiome, and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
- School of BiosciencesUniversity of KentCanterburyUK
- School of Biological SciencesUniversity of East AngliaNorwichUK
| | - Simon R. Carding
- Food, Microbiome, and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
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4
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Hsieh SY, Savva GM, Telatin A, Tiwari SK, Tariq MA, Newberry F, Seton KA, Booth C, Bansal AS, Wileman T, Adriaenssens EM, Carding SR. Investigating the Human Intestinal DNA Virome and Predicting Disease-Associated Virus-Host Interactions in Severe Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). Int J Mol Sci 2023; 24:17267. [PMID: 38139096 PMCID: PMC10744171 DOI: 10.3390/ijms242417267] [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: 11/15/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
Understanding how the human virome, and which of its constituents, contributes to health or disease states is reliant on obtaining comprehensive virome profiles. By combining DNA viromes from isolated virus-like particles (VLPs) and whole metagenomes from the same faecal sample of a small cohort of healthy individuals and patients with severe myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), we have obtained a more inclusive profile of the human intestinal DNA virome. Key features are the identification of a core virome comprising tailed phages of the class Caudoviricetes, and a greater diversity of DNA viruses including extracellular phages and integrated prophages. Using an in silico approach, we predicted interactions between members of the Anaerotruncus genus and unique viruses present in ME/CFS microbiomes. This study therefore provides a framework and rationale for studies of larger cohorts of patients to further investigate disease-associated interactions between the intestinal virome and the bacteriome.
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Affiliation(s)
- Shen-Yuan Hsieh
- Food, Microbiome, and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (S.K.T.); (M.A.T.); (F.N.); (K.A.S.); (T.W.)
| | - George M. Savva
- Core Science Resources, Quadram Institute Bioscience, Norwich NR4 7UQ, UK; (G.M.S.); (C.B.)
| | - Andrea Telatin
- Food, Microbiome, and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (S.K.T.); (M.A.T.); (F.N.); (K.A.S.); (T.W.)
| | - Sumeet K. Tiwari
- Food, Microbiome, and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (S.K.T.); (M.A.T.); (F.N.); (K.A.S.); (T.W.)
| | - Mohammad A. Tariq
- Food, Microbiome, and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (S.K.T.); (M.A.T.); (F.N.); (K.A.S.); (T.W.)
| | - Fiona Newberry
- Food, Microbiome, and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (S.K.T.); (M.A.T.); (F.N.); (K.A.S.); (T.W.)
| | - Katharine A. Seton
- Food, Microbiome, and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (S.K.T.); (M.A.T.); (F.N.); (K.A.S.); (T.W.)
| | - Catherine Booth
- Core Science Resources, Quadram Institute Bioscience, Norwich NR4 7UQ, UK; (G.M.S.); (C.B.)
| | | | - Thomas Wileman
- Food, Microbiome, and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (S.K.T.); (M.A.T.); (F.N.); (K.A.S.); (T.W.)
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Evelien M. Adriaenssens
- Food, Microbiome, and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (S.K.T.); (M.A.T.); (F.N.); (K.A.S.); (T.W.)
| | - Simon R. Carding
- Food, Microbiome, and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (S.K.T.); (M.A.T.); (F.N.); (K.A.S.); (T.W.)
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
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5
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Seton KA, Defernez M, Telatin A, Tiwari SK, Savva GM, Hayhoe A, Noble A, de Carvalho-KoK ALS, James SA, Bansal A, Wileman T, Carding SR. Investigating Antibody Reactivity to the Intestinal Microbiome in Severe Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS): A Feasibility Study. Int J Mol Sci 2023; 24:15316. [PMID: 37895005 PMCID: PMC10607161 DOI: 10.3390/ijms242015316] [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: 09/12/2023] [Revised: 10/03/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a multisystemic disease of unknown aetiology that is characterised by disabling chronic fatigue and involves both the immune and gastrointestinal (GI) systems. Patients display alterations in GI microbiome with a significant proportion experiencing GI discomfort and pain and elevated blood biomarkers for altered intestinal permeability compared with healthy individuals. To investigate a possible GI origin of ME/CFS we designed a feasibility study to test the hypothesis that ME/CFS pathogenesis is a consequence of increased intestinal permeability that results in microbial translocation and a breakdown in immune tolerance leading to generation of antibodies reactive to indigenous intestinal microbes. Secretory immunoglobulin (Ig) A and serum IgG levels and reactivity to intestinal microbes were assessed in five pairs of severe ME/CFS patients and matched same-household healthy controls. For profiling serum IgG, we developed IgG-Seq which combines flow-cytometry based bacterial cell sorting and metagenomics to detect mucosal IgG reactivity to the microbiome. We uncovered evidence for immune dysfunction in severe ME/CFS patients that was characterised by reduced capacity and reactivity of serum IgG to stool microbes, irrespective of their source. This study provides the rationale for additional studies in larger cohorts of ME/CFS patients to further explore immune-microbiome interactions.
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Affiliation(s)
- Katharine A. Seton
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (K.A.S.); (A.T.); (S.K.T.); (G.M.S.); (A.H.); (S.A.J.); (T.W.)
| | - Marianne Defernez
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (K.A.S.); (A.T.); (S.K.T.); (G.M.S.); (A.H.); (S.A.J.); (T.W.)
| | - Andrea Telatin
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (K.A.S.); (A.T.); (S.K.T.); (G.M.S.); (A.H.); (S.A.J.); (T.W.)
| | - Sumeet K. Tiwari
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (K.A.S.); (A.T.); (S.K.T.); (G.M.S.); (A.H.); (S.A.J.); (T.W.)
| | - George M. Savva
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (K.A.S.); (A.T.); (S.K.T.); (G.M.S.); (A.H.); (S.A.J.); (T.W.)
| | - Antonietta Hayhoe
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (K.A.S.); (A.T.); (S.K.T.); (G.M.S.); (A.H.); (S.A.J.); (T.W.)
| | | | - Ana L. S. de Carvalho-KoK
- Experimental Arthritis Treatment Centre for Children, University of Liverpool, Liverpool L12 2AP, UK;
| | - Steve A. James
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (K.A.S.); (A.T.); (S.K.T.); (G.M.S.); (A.H.); (S.A.J.); (T.W.)
| | | | - Thomas Wileman
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (K.A.S.); (A.T.); (S.K.T.); (G.M.S.); (A.H.); (S.A.J.); (T.W.)
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Simon R. Carding
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (K.A.S.); (A.T.); (S.K.T.); (G.M.S.); (A.H.); (S.A.J.); (T.W.)
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
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6
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James SA, Parker A, Purse C, Telatin A, Baker D, Evans R, Holmes S, Funnell SGP, Carding SR. Draft Genome Sequence of a Primate Isolate of Kazachstania pintolopesii. Mycopathologia 2023; 188:821-823. [PMID: 37589873 PMCID: PMC10564811 DOI: 10.1007/s11046-023-00772-8] [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: 05/23/2023] [Accepted: 07/03/2023] [Indexed: 08/18/2023]
Abstract
Kazachstania pintolopesii is an opportunistic mammalian pathobiont from the K. telluris species complex. No draft genomes of this species are currently available. Here, we report the first draft genome sequence of a primate isolate of K. pintolopesii (NCYC 4417).
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Affiliation(s)
- Steve A James
- Food, Microbiome and Health, Quadram Institute Bioscience, Norwich, UK.
| | - Aimee Parker
- Food, Microbiome and Health, Quadram Institute Bioscience, Norwich, UK
| | - Catherine Purse
- Food, Microbiome and Health, Quadram Institute Bioscience, Norwich, UK
| | - Andrea Telatin
- Food, Microbiome and Health, Quadram Institute Bioscience, Norwich, UK
| | - David Baker
- Food, Microbiome and Health, Quadram Institute Bioscience, Norwich, UK
| | - Rhiannon Evans
- Food, Microbiome and Health, Quadram Institute Bioscience, Norwich, UK
| | - Sandy Holmes
- UK Health Security Agency, Porton Down, Salisbury, UK
| | - Simon G P Funnell
- Food, Microbiome and Health, Quadram Institute Bioscience, Norwich, UK
- UK Health Security Agency, Porton Down, Salisbury, UK
| | - Simon R Carding
- Food, Microbiome and Health, Quadram Institute Bioscience, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
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7
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Baldwin L, Jones EJ, Iles A, Carding SR, Pamme N, Dyer CE, Greenman J. Development of a dual-flow tissue perfusion device for modeling the gastrointestinal tract-brain axis. Biomicrofluidics 2023; 17:054104. [PMID: 37840538 PMCID: PMC10569815 DOI: 10.1063/5.0168953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/26/2023] [Indexed: 10/17/2023]
Abstract
Despite the large number of microfluidic devices that have been described over the past decade for the study of tissues and organs, few have become widely adopted. There are many reasons for this lack of adoption, primarily that devices are constructed for a single purpose or because they are highly complex and require relatively expensive investment in facilities and training. Here, we describe a microphysiological system (MPS) that is simple to use and provides fluid channels above and below cells, or tissue biopsies, maintained on a disposable, poly(methyl methacrylate), carrier held between polycarbonate outer plates. All other fittings are standard Luer sizes for ease of adoption. The carrier can be coated with cells on both sides to generate membrane barriers, and the devices can be established in series to allow medium to flow from one cell layer to another. Furthermore, the carrier containing cells can be easily removed after treatment on the device and the cells can be visualized or recovered for additional off-chip analysis. A 0.4 μm membrane with cell monolayers proved most effective in maintaining separate fluid flows, allowing apical and basal surfaces to be perfused independently. A panel of different cell lines (Caco-2, HT29-MTX-E12, SH-SY5Y, and HUVEC) were successfully maintained in the MPS for up to 7 days, either alone or on devices connected in series. The presence of tight junctions and mucin was expressed as expected by Caco-2 and HT-29-MTX-E12, with Concanavalin A showing uniform staining. Addition of Annexin V and PI showed viability of these cells to be >80% at 7 days. Bacterial extracellular vesicles (BEVs) produced by Bacteroides thetaiotaomicron and labeled with 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbo-cyanine perchlorate (DiD) were used as a model component of the human colonic microbiota and were visualized translocating from an apical surface containing Caco-2 cells to differentiated SH-SY5Y neuronal cells cultured on the basal surface of connected devices. The newly described MPS can be easily adapted, by changing the carrier to maintain spheroids, pieces, or slices of biopsy tissue and joined in series to study a variety of cell and tissue processes. The cell layers can be made more complex through the addition of multiple cell types and/or different patterning of extracellular matrix and the ability to culture cells adjacent to one another to allow study of cell:cell transfer, e.g., passive or active drug transfer, virus or bacterial entry or BEV uptake and transfer.
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Affiliation(s)
- Lydia Baldwin
- Centre of Biomedical Sciences, Hull York Medical School, University of Hull, Cottingham Road, Hull, HU6 7RX, United Kingdom
| | - Emily J. Jones
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
| | - Alexander Iles
- Department of Materials and Environmental Chemistry, Stockholm University, 106 91 Stockholm, Sweden
| | | | - Nicole Pamme
- Department of Materials and Environmental Chemistry, Stockholm University, 106 91 Stockholm, Sweden
| | - Charlotte E. Dyer
- Centre of Biomedical Sciences, Hull York Medical School, University of Hull, Cottingham Road, Hull, HU6 7RX, United Kingdom
| | - John Greenman
- Centre of Biomedical Sciences, Hull York Medical School, University of Hull, Cottingham Road, Hull, HU6 7RX, United Kingdom
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Stentz R, Cheema J, Philo M, Carding SR. A Possible Aquatic Origin of the Thiaminase TenA of the Human Gut Symbiont Bacteroides thetaiotaomicron. J Mol Evol 2023; 91:482-491. [PMID: 37022443 PMCID: PMC10277260 DOI: 10.1007/s00239-023-10101-8] [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: 07/21/2022] [Accepted: 02/14/2023] [Indexed: 04/07/2023]
Abstract
TenA thiamin-degrading enzymes are commonly found in prokaryotes, plants, fungi and algae and are involved in the thiamin salvage pathway. The gut symbiont Bacteroides thetaiotaomicron (Bt) produces a TenA protein (BtTenA) which is packaged into its extracellular vesicles. An alignment of BtTenA protein sequence with proteins from different databases using the basic local alignment search tool (BLAST) and the generation of a phylogenetic tree revealed that BtTenA is related to TenA-like proteins not only found in a small number of intestinal bacterial species but also in some aquatic bacteria, aquatic invertebrates, and freshwater fish. This is, to our knowledge, the first report describing the presence of TenA-encoding genes in the genome of members of the animal kingdom. By searching metagenomic databases of diverse host-associated microbial communities, we found that BtTenA homologues were mostly represented in biofilms present on the surface of macroalgae found in Australian coral reefs. We also confirmed the ability of a recombinant BtTenA to degrade thiamin. Our study shows that BttenA-like genes which encode a novel sub-class of TenA proteins are sparingly distributed across two kingdoms of life, a feature of accessory genes known for their ability to spread between species through horizontal gene transfer.
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Affiliation(s)
- Régis Stentz
- Quadram Institute Bioscience, Gut Microbes and Health Research Programme, Norwich, UK.
| | - Jitender Cheema
- Computational and Systems Biology, John Innes Centre, Norwich, UK
| | - Mark Philo
- Core Science Resources, Quadram Institute Bioscience, Norwich, UK
| | - Simon R Carding
- Quadram Institute Bioscience, Gut Microbes and Health Research Programme, Norwich, UK
- Norwich Medical School, University East Anglia, Norwich, UK
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9
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James SA, Telatin A, Baker D, Evans R, Clarke P, Hall LJ, Carding SR. Draft Genome Sequence of a Preterm Infant-Derived Isolate of Candida parapsilosis. Microbiol Resour Announc 2023; 12:e0127322. [PMID: 36847565 PMCID: PMC10019213 DOI: 10.1128/mra.01273-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/10/2023] [Indexed: 03/01/2023] Open
Abstract
Candida parapsilosis is a human fungal pathogen of increasing incidence and causes invasive candidiasis, notably in preterm or low-birthweight neonates. Here, we present the genome sequence of C. parapsilosis NCYC 4289, a fecal isolate from a preterm male infant.
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Affiliation(s)
- Steve A. James
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Andrea Telatin
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - David Baker
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Rhiannon Evans
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Paul Clarke
- Neonatal Intensive Care Unit, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Lindsay J. Hall
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
- Ziel–Institute for Food and Health, Technical University of Munich, Freising, Germany
| | - Simon R. Carding
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
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Abstract
This review focuses on nonlytic outer membrane vesicles (OMVs), a subtype of bacterial extracellular vesicles (BEVs) produced by Gram-negative organisms focusing on the mechanisms of their biogenesis, cargo, and function. Throughout, we highlight issues concerning the characterization of OMVs and distinguishing them from other types of BEVs. We also highlight the shortcomings of commonly used methodologies for the study of BEVs that impact the interpretation of their functionality and suggest solutions to standardize protocols for OMV studies.
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Affiliation(s)
| | - Simon R. Carding
- Quadram Institute Bioscience, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
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11
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Phillips S, Watt R, Atkinson T, Rajan S, Hayhoe A, Savva GM, Hornberger M, Burton BJL, Saada J, Cambell-Kelly M, Rushbrook S, Carding SR. A protocol paper for the MOTION Study-A longitudinal study in a cohort aged 60 years and older to obtain mechanistic knowledge of the role of the gut microbiome during normal healthy ageing in order to develop strategies that will improve lifelong health and wellbeing. PLoS One 2022; 17:e0276118. [PMID: 36399457 PMCID: PMC9674124 DOI: 10.1371/journal.pone.0276118] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/20/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Advances in medicine and public health mean that people are living longer; however, a significant proportion of that increased lifespan is spent in a prolonged state of declining health and wellbeing which places increasing pressure on medical, health and social services. There is a social and economic need to develop strategies to prevent or delay age-related disease and maintain lifelong health. Several studies have suggested links between the gut microbiome and age-related disease, which if confirmed would present a modifiable target for intervention development. The MOTION study aims to determine whether and how changes in the gut microbiome are associated with physical and mental capacity. A comprehensive longitudinal multiparameter study such as this has not been previously undertaken. METHODS MOTION is a longitudinal prospective cohort study with a focus on gut health and cognitive function. 360 healthy individuals aged 60 years and older, living in East Anglia, UK will be recruited to the study, stratified into one of three risk groups (cohorts) for developing dementia based on their cognitive function. Participants will attend study appointments every six months over four years, providing stool and blood samples and a health questionnaire. Participants will also undergo physical measurements and cognitive tests at alternating appointments, and undergo Optical Coherence Tomography scans at 3 timepoints. Two subgroups of participants in the study will provide colonic tissue biopsies (n = ≥30 from each cohort), and brain imaging (n = 30) at two timepoints. DISCUSSION This study will provide new insights into the gut-(microbiota)-brain axis and the relationship between age-associated changes in gut microbe populations and cognitive health. Such insights could help develop new microbe-based strategies to improve lifelong health and wellbeing. TRIAL REGISTRATION This study is registered in the ClinicalTrials.gov Database with ID: NCT04199195 Registered: May 14, 2019.
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Affiliation(s)
- Sarah Phillips
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Rachel Watt
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Thomas Atkinson
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Shelina Rajan
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Antonietta Hayhoe
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - George M. Savva
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Michael Hornberger
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, United Kingdom
| | - Ben J. L. Burton
- James Paget University Hospitals NHS Foundation Trust, Gorleston, Norfolk, United Kingdom
| | - Janak Saada
- Norfolk and Norwich University Hospital, Norwich, United Kingdom
| | | | - Simon Rushbrook
- Norfolk and Norwich University Hospital, Norwich, United Kingdom
| | - Simon R. Carding
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, United Kingdom
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12
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Fonseca S, Carvalho AL, Miquel-Clopés A, Jones EJ, Juodeikis R, Stentz R, Carding SR. Extracellular vesicles produced by the human gut commensal bacterium Bacteroides thetaiotaomicron elicit anti-inflammatory responses from innate immune cells. Front Microbiol 2022; 13:1050271. [PMID: 36439842 PMCID: PMC9684339 DOI: 10.3389/fmicb.2022.1050271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/25/2022] [Indexed: 07/24/2023] Open
Abstract
Bacterial extracellular vesicles (BEVs) produced by gut commensal bacteria have been proposed to play an important role in maintaining host homeostasis via interactions with the immune system. Details of the mediators and pathways of BEV-immune cell interactions are however incomplete. In this study, we provide evidence for the anti-inflammatory and immunomodulatory properties of extracellular vesicles produced by the prominent human gut commensal bacterium Bacteroides thetaiotaomicron (Bt BEVs) and identify the molecular mechanisms underlying their interaction with innate immune cells. Administration of Bt BEVs to mice treated with colitis-inducing dextran sodium sulfate (DSS) ameliorates the symptoms of intestinal inflammation, improving survival rate and reducing weight loss and disease activity index scores, in association with upregulation of IL-10 production in colonic tissue and in splenocytes. Pre-treatment (conditioning) of murine bone marrow derived monocytes (BMDM) with Bt BEVs resulted in higher ratio of IL-10/TNFα production after an LPS challenge when compared to LPS pre-conditioned or non-conditioned BMDM. Using the THP-1 monocytic cell line the interactions between Bt BEVs and monocytes/macrophages were shown to be mediated primarily by TLR2. Histone (H3K4me1) methylation analysis showed that Bt BEVs induced epigenetic reprogramming which persisted after infectious challenge, as revealed by increased levels of H3K4me1 in Bt BEV-conditioned LPS-challenged BMDM. Collectively, our findings highlight the important role of Bt BEVs in maintaining host immune homeostasis and raise the promising possibility of considering their use in immune therapies.
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Affiliation(s)
- Sonia Fonseca
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Ana L. Carvalho
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, United Kingdom
- Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | | | - Emily J. Jones
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Rokas Juodeikis
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Régis Stentz
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Simon R. Carding
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
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13
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Noble A, Pring ET, Durant L, Man R, Dilke SM, Hoyles L, James SA, Carding SR, Jenkins JT, Knight SC. Altered immunity to microbiota, B cell activation and depleted γδ/resident memory T cells in colorectal cancer. Cancer Immunol Immunother 2022. [PMID: 35316367 DOI: 10.1007/s00262-021-03135-8/figures/5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The role of microbiota:immune system dysregulation in the etiology of colorectal cancer (CRC) is poorly understood. CRC develops in gut epithelium, accompanied by low level inflammatory signaling, intestinal microbial dysbiosis and immune dysfunction. We examined populations of intraepithelial lymphocytes in non-affected colonic mucosa of CRC and healthy donors and circulating immune memory to commensal bacterial species and yeasts. γδ T cells and resident memory T cells, populations with a regulatory CD39-expressing phenotype, were found at lower frequencies in the colonic tissue of CRC donors compared to healthy controls. Patterns of T cell proliferative responses to a panel of commensal bacteria were distinct in CRC, while B cell memory responses to several bacteria/yeast were significantly increased, accompanied by increased proportions of effector memory B cells, transitional B cells and plasmablasts in blood. IgA responses to mucosal microbes were unchanged. Our data describe a novel immune signature with similarities to and differences from that of inflammatory bowel disease. They implicate B cell dysregulation as a potential contributor to parainflammation and identify pathways of weakened barrier function and tumor surveillance in CRC-susceptible individuals.
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Affiliation(s)
- Alistair Noble
- Gut Microbes and Health Program, Quadram Institute Bioscience, Norwich, UK
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St. Mark's Campus, Harrow, UK
| | - Edward T Pring
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St. Mark's Campus, Harrow, UK
- St. Mark's Hospital, London North West University Healthcare NHS Trust, Harrow, UK
| | - Lydia Durant
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St. Mark's Campus, Harrow, UK
| | - Ripple Man
- St. Mark's Hospital, London North West University Healthcare NHS Trust, Harrow, UK
| | - Stella M Dilke
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St. Mark's Campus, Harrow, UK
- St. Mark's Hospital, London North West University Healthcare NHS Trust, Harrow, UK
| | - Lesley Hoyles
- Department of Biosciences, Nottingham Trent University, Nottingham, UK
| | - Steve A James
- Gut Microbes and Health Program, Quadram Institute Bioscience, Norwich, UK
| | - Simon R Carding
- Gut Microbes and Health Program, Quadram Institute Bioscience, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - John T Jenkins
- St. Mark's Hospital, London North West University Healthcare NHS Trust, Harrow, UK
| | - Stella C Knight
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St. Mark's Campus, Harrow, UK.
- St. Mark's Hospital, London North West University Healthcare NHS Trust, Harrow, UK.
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14
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Noble A, Pring ET, Durant L, Man R, Dilke SM, Hoyles L, James SA, Carding SR, Jenkins JT, Knight SC. Altered immunity to microbiota, B cell activation and depleted γδ/resident memory T cells in colorectal cancer. Cancer Immunol Immunother 2022; 71:2619-2629. [PMID: 35316367 PMCID: PMC9519644 DOI: 10.1007/s00262-021-03135-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 04/29/2021] [Accepted: 12/20/2021] [Indexed: 12/13/2022]
Abstract
The role of microbiota:immune system dysregulation in the etiology of colorectal cancer (CRC) is poorly understood. CRC develops in gut epithelium, accompanied by low level inflammatory signaling, intestinal microbial dysbiosis and immune dysfunction. We examined populations of intraepithelial lymphocytes in non-affected colonic mucosa of CRC and healthy donors and circulating immune memory to commensal bacterial species and yeasts. γδ T cells and resident memory T cells, populations with a regulatory CD39-expressing phenotype, were found at lower frequencies in the colonic tissue of CRC donors compared to healthy controls. Patterns of T cell proliferative responses to a panel of commensal bacteria were distinct in CRC, while B cell memory responses to several bacteria/yeast were significantly increased, accompanied by increased proportions of effector memory B cells, transitional B cells and plasmablasts in blood. IgA responses to mucosal microbes were unchanged. Our data describe a novel immune signature with similarities to and differences from that of inflammatory bowel disease. They implicate B cell dysregulation as a potential contributor to parainflammation and identify pathways of weakened barrier function and tumor surveillance in CRC-susceptible individuals.
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Affiliation(s)
- Alistair Noble
- Gut Microbes and Health Program, Quadram Institute Bioscience, Norwich, UK
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St. Mark’s Campus, Harrow, UK
| | - Edward T. Pring
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St. Mark’s Campus, Harrow, UK
- St. Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, UK
| | - Lydia Durant
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St. Mark’s Campus, Harrow, UK
| | - Ripple Man
- St. Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, UK
| | - Stella M. Dilke
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St. Mark’s Campus, Harrow, UK
- St. Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, UK
| | - Lesley Hoyles
- Department of Biosciences, Nottingham Trent University, Nottingham, UK
| | - Steve A. James
- Gut Microbes and Health Program, Quadram Institute Bioscience, Norwich, UK
| | - Simon R. Carding
- Gut Microbes and Health Program, Quadram Institute Bioscience, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - John T. Jenkins
- St. Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, UK
| | - Stella C. Knight
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St. Mark’s Campus, Harrow, UK
- St. Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, UK
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15
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James SA, Parker A, Purse C, Telatin A, Baker D, Holmes S, Durham J, Funnell SGP, Carding SR. The Cynomolgus Macaque Intestinal Mycobiome Is Dominated by the Kazachstania Genus and K. pintolopesii Species. J Fungi (Basel) 2022; 8:1054. [PMID: 36294619 PMCID: PMC9605169 DOI: 10.3390/jof8101054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/02/2022] [Accepted: 09/30/2022] [Indexed: 08/10/2023] Open
Abstract
The cynomolgus macaque, Macaca fascicularis, is a non-human primate (NHP) widely used in biomedical research as its genetics, immunology and physiology are similar to those of humans. They may also be a useful model of the intestinal microbiome as their prokaryome resembles that of humans. However, beyond the prokaryome relatively little is known about other constituents of the macaque intestinal microbiome including the mycobiome. Here, we conducted a region-by-region taxonomic survey of the cynomolgus intestinal mycobiota, from duodenum to distal colon, of sixteen captive animals of differing age (from young to old). Using a high-throughput ITS1 amplicon sequencing-based approach, the cynomolgus gut mycobiome was dominated by fungi from the Ascomycota phylum. The budding yeast genus Kazachstania was most abundant, with the thermotolerant species K. pintolopesii highly prevalent, and the predominant species in both the small and large intestines. This is in marked contrast to humans, in which the intestinal mycobiota is characterised by other fungal genera including Candida and Saccharomyces, and Candida albicans. This study provides a comprehensive insight into the fungal communities present within the captive cynomolgus gut, and for the first time identifies K. pintolopesii as a candidate primate gut commensal.
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Affiliation(s)
- Steve A. James
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Aimee Parker
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Catherine Purse
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Andrea Telatin
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - David Baker
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Sandy Holmes
- UK Health Security Agency, Porton Down, Salisbury SP4 0JG, UK
| | - James Durham
- UK Health Security Agency, Porton Down, Salisbury SP4 0JG, UK
| | - Simon G. P. Funnell
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
- UK Health Security Agency, Porton Down, Salisbury SP4 0JG, UK
| | - Simon R. Carding
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
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16
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Jordan A, Carding SR, Hall LJ. The early-life gut microbiome and vaccine efficacy. Lancet Microbe 2022; 3:e787-e794. [PMID: 36088916 DOI: 10.1016/s2666-5247(22)00185-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 05/31/2022] [Accepted: 06/08/2022] [Indexed: 12/24/2022]
Abstract
Vaccines are one of the greatest successes of public health, preventing millions of cases of disease and death in children each year. However, the efficacy of many vaccines can vary greatly between infants from geographically and socioeconomically distinct locations. Differences in the composition of the intestinal microbiome have emerged as one of the main factors that can account for variations in immunisation outcomes. In this Review, we assess the influence of the gut microbiota upon early life immunity, focusing on two important members of the microbiota with health-promoting and immunomodulatory properties: Bifidobacterium and Bacteroides. Additionally, we discuss their immune stimulatory microbial properties, interactions with the host, and their effect on vaccine responses and efficacy in infants. We also provide an overview of current microbiota-based approaches to enhance vaccine outcomes, and describe novel microbe-derived components that could lead to safer, more effective vaccines and vaccine adjuvants.
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Affiliation(s)
- Anne Jordan
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Simon R Carding
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK; Norwich Medical School, University of East Anglia, Norwich, UK
| | - Lindsay J Hall
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK; Norwich Medical School, University of East Anglia, Norwich, UK; Intestinal Microbiome, School of Life Sciences, ZIEL Institute for Food & Health, Technical University of Munich, Munich, Germany.
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17
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Stentz R, Jones E, Juodeikis R, Wegmann U, Guirro M, Goldson AJ, Brion A, Booth C, Sudhakar P, Brown IR, Korcsmáros T, Carding SR. The Proteome of Extracellular Vesicles Produced by the Human Gut Bacteria Bacteroides thetaiotaomicron In Vivo Is Influenced by Environmental and Host-Derived Factors. Appl Environ Microbiol 2022; 88:e0053322. [PMID: 35916501 PMCID: PMC9397113 DOI: 10.1128/aem.00533-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 03/30/2022] [Accepted: 07/11/2022] [Indexed: 11/20/2022] Open
Abstract
Bacterial extracellular vesicles (BEVs) released from both Gram-negative and Gram-positive bacteria provide an effective means of communication and trafficking of cell signaling molecules. In the gastrointestinal tract (GIT) BEVs produced by members of the intestinal microbiota can impact host health by mediating microbe-host cell interactions. A major unresolved question, however, is what factors influence the composition of BEV proteins and whether the host influences protein packaging into BEVs and secretion into the GIT. To address this, we have analyzed the proteome of BEVs produced by the major human gut symbiont Bacteroides thetaiotaomicron both in vitro and in vivo in the murine GIT in order to identify proteins specifically enriched in BEVs produced in vivo. We identified 113 proteins enriched in BEVs produced in vivo, the majority (62/113) of which accumulated in BEVs in the absence of any changes in their expression by the parental cells. Among these selectively enriched proteins, we identified dipeptidyl peptidases and an asparaginase and confirmed their increased activity in BEVs produced in vivo. We also showed that intact BEVs are capable of degrading bile acids via a bile salt hydrolase. Collectively these findings provide additional evidence for the dynamic interplay of host-microbe interactions in the GIT and the existence of an active mechanism to drive and enrich a selected group of proteins for secretion into BEVs in the GIT. IMPORTANCE The gastrointestinal tract (GIT) harbors a complex community of microbes termed the microbiota that plays a role in maintaining the host's health and wellbeing. How this comes about and the nature of microbe-host cell interactions in the GIT is still unclear. Recently, nanosized vesicles naturally produced by bacterial constituents of the microbiota have been shown to influence responses of different host cells although the molecular basis and identity of vesicle-born bacterial proteins that mediate these interactions is unclear. We show here that bacterial extracellular vesicles (BEVs) produced by the human symbiont Bacteroides thetaiotaomicron in the GIT are enriched in a set of proteins and enzymes, including dipeptidyl peptidases, an asparaginase and a bile salt hydrolase that can influence host cell biosynthetic pathways. Our results provide new insights into the molecular basis of microbiota-host interactions that are central to maintaining GIT homeostasis and health.
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Affiliation(s)
- Régis Stentz
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Emily Jones
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Rokas Juodeikis
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Udo Wegmann
- School of Chemistry, University East Anglia, Norwich, United Kingdom
| | - Maria Guirro
- Biochemistry and Biotechnology Department, Nutrigenomics Research Group, Universitat Rovira i Virgili, Tarragona, Spain
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), Reus, Spain
| | - Andrew J. Goldson
- Core Science Resources Quadram Institute Bioscience, Norwich, United Kingdom
| | - Arlaine Brion
- Core Science Resources Quadram Institute Bioscience, Norwich, United Kingdom
| | - Catherine Booth
- Core Science Resources Quadram Institute Bioscience, Norwich, United Kingdom
| | - Padhmanand Sudhakar
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
- Earlham Institute, Norwich, United Kingdom
- Department of Chronic Diseases, Metabolism and Ageing, TARGID, KU Leuven, Leuven, Belgium
| | - Ian R. Brown
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Tamás Korcsmáros
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
- Earlham Institute, Norwich, United Kingdom
| | - Simon R. Carding
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
- Norwich Medical School, University East Anglia, Norwich, United Kingdom
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18
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Parker A, James SA, Purse C, Brion A, Goldson A, Telatin A, Baker D, Carding SR. Absence of Bacteria Permits Fungal Gut-To-Brain Translocation and Invasion in Germfree Mice but Ageing Alone Does Not Drive Pathobiont Expansion in Conventionally Raised Mice. Front Aging Neurosci 2022; 14:828429. [PMID: 35923548 PMCID: PMC9339909 DOI: 10.3389/fnagi.2022.828429] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Age-associated changes in the structure of the intestinal microbiome and in its interaction with the brain via the gut-brain axis are increasingly being implicated in neurological and neurodegenerative diseases. Intestinal microbial dysbiosis and translocation of microbes and microbial products including fungal species into the brain have been implicated in the development of dementias such as Alzheimer's disease. Using germ-free mice, we investigated if the fungal gut commensal, Candida albicans, an opportunistic pathogen in humans, can traverse the gastrointestinal barrier and disseminate to brain tissue and whether ageing impacts on the gut mycobiome as a pre-disposing factor in fungal brain infection. C. albicans was detected in different regions of the brain of colonised germ-free mice in both yeast and hyphal cell forms, often in close association with activated (Iba-1+) microglial cells. Using high-throughput ITS1 amplicon sequencing to characterise the faecal gut fungal composition of aged and young SPF mice, we identified several putative gut commensal fungal species with pathobiont potential although their abundance was not significantly different between young and aged mice. Collectively, these results suggest that although some fungal species can travel from the gut to brain where they can induce an inflammatory response, ageing alone is not correlated with significant changes in gut mycobiota composition which could predispose to these events. These results are consistent with a scenario in which significant disruptions to the gut microbiota or intestinal barrier, beyond those which occur with natural ageing, are required to allow fungal escape and brain infection.
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Affiliation(s)
- Aimée Parker
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, United Kingdom
| | - Steve A. James
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, United Kingdom
| | - Catherine Purse
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, United Kingdom
| | - Arlaine Brion
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, United Kingdom
| | - Andrew Goldson
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, United Kingdom
| | - Andrea Telatin
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, United Kingdom
| | - David Baker
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, United Kingdom
| | - Simon R. Carding
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
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Noble A, Durant L, Dilke SM, Man R, Martin I, Patel R, Hoyles L, Pring ET, Latchford A, Clark SK, Carding SR, Knight SC. Altered Mucosal Immune-Microbiota Interactions in Familial Adenomatous Polyposis. Clin Transl Gastroenterol 2022; 13:e00428. [PMID: 35297393 PMCID: PMC10476795 DOI: 10.14309/ctg.0000000000000428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 09/23/2021] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION Familial adenomatous polyposis (FAP) is a condition caused by a constitutional pathogenic variant of the adenomatous polyposis coli gene that results in intestinal adenoma formation and colorectal cancer, necessitating pre-emptive colectomy. We sought to examine interaction between the mucosal immune system and commensal bacteria in FAP to test for immune dysfunction that might accelerate tumorigenesis. METHODS Colonic biopsies were obtained from macroscopically normal mucosal tissue from 14 healthy donors and 13 patients with FAP during endoscopy or from surgical specimens. Intraepithelial and lamina propria lymphocytes were phenotyped. Intraepithelial microbes were labeled with anti-IgA/IgG and analyzed by flow cytometry. RESULTS Proportions of resident memory CD103-expressing CD8 + and γδ T-cell receptor + intraepithelial lymphocytes were dramatically reduced in both the left and right colon of patients with FAP compared with healthy controls. In lamina propria, T cells expressed less CD103, and CD4 + CD103 + cells expressed less CD73 ectonucleotidase. IgA coating of epithelia-associated bacteria, IgA + peripheral B cells, and CD4 T-cell memory responses to commensal bacteria were increased in FAP. DISCUSSION Loss of resident memory T cells and γδ T cells in mucosal tissue of patients with FAP accompanies intestinal microbial dysbiosis previously reported in this precancerous state and suggests impaired cellular immunity and tumor surveillance. This may lead to barrier dysfunction, possible loss of regulatory T-cell function, and excess IgA antibody secretion. Our data are the first to implicate mucosal immune dysfunction as a contributing factor in this genetically driven disease and identify potentially critical pathways in the etiology of CRC.
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Affiliation(s)
- Alistair Noble
- Gut Microbes and Health Program, Quadram Institute Bioscience, Norwich, United Kingdom;
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St. Mark's Campus, Harrow, United Kingdom;
| | - Lydia Durant
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St. Mark's Campus, Harrow, United Kingdom;
| | - Stella M. Dilke
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St. Mark's Campus, Harrow, United Kingdom;
| | - Ripple Man
- The Polyposis Registry, St. Mark's Hospital, London North West University Healthcare NHS Trust, Harrow, United Kingdom;
| | - Isabel Martin
- The Polyposis Registry, St. Mark's Hospital, London North West University Healthcare NHS Trust, Harrow, United Kingdom;
| | - Roshani Patel
- The Polyposis Registry, St. Mark's Hospital, London North West University Healthcare NHS Trust, Harrow, United Kingdom;
| | - Lesley Hoyles
- Department of Biosciences, Nottingham Trent University, Nottingham, United Kingdom;
| | - Edward T. Pring
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St. Mark's Campus, Harrow, United Kingdom;
| | - Andrew Latchford
- The Polyposis Registry, St. Mark's Hospital, London North West University Healthcare NHS Trust, Harrow, United Kingdom;
- Department of Surgery and Cancer, Imperial College London, United Kingdom;
| | - Susan K. Clark
- The Polyposis Registry, St. Mark's Hospital, London North West University Healthcare NHS Trust, Harrow, United Kingdom;
- Department of Surgery and Cancer, Imperial College London, United Kingdom;
| | - Simon R. Carding
- Gut Microbes and Health Program, Quadram Institute Bioscience, Norwich, United Kingdom;
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom.
| | - Stella C. Knight
- Gut Microbes and Health Program, Quadram Institute Bioscience, Norwich, United Kingdom;
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St. Mark's Campus, Harrow, United Kingdom;
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20
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Parker A, Romano S, Ansorge R, Aboelnour A, Le Gall G, Savva GM, Pontifex MG, Telatin A, Baker D, Jones E, Vauzour D, Rudder S, Blackshaw LA, Jeffery G, Carding SR. Fecal microbiota transfer between young and aged mice reverses hallmarks of the aging gut, eye, and brain. Microbiome 2022; 10:68. [PMID: 35501923 PMCID: PMC9063061 DOI: 10.1186/s40168-022-01243-w] [Citation(s) in RCA: 88] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/04/2022] [Indexed: 05/11/2023]
Abstract
BACKGROUND Altered intestinal microbiota composition in later life is associated with inflammaging, declining tissue function, and increased susceptibility to age-associated chronic diseases, including neurodegenerative dementias. Here, we tested the hypothesis that manipulating the intestinal microbiota influences the development of major comorbidities associated with aging and, in particular, inflammation affecting the brain and retina. METHODS Using fecal microbiota transplantation, we exchanged the intestinal microbiota of young (3 months), old (18 months), and aged (24 months) mice. Whole metagenomic shotgun sequencing and metabolomics were used to develop a custom analysis workflow, to analyze the changes in gut microbiota composition and metabolic potential. Effects of age and microbiota transfer on the gut barrier, retina, and brain were assessed using protein assays, immunohistology, and behavioral testing. RESULTS We show that microbiota composition profiles and key species enriched in young or aged mice are successfully transferred by FMT between young and aged mice and that FMT modulates resulting metabolic pathway profiles. The transfer of aged donor microbiota into young mice accelerates age-associated central nervous system (CNS) inflammation, retinal inflammation, and cytokine signaling and promotes loss of key functional protein in the eye, effects which are coincident with increased intestinal barrier permeability. Conversely, these detrimental effects can be reversed by the transfer of young donor microbiota. CONCLUSIONS These findings demonstrate that the aging gut microbiota drives detrimental changes in the gut-brain and gut-retina axes suggesting that microbial modulation may be of therapeutic benefit in preventing inflammation-related tissue decline in later life. Video abstract.
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Affiliation(s)
- Aimée Parker
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, NR4 7UQ, UK.
| | - Stefano Romano
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, NR4 7UQ, UK
| | - Rebecca Ansorge
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, NR4 7UQ, UK
| | - Asmaa Aboelnour
- Institute of Ophthalmology, University College London, London, EC1V 9EL, UK
| | - Gwenaelle Le Gall
- Norwich Medical School, University of East Anglia, Norwich, NR4 7TJ, UK
| | - George M Savva
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, NR4 7UQ, UK
| | | | - Andrea Telatin
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, NR4 7UQ, UK
| | - David Baker
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, NR4 7UQ, UK
| | - Emily Jones
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, NR4 7UQ, UK
| | - David Vauzour
- Norwich Medical School, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Steven Rudder
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, NR4 7UQ, UK
| | - L Ashley Blackshaw
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, NR4 7UQ, UK
| | - Glen Jeffery
- Institute of Ophthalmology, University College London, London, EC1V 9EL, UK
| | - Simon R Carding
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, NR4 7UQ, UK.
- Norwich Medical School, University of East Anglia, Norwich, NR4 7TJ, UK.
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21
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Gul L, Modos D, Fonseca S, Madgwick M, Thomas JP, Sudhakar P, Booth C, Stentz R, Carding SR, Korcsmaros T. Extracellular vesicles produced by the human commensal gut bacterium Bacteroides thetaiotaomicron affect host immune pathways in a cell-type specific manner that are altered in inflammatory bowel disease. J Extracell Vesicles 2022; 11:e12189. [PMID: 35064769 PMCID: PMC8783345 DOI: 10.1002/jev2.12189] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [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: 02/27/2021] [Revised: 10/04/2021] [Accepted: 12/31/2021] [Indexed: 12/14/2022] Open
Abstract
The gastrointestinal (GI) tract harbours a complex microbial community, which contributes to its homeostasis. A disrupted microbiome can cause GI-related diseases, including inflammatory bowel disease (IBD), therefore identifying host-microbe interactions is crucial for better understanding gut health. Bacterial extracellular vesicles (BEVs), released into the gut lumen, can cross the mucus layer and access underlying immune cells. To study BEV-host interactions, we examined the influence of BEVs generated by the gut commensal bacterium, Bacteroides thetaiotaomicron, on host immune cells. Single-cell RNA sequencing data and host-microbe protein-protein interaction networks were used to predict the effect of BEVs on dendritic cells, macrophages and monocytes focusing on the Toll-like receptor (TLR) pathway. We identified biological processes affected in each immune cell type and cell-type specific processes including myeloid cell differentiation. TLR pathway analysis highlighted that BEV targets differ among cells and between the same cells in healthy versus disease (ulcerative colitis) conditions. The in silico findings were validated in BEV-monocyte co-cultures demonstrating the requirement for TLR4 and Toll-interleukin-1 receptor domain-containing adaptor protein (TIRAP) in BEV-elicited NF-kB activation. This study demonstrates that both cell-type and health status influence BEV-host communication. The results and the pipeline could facilitate BEV-based therapies for the treatment of IBD.
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Affiliation(s)
| | - Dezso Modos
- Earlham Institute, NorwichNorwichUK
- Gut Microbes and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
| | - Sonia Fonseca
- Gut Microbes and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
| | - Matthew Madgwick
- Earlham Institute, NorwichNorwichUK
- Gut Microbes and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
| | - John P. Thomas
- Earlham Institute, NorwichNorwichUK
- Department of GastroenterologyNorfolk and Norwich University HospitalNorwichUK
| | - Padhmanand Sudhakar
- Earlham Institute, NorwichNorwichUK
- Gut Microbes and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
- KU Leuven Department of Chronic DiseasesMetabolism and AgeingTranslational Research Centre for Gastrointestinal Disorders (TARGID)LeuvenBelgium
| | | | - Régis Stentz
- Gut Microbes and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
| | - Simon R. Carding
- Gut Microbes and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
| | - Tamas Korcsmaros
- Earlham Institute, NorwichNorwichUK
- Gut Microbes and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
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22
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Hoyles L, Pontifex MG, Rodriguez-Ramiro I, Anis-Alavi MA, Jelane KS, Snelling T, Solito E, Fonseca S, Carvalho AL, Carding SR, Müller M, Glen RC, Vauzour D, McArthur S. Regulation of blood-brain barrier integrity by microbiome-associated methylamines and cognition by trimethylamine N-oxide. Microbiome 2021; 9:235. [PMID: 34836554 PMCID: PMC8626999 DOI: 10.1186/s40168-021-01181-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 10/18/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND Communication between the gut microbiota and the brain is primarily mediated via soluble microbe-derived metabolites, but the details of this pathway remain poorly defined. Methylamines produced by microbial metabolism of dietary choline and L-carnitine have received attention due to their proposed association with vascular disease, but their effects upon the cerebrovascular circulation have hitherto not been studied. RESULTS Here, we use an integrated in vitro/in vivo approach to show that physiologically relevant concentrations of the dietary methylamine trimethylamine N-oxide (TMAO) enhanced blood-brain barrier (BBB) integrity and protected it from inflammatory insult, acting through the tight junction regulator annexin A1. In contrast, the TMAO precursor trimethylamine (TMA) impaired BBB function and disrupted tight junction integrity. Moreover, we show that long-term exposure to TMAO protects murine cognitive function from inflammatory challenge, acting to limit astrocyte and microglial reactivity in a brain region-specific manner. CONCLUSION Our findings demonstrate the mechanisms through which microbiome-associated methylamines directly interact with the mammalian BBB, with consequences for cerebrovascular and cognitive function. Video abstract.
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Affiliation(s)
- Lesley Hoyles
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Clifton, Nottingham, UK.
| | | | - Ildefonso Rodriguez-Ramiro
- Norwich Medical School, University of East Anglia, Norwich, UK
- Metabolic Syndrome Group, Madrid Institute for Advanced Studies (IMDEA) in Food, E28049, Madrid, Spain
| | - M Areeb Anis-Alavi
- Institute of Dentistry, Faculty of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - Khadija S Jelane
- Institute of Dentistry, Faculty of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - Tom Snelling
- Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Egle Solito
- William Harvey Research Institute, Faculty of Medicine & Dentistry, Queen Mary University of London, London, UK
- Dipartimento di Medicina molecolare e Biotecnologie mediche, Federico II University, Naples, Italy
| | - Sonia Fonseca
- The Gut Microbes and Health Research Programme, The Quadram Institute, Norwich Research Park, Norwich, UK
| | - Ana L Carvalho
- The Gut Microbes and Health Research Programme, The Quadram Institute, Norwich Research Park, Norwich, UK
| | - Simon R Carding
- Norwich Medical School, University of East Anglia, Norwich, UK
- The Gut Microbes and Health Research Programme, The Quadram Institute, Norwich Research Park, Norwich, UK
| | - Michael Müller
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Robert C Glen
- Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK
| | - David Vauzour
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Simon McArthur
- Institute of Dentistry, Faculty of Medicine & Dentistry, Queen Mary University of London, London, UK.
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23
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Jones E, Stentz R, Telatin A, Savva GM, Booth C, Baker D, Rudder S, Knight SC, Noble A, Carding SR. The Origin of Plasma-Derived Bacterial Extracellular Vesicles in Healthy Individuals and Patients with Inflammatory Bowel Disease: A Pilot Study. Genes (Basel) 2021; 12:1636. [PMID: 34681030 PMCID: PMC8535827 DOI: 10.3390/genes12101636] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 08/09/2021] [Revised: 09/10/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
The gastrointestinal tract harbors the gut microbiota, structural alterations of which (dysbiosis) are linked with an increase in gut permeability ("leaky gut"), enabling luminal antigens and bacterial products such as nanosized bacterial extracellular vesicles (BEVs) to access the circulatory system. Blood-derived BEVs contain various cargoes and may be useful biomarkers for diagnosis and monitoring of disease status and relapse in conditions such as inflammatory bowel disease (IBD). To progress this concept, we developed a rapid, cost-effective protocol to isolate BEV-associated DNA and used 16S rRNA gene sequencing to identify bacterial origins of the blood microbiome of healthy individuals and patients with Crohn's disease and ulcerative colitis. The 16S rRNA gene sequencing successfully identified the origin of plasma-derived BEV DNA. The analysis showed that the blood microbiota richness, diversity, or composition in IBD, healthy control, and protocol control groups were not significantly distinct, highlighting the issue of 'kit-ome' contamination in low-biomass studies. Our pilot study provides the basis for undertaking larger studies to determine the potential use of blood microbiota profiling as a diagnostic aid in IBD.
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Affiliation(s)
- Emily Jones
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, UK; (E.J.); (R.S.); (A.T.); (G.M.S.); (D.B.); (S.R.)
| | - Régis Stentz
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, UK; (E.J.); (R.S.); (A.T.); (G.M.S.); (D.B.); (S.R.)
| | - Andrea Telatin
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, UK; (E.J.); (R.S.); (A.T.); (G.M.S.); (D.B.); (S.R.)
| | - George M. Savva
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, UK; (E.J.); (R.S.); (A.T.); (G.M.S.); (D.B.); (S.R.)
| | - Catherine Booth
- Core Science Resources, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, UK;
| | - David Baker
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, UK; (E.J.); (R.S.); (A.T.); (G.M.S.); (D.B.); (S.R.)
| | - Steven Rudder
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, UK; (E.J.); (R.S.); (A.T.); (G.M.S.); (D.B.); (S.R.)
| | - Stella C. Knight
- Antigen Presentation Research Group, Northwick Park & St. Mark’s Hospital Campus, Imperial College London, Harrow HA1 3UJ, UK; (S.C.K.); (A.N.)
| | - Alistair Noble
- Antigen Presentation Research Group, Northwick Park & St. Mark’s Hospital Campus, Imperial College London, Harrow HA1 3UJ, UK; (S.C.K.); (A.N.)
| | - Simon R. Carding
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, UK; (E.J.); (R.S.); (A.T.); (G.M.S.); (D.B.); (S.R.)
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
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24
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Hsieh SY, Tariq MA, Telatin A, Ansorge R, Adriaenssens EM, Savva GM, Booth C, Wileman T, Hoyles L, Carding SR. Comparison of PCR versus PCR-Free DNA Library Preparation for Characterising the Human Faecal Virome. Viruses 2021; 13:2093. [PMID: 34696523 PMCID: PMC8537689 DOI: 10.3390/v13102093] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 09/22/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 01/04/2023] Open
Abstract
The human intestinal microbiota is abundant in viruses, comprising mainly bacteriophages, occasionally outnumbering bacteria 10:1 and is termed the virome. Due to their high genetic diversity and the lack of suitable tools and reference databases, the virome remains poorly characterised and is often referred to as "viral dark matter". However, the choice of sequencing platforms, read lengths and library preparation make study design challenging with respect to the virome. Here we have compared the use of PCR and PCR-free methods for sequence-library construction on the Illumina sequencing platform for characterising the human faecal virome. Viral DNA was extracted from faecal samples of three healthy donors and sequenced. Our analysis shows that most variation was reflecting the individually specific faecal virome. However, we observed differences between PCR and PCR-free library preparation that affected the recovery of low-abundance viral genomes. Using three faecal samples in this study, the PCR library preparation samples led to a loss of lower-abundance vOTUs evident in their PCR-free pairs (vOTUs 128, 6202 and 8364) and decreased the alpha-diversity indices (Chao1 p-value = 0.045 and Simpson p-value = 0.044). Thus, differences between PCR and PCR-free methods are important to consider when investigating "rare" members of the gut virome, with these biases likely negligible when investigating moderately and highly abundant viruses.
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Affiliation(s)
- Shen-Yuan Hsieh
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (R.A.); (E.M.A.); (G.M.S.); (C.B.); (T.W.); (S.R.C.)
| | - Mohammad A. Tariq
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (R.A.); (E.M.A.); (G.M.S.); (C.B.); (T.W.); (S.R.C.)
| | - Andrea Telatin
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (R.A.); (E.M.A.); (G.M.S.); (C.B.); (T.W.); (S.R.C.)
| | - Rebecca Ansorge
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (R.A.); (E.M.A.); (G.M.S.); (C.B.); (T.W.); (S.R.C.)
| | - Evelien M. Adriaenssens
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (R.A.); (E.M.A.); (G.M.S.); (C.B.); (T.W.); (S.R.C.)
| | - George M. Savva
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (R.A.); (E.M.A.); (G.M.S.); (C.B.); (T.W.); (S.R.C.)
| | - Catherine Booth
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (R.A.); (E.M.A.); (G.M.S.); (C.B.); (T.W.); (S.R.C.)
| | - Tom Wileman
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (R.A.); (E.M.A.); (G.M.S.); (C.B.); (T.W.); (S.R.C.)
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Lesley Hoyles
- Department of Biosciences, School of Science & Technology, Nottingham Trent University, Nottingham NG11 8NS, UK;
| | - Simon R. Carding
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (R.A.); (E.M.A.); (G.M.S.); (C.B.); (T.W.); (S.R.C.)
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
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25
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Tariq MA, Carding SR. Complete Genome Sequence of a Bacteroides fragilis Bacteriophage, vB_BfrS_NCTC. Microbiol Resour Announc 2021; 10:e0054821. [PMID: 34292066 PMCID: PMC8297453 DOI: 10.1128/mra.00548-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 06/21/2021] [Indexed: 11/26/2022] Open
Abstract
Bacteroides fragilis is an obligate anaerobe and a common gut commensal bacterium that is also an important opportunistic pathogen. Here, we present the complete genome sequence of the circularly permuted B. fragilis bacteriophage vB_BfrS_NCTC. It comprises 47,160 bp, with 69 open reading frames.
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Affiliation(s)
- Mohammad A. Tariq
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Simon R. Carding
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
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26
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Wang Y, Sharma P, Jefferson M, Zhang W, Bone B, Kipar A, Bitto D, Coombes JL, Pearson T, Man A, Zhekova A, Bao Y, Tripp RA, Carding SR, Yamauchi Y, Mayer U, Powell PP, Stewart JP, Wileman T. Non-canonical autophagy functions of ATG16L1 in epithelial cells limit lethal infection by influenza A virus. EMBO J 2021; 40:e105543. [PMID: 33586810 PMCID: PMC7957399 DOI: 10.15252/embj.2020105543] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [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: 05/06/2020] [Revised: 12/23/2020] [Accepted: 01/08/2021] [Indexed: 12/17/2022] Open
Abstract
Influenza A virus (IAV) and SARS-CoV-2 (COVID-19) cause pandemic infections where cytokine storm syndrome and lung inflammation lead to high mortality. Given the high social and economic cost of respiratory viruses, there is an urgent need to understand how the airways defend against virus infection. Here we use mice lacking the WD and linker domains of ATG16L1 to demonstrate that ATG16L1-dependent targeting of LC3 to single-membrane, non-autophagosome compartments - referred to as non-canonical autophagy - protects mice from lethal IAV infection. Mice with systemic loss of non-canonical autophagy are exquisitely sensitive to low-pathogenicity IAV where extensive viral replication throughout the lungs, coupled with cytokine amplification mediated by plasmacytoid dendritic cells, leads to fulminant pneumonia, lung inflammation and high mortality. IAV was controlled within epithelial barriers where non-canonical autophagy reduced IAV fusion with endosomes and activation of interferon signalling. Conditional mouse models and ex vivo analysis showed that protection against IAV infection of lung was independent of phagocytes and other leucocytes. This establishes non-canonical autophagy in airway epithelial cells as a novel innate defence that restricts IAV infection and lethal inflammation at respiratory surfaces.
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Affiliation(s)
- Yingxue Wang
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
| | - Parul Sharma
- Department of Infection Biology and MicrobiomesUniversity of LiverpoolLiverpoolUK
| | | | - Weijiao Zhang
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
| | - Ben Bone
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
| | - Anja Kipar
- Department of Infection Biology and MicrobiomesUniversity of LiverpoolLiverpoolUK
- Institute of Veterinary PathologyUniversity of ZurichZurichSwitzerland
| | - David Bitto
- School of Cellular and Molecular MedicineFaculty of Life SciencesUniversity of BristolBristolUK
| | - Janine L Coombes
- Department of Infection Biology and MicrobiomesUniversity of LiverpoolLiverpoolUK
| | | | | | - Alex Zhekova
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
| | - Yongping Bao
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
| | - Ralph A Tripp
- Department of Infectious DiseaseUniversity of GeorgiaGeorgiaUSA
| | - Simon R Carding
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
- Gut Microbes and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
| | - Yohei Yamauchi
- School of Cellular and Molecular MedicineFaculty of Life SciencesUniversity of BristolBristolUK
| | - Ulrike Mayer
- School of Biological SciencesUniversity of East AngliaNorwichUK
| | - Penny P Powell
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
| | - James P Stewart
- Department of Infection Biology and MicrobiomesUniversity of LiverpoolLiverpoolUK
- Department of Infectious DiseaseUniversity of GeorgiaGeorgiaUSA
| | - Thomas Wileman
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
- Gut Microbes and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
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27
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Treveil A, Sudhakar P, Matthews ZJ, Wrzesiński T, Jones EJ, Brooks J, Ölbei M, Hautefort I, Hall LJ, Carding SR, Mayer U, Powell PP, Wileman T, Di Palma F, Haerty W, Korcsmáros T. Regulatory network analysis of Paneth cell and goblet cell enriched gut organoids using transcriptomics approaches. Mol Omics 2021; 16:39-58. [PMID: 31819932 DOI: 10.1039/c9mo00130a] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The epithelial lining of the small intestine consists of multiple cell types, including Paneth cells and goblet cells, that work in cohort to maintain gut health. 3D in vitro cultures of human primary epithelial cells, called organoids, have become a key model to study the functions of Paneth cells and goblet cells in normal and diseased conditions. Advances in these models include the ability to skew differentiation to particular lineages, providing a useful tool to study cell type specific function/dysfunction in the context of the epithelium. Here, we use comprehensive profiling of mRNA, microRNA and long non-coding RNA expression to confirm that Paneth cell and goblet cell enrichment of murine small intestinal organoids (enteroids) establishes a physiologically accurate model. We employ network analysis to infer the regulatory landscape altered by skewing differentiation, and using knowledge of cell type specific markers, we predict key regulators of cell type specific functions: Cebpa, Jun, Nr1d1 and Rxra specific to Paneth cells, Gfi1b and Myc specific for goblet cells and Ets1, Nr3c1 and Vdr shared between them. Links identified between these regulators and cellular phenotypes of inflammatory bowel disease (IBD) suggest that global regulatory rewiring during or after differentiation of Paneth cells and goblet cells could contribute to IBD aetiology. Future application of cell type enriched enteroids combined with the presented computational workflow can be used to disentangle multifactorial mechanisms of these cell types and propose regulators whose pharmacological targeting could be advantageous in treating IBD patients with Crohn's disease or ulcerative colitis.
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Affiliation(s)
- A Treveil
- Earlham Institute, Norwich Research Park, Norwich, Norfolk NR4 7UZ, UK.
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28
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James SA, Phillips S, Telatin A, Baker D, Ansorge R, Clarke P, Hall LJ, Carding SR. Preterm Infants Harbour a Rapidly Changing Mycobiota That Includes Candida Pathobionts. J Fungi (Basel) 2020; 6:E273. [PMID: 33182444 PMCID: PMC7712117 DOI: 10.3390/jof6040273] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 10/26/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 12/22/2022] Open
Abstract
Fungi and the mycobiome are a fundamental part of the human microbiome that contributes to human health and development. Despite this, relatively little is known about the mycobiome of the preterm infant gut. Here, we have characterised faecal fungal communities present in 11 premature infants born with differing degrees of prematurity and mapped how the mycobiome develops during early infancy. Using an ITS1 sequencing-based approach, the preterm infant gut mycobiome was found to be often dominated by a single species, typically a yeast. Candida was the most abundant genus, with the pathobionts C.albicans and C.parapsilosis highly prevalent and persistent in these infants. Gestational maturity at birth affected the distribution and abundance of these Candida, with hospital-associated C.parapsilosis more prevalent and abundant in infants born at less than 31 weeks. Fungal diversity was lowest at 6 months, but increased with age and change of diet, with food-associated Saccharomycescerevisiae most abundant in infants post weaning. This study provides a first insight into the fungal communities present within the preterm infant gut, identifying distinctive features including the prominence of pathobiont species, and the influence age and environmental factors play in shaping the development of the mycobiome.
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Affiliation(s)
- Stephen A. James
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.A.J.); (S.P.); (A.T.); (D.B.); (R.A.)
| | - Sarah Phillips
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.A.J.); (S.P.); (A.T.); (D.B.); (R.A.)
| | - Andrea Telatin
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.A.J.); (S.P.); (A.T.); (D.B.); (R.A.)
| | - David Baker
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.A.J.); (S.P.); (A.T.); (D.B.); (R.A.)
| | - Rebecca Ansorge
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.A.J.); (S.P.); (A.T.); (D.B.); (R.A.)
| | - Paul Clarke
- Neonatal Intensive Care Unit, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich NR4 7UY, UK;
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Lindsay J. Hall
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.A.J.); (S.P.); (A.T.); (D.B.); (R.A.)
- Ziel—Institute for Food and Health, Technical University of Munich, 85354 Freising, Germany
| | - Simon R. Carding
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.A.J.); (S.P.); (A.T.); (D.B.); (R.A.)
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
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Modasia A, Parker A, Jones E, Stentz R, Brion A, Goldson A, Defernez M, Wileman T, Ashley Blackshaw L, Carding SR. Regulation of Enteroendocrine Cell Networks by the Major Human Gut Symbiont Bacteroides thetaiotaomicron. Front Microbiol 2020; 11:575595. [PMID: 33240233 PMCID: PMC7677362 DOI: 10.3389/fmicb.2020.575595] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 06/23/2020] [Accepted: 10/16/2020] [Indexed: 12/12/2022] Open
Abstract
Gut microbes have critical roles in maintaining host physiology, but their effects on epithelial chemosensory enteroendocrine cells (EEC) remain unclear. We investigated the role that the ubiquitous commensal gut bacterium Bacteriodes thetaiotaomicron (Bt) and its major fermentation products, acetate, propionate, and succinate (APS) have in shaping EEC networks in the murine gastrointestinal tract (GIT). The distribution and numbers of EEC populations were assessed in tissues along the GIT by fluorescent immunohistochemistry in specific pathogen free (SPF), germfree (GF) mice, GF mice conventionalized by Bt or Lactobacillus reuteri (Lr), and GF mice administered APS. In parallel, we also assessed the suitability of using intestinal crypt-derived epithelial monolayer cultures for these studies. GF mice up-regulated their EEC network, in terms of a general EEC marker chromogranin A (ChrA) expression, numbers of serotonin-producing enterochromaffin cells, and both hormone-producing K- and L-cells, with a corresponding increase in serum glucagon-like peptide-1 (GLP-1) levels. Bt conventionalization restored EEC numbers to levels in SPF mice with regional specificity; the effects on ChrA and L-cells were mainly in the small intestine, the effects on K-cells and EC cells were most apparent in the colon. By contrast, Lr did not restore EEC networks in conventionalized GF mice. Analysis of secretory epithelial cell monolayer cultures from whole small intestine showed that intestinal monolayers are variable and with the possible exclusion of GIP expressing cells, did not accurately reflect the EEC cell makeup seen in vivo. Regarding the mechanism of action of Bt on EECs, colonization of GF mice with Bt led to the production and accumulation of acetate, propionate and succinate (APS) in the caecum and colon, which when administered at physiological concentrations to GF mice via their drinking water for 10 days mimicked to a large extent the effects of Bt in GF mice. After withdrawal of APS, the changes in some EEC were maintained and, in some cases, were greater than during APS treatment. This data provides evidence of microbiota influences on regulating EEC networks in different regions of the GIT, with a single microbe, Bt, recapitulating its role in a process that may be dependent upon its fermentation products.
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Affiliation(s)
- Amisha Modasia
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Aimee Parker
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Emily Jones
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Regis Stentz
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Arlaine Brion
- Core Science Resources, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Andrew Goldson
- Core Science Resources, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Marianne Defernez
- Core Science Resources, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Tom Wileman
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
- Norwich Medical School, Faculty of Medicine and Health Sciences, University of East Anglia, Norwich, United Kingdom
| | - L. Ashley Blackshaw
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Simon R. Carding
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
- Norwich Medical School, Faculty of Medicine and Health Sciences, University of East Anglia, Norwich, United Kingdom
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30
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Tariq MA, Newberry F, Haagmans R, Booth C, Wileman T, Hoyles L, Clokie MRJ, Ebdon J, Carding SR. Genome Characterization of a Novel Wastewater Bacteroides fragilis Bacteriophage (vB_BfrS_23) and its Host GB124. Front Microbiol 2020; 11:583378. [PMID: 33193224 PMCID: PMC7644841 DOI: 10.3389/fmicb.2020.583378] [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] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/05/2020] [Indexed: 12/31/2022] Open
Abstract
Bacteroides spp. are part of the human intestinal microbiota but can under some circumstances become clinical pathogens. Phages are a potentially valuable therapeutic treatment option for many pathogens, but phage therapy for pathogenic Bacteroides spp. including Bacteroides fragilis is currently limited to three genome-sequenced phages. Here we describe the isolation from sewage wastewater and genome of a lytic phage, vB_BfrS_23, that infects and kills B. fragilis strain GB124. Transmission electron microscopy identified this phage as a member of the Siphoviridae family. The phage is stable when held at temperatures of 4 and 60°C for 1 h. It has a very narrow host range, only infecting one host from a panel of B. fragilis strains (n = 8). Whole-genome sequence analyses of vB_BfrS_23 determined it is double-stranded DNA phage and is circularly permuted, with a genome of 48,011 bp. The genome encodes 73 putative open reading frames. We also sequenced the host bacterium, B. fragilis GB124 (5.1 Mb), which has two plasmids of 43,923 and 4,138 bp. Although this phage is host specific, its isolation together with the detailed characterization of the host B. fragilis GB124 featured in this study represent a useful starting point from which to facilitate the future development of highly specific therapeutic agents. Furthermore, the phage could be a novel tool in determining water (and water reuse) treatment efficacy, and for identifying human fecal transmission pathways within contaminated environmental waters and foodstuffs.
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Affiliation(s)
- Mohammad A. Tariq
- Gut Microbes and Health Research Programme, Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Fiona Newberry
- Gut Microbes and Health Research Programme, Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Rik Haagmans
- Gut Microbes and Health Research Programme, Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Catherine Booth
- Gut Microbes and Health Research Programme, Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Tom Wileman
- Gut Microbes and Health Research Programme, Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Lesley Hoyles
- Department of Biosciences, Nottingham Trent University, Nottingham, United Kingdom
| | - Martha R. J. Clokie
- Department of Genetics and Genome Biology, Leicester University, Leicester, United Kingdom
| | - James Ebdon
- Environment and Public Health Research Group, School of Environment and Technology, University of Brighton, Brighton, United Kingdom
| | - Simon R. Carding
- Gut Microbes and Health Research Programme, Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
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31
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Durant L, Stentz R, Noble A, Brooks J, Gicheva N, Reddi D, O’Connor MJ, Hoyles L, McCartney AL, Man R, Pring ET, Dilke S, Hendy P, Segal JP, Lim DNF, Misra R, Hart AL, Arebi N, Carding SR, Knight SC. Bacteroides thetaiotaomicron-derived outer membrane vesicles promote regulatory dendritic cell responses in health but not in inflammatory bowel disease. Microbiome 2020; 8:88. [PMID: 32513301 PMCID: PMC7282036 DOI: 10.1186/s40168-020-00868-z] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/13/2020] [Indexed: 06/09/2023]
Abstract
BACKGROUND Bacteroides thetaiotaomicron (Bt) is a prominent member of the human intestinal microbiota that, like all gram-negative bacteria, naturally generates nanosized outer membrane vesicles (OMVs) which bud off from the cell surface. Importantly, OMVs can cross the intestinal epithelial barrier to mediate microbe-host cell crosstalk involving both epithelial and immune cells to help maintain intestinal homeostasis. Here, we have examined the interaction between Bt OMVs and blood or colonic mucosa-derived dendritic cells (DC) from healthy individuals and patients with Crohn's disease (CD) or ulcerative colitis (UC). RESULTS In healthy individuals, Bt OMVs stimulated significant (p < 0.05) IL-10 expression by colonic DC, whereas in peripheral blood-derived DC they also stimulated significant (p < 0.001 and p < 0.01, respectively) expression of IL-6 and the activation marker CD80. Conversely, in UC Bt OMVs were unable to elicit IL-10 expression by colonic DC. There were also reduced numbers of CD103+ DC in the colon of both UC and CD patients compared to controls, supporting a loss of regulatory DC in both diseases. Furthermore, in CD and UC, Bt OMVs elicited a significantly lower proportion of DC which expressed IL-10 (p < 0.01 and p < 0.001, respectively) in blood compared to controls. These alterations in DC responses to Bt OMVs were seen in patients with inactive disease, and thus are indicative of intrinsic defects in immune responses to this commensal in inflammatory bowel disease (IBD). CONCLUSIONS Overall, our findings suggest a key role for OMVs generated by the commensal gut bacterium Bt in directing a balanced immune response to constituents of the microbiota locally and systemically during health which is altered in IBD patients. Video Abstract.
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Affiliation(s)
- Lydia Durant
- Antigen Presentation Research Group, Imperial College London, Northwick Park & St. Mark’s Hospital Campus, Watford Rd, Harrow, Greater London HA1 3UJ UK
| | - Régis Stentz
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, NR4 7UQ UK
| | - Alistair Noble
- Antigen Presentation Research Group, Imperial College London, Northwick Park & St. Mark’s Hospital Campus, Watford Rd, Harrow, Greater London HA1 3UJ UK
| | - Johanne Brooks
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, NR4 7UQ UK
- Norwich Medical School, University of East Anglia, Norwich, NR4 7TJ UK
| | - Nadezhda Gicheva
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, NR4 7UQ UK
| | - Durga Reddi
- Antigen Presentation Research Group, Imperial College London, Northwick Park & St. Mark’s Hospital Campus, Watford Rd, Harrow, Greater London HA1 3UJ UK
| | - Matthew J. O’Connor
- Antigen Presentation Research Group, Imperial College London, Northwick Park & St. Mark’s Hospital Campus, Watford Rd, Harrow, Greater London HA1 3UJ UK
| | - Lesley Hoyles
- Department of Biosciences, Nottingham Trent University, Clifton Campus, Nottingham, NG11 8NS UK
| | - Anne L. McCartney
- Food Microbial Sciences Unit, University of Reading, Whiteknights, Reading, RG6 6UR UK
| | - Ripple Man
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, Greater London HA1 3UJ UK
| | - E. Tobias Pring
- Antigen Presentation Research Group, Imperial College London, Northwick Park & St. Mark’s Hospital Campus, Watford Rd, Harrow, Greater London HA1 3UJ UK
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, Greater London HA1 3UJ UK
| | - Stella Dilke
- Antigen Presentation Research Group, Imperial College London, Northwick Park & St. Mark’s Hospital Campus, Watford Rd, Harrow, Greater London HA1 3UJ UK
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, Greater London HA1 3UJ UK
| | - Philip Hendy
- Antigen Presentation Research Group, Imperial College London, Northwick Park & St. Mark’s Hospital Campus, Watford Rd, Harrow, Greater London HA1 3UJ UK
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, Greater London HA1 3UJ UK
| | - Jonathan P. Segal
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, Greater London HA1 3UJ UK
| | - Dennis N. F. Lim
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, Greater London HA1 3UJ UK
| | - Ravi Misra
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, Greater London HA1 3UJ UK
| | - Ailsa L. Hart
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, Greater London HA1 3UJ UK
| | - Naila Arebi
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, Greater London HA1 3UJ UK
| | - Simon R. Carding
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, NR4 7UQ UK
- Norwich Medical School, University of East Anglia, Norwich, NR4 7TJ UK
| | - Stella C. Knight
- Antigen Presentation Research Group, Imperial College London, Northwick Park & St. Mark’s Hospital Campus, Watford Rd, Harrow, Greater London HA1 3UJ UK
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, Greater London HA1 3UJ UK
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32
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Noble A, Durant L, Hoyles L, Mccartney AL, Man R, Segal J, Costello SP, Hendy P, Reddi D, Bouri S, Lim DNF, Pring T, O’Connor MJ, Datt P, Wilson A, Arebi N, Akbar A, Hart AL, Carding SR, Knight SC. Deficient Resident Memory T Cell and CD8 T Cell Response to Commensals in Inflammatory Bowel Disease. J Crohns Colitis 2020; 14:525-537. [PMID: 31665283 PMCID: PMC7242004 DOI: 10.1093/ecco-jcc/jjz175] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND AND AIMS The intestinal microbiota is closely associated with resident memory lymphocytes in mucosal tissue. We sought to understand how acquired cellular and humoral immunity to the microbiota differ in health versus inflammatory bowel disease [IBD]. METHODS Resident memory T cells [Trm] in colonic biopsies and local antibody responses to intraepithelial microbes were analysed. Systemic antigen-specific immune T and B cell memory to a panel of commensal microbes was assessed. RESULTS Systemically, healthy blood showed CD4 and occasional CD8 memory T cell responses to selected intestinal bacteria, but few memory B cell responses. In IBD, CD8 memory T cell responses decreased although B cell responses and circulating plasmablasts increased. Possibly secondary to loss of systemic CD8 T cell responses in IBD, dramatically reduced numbers of mucosal CD8+ Trm and γδ T cells were observed. IgA responses to intraepithelial bacteria were increased. Colonic Trm expressed CD39 and CD73 ectonucleotidases, characteristic of regulatory T cells. Cytokines/factors required for Trm differentiation were identified, and in vitro-generated Trm expressed regulatory T cell function via CD39. Cognate interaction between T cells and dendritic cells induced T-bet expression in dendritic cells, a key mechanism in regulating cell-mediated mucosal responses. CONCLUSIONS A previously unrecognised imbalance exists between cellular and humoral immunity to the microbiota in IBD, with loss of mucosal T cell-mediated barrier immunity and uncontrolled antibody responses. Regulatory function of Trm may explain their association with intestinal health. Promoting Trm and their interaction with dendritic cells, rather than immunosuppression, may reinforce tissue immunity, improve barrier function, and prevent B cell dysfunction in microbiota-associated disease and IBD aetiology.
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Affiliation(s)
- Alistair Noble
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich, UK,Antigen Presentation Research Group, Imperial College London, Northwick Park and St Mark’s Campus, Harrow, London, UK,Corresponding author: Alistair Noble, PhD, Antigen Presentation Research Group, Northwick Park and St Mark’s Hospital, Level 7W, Watford Road, Harrow HA1 3UJ, UK. Tel.: [44] 20 8869 3255;
| | - Lydia Durant
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St Mark’s Campus, Harrow, London, UK
| | - Lesley Hoyles
- Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK,Department of Bioscience, Nottingham Trent University, Nottingham, UK
| | - Anne L Mccartney
- Department of Food and Nutritional Sciences, University of Reading, Reading, UK
| | - Ripple Man
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, UK
| | - Jonathan Segal
- Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK,St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, UK
| | - Samuel P Costello
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, UK,Department of Gastroenterology, Queen Elizabeth Hospital, Adelaide, SA, Australia
| | - Philip Hendy
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St Mark’s Campus, Harrow, London, UK,St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, UK
| | - Durga Reddi
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St Mark’s Campus, Harrow, London, UK
| | - Sonia Bouri
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, UK
| | - Dennis N F Lim
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, UK
| | - Toby Pring
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, UK
| | - Matthew J O’Connor
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St Mark’s Campus, Harrow, London, UK
| | - Pooja Datt
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, UK
| | - Ana Wilson
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, UK
| | - Naila Arebi
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, UK
| | - Ayesha Akbar
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, UK
| | - Ailsa L Hart
- Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK,St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, UK
| | - Simon R Carding
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich, UK,Norwich Medical School, University of East Anglia, Norwich, UK
| | - Stella C Knight
- Antigen Presentation Research Group, Imperial College London, Northwick Park and St Mark’s Campus, Harrow, London, UK,St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, UK
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Jones EJ, Booth C, Fonseca S, Parker A, Cross K, Miquel-Clopés A, Hautefort I, Mayer U, Wileman T, Stentz R, Carding SR. The Uptake, Trafficking, and Biodistribution of Bacteroides thetaiotaomicron Generated Outer Membrane Vesicles. Front Microbiol 2020; 11:57. [PMID: 32117106 PMCID: PMC7015872 DOI: 10.3389/fmicb.2020.00057] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [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: 10/31/2019] [Accepted: 01/13/2020] [Indexed: 12/29/2022] Open
Abstract
Gram-negative bacteria ubiquitously produce and release nano-size, non-replicative outer membrane vesicles (OMVs). In the gastrointestinal (GI-) tract, OMVs generated by members of the intestinal microbiota are believed to contribute to maintaining the intestinal microbial ecosystem and mediating bacteria-host interactions, including the delivery of bacterial effector molecules to host cells to modulate their physiology. Bacterial OMVs have also been found in the bloodstream although their origin and fate are unclear. Here we have investigated the interactions between OMVs produced by the major human gut commensal bacterium, Bacteroides thetaiotaomicron (Bt), with cells of the GI-tract. Using a combination of in vitro culture systems including intestinal epithelial organoids and in vivo imaging we show that intestinal epithelial cells principally acquire Bt OMVs via dynamin-dependent endocytosis followed by intracellular trafficking to LAMP-1 expressing endo-lysosomal vesicles and co-localization with the perinuclear membrane. We observed that Bt OMVs can also transmigrate through epithelial cells via a paracellular route with in vivo imaging demonstrating that within hours of oral administration Bt OMVs can be detected in systemic tissues and in particular, the liver. Our findings raise the intriguing possibility that OMVs may act as a long-distance microbiota-host communication system.
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Affiliation(s)
- Emily J. Jones
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Catherine Booth
- Core Science Resources, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Sonia Fonseca
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Aimee Parker
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Kathryn Cross
- Core Science Resources, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Ariadna Miquel-Clopés
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | | | - Ulrike Mayer
- Biomedical Research Centre, University of East Anglia, Norwich, United Kingdom
| | - Tom Wileman
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Régis Stentz
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Simon R. Carding
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
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34
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Parker A, Fonseca S, Carding SR. Gut microbes and metabolites as modulators of blood-brain barrier integrity and brain health. Gut Microbes 2019; 11:135-157. [PMID: 31368397 PMCID: PMC7053956 DOI: 10.1080/19490976.2019.1638722] [Citation(s) in RCA: 270] [Impact Index Per Article: 54.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/22/2019] [Accepted: 06/26/2019] [Indexed: 02/03/2023] Open
Abstract
The human gastrointestinal (gut) microbiota comprises diverse and dynamic populations of bacteria, archaea, viruses, fungi, and protozoa, coexisting in a mutualistic relationship with the host. When intestinal homeostasis is perturbed, the function of the gastrointestinal tract and other organ systems, including the brain, can be compromised. The gut microbiota is proposed to contribute to blood-brain barrier disruption and the pathogenesis of neurodegenerative diseases. While progress is being made, a better understanding of interactions between gut microbes and host cells, and the impact these have on signaling from gut to brain is now required. In this review, we summarise current evidence of the impact gut microbes and their metabolites have on blood-brain barrier integrity and brain function, and the communication networks between the gastrointestinal tract and brain, which they may modulate. We also discuss the potential of microbiota modulation strategies as therapeutic tools for promoting and restoring brain health.
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Affiliation(s)
- Aimée Parker
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, UK
| | - Sonia Fonseca
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, UK
| | - Simon R. Carding
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
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35
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Carvalho AL, Fonseca S, Miquel-Clopés A, Cross K, Kok KS, Wegmann U, Gil-Cordoso K, Bentley EG, Al Katy SH, Coombes JL, Kipar A, Stentz R, Stewart JP, Carding SR. Bioengineering commensal bacteria-derived outer membrane vesicles for delivery of biologics to the gastrointestinal and respiratory tract. J Extracell Vesicles 2019; 8:1632100. [PMID: 31275534 PMCID: PMC6598475 DOI: 10.1080/20013078.2019.1632100] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [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: 11/20/2018] [Revised: 05/16/2019] [Accepted: 06/10/2019] [Indexed: 12/27/2022] Open
Abstract
Gram-negative bacteria naturally produce and secrete nanosized outer membrane vesicles (OMVs). In the human gastrointestinal tract, OMVs produced by commensal Gram-negative bacteria can mediate interactions amongst host cells (including between epithelial cells and immune cells) and maintain microbial homeostasis. This OMV-mediated pathway for host-microbe interactions could be exploited to deliver biologically active proteins to the body. To test this we engineered the Gram-negative bacterium Bacteroides thetaiotaomicron (Bt), a prominent member of the intestinal microbiota of all animals, to incorporate bacteria-, virus- and human-derived proteins into its OMVs. We then used the engineered Bt OMVs to deliver these proteins to the respiratory and gastrointestinal (GI)-tract to protect against infection, tissue inflammation and injury. Our findings demonstrate the ability to express and package both Salmonella enterica ser. Typhimurium-derived vaccine antigens and influenza A virus (IAV)-derived vaccine antigens within or on the outer membrane of Bt OMVs. These antigens were in a form capable of eliciting antigen-specific immune and antibody responses in both mucosal tissues and systemically. Furthermore, immunisation with OMVs containing the core stalk region of the IAV H5 hemagglutinin from an H5N1 strain induced heterotypic protection in mice to a 10-fold lethal dose of an unrelated subtype (H1N1) of IAV. We also showed that OMVs could express the human therapeutic protein, keratinocyte growth factor-2 (KGF-2), in a stable form that, when delivered orally, reduced disease severity and promoted intestinal epithelial repair and recovery in animals administered colitis-inducing dextran sodium sulfate. Collectively, our data demonstrates the utility and effectiveness of using Bt OMVs as a mucosal biologics and drug delivery platform technology.
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Affiliation(s)
- Ana L. Carvalho
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, UK
| | - Sonia Fonseca
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, UK
| | - Ariadna Miquel-Clopés
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, UK
| | - Kathryn Cross
- Core Science Resources, Quadram Institute Bioscience, Norwich, UK
| | - Khoon-S. Kok
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Udo Wegmann
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, UK
| | - Katherine Gil-Cordoso
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, UK
- Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, Tarragona, Spain
| | | | | | - Janine L. Coombes
- Department of Infection Biology, University of Liverpool, Liverpool, UK
| | - Anja Kipar
- Instiute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Regis Stentz
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, UK
| | - James P. Stewart
- Department of Infection Biology, University of Liverpool, Liverpool, UK
| | - Simon R. Carding
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
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36
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Carvalho AL, Miquel-Clopés A, Wegmann U, Jones E, Stentz R, Telatin A, Walker NJ, Butcher WA, Brown PJ, Holmes S, Dennis MJ, Williamson ED, Funnell SGP, Stock M, Carding SR. Use of bioengineered human commensal gut bacteria-derived microvesicles for mucosal plague vaccine delivery and immunization. Clin Exp Immunol 2019; 196:287-304. [PMID: 30985006 PMCID: PMC6514708 DOI: 10.1111/cei.13301] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [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] [Accepted: 03/25/2019] [Indexed: 12/19/2022] Open
Abstract
Plague caused by the Gram‐negative bacterium, Yersinia pestis, is still endemic in parts of the world today. Protection against pneumonic plague is essential to prevent the development and spread of epidemics. Despite this, there are currently no licensed plague vaccines in the western world. Here we describe the means of delivering biologically active plague vaccine antigens directly to mucosal sites of plague infection using highly stable microvesicles (outer membrane vesicles; OMVs) that are naturally produced by the abundant and harmless human commensal gut bacterium Bacteroides thetaiotaomicron (Bt). Bt was engineered to express major plague protective antigens in its OMVs, specifically Fraction 1 (F1) in the outer membrane and LcrV (V antigen) in the lumen, for targeted delivery to the gastrointestinal (GI) and respiratory tracts in a non‐human primate (NHP) host. Our key findings were that Bt OMVs stably expresses F1 and V plague antigens, particularly the V antigen, in the correct, immunogenic form. When delivered intranasally V‐OMVs elicited substantive and specific immune and antibody responses, both in the serum [immunoglobulin (Ig)G] and in the upper and lower respiratory tract (IgA); this included the generation of serum antibodies able to kill plague bacteria. Our results also showed that Bt OMV‐based vaccines had many desirable characteristics, including: biosafety and an absence of any adverse effects, pathology or gross alteration of resident microbial communities (microbiotas); high stability and thermo‐tolerance; needle‐free delivery; intrinsic adjuvanticity; the ability to stimulate both humoral and cell‐mediated immune responses; and targeting of primary sites of plague infection.
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Affiliation(s)
- A L Carvalho
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, UK
| | - A Miquel-Clopés
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, UK
| | - U Wegmann
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, UK
| | - E Jones
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, UK
| | - R Stentz
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, UK
| | - A Telatin
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, UK
| | - N J Walker
- Defence Science and Technology Laboratory, Porton, Salisbury, UK
| | - W A Butcher
- Defence Science and Technology Laboratory, Porton, Salisbury, UK
| | - P J Brown
- Public Health England, Porton, Porton, Salisbury, UK
| | - S Holmes
- Public Health England, Porton, Porton, Salisbury, UK
| | - M J Dennis
- Public Health England, Porton, Porton, Salisbury, UK
| | - E D Williamson
- Defence Science and Technology Laboratory, Porton, Salisbury, UK
| | - S G P Funnell
- Public Health England, Porton, Porton, Salisbury, UK
| | - M Stock
- Plant Biotechnology Ltd, Norwich, UK
| | - S R Carding
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, UK.,Norwich Medical School, University East Anglia, Norwich, UK
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37
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Abstract
There is an urgent and unmet need to develop effective vaccines to reduce the global burden of infectious disease in both animals and humans, and in particular for the majority of pathogens that infect via mucosal sites. Here we summarise the impediments to developing mucosal vaccines and review the new and emerging technologies aimed at overcoming the lack of effective vaccine delivery systems that is the major obstacle to developing new mucosal vaccines.
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Affiliation(s)
- A Miquel-Clopés
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, UK
| | - E G Bentley
- Department of Infection Biology, University of Liverpool, Liverpool, UK
| | - J P Stewart
- Department of Infection Biology, University of Liverpool, Liverpool, UK
| | - S R Carding
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, UK.,Norwich Medical School, University of East Anglia, Norwich, UK
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38
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Rai S, Arasteh M, Jefferson M, Pearson T, Wang Y, Zhang W, Bicsak B, Divekar D, Powell PP, Naumann R, Beraza N, Carding SR, Florey O, Mayer U, Wileman T. The ATG5-binding and coiled coil domains of ATG16L1 maintain autophagy and tissue homeostasis in mice independently of the WD domain required for LC3-associated phagocytosis. Autophagy 2019; 15:599-612. [PMID: 30403914 PMCID: PMC6526875 DOI: 10.1080/15548627.2018.1534507] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [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: 02/08/2018] [Revised: 09/28/2018] [Accepted: 10/05/2018] [Indexed: 11/11/2022] Open
Abstract
Macroautophagy/autophagy delivers damaged proteins and organelles to lysosomes for degradation, and plays important roles in maintaining tissue homeostasis by reducing tissue damage. The translocation of LC3 to the limiting membrane of the phagophore, the precursor to the autophagosome, during autophagy provides a binding site for autophagy cargoes, and facilitates fusion with lysosomes. An autophagy-related pathway called LC3-associated phagocytosis (LAP) targets LC3 to phagosome and endosome membranes during uptake of bacterial and fungal pathogens, and targets LC3 to swollen endosomes containing particulate material or apoptotic cells. We have investigated the roles played by autophagy and LAP in vivo by exploiting the observation that the WD domain of ATG16L1 is required for LAP, but not autophagy. Mice lacking the linker and WD domains, activate autophagy, but are deficient in LAP. The LAP-/- mice survive postnatal starvation, grow at the same rate as littermate controls, and are fertile. The liver, kidney, brain and muscle of these mice maintain levels of autophagy cargoes such as LC3 and SQSTM1/p62 similar to littermate controls, and prevent accumulation of SQSTM1 inclusions and tissue damage associated with loss of autophagy. The results suggest that autophagy maintains tissue homeostasis in mice independently of LC3-associated phagocytosis. Further deletion of glutamate E230 in the coiled-coil domain required for WIPI2 binding produced mice with defective autophagy that survived neonatal starvation. Analysis of brain lysates suggested that interactions between WIPI2 and ATG16L1 were less critical for autophagy in the brain, which may allow a low level of autophagy to overcome neonatal lethality. Abbreviations: CCD: coiled-coil domain; CYBB/NOX2: cytochrome b-245: beta polypeptide; GPT/ALT: glutamic pyruvic transaminase: soluble; LAP: LC3-associated phagocytosis; LC3: microtubule-associated protein 1 light chain 3; MEF: mouse embryonic fibroblast; NOD: nucleotide-binding oligomerization domain; NADPH: nicotinamide adenine dinucleotide phosphate; RUBCN/Rubicon: RUN domain and cysteine-rich domain containing Beclin 1-interacting protein; SLE: systemic lupus erythematosus; SQSTM1/p62: sequestosome 1; TLR: toll-like receptor; TMEM: transmembrane protein; TRIM: tripartite motif-containing protein; UVRAG: UV radiation resistance associated gene; WD: tryptophan-aspartic acid; WIPI: WD 40 repeat domain: phosphoinositide interacting.
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Affiliation(s)
- Shashank Rai
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, UK
| | - Maryam Arasteh
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, UK
| | - Matthew Jefferson
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, UK
| | - Timothy Pearson
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, UK
| | - Yingxue Wang
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, UK
| | - Weijiao Zhang
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, UK
| | - Bertalan Bicsak
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, UK
| | - Devina Divekar
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, UK
| | - Penny P. Powell
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, UK
| | - Ronald Naumann
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | | | - Oliver Florey
- Signalling Programme, Babraham Institute, Cambridge, UK
| | - Ulrike Mayer
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK
| | - Thomas Wileman
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, UK
- Quadram Institute Bioscience, Norwich, Norfolk, UK
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39
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Sayers E, Dainty JR, Yates M, Verstappen SM, Chipping J, Carding SR, Luben RN, Khaw KT, Wareham NJ, MacGregor AJ. O14 Pro-inflammatory diets are associated with increased C-reactive protein and subsequent rheumatoid arthritis in the European Investigation of Cancer: Norfolk Arthritis Register cohort. Rheumatology (Oxford) 2019. [DOI: 10.1093/rheumatology/kez105.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Ellie Sayers
- Faculty of Medicine and Health Sciences, University of East Anglia, Norwich, United Kingdom
| | - Jack R Dainty
- Faculty of Medicine and Health Sciences, University of East Anglia, Norwich, United Kingdom
| | - Max Yates
- Faculty of Medicine and Health Sciences, University of East Anglia, Norwich, United Kingdom
| | - Suzanne M Verstappen
- Arthritis Research UK Centre for Epidemiology, University of Manchester, Manchester, United Kingdom
| | - Jacqueline Chipping
- Faculty of Medicine and Health Sciences, University of East Anglia, Norwich, United Kingdom
| | - Simon R Carding
- Gut Health and Food Safety, Quadram Insitute Bioscience, Norwich, United Kingdom
| | - Robert N Luben
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Kay-Tee Khaw
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Nick J Wareham
- MRC Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Alexander J MacGregor
- Faculty of Medicine and Health Sciences, University of East Anglia, Norwich, United Kingdom
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40
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Mukhopadhya I, Segal JP, Carding SR, Hart AL, Hold GL. The gut virome: the 'missing link' between gut bacteria and host immunity? Therap Adv Gastroenterol 2019; 12:1756284819836620. [PMID: 30936943 PMCID: PMC6435874 DOI: 10.1177/1756284819836620] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [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: 01/05/2019] [Accepted: 02/14/2019] [Indexed: 02/04/2023] Open
Abstract
The human gut virome includes a diverse collection of viruses that infect our own cells as well as other commensal organisms, directly impacting on our well-being. Despite its predominance, the virome remains one of the least understood components of the gut microbiota, with appropriate analysis toolkits still in development. Based on its interconnectivity with all living cells, it is clear that the virome cannot be studied in isolation. Here we review the current understanding of the human gut virome, specifically in relation to other constituents of the microbiome, its evolution and life-long association with its host, and our current understanding in the context of inflammatory bowel disease and associated therapies. We propose that the gut virome and the gut bacterial microbiome share similar trajectories and interact in both health and disease and that future microbiota studies should in parallel characterize the gut virome to uncover its role in health and disease.
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Affiliation(s)
- Indrani Mukhopadhya
- Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Foresterhill, Aberdeen, UK Gut Health Group, The Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - Jonathan P. Segal
- St. Mark’s Hospital, Watford Road, Harrow, UK Imperial College London, South Kensington Campus, Department of Surgery and Cancer, London, UK
| | - Simon R. Carding
- Gut Microbes and Health Research Programme, The Quadram Institute, Norwich Research Park, Norwich, Norfolk, UK Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk, UK
| | - Ailsa L. Hart
- St. Mark’s Hospital, Watford Road, Harrow, UK Imperial College London, South Kensington Campus, Department of Surgery and Cancer, London, UK
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41
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Jones EJ, Matthews ZJ, Gul L, Sudhakar P, Treveil A, Divekar D, Buck J, Wrzesinski T, Jefferson M, Armstrong SD, Hall LJ, Watson AJM, Carding SR, Haerty W, Di Palma F, Mayer U, Powell PP, Hautefort I, Wileman T, Korcsmaros T. Integrative analysis of Paneth cell proteomic and transcriptomic data from intestinal organoids reveals functional processes dependent on autophagy. Dis Model Mech 2019; 12:dmm.037069. [PMID: 30814064 PMCID: PMC6451430 DOI: 10.1242/dmm.037069] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 02/01/2019] [Indexed: 12/12/2022] Open
Abstract
Paneth cells are key epithelial cells that provide an antimicrobial barrier and maintain integrity of the small-intestinal stem cell niche. Paneth cell abnormalities are unfortunately detrimental to gut health and are often associated with digestive pathologies such as Crohn's disease or infections. Similar alterations are observed in individuals with impaired autophagy, a process that recycles cellular components. The direct effect of autophagy impairment on Paneth cells has not been analysed. To investigate this, we generated a mouse model lacking Atg16l1 specifically in intestinal epithelial cells, making these cells impaired in autophagy. Using three-dimensional intestinal organoids enriched for Paneth cells, we compared the proteomic profiles of wild-type and autophagy-impaired organoids. We used an integrated computational approach combining protein-protein interaction networks, autophagy-targeted proteins and functional information to identify the mechanistic link between autophagy impairment and disrupted pathways. Of the 284 altered proteins, 198 (70%) were more abundant in autophagy-impaired organoids, suggesting reduced protein degradation. Interestingly, these differentially abundant proteins comprised 116 proteins (41%) that are predicted targets of the selective autophagy proteins p62, LC3 and ATG16L1. Our integrative analysis revealed autophagy-mediated mechanisms that degrade key proteins in Paneth cell functions, such as exocytosis, apoptosis and DNA damage repair. Transcriptomic profiling of additional organoids confirmed that 90% of the observed changes upon autophagy alteration have effects at the protein level, not on gene expression. We performed further validation experiments showing differential lysozyme secretion, confirming our computationally inferred downregulation of exocytosis. Our observations could explain how protein-level alterations affect Paneth cell homeostatic functions upon autophagy impairment. This article has an associated First Person interview with the joint first authors of the paper. Editor's choice: Using an integrative approach encompassing intestinal organoid culture, proteomics, transcriptomics and protein-protein interaction networks, we list Paneth cell functions dependent on autophagy.
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Affiliation(s)
- Emily J Jones
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK.,Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK.,Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Zoe J Matthews
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Lejla Gul
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Padhmanand Sudhakar
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK.,Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK
| | - Agatha Treveil
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK.,Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK
| | - Devina Divekar
- Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK.,Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Jasmine Buck
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | | | - Matthew Jefferson
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Stuart D Armstrong
- National Institute of Health Research, University of Liverpool, Liverpool L3 5RF, UK
| | - Lindsay J Hall
- Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK
| | - Alastair J M Watson
- Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK.,Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Simon R Carding
- Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK.,Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | | | - Ulrike Mayer
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Penny P Powell
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | | | - Tom Wileman
- Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK.,Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Tamas Korcsmaros
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK .,Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK
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42
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Miquel-Clopes A, Carvalho AL, Wegmann U, Bentley EG, Al-Katy SH, Coombes JL, Kipar A, Stentz R, Stewart JP, Carding SR. Use of Bacteroides-derived microvesicles for mucosal vaccines. Access Microbiol 2019. [DOI: 10.1099/acmi.ac2019.po0514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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)
| | | | - Udo Wegmann
- 1Quadram Institute Bioscience, Norwich, United Kingdom
| | | | | | | | - Anja Kipar
- 3Instiute of Veterinary Pathology, Zurich, Switzerland
| | - Regis Stentz
- 1Quadram Institute Bioscience, Norwich, United Kingdom
| | | | - Simon R. Carding
- 4University of East Anglia, Norwich, United Kingdom
- 1Quadram Institute Bioscience, Norwich, United Kingdom
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43
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Bentley E, Al Katy S, Kipar A, Stenz R, Carding SR, Stewart J. Development of Bacteroides thetaiotaomicron outer membrane vesicles as a universal, mucosal vaccine for Influenza A virus. Access Microbiol 2019. [DOI: 10.1099/acmi.ac2019.po0491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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)
- Eleanor Bentley
- 1Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Sanaria Al Katy
- 2Department of Pathology and Poultry Diseases, College of Veterinary Medicine, University of Mosul, Mosul, Iraq
- 1Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Anja Kipar
- 3Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | - Regis Stenz
- 4Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Simon R Carding
- 5Norwich Medical School, University of East Anglia, Norwich, United Kingdom
- 4Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - James Stewart
- 1Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
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44
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Sayers E, MacGregor A, Carding SR. Drug-microbiota interactions and treatment response: Relevance to rheumatoid arthritis. AIMS Microbiol 2018; 4:642-654. [PMID: 31294239 PMCID: PMC6613334 DOI: 10.3934/microbiol.2018.4.642] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 08/20/2018] [Accepted: 10/24/2018] [Indexed: 01/16/2023] Open
Abstract
Knowledge about associations between changes in the structure and/or function of intestinal microbes (the microbiota) and the pathogenesis of various diseases is expanding. However, interactions between the intestinal microbiota and different pharmaceuticals and the impact of these on responses to treatment are less well studied. Several mechanisms are known by which drug-microbiota interactions can influence drug bioavailability, efficacy, and/or toxicity. This includes direct activation or inactivation of drugs by microbial enzymes which can enhance or reduce drug effectiveness. The extensive metabolic capabilities of the intestinal microbiota make it a hotspot for drug modification. However, drugs can also influence the microbiota profoundly and change the outcome of interactions with the host. Additionally, individual microbiota signatures are unique, leading to substantial variation in host responses to particular drugs. In this review, we describe several known and emerging examples of how drug-microbiota interactions influence the responses of patients to treatment for various diseases, including inflammatory bowel disease, type 2 diabetes and cancer. Focussing on rheumatoid arthritis (RA), a chronic inflammatory disease of the joints which has been linked with microbial dysbiosis, we propose mechanisms by which the intestinal microbiota may affect responses to treatment with methotrexate which are highly variable. Furthering our knowledge of this subject will eventually lead to the adoption of new treatment strategies incorporating microbiota signatures to predict or improve treatment outcomes.
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Affiliation(s)
- Ellie Sayers
- Gut Health and Food Safety Programme, Quadram Institute Bioscience, Norwich, Norfolk, NR4 7UA, UK.,Norwich Medical School, Faculty of Medicine and Health Sciences, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - Alex MacGregor
- Gut Health and Food Safety Programme, Quadram Institute Bioscience, Norwich, Norfolk, NR4 7UA, UK
| | - Simon R Carding
- Gut Health and Food Safety Programme, Quadram Institute Bioscience, Norwich, Norfolk, NR4 7UA, UK.,Norwich Medical School, Faculty of Medicine and Health Sciences, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
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45
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Maijo M, Ivory K, Clements SJ, Dainty JR, Jennings A, Gillings R, Fairweather-Tait S, Gulisano M, Santoro A, Franceschi C, Carding SR, Nicoletti C. One-Year Consumption of a Mediterranean-Like Dietary Pattern With Vitamin D3 Supplements Induced Small Scale but Extensive Changes of Immune Cell Phenotype, Co-receptor Expression and Innate Immune Responses in Healthy Elderly Subjects: Results From the United Kingdom Arm of the NU-AGE Trial. Front Physiol 2018; 9:997. [PMID: 30093866 PMCID: PMC6070774 DOI: 10.3389/fphys.2018.00997] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 03/01/2018] [Accepted: 07/09/2018] [Indexed: 11/13/2022] Open
Abstract
Amongst the major features of aging are chronic low grade inflammation and a decline in immune function. The Mediterranean diet (MedDiet) is considered to be a valuable tool to improve health status, and although beneficial effects have been reported, to date, immunological outcomes have not been extensively studied. We aimed to test the hypothesis that 1 year of a tailored intervention based on the MedDiet with vitamin D (10 μg/day) would improve innate immune responses in healthy elderly subjects (65-79 years) from the English cohort (272 subjects recruited) of the NU-AGE randomized, controlled study (clinicaltrials.gov, NCT01754012). Of the 272 subjects forming the United Kingdom cohort a subgroup of 122 subjects (61 in the intervention group and 61 in the control group) was used to evaluate ex vivo innate immune response, phenotype of circulating immune cells, and levels of pro- and anti-inflammatory markers. Odds Ratio (OR) was calculated for all the parameters analyzed. After adjustment by gender, MedDiet-females with a BMI < 31 kg/m2 had a significant upregulation of circulating CD40+CD86+ cells (OR 3.44, 95% CI 1.01-11.75, P = 0.0437). Furthermore, in all MedDiet subjects, regardless of gender, we observed a MedDiet-dependent changes, although not statistically significant of immune-critical parameters including T cell degranulation, cytokine production and co-receptor expression. Overall, our study showed that adherence to an individually tailored Mediterranean-like dietary pattern with a daily low dose of vitamin D3 supplements for 1 year modified a large variety of parameters of immune function in healthy, elderly subjects. We interpreted these data as showing that the MedDiet in later life could improve aspects of innate immunity and thus it could aid the design of strategies to counteract age-associated disturbances. Clinical Trial Registration: clinicaltrials.gov, NCT01754012.
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Affiliation(s)
- Monica Maijo
- Gut Health Programme, Institute Strategic Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Kamal Ivory
- Gut Health Programme, Institute Strategic Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Sarah J Clements
- Gut Health Programme, Institute Strategic Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Jack R Dainty
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Amy Jennings
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Rachel Gillings
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | | | - Massimo Gulisano
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Aurelia Santoro
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.,C.I.G. Interdepartmental Centre "L. Galvani", University of Bologna, Bologna, Italy
| | - Claudio Franceschi
- C.I.G. Interdepartmental Centre "L. Galvani", University of Bologna, Bologna, Italy
| | - Simon R Carding
- Gut Health Programme, Institute Strategic Programme, Quadram Institute Bioscience, Norwich, United Kingdom.,Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Claudio Nicoletti
- Gut Health Programme, Institute Strategic Programme, Quadram Institute Bioscience, Norwich, United Kingdom.,Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
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Calder PC, Carding SR, Christopher G, Kuh D, Langley-Evans SC, McNulty H. A holistic approach to healthy ageing: how can people live longer, healthier lives? J Hum Nutr Diet 2018; 31:439-450. [PMID: 29862589 DOI: 10.1111/jhn.12566] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [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: 12/18/2022]
Abstract
BACKGROUND Although lifespan is increasing, there is no evidence to suggest that older people are experiencing better health in their later years than previous generations. Nutrition, at all stages of life, plays an important role in determining health and wellbeing. METHODS A roundtable meeting of UK experts on nutrition and ageing considered key aspects of the diet-ageing relationship and developed a consensus position on the main priorities for research and public health actions that are required to help people live healthier lives as they age. RESULTS The group consensus highlighted the requirement for a life course approach, recognising the multifactorial nature of the impact of ageing. Environmental and lifestyle influences at any life stage are modified by genetic factors and early development. The response to the environment at each stage of life can determine the impact of lifestyle later on. There are no key factors that act in isolation to determine patterns of ageing and it is a combination of environmental and social factors that drives healthy or unhealthy ageing. Too little is known about how contemporary dietary patterns and sedentary lifestyles will impact upon healthy ageing in future generations and this is a priority for future research. CONCLUSIONS There is good evidence to support change to lifestyle (i.e. diet, nutrition and physical) activity in relation to maintaining or improving body composition, cognitive health and emotional intelligence, immune function and vascular health. Lifestyle change at any stage of life may extend healthy lifespan, although the impact of early changes appears to be greatest.
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Affiliation(s)
- P C Calder
- Faculty of Medicine, University of Southampton, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, Southampton, UK
| | - S R Carding
- Quadram Institute Bioscience and Norwich Medical School, University of East Anglia, Norwich, UK
| | - G Christopher
- Faculty of Health and Applied Sciences, University of the West of England, Bristol, UK
| | - D Kuh
- Medical Research Council Unit for Lifelong Health and Ageing, University College London, London, UK
| | - S C Langley-Evans
- School of Biosciences, University of Nottingham, Sutton Bonnington, UK
| | - H McNulty
- Nutrition Innovation Centre for Food and Health, School of Biomedical Sciences, Ulster University, Coleraine, UK
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Hoyles L, Snelling T, Umlai UK, Nicholson JK, Carding SR, Glen RC, McArthur S. Microbiome-host systems interactions: protective effects of propionate upon the blood-brain barrier. Microbiome 2018; 6:55. [PMID: 29562936 PMCID: PMC5863458 DOI: 10.1186/s40168-018-0439-y] [Citation(s) in RCA: 276] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 03/09/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Gut microbiota composition and function are symbiotically linked with host health and altered in metabolic, inflammatory and neurodegenerative disorders. Three recognised mechanisms exist by which the microbiome influences the gut-brain axis: modification of autonomic/sensorimotor connections, immune activation, and neuroendocrine pathway regulation. We hypothesised interactions between circulating gut-derived microbial metabolites, and the blood-brain barrier (BBB) also contribute to the gut-brain axis. Propionate, produced from dietary substrates by colonic bacteria, stimulates intestinal gluconeogenesis and is associated with reduced stress behaviours, but its potential endocrine role has not been addressed. RESULTS After demonstrating expression of the propionate receptor FFAR3 on human brain endothelium, we examined the impact of a physiologically relevant propionate concentration (1 μM) on BBB properties in vitro. Propionate inhibited pathways associated with non-specific microbial infections via a CD14-dependent mechanism, suppressed expression of LRP-1 and protected the BBB from oxidative stress via NRF2 (NFE2L2) signalling. CONCLUSIONS Together, these results suggest gut-derived microbial metabolites interact with the BBB, representing a fourth facet of the gut-brain axis that warrants further attention.
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Affiliation(s)
- Lesley Hoyles
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Imperial College London, London, UK.
| | - Tom Snelling
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Umm-Kulthum Umlai
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Jeremy K Nicholson
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Simon R Carding
- Norwich Medical School, University of East Anglia, Norwich, UK
- The Gut Health and Food Safety Research Programme, The Quadram Institute, Norwich Research Park, Norwich, UK
| | - Robert C Glen
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Imperial College London, London, UK
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Simon McArthur
- Institute of Dentistry, Barts and the London School of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, UK.
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Fletcher K, Ulferts R, Jacquin E, Veith T, Gammoh N, Arasteh JM, Mayer U, Carding SR, Wileman T, Beale R, Florey O. The WD40 domain of ATG16L1 is required for its non-canonical role in lipidation of LC3 at single membranes. EMBO J 2018; 37:e97840. [PMID: 29317426 PMCID: PMC5813257 DOI: 10.15252/embj.201797840] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [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: 07/24/2017] [Revised: 12/06/2017] [Accepted: 12/14/2017] [Indexed: 11/17/2022] Open
Abstract
A hallmark of macroautophagy is the covalent lipidation of LC3 and insertion into the double-membrane phagophore, which is driven by the ATG16L1/ATG5-ATG12 complex. In contrast, non-canonical autophagy is a pathway through which LC3 is lipidated and inserted into single membranes, particularly endolysosomal vacuoles during cell engulfment events such as LC3-associated phagocytosis. Factors controlling the targeting of ATG16L1 to phagophores are dispensable for non-canonical autophagy, for which the mechanism of ATG16L1 recruitment is unknown. Here we show that the WD repeat-containing C-terminal domain (WD40 CTD) of ATG16L1 is essential for LC3 recruitment to endolysosomal membranes during non-canonical autophagy, but dispensable for canonical autophagy. Using this strategy to inhibit non-canonical autophagy specifically, we show a reduction of MHC class II antigen presentation in dendritic cells from mice lacking the WD40 CTD Further, we demonstrate activation of non-canonical autophagy dependent on the WD40 CTD during influenza A virus infection. This suggests dependence on WD40 CTD distinguishes between macroautophagy and non-canonical use of autophagy machinery.
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Affiliation(s)
| | - Rachel Ulferts
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Elise Jacquin
- Signalling Programme, Babraham Institute, Cambridge, UK
| | - Talitha Veith
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Noor Gammoh
- Edinburgh Cancer Research UK Centre University of Edinburgh, Edinburgh, UK
| | | | | | - Simon R Carding
- Quadrum Institute Bioscience, Norwich Research Park, Norwich, UK
| | | | - Rupert Beale
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Oliver Florey
- Signalling Programme, Babraham Institute, Cambridge, UK
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Clements SJ, Maijo M, Ivory K, Nicoletti C, Carding SR. Age-Associated Decline in Dendritic Cell Function and the Impact of Mediterranean Diet Intervention in Elderly Subjects. Front Nutr 2017; 4:65. [PMID: 29312949 PMCID: PMC5742184 DOI: 10.3389/fnut.2017.00065] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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: 07/10/2017] [Accepted: 12/04/2017] [Indexed: 12/21/2022] Open
Abstract
Introduction Aging is accompanied by increased susceptibility to infection and age-associated chronic diseases. It is also associated with reduced vaccine responses, which is often attributed to immunosenescence and the functional decline of the immune system. Immunosenescence is characterized by a chronic, low-grade, inflammatory state termed inflammaging. Habitants of Mediterranean (MED) regions maintain good health into old age; often attributed to MED diets. Hypothesis Adoption of a MED-diet by elderly subjects, in Norfolk (UK), may improve immune responses of these individuals and in particular, dendritic cell (DC) function. Experimental approach A total of 120 elderly subjects (65–79 years old) recruited onto the Nu-AGE study, a multicenter European dietary study specifically addressing the needs of the elderly, across five countries, and were randomized to the control or MED-diet groups, for one year. Blood samples were taken pre- and post-intervention for DC analysis and were compared with each other, and to samples obtained from 45 young (18–40 years old) subjects. MED-diet compliance was assessed using high performance liquid chromatography-with tandem mass spectrometry analysis of urine samples. Immune cell and DC subset numbers and concentrations of secreted proteins were determined by flow cytometric analysis. Results As expected, reduced myeloid DC numbers were observed in blood samples from elderly subjects compared with young. The elevated secretion of the adipokine, resistin, after ex vivo stimulation of peripheral blood mononuclear cells from elderly subjects, was significantly reduced after MED-diet intervention. Conclusion This study provides further evidence of numerical and functional effects of aging on DCs. The MED-diet showed potential to impact on the aging immune cells investigated and could provide an economical approach to address problems associated with our aging population.
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Affiliation(s)
- Sarah J Clements
- Gut Health and Food Safety Research Programme, The Quadram Institute, Norwich Research Park, Norwich, United Kingdom.,Faculty of Medicine and Health Sciences, Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Monica Maijo
- Gut Health and Food Safety Research Programme, The Quadram Institute, Norwich Research Park, Norwich, United Kingdom
| | - Kamal Ivory
- Gut Health and Food Safety Research Programme, The Quadram Institute, Norwich Research Park, Norwich, United Kingdom
| | - Claudio Nicoletti
- Gut Health and Food Safety Research Programme, The Quadram Institute, Norwich Research Park, Norwich, United Kingdom.,Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Simon R Carding
- Gut Health and Food Safety Research Programme, The Quadram Institute, Norwich Research Park, Norwich, United Kingdom.,Faculty of Medicine and Health Sciences, Norwich Medical School, University of East Anglia, Norwich, United Kingdom
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Tomlinson ML, Butelli E, Martin C, Carding SR. Flavonoids from Engineered Tomatoes Inhibit Gut Barrier Pro-inflammatory Cytokines and Chemokines, via SAPK/JNK and p38 MAPK Pathways. Front Nutr 2017; 4:61. [PMID: 29326940 PMCID: PMC5741681 DOI: 10.3389/fnut.2017.00061] [Citation(s) in RCA: 14] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 11/24/2017] [Indexed: 12/29/2022] Open
Abstract
Flavonoids are a diverse group of plant secondary metabolites, known to reduce inflammatory bowel disease symptoms. How they achieve this is largely unknown. Our study focuses on the gut epithelium as it receives high topological doses of dietary constituents, maintains gut homeostasis, and orchestrates gut immunity. Dysregulation leads to chronic gut inflammation, via dendritic cell (DC)-driven immune responses. Tomatoes engineered for enriched sets of flavonoids (anthocyanins or flavonols) provided a unique and complex naturally consumed food matrix to study the effect of diet on chronic inflammation. Primary murine colonic epithelial cell-based inflammation assays consist of chemokine induction, apoptosis and proliferation, and effects on kinase pathways. Primary murine leukocytes and DCs were used to assay effects on transmigration. A murine intestinal cell line was used to assay wound healing. Engineered tomato extracts (enriched in anthocyanins or flavonols) showed strong and specific inhibitory effects on a set of key epithelial pro-inflammatory cytokines and chemokines. Chemotaxis assays showed a resulting reduction in the migration of primary leukocytes and DCs. Activation of epithelial cell SAPK/JNK and p38 MAPK signaling pathways were specifically inhibited. The epithelial wound healing-associated STAT3 pathway was unaffected. Cellular migration, proliferation, and apoptosis assays confirmed that wound healing processes were not affected by flavonoids. We show flavonoids target epithelial pro-inflammatory kinase pathways, inhibiting chemotactic signals resulting in reduced leukocyte and DC chemotaxis. Thus, both anthocyanins and flavonols modulate epithelial cells to become hyporesponsive to bacterial stimulation. Our results identify a viable mechanism to explain the in vivo anti-inflammatory effects of flavonoids.
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Affiliation(s)
- Matthew L. Tomlinson
- Gut Health and Food Safety Research Programme, Quadram Institute, Norwich, United Kingdom
- Martin Laboratory, The John Innes Centre, Norwich, United Kingdom
| | - Eugenio Butelli
- Martin Laboratory, The John Innes Centre, Norwich, United Kingdom
| | - Cathie Martin
- Martin Laboratory, The John Innes Centre, Norwich, United Kingdom
| | - Simon R. Carding
- Gut Health and Food Safety Research Programme, Quadram Institute, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
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