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Arega AM, Dhal AK, Pattanaik KP, Nayak S, Mahapatra RK. An Immunoinformatics-Based Study of Mycobacterium tuberculosis Region of Difference-2 Uncharacterized Protein (Rv1987) as a Potential Subunit Vaccine Candidate for Preliminary Ex Vivo Analysis. Appl Biochem Biotechnol 2024; 196:2367-2395. [PMID: 37498378 DOI: 10.1007/s12010-023-04658-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2023] [Indexed: 07/28/2023]
Abstract
Mycobacterium tuberculosis (Mtb) is the pathogen that causes tuberculosis and develops resistance to many of the existing drugs. The sole licensed TB vaccine, BCG, is unable to provide a comprehensive defense. So, it is crucial to maintain the immunological response to eliminate tuberculosis. Our previous in silico study reported five uncharacterized proteins as potential vaccine antigens. In this article, we considered the uncharacterized Mtb H37Rv regions of difference (RD-2) Rv1987 protein as a promising vaccine candidate. The vaccine quality of the protein was analyzed using reverse vaccinology and immunoinformatics-based quality-checking parameters followed by an ex vivo preliminary investigation. In silico analysis of Rv1987 protein predicted it as surface localized, secretory, single helix, antigenic, non-allergenic, and non-homologous to the host protein. Immunoinformatics analysis of Rv1987 by CD4 + and CD8 + T-cells via MHC-I and MHC-II binding affinity and presence of B-cell epitope predicted its immunogenicity. The docked complex analysis of the 3D model structure of the protein with immune cell receptor TLR-4 revealed the protein's capability for potential interaction. Furthermore, the target protein-encoded gene Rv1987 was cloned, over-expressed, purified, and analyzed by mass spectrometry (MS) to report the target peptides. The qRT-PCR gene expression analysis shows that it is capable of activating macrophages and significantly increasing the production of a number of key cytokines (TNF-α, IL-1β, and IL-10). Our in-silico analysis and ex vivo preliminary investigations revealed the immunogenic potential of the target protein. These findings suggest that the Rv1987 be undertaken as a potent subunit vaccine antigen and that further animal model immuno-modulation studies would boost the novel TB vaccine discovery and/or BCG vaccine supplement pipeline.
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Affiliation(s)
- Aregitu Mekuriaw Arega
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, Odisha, India
- National Veterinary Institute, Debre Zeit, Ethiopia
| | - Ajit Kumar Dhal
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, Odisha, India
| | | | - Sasmita Nayak
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, Odisha, India
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Jang SH, Cha JW, Han NS, Jeong KJ. Development of bicistronic expression system for the enhanced and reliable production of recombinant proteins in Leuconostoc citreum. Sci Rep 2018; 8:8852. [PMID: 29891982 PMCID: PMC5995908 DOI: 10.1038/s41598-018-27091-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 05/22/2018] [Indexed: 01/13/2023] Open
Abstract
The lactic acid bacteria (LAB) Leuconostoc citreum are non-sporulating hetero-fermentative bacteria that play an important role in the fermented food industry. In this study, for the enhanced and reliable production of recombinant proteins in L. citreum, we developed a bicistronic design (BCD) expression system which includes a short leader peptide (1st cistron) followed by target genes (2nd cistron) under the control of a single promoter. Using superfolder green fluorescent protein (sfGFP) as a reporter, the functionality of BCD in L. citreum was verified. Further, to improve the expression in BCD, we tried to engineer a Shine-Dalgarno sequence (SD2) for the 2nd cistron and a promoter by FACS screening of random libraries, and both strong SD2 (eSD2) and promoter (P710V4) were successfully isolated. The usefulness of the engineered BCD with P710V4 and eSD2 was further validated using three model proteins—glutathione-s-transferase, human growth hormone, and α-amylase. All examined proteins were successfully produced with levels highly increased compared with those in the original BCD as well as the monocistronic design (MCD) expression system.
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Affiliation(s)
- Seung Hoon Jang
- Department of Chemical and Biomolecular Engineering (BK21 Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Ji Won Cha
- Department of Chemical and Biomolecular Engineering (BK21 Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Nam Soo Han
- Brain Korea 21 Center for Bio-Resource Development, Division of Animal, Horticultural and Food Sciences, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Ki Jun Jeong
- Department of Chemical and Biomolecular Engineering (BK21 Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea. .,KAIST Institute for the BioCentury, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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LeCureux JS, Dean GA. Lactobacillus Mucosal Vaccine Vectors: Immune Responses against Bacterial and Viral Antigens. mSphere 2018; 3:e00061-18. [PMID: 29769376 PMCID: PMC5956152 DOI: 10.1128/msphere.00061-18] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Lactic acid bacteria (LAB) have been utilized since the 1990s for therapeutic heterologous gene expression. The ability of LAB to elicit an immune response against expressed foreign antigens has led to their exploration as potential mucosal vaccine candidates. LAB vaccine vectors offer many attractive advantages: simple, noninvasive administration (usually oral or intranasal), the acceptance and stability of genetic modifications, relatively low cost, and the highest level of safety possible. Experimentation using LAB of the genus Lactobacillus has become popular in recent years due to their ability to elicit strong systemic and mucosal immune responses. This article reviews Lactobacillus vaccine constructs, including Lactobacillus species, antigen expression, model organisms, and in vivo immune responses, with a primary focus on viral and bacterial antigens.
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Affiliation(s)
- Jonathan S LeCureux
- Department of Natural and Applied Sciences, Evangel University, Springfield, Missouri, USA
| | - Gregg A Dean
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
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Rathnaiah G, Zinniel DK, Bannantine JP, Stabel JR, Gröhn YT, Collins MT, Barletta RG. Pathogenesis, Molecular Genetics, and Genomics of Mycobacterium avium subsp. paratuberculosis, the Etiologic Agent of Johne's Disease. Front Vet Sci 2017; 4:187. [PMID: 29164142 PMCID: PMC5681481 DOI: 10.3389/fvets.2017.00187] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 10/20/2017] [Indexed: 12/12/2022] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the etiologic agent of Johne's disease in ruminants causing chronic diarrhea, malnutrition, and muscular wasting. Neonates and young animals are infected primarily by the fecal-oral route. MAP attaches to, translocates via the intestinal mucosa, and is phagocytosed by macrophages. The ensuing host cellular immune response leads to granulomatous enteritis characterized by a thick and corrugated intestinal wall. We review various tissue culture systems, ileal loops, and mice, goats, and cattle used to study MAP pathogenesis. MAP can be detected in clinical samples by microscopy, culturing, PCR, and an enzyme-linked immunosorbent assay. There are commercial vaccines that reduce clinical disease and shedding, unfortunately, their efficacies are limited and may not engender long-term protective immunity. Moreover, the potential linkage with Crohn's disease and other human diseases makes MAP a concern as a zoonotic pathogen. Potential therapies with anti-mycobacterial agents are also discussed. The completion of the MAP K-10 genome sequence has greatly improved our understanding of MAP pathogenesis. The analysis of this sequence has identified a wide range of gene functions involved in virulence, lipid metabolism, transcriptional regulation, and main metabolic pathways. We also review the transposons utilized to generate random transposon mutant libraries and the recent advances in the post-genomic era. This includes the generation and characterization of allelic exchange mutants, transcriptomic analysis, transposon mutant banks analysis, new efforts to generate comprehensive mutant libraries, and the application of transposon site hybridization mutagenesis and transposon sequencing for global analysis of the MAP genome. Further analysis of candidate vaccine strains development is also provided with critical discussions on their benefits and shortcomings, and strategies to develop a highly efficacious live-attenuated vaccine capable of differentiating infected from vaccinated animals.
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Affiliation(s)
- Govardhan Rathnaiah
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, NE, United States
| | - Denise K. Zinniel
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, NE, United States
| | - John P. Bannantine
- Infectious Bacterial Diseases, National Animal Disease Center, USDA-ARS, Ames, IA, United States
| | - Judith R. Stabel
- Infectious Bacterial Diseases, National Animal Disease Center, USDA-ARS, Ames, IA, United States
| | - Yrjö T. Gröhn
- Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Michael T. Collins
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Raúl G. Barletta
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, NE, United States
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Taghinezhad-S S, Razavilar V, Keyvani H, Razavi MR, Nejadsattari T. Codon optimization of Iranian human papillomavirus Type 16 E6 oncogene for Lactococcus lactis subsp. cremoris MG1363. Future Virol 2017. [DOI: 10.2217/fvl-2017-0032] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: The present study aimed to investigate the effect of codon optimization on E6 recombinant protein production in Lactococcus lactis. Method: Here we define the construction of shuttle vector harboring wild-type and codon-optimized HPV16 E6 oncogene, with maximum number of infrequent codons exchanged with codons that are frequently used in Lactococcus lactis subsp. cremoris MG1363. Results: Hence, the codons encoding 159 amino acids were modified, in which a total of 91 codons were changed, resulting in approximately threefold increase in protein expression of recombinant E6 (rE6). Conclusion: Our data revealed that codon usage optimization according to L. lactis desired codon usage can dramatically increase the expression of HPV16 E6, suggesting that this strategy is a valuable approach for immunization through DNA vaccine.
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Affiliation(s)
- Sedigheh Taghinezhad-S
- Department of Microbiology, Faculty of Basic Sciences, Science & Research Branch, Islamic Azad University, Tehran, Iran
| | - Vadood Razavilar
- Department of Food Hygiene, Faculty of Veterinary Sciences, Science & Research Branch, Islamic Azad University, Tehran, Iran
| | - Hossein Keyvani
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | | | - Taher Nejadsattari
- Department of Biology, Faculty of Basic Sciences, Science & Research Branch, Islamic Azad University, Tehran, Iran
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Sola-Oladokun B, Culligan EP, Sleator RD. Engineered Probiotics: Applications and Biological Containment. Annu Rev Food Sci Technol 2017; 8:353-370. [PMID: 28125354 DOI: 10.1146/annurev-food-030216-030256] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bioengineered probiotics represent the next generation of whole cell-mediated biotherapeutics. Advances in synthetic biology, genome engineering, and DNA sequencing and synthesis have enabled scientists to design and develop probiotics with increased stress tolerance and the ability to target specific pathogens and their associated toxins, as well as to mediate targeted delivery of vaccines, drugs, and immunomodulators directly to host cells. Herein, we review the most significant advances in the development of this field. We discuss the critical issue of biological containment and consider the role of synthetic biology in the design and construction of the probiotics of the future.
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Affiliation(s)
- Babasola Sola-Oladokun
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland; , ,
| | - Eamonn P Culligan
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland; , ,
| | - Roy D Sleator
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland; , , .,APC Microbiome Institute, University College Cork, Cork, Ireland
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Abstract
The review centers on the human gastrointestinal tract; focusing first on the bacterial stress responses needed to overcome the physiochemical defenses of the host, specifically how these stress survival strategies can be used as targets for alternative infection control strategies. The concluding section focuses on recent developments in molecular diagnostics; centring on the shifting paradigm from culture to molecular based diagnostics.
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Affiliation(s)
- Roy D Sleator
- a Department of Biological Sciences ; Cork Institute of Technology ; Bishopstown , Cork , Ireland
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Sleator RD. Designer probiotics: Development and applications in gastrointestinal health. World J Gastrointest Pathophysiol 2015; 6:73-78. [PMID: 26301121 PMCID: PMC4540709 DOI: 10.4291/wjgp.v6.i3.73] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 04/23/2015] [Accepted: 07/14/2015] [Indexed: 02/06/2023] Open
Abstract
Given the increasing commercial and clinical relevance of probiotics, improving their stress tolerance profile and ability to overcome the physiochemical defences of the host is an important biological goal. Herein, I review the current state of the art in the design of engineered probiotic cultures, with a specific focus on their utility as therapeutics for the developing world; from the treatment of chronic and acute enteric infections, and their associated diarrhoeal complexes, to targeting HIV and application as novel mucosal vaccine delivery vehicles.
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Sleator RD. The genetic code. Rewritten, revised, repurposed. ARTIFICIAL DNA, PNA & XNA 2014; 5:e29408. [PMID: 25483933 DOI: 10.4161/adna.29408] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Despite remaining apparently frozen through the millennia, the genetic code is far more flexible than previously believed and can be extended and repurposed with relative ease.
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Affiliation(s)
- Roy D Sleator
- a Department of Biological Sciences; Cork Institute of Technology; Cork, Ireland
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Hoang PM, Cho S, Kim KE, Byun SJ, Lee TK, Lee S. Development of Lactobacillus paracasei harboring nucleic acid-hydrolyzing 3D8 scFv as a preventive probiotic against murine norovirus infection. Appl Microbiol Biotechnol 2014; 99:2793-803. [PMID: 25487889 DOI: 10.1007/s00253-014-6257-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 11/18/2014] [Accepted: 11/20/2014] [Indexed: 01/15/2023]
Abstract
The protein 3D8 single-chain variable fragment (3D8 scFv) has potential anti-viral activity due to its ability to penetrate into cells and hydrolyze nucleic acids. Probiotic Lactobacillus paracasei engineered to secrete 3D8 scFv for oral administration was used to test the anti-viral effects of 3D8 scFv against gastrointestinal virus infections. We found that injection of 3D8 scFv into the intestinal lumen resulted in the penetration of 3D8 scFv into the intestinal villi and lamina propria. 3D8 scFv secreted from engineered L. paracasei retained its cell-penetrating and nucleic acid-hydrolyzing activities, which were previously shown with 3D8 scFv expressed in Escherichia coli. Pretreatment of RAW264.7 cells with 3D8 scFv purified from L. paracasei prevented apoptosis induction by murine norovirus infection and decreased messenger RNA (mRNA) expression of the viral capsid protein VP1. In a mouse model, oral administration of the engineered L. paracasei prior to murine norovirus infection reduced the expression level of mRNA encoding viral polymerase. Taken together, these results suggest that L. paracasei secreting 3D8 scFv provides a basis for the development of ingestible anti-viral probiotics active against gastrointestinal viral infection.
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Affiliation(s)
- Phuong Mai Hoang
- Department of Genetic Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, 440-746, Korea
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Johnston CD, Bannantine JP, Govender R, Endersen L, Pletzer D, Weingart H, Coffey A, O'Mahony J, Sleator RD. Enhanced expression of codon optimized Mycobacterium avium subsp. paratuberculosis antigens in Lactobacillus salivarius. Front Cell Infect Microbiol 2014; 4:120. [PMID: 25237653 PMCID: PMC4154528 DOI: 10.3389/fcimb.2014.00120] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 08/15/2014] [Indexed: 01/03/2023] Open
Abstract
It is well documented that open reading frames containing high GC content show poor expression in A+T rich hosts. Specifically, G+C-rich codon usage is a limiting factor in heterologous expression of Mycobacterium avium subsp. paratuberculosis (MAP) proteins using Lactobacillus salivarius. However, re-engineering opening reading frames through synonymous substitutions can offset codon bias and greatly enhance MAP protein production in this host. In this report, we demonstrate that codon-usage manipulation of MAP2121c can enhance the heterologous expression of the major membrane protein (MMP), analogous to the form in which it is produced natively by MAP bacilli. When heterologously over-expressed, antigenic determinants were preserved in synthetic MMP proteins as shown by monoclonal antibody mediated ELISA. Moreover, MMP is a membrane protein in MAP, which is also targeted to the cellular surface of recombinant L. salivarius at levels comparable to MAP. Additionally, we previously engineered MAP3733c (encoding MptD) and show herein that MptD displays the tendency to associate with the cytoplasmic membrane boundary under confocal microscopy and the intracellularly accumulated protein selectively adheres to the MptD-specific bacteriophage fMptD. This work demonstrates there is potential for L. salivarius as a viable antigen delivery vehicle for MAP, which may provide an effective mucosal vaccine against Johne's disease.
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Affiliation(s)
| | - John P Bannantine
- United States Department of Agriculture - Agricultural Research Service, National Animal Disease Center Ames, IA, USA
| | - Rodney Govender
- Biological Sciences Department, Cork Institute of Technology Cork, Ireland
| | - Lorraine Endersen
- Biological Sciences Department, Cork Institute of Technology Cork, Ireland
| | - Daniel Pletzer
- School of Engineering and Science, Jacobs University Bremen Bremen, Germany
| | - Helge Weingart
- School of Engineering and Science, Jacobs University Bremen Bremen, Germany
| | - Aidan Coffey
- Biological Sciences Department, Cork Institute of Technology Cork, Ireland
| | - Jim O'Mahony
- Biological Sciences Department, Cork Institute of Technology Cork, Ireland
| | - Roy D Sleator
- Biological Sciences Department, Cork Institute of Technology Cork, Ireland
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Culligan EP, Sleator RD, Marchesi JR, Hill C. Metagenomics and novel gene discovery: promise and potential for novel therapeutics. Virulence 2014; 5:399-412. [PMID: 24317337 PMCID: PMC3979868 DOI: 10.4161/viru.27208] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 10/21/2013] [Accepted: 11/14/2013] [Indexed: 02/06/2023] Open
Abstract
Metagenomics provides a means of assessing the total genetic pool of all the microbes in a particular environment, in a culture-independent manner. It has revealed unprecedented diversity in microbial community composition, which is further reflected in the encoded functional diversity of the genomes, a large proportion of which consists of novel genes. Herein, we review both sequence-based and functional metagenomic methods to uncover novel genes and outline some of the associated problems of each type of approach, as well as potential solutions. Furthermore, we discuss the potential for metagenomic biotherapeutic discovery, with a particular focus on the human gut microbiome and finally, we outline how the discovery of novel genes may be used to create bioengineered probiotics.
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Affiliation(s)
- Eamonn P Culligan
- Alimentary Pharmabiotic Centre; University College Cork; Cork, Ireland
- School of Microbiology; University College Cork; Cork, Ireland
| | - Roy D Sleator
- Alimentary Pharmabiotic Centre; University College Cork; Cork, Ireland
- Department of Biological Sciences; Cork Institute of Technology; Bishopstown, Cork, Ireland
| | - Julian R Marchesi
- Alimentary Pharmabiotic Centre; University College Cork; Cork, Ireland
- Cardiff School of Biosciences; Cardiff University; Cardiff, UK
- Department of Hepatology and Gastroenterology; Imperial College London; London, UK
| | - Colin Hill
- Alimentary Pharmabiotic Centre; University College Cork; Cork, Ireland
- School of Microbiology; University College Cork; Cork, Ireland
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