51
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Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Ter Horst R, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LAB, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ. Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity. Cell 2017; 167:1125-1136.e8. [PMID: 27814509 DOI: 10.1016/j.cell.2016.10.020] [Citation(s) in RCA: 610] [Impact Index Per Article: 87.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/09/2016] [Accepted: 10/12/2016] [Indexed: 12/12/2022]
Abstract
Gut microbial dysbioses are linked to aberrant immune responses, which are often accompanied by abnormal production of inflammatory cytokines. As part of the Human Functional Genomics Project (HFGP), we investigate how differences in composition and function of gut microbial communities may contribute to inter-individual variation in cytokine responses to microbial stimulations in healthy humans. We observe microbiome-cytokine interaction patterns that are stimulus specific, cytokine specific, and cytokine and stimulus specific. Validation of two predicted host-microbial interactions reveal that TNFα and IFNγ production are associated with specific microbial metabolic pathways: palmitoleic acid metabolism and tryptophan degradation to tryptophol. Besides providing a resource of predicted microbially derived mediators that influence immune phenotypes in response to common microorganisms, these data can help to define principles for understanding disease susceptibility. The three HFGP studies presented in this issue lay the groundwork for further studies aimed at understanding the interplay between microbial, genetic, and environmental factors in the regulation of the immune response in humans. PAPERCLIP.
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Affiliation(s)
- Melanie Schirmer
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Sanne P Smeekens
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Hera Vlamakis
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Martin Jaeger
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Marije Oosting
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Eric A Franzosa
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Rob Ter Horst
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Trees Jansen
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Liesbeth Jacobs
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Marc Jan Bonder
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 EX Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 EX Groningen, the Netherlands; Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 EX Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Centre Groningen, 9713 EX Groningen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 EX Groningen, the Netherlands
| | - Curtis Huttenhower
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 EX Groningen, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboudumc, 6525 GA Nijmegen, the Netherlands.
| | - Ramnik J Xavier
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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52
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Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Horst RT, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LAB, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ. Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity. Cell 2016; 167:1897. [PMID: 27984736 DOI: 10.1016/j.cell.2016.11.046] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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53
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Bonder MJ, Kurilshikov A, Tigchelaar EF, Mujagic Z, Imhann F, Vila AV, Deelen P, Vatanen T, Schirmer M, Smeekens SP, Zhernakova DV, Jankipersadsing SA, Jaeger M, Oosting M, Cenit MC, Masclee AAM, Swertz MA, Li Y, Kumar V, Joosten L, Harmsen H, Weersma RK, Franke L, Hofker MH, Xavier RJ, Jonkers D, Netea MG, Wijmenga C, Fu J, Zhernakova A. The effect of host genetics on the gut microbiome. Nat Genet 2016; 48:1407-1412. [PMID: 27694959 DOI: 10.1038/ng.3663] [Citation(s) in RCA: 511] [Impact Index Per Article: 63.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 08/10/2016] [Indexed: 02/07/2023]
Abstract
The gut microbiome is affected by multiple factors, including genetics. In this study, we assessed the influence of host genetics on microbial species, pathways and gene ontology categories, on the basis of metagenomic sequencing in 1,514 subjects. In a genome-wide analysis, we identified associations of 9 loci with microbial taxonomies and 33 loci with microbial pathways and gene ontology terms at P < 5 × 10-8. Additionally, in a targeted analysis of regions involved in complex diseases, innate and adaptive immunity, or food preferences, 32 loci were identified at the suggestive level of P < 5 × 10-6. Most of our reported associations are new, including genome-wide significance for the C-type lectin molecules CLEC4F-CD207 at 2p13.3 and CLEC4A-FAM90A1 at 12p13. We also identified association of a functional LCT SNP with the Bifidobacterium genus (P = 3.45 × 10-8) and provide evidence of a gene-diet interaction in the regulation of Bifidobacterium abundance. Our results demonstrate the importance of understanding host-microbe interactions to gain better insight into human health.
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Affiliation(s)
- Marc Jan Bonder
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Alexander Kurilshikov
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands.,Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Ettje F Tigchelaar
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands.,Top Institute Food and Nutrition, Wageningen, the Netherlands
| | - Zlatan Mujagic
- Top Institute Food and Nutrition, Wageningen, the Netherlands.,Division of Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Floris Imhann
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands
| | - Arnau Vich Vila
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands
| | - Patrick Deelen
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - Tommi Vatanen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Computer Science, Aalto University School of Science, Espoo, Finland
| | - Melanie Schirmer
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Sanne P Smeekens
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Center of Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Daria V Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Soesma A Jankipersadsing
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, the Netherlands
| | - Martin Jaeger
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Center of Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marije Oosting
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Center of Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Maria Carmen Cenit
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Ad A M Masclee
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Morris A Swertz
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - Yang Li
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Vinod Kumar
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Leo Joosten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Center of Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Hermie Harmsen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands
| | - Rinse K Weersma
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands
| | - Lude Franke
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Marten H Hofker
- University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, the Netherlands
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.,Gastrointestinal Unit, Massachusetts General Hospital, Boston, Massachusetts, USA.,Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Daisy Jonkers
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Center of Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Jingyuan Fu
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, the Netherlands
| | - Alexandra Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands.,Top Institute Food and Nutrition, Wageningen, the Netherlands
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54
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Morozova V, Kozlova Y, Shedko E, Kurilshikov A, Babkin I, Tupikin A, Yunusova A, Chernonosov A, Baykov I, Кondratov I, Kabilov M, Ryabchikova E, Vlassov V, Tikunova N. Lytic bacteriophage PM16 specific for Proteus mirabilis: a novel member of the genus Phikmvvirus. Arch Virol 2016; 161:2457-72. [PMID: 27350061 DOI: 10.1007/s00705-016-2944-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 06/18/2016] [Indexed: 12/19/2022]
Abstract
Lytic Proteus phage PM16, isolated from human faeces, is a novel virus that is specific for Proteus mirabilis cells. Bacteriophage PM16 is characterized by high stability, a short latency period, large burst size and the occurrence of low phage resistance. Phage PM16 was classified as a member of the genus Phikmvvirus on the basis of genome organization, gene synteny, and protein sequences similarities. Within the genus Phikmvvirus, phage PM16 is grouped with Vibrio phage VP93, Pantoea phage LIMElight, Acinetobacter phage Petty, Enterobacter phage phiKDA1, and KP34-like bacteriophages. An investigation of the phage-cell interaction demonstrated that phage PM16 attached to the cell surface, not to the bacterial flagella. The study of P. mirabilis mutant cells obtained during the phage-resistant bacterial cell assay that were resistant to phage PM16 re-infection revealed a non-swarming phenotype, changes in membrane characteristics, and the absence of flagella. Presumably, the resistance of non-swarming P. mirabilis cells to phage PM16 re-infection is determined by changes in membrane macromolecular composition and is associated with the absence of flagella and a non-swarming phenotype.
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Affiliation(s)
- V Morozova
- Institute of Chemical Biology and Fundamental Medicine, Lavrentieva Ave., 8, Novosibirsk, Russia.
| | - Yu Kozlova
- Institute of Chemical Biology and Fundamental Medicine, Lavrentieva Ave., 8, Novosibirsk, Russia
| | - E Shedko
- Institute of Chemical Biology and Fundamental Medicine, Lavrentieva Ave., 8, Novosibirsk, Russia
| | - A Kurilshikov
- Institute of Chemical Biology and Fundamental Medicine, Lavrentieva Ave., 8, Novosibirsk, Russia
| | - I Babkin
- Institute of Chemical Biology and Fundamental Medicine, Lavrentieva Ave., 8, Novosibirsk, Russia
| | - A Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Lavrentieva Ave., 8, Novosibirsk, Russia
| | - A Yunusova
- Institute of Chemical Biology and Fundamental Medicine, Lavrentieva Ave., 8, Novosibirsk, Russia
| | - A Chernonosov
- Institute of Chemical Biology and Fundamental Medicine, Lavrentieva Ave., 8, Novosibirsk, Russia
| | - I Baykov
- Institute of Chemical Biology and Fundamental Medicine, Lavrentieva Ave., 8, Novosibirsk, Russia
| | - I Кondratov
- Limnological Institute of SB RAS, Ulan-Batorskaya Str., 3, Irkutsk, Russia
| | - M Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Lavrentieva Ave., 8, Novosibirsk, Russia
| | - E Ryabchikova
- Institute of Chemical Biology and Fundamental Medicine, Lavrentieva Ave., 8, Novosibirsk, Russia
| | - V Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Lavrentieva Ave., 8, Novosibirsk, Russia
| | - N Tikunova
- Institute of Chemical Biology and Fundamental Medicine, Lavrentieva Ave., 8, Novosibirsk, Russia
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55
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Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, Kurilshikov A, Bonder MJ, Valles-Colomer M, Vandeputte D, Tito RY, Chaffron S, Rymenans L, Verspecht C, De Sutter L, Lima-Mendez G, D'hoe K, Jonckheere K, Homola D, Garcia R, Tigchelaar EF, Eeckhaudt L, Fu J, Henckaerts L, Zhernakova A, Wijmenga C, Raes J. Population-level analysis of gut microbiome variation. Science 2016; 352:560-4. [PMID: 27126039 DOI: 10.1126/science.aad3503] [Citation(s) in RCA: 1393] [Impact Index Per Article: 174.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 03/11/2016] [Indexed: 12/14/2022]
Abstract
Fecal microbiome variation in the average, healthy population has remained under-investigated. Here, we analyzed two independent, extensively phenotyped cohorts: the Belgian Flemish Gut Flora Project (FGFP; discovery cohort; N = 1106) and the Dutch LifeLines-DEEP study (LLDeep; replication; N = 1135). Integration with global data sets (N combined = 3948) revealed a 14-genera core microbiota, but the 664 identified genera still underexplore total gut diversity. Sixty-nine clinical and questionnaire-based covariates were found associated to microbiota compositional variation with a 92% replication rate. Stool consistency showed the largest effect size, whereas medication explained largest total variance and interacted with other covariate-microbiota associations. Early-life events such as birth mode were not reflected in adult microbiota composition. Finally, we found that proposed disease marker genera associated to host covariates, urging inclusion of the latter in study design.
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Affiliation(s)
- Gwen Falony
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Marie Joossens
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Sara Vieira-Silva
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Jun Wang
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Youssef Darzi
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Karoline Faust
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Alexander Kurilshikov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia. Novosibirsk State University, Novosibirsk, Russia
| | - Marc Jan Bonder
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, Netherlands
| | - Mireia Valles-Colomer
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Doris Vandeputte
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Raul Y Tito
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Samuel Chaffron
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Leen Rymenans
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Chloë Verspecht
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Lise De Sutter
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Gipsi Lima-Mendez
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Kevin D'hoe
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Karl Jonckheere
- VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Daniel Homola
- VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Roberto Garcia
- VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Ettje F Tigchelaar
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, Netherlands. Top Institute Food and Nutrition, Wageningen, Netherlands
| | - Linda Eeckhaudt
- VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Jingyuan Fu
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, Netherlands. University of Groningen, University Medical Center Groningen, Department of Pediatrics, 9700 RB Groningen, Netherlands
| | - Liesbet Henckaerts
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. KU Leuven-University Hospitals Leuven, Department of General Internal Medicine, Leuven, Belgium
| | - Alexandra Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, Netherlands. Top Institute Food and Nutrition, Wageningen, Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, Netherlands
| | - Jeroen Raes
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium.
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56
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Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, Mujagic Z, Vila AV, Falony G, Vieira-Silva S, Wang J, Imhann F, Brandsma E, Jankipersadsing SA, Joossens M, Cenit MC, Deelen P, Swertz MA, Weersma RK, Feskens EJM, Netea MG, Gevers D, Jonkers D, Franke L, Aulchenko YS, Huttenhower C, Raes J, Hofker MH, Xavier RJ, Wijmenga C, Fu J. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science 2016; 352:565-9. [PMID: 27126040 DOI: 10.1126/science.aad3369] [Citation(s) in RCA: 1121] [Impact Index Per Article: 140.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 03/11/2016] [Indexed: 12/11/2022]
Abstract
Deep sequencing of the gut microbiomes of 1135 participants from a Dutch population-based cohort shows relations between the microbiome and 126 exogenous and intrinsic host factors, including 31 intrinsic factors, 12 diseases, 19 drug groups, 4 smoking categories, and 60 dietary factors. These factors collectively explain 18.7% of the variation seen in the interindividual distance of microbial composition. We could associate 110 factors to 125 species and observed that fecal chromogranin A (CgA), a protein secreted by enteroendocrine cells, was exclusively associated with 61 microbial species whose abundance collectively accounted for 53% of microbial composition. Low CgA concentrations were seen in individuals with a more diverse microbiome. These results are an important step toward a better understanding of environment-diet-microbe-host interactions.
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Affiliation(s)
- Alexandra Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, Netherlands. Top Institute Food and Nutrition, Wageningen, Netherlands.
| | - Alexander Kurilshikov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia. Novosibirsk State University, Novosibirsk, Russia
| | - Marc Jan Bonder
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Ettje F Tigchelaar
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, Netherlands. Top Institute Food and Nutrition, Wageningen, Netherlands
| | - Melanie Schirmer
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA. Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Tommi Vatanen
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA. Department of Computer Science, Aalto University School of Science, Espoo, Finland
| | - Zlatan Mujagic
- Top Institute Food and Nutrition, Wageningen, Netherlands. Division of Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center, Maastricht, Netherlands
| | - Arnau Vich Vila
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands
| | - Gwen Falony
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Sara Vieira-Silva
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Jun Wang
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Floris Imhann
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands
| | - Eelke Brandsma
- University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, Netherlands
| | - Soesma A Jankipersadsing
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Marie Joossens
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Maria Carmen Cenit
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, Netherlands. Microbial Ecology, Nutrition and Health Research Group, Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Valencia, Spain. Department of Pediatrics, Dr. Peset University Hospital, Valencia, Spain
| | - Patrick Deelen
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, Netherlands. University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, Netherlands
| | - Morris A Swertz
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, Netherlands. University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, Netherlands
| | | | - Rinse K Weersma
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands
| | - Edith J M Feskens
- Top Institute Food and Nutrition, Wageningen, Netherlands. Division of Human Nutrition, Wageningen University, Wageningen, Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Dirk Gevers
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daisy Jonkers
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center, Maastricht, Netherlands
| | - Lude Franke
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Yurii S Aulchenko
- Novosibirsk State University, Novosibirsk, Russia. Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK. PolyOmica, Groningen, Netherlands. Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Curtis Huttenhower
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA. Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Jeroen Raes
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Marten H Hofker
- University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, Netherlands
| | - Ramnik J Xavier
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA. Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA. Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA. Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, Netherlands.
| | - Jingyuan Fu
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, Netherlands. University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, Netherlands.
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Morozkin E, Rykova E, Bondar A, Skvortsova T, Zaporozhchenko I, Kurilshikov A, Anikeeva O, Krasnova N, Polovnikov E, Ponomaryova A, Laktionov P. P124. European Journal of Cancer Supplements 2015. [DOI: 10.1016/j.ejcsup.2015.08.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Bondar A, Kurilshikov A, Morozkin E, Zaripov M, Kabilov M, Voytsitskiy V, Vlassov V, Laktionov P. P124. EJC Suppl 2015. [DOI: 10.1016/j.ejcsup.2015.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Bondar A, Kurilshikov A, Morozkin E, Zaripov M, Kabilov M, Voytsitskiy V, Vlassov V, Laktionov P. 430 Epigenetic cell-free DNA biomarkers of prostate cancer: The search by massively parallel sequencing. Eur J Cancer 2015. [DOI: 10.1016/s0959-8049(16)30264-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Kurilshikov A, Livanova NN, Fomenko NV, Tupikin AE, Rar VA, Kabilov MR, Livanov SG, Tikunova NV. Comparative Metagenomic Profiling of Symbiotic Bacterial Communities Associated with Ixodes persulcatus, Ixodes pavlovskyi and Dermacentor reticulatus Ticks. PLoS One 2015; 10:e0131413. [PMID: 26154300 PMCID: PMC4496043 DOI: 10.1371/journal.pone.0131413] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/01/2015] [Indexed: 12/29/2022] Open
Abstract
Ixodes persulcatus, Ixodes pavlovskyi, and Dermacentor reticulatus ticks inhabiting Western Siberia are responsible for the transmission of a number of etiological agents that cause human and animal tick-borne diseases. Because these ticks are abundant in the suburbs of large cities, agricultural areas, and popular tourist sites and frequently attack people and livestock, data regarding the microbiomes of these organisms are required. Using metagenomic 16S profiling, we evaluate bacterial communities associated with I. persulcatus, I. pavlovskyi, and D. reticulatus ticks collected from the Novosibirsk region of Russia. A total of 1214 ticks were used for this study. DNA extracted from the ticks was pooled according to tick species and sex. Sequencing of the V3-V5 domains of 16S rRNA genes was performed using the Illumina Miseq platform. The following bacterial genera were prevalent in the examined communities: Acinetobacter (all three tick species), Rickettsia (I. persulcatus and D. reticulatus) and Francisella (D. reticulatus). B. burgdorferi sensu lato and B. miyamotoi sequences were detected in I. persulcatus and I. pavlovskyi but not in D. reticulatus ticks. The pooled samples of all tick species studied contained bacteria from the Anaplasmataceae family, although their occurrence was low. DNA from A. phagocytophilum and Candidatus Neoehrlichia mikurensis was first observed in I. pavlovskyi ticks. Significant inter-species differences in the number of bacterial taxa as well as intra-species diversity related to tick sex were observed. The bacterial communities associated with the I. pavlovskyi ticks displayed a higher biodiversity compared with those of the I. persulcatus and D. reticulatus ticks. Bacterial community structure was also diverse across the studied tick species, as shown by permutational analysis of variance using the Bray-Curtis dissimilarity metric (p = 0.002). Between-sex variation was confirmed by PERMANOVA testing in I. persulcatus (p = 0.042) and I. pavlovskyi (p = 0.042) ticks. Our study indicated that 16S metagenomic profiling could be used for rapid assessment of the occurrence of medically important bacteria in tick populations inhabiting different natural biotopes and therefore the epidemic danger of studied foci.
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Affiliation(s)
- Alexander Kurilshikov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
- * E-mail:
| | - Natalya N. Livanova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
- Institute of Systematics and Ecology of Animals SB RAS, Novosibirsk, Russia
| | - Nataliya V. Fomenko
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Alexey E. Tupikin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Vera A. Rar
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | | | - Nina V. Tikunova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
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Mironova N, Patutina O, Brenner E, Kurilshikov A, Vlassov V, Zenkova M. MicroRNA drop in the bloodstream and microRNA boost in the tumour caused by treatment with ribonuclease A leads to an attenuation of tumour malignancy. PLoS One 2013; 8:e83482. [PMID: 24386211 PMCID: PMC3875445 DOI: 10.1371/journal.pone.0083482] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 11/03/2013] [Indexed: 12/27/2022] Open
Abstract
Novel data showing an important role of microRNAs in mediating tumour progression opened a new field of possible molecular targets for cytotoxic ribonucleases. Recently, antitumour and antimetastatic activities of pancreatic ribonuclease A were demonstrated and here genome-wide profiles of microRNAs in the tumour and blood of mice bearing Lewis lung carcinoma after treatment with RNase A were analysed by high-throughput Sequencing by Oligonucleotide Ligation and Detection (SOLiD™) sequencing technology. Sequencing data showed that RNase A therapy resulted in the boost of 116 microRNAs in tumour tissue and a significant drop of 137 microRNAs in the bloodstream that were confirmed by qPCR. The microRNA boost in the tumour was accompanied by the overexpression of microRNA processing genes: RNASEN (Drosha), xpo5, dicer1, and eif2c2 (Ago2). Ribonuclease activity of RNase A was shown to be crucial for the activation of both microRNA synthesis and expression of the microRNA processing genes. In the tumour tissue, RNase A caused the upregulation of both oncomirs and tumour-suppressor microRNAs, including microRNAs of the let-7 family, known to negatively regulate tumour progression. Our results suggest that the alteration of microRNA signature caused by RNase A treatment leads to the attenuation of tumour malignancy.
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Affiliation(s)
- Nadezhda Mironova
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Olga Patutina
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Evgenyi Brenner
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Alexander Kurilshikov
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Valentin Vlassov
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Marina Zenkova
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russian Federation
- * E-mail:
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