1
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Fernández-Pato A, Sinha T, Gacesa R, Andreu-Sánchez S, Gois MFB, Gelderloos-Arends J, Jansen DBH, Kruk M, Jaeger M, Joosten LAB, Netea MG, Weersma RK, Wijmenga C, Harmsen HJM, Fu J, Zhernakova A, Kurilshikov A. Choice of DNA extraction method affects stool microbiome recovery and subsequent phenotypic association analyses. Sci Rep 2024; 14:3911. [PMID: 38366085 PMCID: PMC10873414 DOI: 10.1038/s41598-024-54353-w] [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: 06/29/2023] [Accepted: 02/12/2024] [Indexed: 02/18/2024] Open
Abstract
The lack of standardization in the methods of DNA extraction from fecal samples represents the major source of experimental variation in the microbiome research field. In this study, we aimed to compare the metagenomic profiles and microbiome-phenotype associations obtained by applying two commercially available DNA extraction kits: the AllPrep DNA/RNA Mini Kit (APK) and the QIAamp Fast DNA Stool Mini Kit (FSK). Using metagenomic sequencing data available from 745 paired fecal samples from two independent population cohorts, Lifelines-DEEP (LLD, n = 292) and the 500 Functional Genomics project (500FG, n = 453), we confirmed significant differences in DNA yield and the recovered microbial communities between protocols, with the APK method resulting in a higher DNA concentration and microbial diversity. Further, we observed a massive difference in bacterial relative abundances at species-level between the APK and the FSK protocols, with > 75% of species differentially abundant between protocols in both cohorts. Specifically, comparison with a standard mock community revealed that the APK method provided higher accuracy in the recovery of microbial relative abundances, with the absence of a bead-beating step in the FSK protocol causing an underrepresentation of gram-positive bacteria. This heterogeneity in the recovered microbial composition led to remarkable differences in the association with anthropometric and lifestyle phenotypes. The results of this study further reinforce that the choice of DNA extraction method impacts the metagenomic profile of human gut microbiota and highlight the importance of harmonizing protocols in microbiome studies.
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Affiliation(s)
- Asier Fernández-Pato
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Trishla Sinha
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Ranko Gacesa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Milla F Brandao Gois
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Jody Gelderloos-Arends
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Dianne B H Jansen
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Marloes Kruk
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Martin Jaeger
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Hermie J M Harmsen
- Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands.
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2
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Gois MFB, Fernández-Pato A, Huss A, Gacesa R, Wijmenga C, Weersma RK, Fu J, Vermeulen RCH, Zhernakova A, Lenters VC, Kurilshikov A. Impact of occupational pesticide exposure on the human gut microbiome. Front Microbiol 2023; 14:1223120. [PMID: 37637104 PMCID: PMC10448898 DOI: 10.3389/fmicb.2023.1223120] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023] Open
Abstract
The rising use of pesticides in modern agriculture has led to a shift in disease burden in which exposure to these chemicals plays an increasingly important role. The human gut microbiome, which is partially responsible for the biotransformation of xenobiotics, is also known to promote biotransformation of environmental pollutants. Understanding the effects of occupational pesticide exposure on the gut microbiome can thus provide valuable insights into the mechanisms underlying the impact of pesticide exposure on health. Here we investigate the impact of occupational pesticide exposure on human gut microbiome composition in 7198 participants from the Dutch Microbiome Project of the Lifelines Study. We used job-exposure matrices in combination with occupational codes to retrieve categorical and cumulative estimates of occupational exposures to general pesticides, herbicides, insecticides and fungicides. Approximately 4% of our cohort was occupationally exposed to at least one class of pesticides, with predominant exposure to multiple pesticide classes. Most participants reported long-term employment, suggesting a cumulative profile of exposure. We demonstrate that contact with insecticides, fungicides and a general "all pesticides" class was consistently associated with changes in the gut microbiome, showing significant associations with decreased alpha diversity and a differing beta diversity. We also report changes in the abundance of 39 different bacterial taxa upon exposure to the different pesticide classes included in this study. Together, the extent of statistically relevant associations between gut microbial changes and pesticide exposure in our findings highlights the impact of these compounds on the human gut microbiome.
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Affiliation(s)
- Milla F. Brandao Gois
- Department of Genetics and Department of Gastroenterology and Hepatology University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Asier Fernández-Pato
- Department of Genetics and Department of Gastroenterology and Hepatology University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Anke Huss
- Department of Population Health Sciences, Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, Netherlands
| | - Ranko Gacesa
- Department of Genetics and Department of Gastroenterology and Hepatology University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Cisca Wijmenga
- Department of Genetics and Department of Gastroenterology and Hepatology University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Rinse K. Weersma
- Department of Genetics and Department of Gastroenterology and Hepatology University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Jingyuan Fu
- Department of Genetics and Department of Gastroenterology and Hepatology University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Roel C. H. Vermeulen
- Department of Population Health Sciences, Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, Netherlands
| | - Alexandra Zhernakova
- Department of Genetics and Department of Gastroenterology and Hepatology University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Virissa C. Lenters
- Department of Population Health Sciences, Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, Netherlands
| | - Alexander Kurilshikov
- Department of Genetics and Department of Gastroenterology and Hepatology University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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3
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Lopera-Maya EA, Kurilshikov A, van der Graaf A, Hu S, Andreu-Sánchez S, Chen L, Vila AV, Gacesa R, Sinha T, Collij V, Klaassen MAY, Bolte LA, Gois MFB, Neerincx PBT, Swertz MA, Harmsen HJM, Wijmenga C, Fu J, Weersma RK, Zhernakova A, Sanna S. Author Correction: Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project. Nat Genet 2022; 54:1448. [PMID: 35879415 DOI: 10.1038/s41588-022-01164-2] [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: 11/09/2022]
Affiliation(s)
- Esteban A Lopera-Maya
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Adriaan van der Graaf
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Shixian Hu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Lianmin Chen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Trishla Sinha
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Valerie Collij
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marjiolein A Y Klaassen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Laura A Bolte
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Milla F Brandao Gois
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Pieter B T Neerincx
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - Morris A Swertz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | | | - Hermie J M Harmsen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
| | - Serena Sanna
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands. .,Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Cagliari, Italy.
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4
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Beulens JWJ, Pinho MGM, Abreu TC, den Braver NR, Lam TM, Huss A, Vlaanderen J, Sonnenschein T, Siddiqui NZ, Yuan Z, Kerckhoffs J, Zhernakova A, Brandao Gois MF, Vermeulen RCH. Environmental risk factors of type 2 diabetes-an exposome approach. Diabetologia 2022; 65:263-274. [PMID: 34792619 DOI: 10.1007/s00125-021-05618-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 10/07/2021] [Indexed: 12/11/2022]
Abstract
Type 2 diabetes is one of the major chronic diseases accounting for a substantial proportion of disease burden in Western countries. The majority of the burden of type 2 diabetes is attributed to environmental risks and modifiable risk factors such as lifestyle. The environment we live in, and changes to it, can thus contribute substantially to the prevention of type 2 diabetes at a population level. The 'exposome' represents the (measurable) totality of environmental, i.e. nongenetic, drivers of health and disease. The external exposome comprises aspects of the built environment, the social environment, the physico-chemical environment and the lifestyle/food environment. The internal exposome comprises measurements at the epigenetic, transcript, proteome, microbiome or metabolome level to study either the exposures directly, the imprints these exposures leave in the biological system, the potential of the body to combat environmental insults and/or the biology itself. In this review, we describe the evidence for environmental risk factors of type 2 diabetes, focusing on both the general external exposome and imprints of this on the internal exposome. Studies provided established associations of air pollution, residential noise and area-level socioeconomic deprivation with an increased risk of type 2 diabetes, while neighbourhood walkability and green space are consistently associated with a reduced risk of type 2 diabetes. There is little or inconsistent evidence on the contribution of the food environment, other aspects of the social environment and outdoor temperature. These environmental factors are thought to affect type 2 diabetes risk mainly through mechanisms incorporating lifestyle factors such as physical activity or diet, the microbiome, inflammation or chronic stress. To further assess causality of these associations, future studies should focus on investigating the longitudinal effects of our environment (and changes to it) in relation to type 2 diabetes risk and whether these associations are explained by these proposed mechanisms.
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Affiliation(s)
- Joline W J Beulens
- Department of Epidemiology & Data Science, Amsterdam Public Health, Amsterdam Cardiovascular Sciences, Amsterdam UMC, location VUmc, Amsterdam, the Netherlands.
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Maria G M Pinho
- Department of Epidemiology & Data Science, Amsterdam Public Health, Amsterdam Cardiovascular Sciences, Amsterdam UMC, location VUmc, Amsterdam, the Netherlands
| | - Taymara C Abreu
- Department of Epidemiology & Data Science, Amsterdam Public Health, Amsterdam Cardiovascular Sciences, Amsterdam UMC, location VUmc, Amsterdam, the Netherlands
| | - Nicole R den Braver
- Department of Epidemiology & Data Science, Amsterdam Public Health, Amsterdam Cardiovascular Sciences, Amsterdam UMC, location VUmc, Amsterdam, the Netherlands
| | - Thao M Lam
- Department of Epidemiology & Data Science, Amsterdam Public Health, Amsterdam Cardiovascular Sciences, Amsterdam UMC, location VUmc, Amsterdam, the Netherlands
| | - Anke Huss
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | - Jelle Vlaanderen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | - Tabea Sonnenschein
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
- Department of Human Geography and Spatial Planning, Utrecht University, Utrecht, the Netherlands
| | - Noreen Z Siddiqui
- Department of Epidemiology & Data Science, Amsterdam Public Health, Amsterdam Cardiovascular Sciences, Amsterdam UMC, location VUmc, Amsterdam, the Netherlands
| | - Zhendong Yuan
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | - Jules Kerckhoffs
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, Groningen, the Netherlands
| | - Milla F Brandao Gois
- Department of Genetics, University Medical Center Groningen, Groningen, the Netherlands
| | - Roel C H Vermeulen
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
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5
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Lopera-Maya EA, Kurilshikov A, van der Graaf A, Hu S, Andreu-Sánchez S, Chen L, Vila AV, Gacesa R, Sinha T, Collij V, Klaassen MAY, Bolte LA, Gois MFB, Neerincx PBT, Swertz MA, Harmsen HJM, Wijmenga C, Fu J, Weersma RK, Zhernakova A, Sanna S. Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project. Nat Genet 2022; 54:143-151. [PMID: 35115690 DOI: 10.1038/s41588-021-00992-y] [Citation(s) in RCA: 101] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 11/19/2021] [Indexed: 02/07/2023]
Abstract
Host genetics are known to influence the gut microbiome, yet their role remains poorly understood. To robustly characterize these effects, we performed a genome-wide association study of 207 taxa and 205 pathways representing microbial composition and function in 7,738 participants of the Dutch Microbiome Project. Two robust, study-wide significant (P < 1.89 × 10-10) signals near the LCT and ABO genes were found to be associated with multiple microbial taxa and pathways and were replicated in two independent cohorts. The LCT locus associations seemed modulated by lactose intake, whereas those at ABO could be explained by participant secretor status determined by their FUT2 genotype. Twenty-two other loci showed suggestive evidence (P < 5 × 10-8) of association with microbial taxa and pathways. At a more lenient threshold, the number of loci we identified strongly correlated with trait heritability, suggesting that much larger sample sizes are needed to elucidate the remaining effects of host genetics on the gut microbiome.
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Affiliation(s)
- Esteban A Lopera-Maya
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Adriaan van der Graaf
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Shixian Hu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Lianmin Chen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Trishla Sinha
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Valerie Collij
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marjiolein A Y Klaassen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Laura A Bolte
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Milla F Brandao Gois
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Pieter B T Neerincx
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - Morris A Swertz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - Hermie J M Harmsen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
| | - Serena Sanna
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Cagliari, Italy.
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