LifeLines-DEEP population multi-omix cohort from the noth of the Netherlands.

The LifeLines-DEEP cohort is a sub-cohort of the LifeLines cohort (167,729 participants) that employs a broad range of investigative procedures to assess the biomedical, socio-demographic, behavioral, physical and psychological factors that contribute to health and disease in the general Dutch population, (Scholtens 2015). A subset of approximately 1,500 participants also took part in LifeLines-DEEP. For these participants, additional biological materials were collected, including analysis of the gut microbiome composition. The phenotyping and processing of LifeLines-DEEP has been described in Tigchelaar (2015).

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

5 Datasets 32 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001001991	Meta-genomic sequencing of 1,200 LifeLines-DEEP participants	Illumina HiSeq 2000	1135
EGAD00001003453	16S sequencing of stool samples of LifeLines-DEEP, domain V4	Illumina MiSeq	1010
EGAD00001006953	Lifelines-DEEP plasma un-targeted metabolomics		-
EGAD00001006959	Second round of follow-up of population-based LifeLines-DEEP cohort		676
EGAD00001009268	levels of 92 circulating proteins measured by Olink platform, CVDIII panel		1

Publications	Citations
Cohort profile: LifeLines DEEP, a prospective, general population cohort study in the northern Netherlands: study design and baseline characteristics. Tigchelaar EF, Zhernakova A, Dekens JA, Hermes G, Baranska A, Mujagic Z, Swertz MA, Muñoz AM, Deelen P, Cénit MC, Franke L, Scholtens S, Stolk RP, Wijmenga C, Feskens EJ. BMJ Open 5: 2015 e006772	136
Detection of stable community structures within gut microbiota co-occurrence networks from different human populations. Jackson MA, Bonder MJ, Kuncheva Z, Zierer J, Fu J, Kurilshikov A, Wijmenga C, Zhernakova A, Bell JT, Spector TD, Steves CJ. PeerJ 6: 2018 e4303	28
Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome. Zhernakova DV, Le TH, Kurilshikov A, Atanasovska B, Bonder MJ, Sanna S, Claringbould A, Võsa U, Deelen P, Franke L, de Boer RA, Kuipers F, Netea MG, Hofker MH, Wijmenga C, Zhernakova A, Fu J, LifeLines cohort study, BIOS consortium. Nat Genet 50: 2018 1524-1532	47
Causal relationships among the gut microbiome, short-chain fatty acids and metabolic diseases. Sanna S, van Zuydam NR, Mahajan A, Kurilshikov A, Vich Vila A, Võsa U, Mujagic Z, Masclee AAM, Jonkers DMAE, Oosting M, Joosten LAB, Netea MG, Franke L, Zhernakova A, Fu J, Wijmenga C, McCarthy MI. Nat Genet 51: 2019 600-605	629
Microbial genes and pathways in inflammatory bowel disease. Schirmer M, Garner A, Vlamakis H, Xavier RJ. Nat Rev Microbiol 17: 2019 497-511	313
Relationship between gut microbiota and circulating metabolites in population-based cohorts. Vojinovic D, Radjabzadeh D, Kurilshikov A, Amin N, Wijmenga C, Franke L, Ikram MA, Uitterlinden AG, Zhernakova A, Fu J, Kraaij R, van Duijn CM. Nat Commun 10: 2019 5813	115
Impact of commonly used drugs on the composition and metabolic function of the gut microbiota. Vich Vila A, Collij V, Sanna S, Sinha T, Imhann F, Bourgonje AR, Mujagic Z, Jonkers DMAE, Masclee AAM, Fu J, Kurilshikov A, Wijmenga C, Zhernakova A, Weersma RK. Nat Commun 11: 2020 362	288
Distribution of Bacterial α1,3-Galactosyltransferase Genes in the Human Gut Microbiome. Montassier E, Al-Ghalith GA, Mathé C, Le Bastard Q, Douillard V, Garnier A, Guimon R, Raimondeau B, Touchefeu Y, Duchalais E, Vince N, Limou S, Gourraud PA, Laplaud DA, Nicot AB, Soulillou JP, Berthelot L. Front Immunol 10: 2019 3000	28
Binning unassembled short reads based on k-mer abundance covariance using sparse coding. Kyrgyzov O, Prost V, Gazut S, Farcy B, Brüls T. Gigascience 9: 2020 giaa028	3
Whole exome sequencing analyses reveal gene-microbiota interactions in the context of IBD. Hu S, Vich Vila A, Gacesa R, Collij V, Stevens C, Fu JM, Wong I, Talkowski ME, Rivas MA, Imhann F, Bolte L, van Dullemen H, Dijkstra G, Visschedijk MC, Festen EA, Xavier RJ, Fu J, Daly MJ, Wijmenga C, Zhernakova A, Kurilshikov A, Weersma RK. Gut 70: 2021 285-296	26
Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity. Chen L, Collij V, Jaeger M, van den Munckhof ICL, Vich Vila A, Kurilshikov A, Gacesa R, Sinha T, Oosting M, Joosten LAB, Rutten JHW, Riksen NP, Xavier RJ, Kuipers F, Wijmenga C, Zhernakova A, Netea MG, Weersma RK, Fu J. Nat Commun 11: 2020 4018	69
An association between chronic widespread pain and the gut microbiome. Freidin MB, Stalteri MA, Wells PM, Lachance G, Baleanu AF, Bowyer RCE, Kurilshikov A, Zhernakova A, Steves CJ, Williams FMK. Rheumatology (Oxford) 60: 2021 3727-3737	34
Large-scale association analyses identify host factors influencing human gut microbiome composition. Kurilshikov A, Medina-Gomez C, Bacigalupe R, Radjabzadeh D, Wang J, Demirkan A, Le Roy CI, Raygoza Garay JA, Finnicum CT, Liu X, Zhernakova DV, Bonder MJ, Hansen TH, Frost F, Rühlemann MC, Turpin W, Moon JY, Kim HN, Lüll K, Barkan E, Shah SA, Fornage M, Szopinska-Tokov J, Wallen ZD, Borisevich D, Agreus L, Andreasson A, Bang C, Bedrani L, Bell JT, Bisgaard H, Boehnke M, Boomsma DI, Burk RD, Claringbould A, Croitoru K, Davies GE, van Duijn CM, Duijts L, Falony G, Fu J, van der Graaf A, Hansen T, Homuth G, Hughes DA, Ijzerman RG, Jackson MA, Jaddoe VWV, Joossens M, Jørgensen T, Keszthelyi D, Knight R, Laakso M, Laudes M, Launer LJ, Lieb W, Lusis AJ, Masclee AAM, Moll HA, Mujagic Z, Qibin Q, Rothschild D, Shin H, Sørensen SJ, Steves CJ, Thorsen J, Timpson NJ, Tito RY, Vieira-Silva S, Völker U, Völzke H, Võsa U, Wade KH, Walter S, Watanabe K, Weiss S, Weiss FU, Weissbrod O, Westra HJ, Willemsen G, Payami H, Jonkers DMAE, Arias Vasquez A, de Geus EJC, Meyer KA, Stokholm J, Segal E, Org E, Wijmenga C, Kim HL, Kaplan RC, Spector TD, Uitterlinden AG, Rivadeneira F, Franke A, Lerch MM, Franke L, Sanna S, D'Amato M, Pedersen O, Paterson AD, Kraaij R, Raes J, Zhernakova A. Nat Genet 53: 2021 156-165	710
The Composition and Metabolic Potential of the Human Small Intestinal Microbiota Within the Context of Inflammatory Bowel Disease. Ruigrok RAAA, Collij V, Sureda P, Klaassen MAY, Bolte LA, Jansen BH, Voskuil MD, Fu J, Wijmenga C, Zhernakova A, Weersma RK, Vich Vila A. J Crohns Colitis 15: 2021 1326-1338	13
Metabolic Phenotypes as Potential Biomarkers for Linking Gut Microbiome With Inflammatory Bowel Diseases. Iablokov SN, Klimenko NS, Efimova DA, Shashkova T, Novichkov PS, Rodionov DA, Tyakht AV. Front Mol Biosci 7: 2020 603740	7
Long-term dietary patterns are associated with pro-inflammatory and anti-inflammatory features of the gut microbiome. Bolte LA, Vich Vila A, Imhann F, Collij V, Gacesa R, Peters V, Wijmenga C, Kurilshikov A, Campmans-Kuijpers MJE, Fu J, Dijkstra G, Zhernakova A, Weersma RK. Gut 70: 2021 1287-1298	205
Binary Metabolic Phenotypes and Phenotype Diversity Metrics for the Functional Characterization of Microbial Communities. Iablokov SN, Novichkov PS, Osterman AL, Rodionov DA. Front Microbiol 12: 2021 653314	5
A zero inflated log-normal model for inference of sparse microbial association networks. Prost V, Gazut S, Brüls T. PLoS Comput Biol 17: 2021 e1009089	5
A combination of fecal calprotectin and human beta-defensin 2 facilitates diagnosis and monitoring of inflammatory bowel disease. Gacesa R, Vich Vila A, Collij V, Mujagic Z, Kurilshikov A, Voskuil MD, Festen EAM, Wijmenga C, Jonkers DMAE, Dijkstra G, Fu J, Zhernakova A, Imhann F, Weersma RK. Gut Microbes 13: 2021 1943288	3
Inulin-grown <i>Faecalibacterium prausnitzii</i> cross-feeds fructose to the human intestinal epithelium. Fagundes RR, Bourgonje AR, Saeed A, Vich Vila A, Plomp N, Blokzijl T, Sadaghian Sadabad M, von Martels JZH, van Leeuwen SS, Weersma RK, Dijkstra G, Harmsen HJM, Faber KN. Gut Microbes 13: 2021 1993582	11
Influence of the microbiome, diet and genetics on inter-individual variation in the human plasma metabolome. Chen L, Zhernakova DV, Kurilshikov A, Andreu-Sánchez S, Wang D, Augustijn HE, Vich Vila A, Lifelines Cohort Study, Weersma RK, Medema MH, Netea MG, Kuipers F, Wijmenga C, Zhernakova A, Fu J. Nat Med 28: 2022 2333-2343	80
Microbial vitamin production mediates dietary effects on diabetic risk. Wang D, Pham VT, Steinert RE, Zhernakova A, Fu J. Gut Microbes 14: 2022 2154550	2
gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota. Pascal Andreu V, Augustijn HE, Chen L, Zhernakova A, Fu J, Fischbach MA, Dodd D, Medema MH. Nat Biotechnol 41: 2023 1416-1423	33
Faecal metabolome and its determinants in inflammatory bowel disease. Vich Vila A, Hu S, Andreu-Sánchez S, Collij V, Jansen BH, Augustijn HE, Bolte LA, Ruigrok RAAA, Abu-Ali G, Giallourakis C, Schneider J, Parkinson J, Al-Garawi A, Zhernakova A, Gacesa R, Fu J, Weersma RK. Gut 72: 2023 1472-1485	31
Assessing the relationship between gut microbiota and irritable bowel syndrome: a two-sample Mendelian randomization analysis. Liu B, Ye D, Yang H, Song J, Sun X, He Z, Mao Y, Hao G. BMC Gastroenterol 23: 2023 150	13
Amino acid auxotrophies in human gut bacteria are linked to higher microbiome diversity and long-term stability. Starke S, Harris DMM, Zimmermann J, Schuchardt S, Oumari M, Frank D, Bang C, Rosenstiel P, Schreiber S, Frey N, Franke A, Aden K, Waschina S. ISME J 17: 2023 2370-2380	4
Microbiome and metabolome features in inflammatory bowel disease via multi-omics integration analyses across cohorts. Ning L, Zhou YL, Sun H, Zhang Y, Shen C, Wang Z, Xuan B, Zhao Y, Ma Y, Yan Y, Tong T, Huang X, Hu M, Zhu X, Ding J, Zhang Y, Cui Z, Fang JY, Chen H, Hong J. Nat Commun 14: 2023 7135	22
Host genetic regulation of human gut microbial structural variation. Zhernakova DV, Wang D, Liu L, Andreu-Sánchez S, Zhang Y, Ruiz-Moreno AJ, Peng H, Plomp N, Del Castillo-Izquierdo Á, Gacesa R, Lopera-Maya EA, Temba GS, Kullaya VI, van Leeuwen SS, Lifelines Cohort Study, Xavier RJ, de Mast Q, Joosten LAB, Riksen NP, Rutten JHW, Netea MG, Sanna S, Wijmenga C, Weersma RK, Zhernakova A, Harmsen HJM, Fu J. Nature 625: 2024 813-821	12
Unraveling interindividual variation of trimethylamine <i>N</i>-oxide and its precursors at the population level. Andreu-Sánchez S, Ahmad S, Kurilshikov A, Beekman M, Ghanbari M, van Faassen M, van den Munckhof ICL, Steur M, Harms A, Hankemeier T, Ikram MA, Kavousi M, Voortman T, Kraaij R, Netea MG, Rutten JHW, Riksen NP, Zhernakova A, Kuipers F, Slagboom PE, van Duijn CM, Fu J, Vojinovic D. Imeta 3: 2024 e183	0
Epigenome-wide association study on the plasma metabolome suggests self-regulation of the glycine and serine pathway through DNA methylation. Wu J, Palasantzas V, Andreu-Sánchez S, Plösch T, Leonard S, Li S, Bonder MJ, Westra HJ, van Meurs J, Ghanbari M, Franke L, Zhernakova A, Fu J, Hoogerland JA, Zhernakova DV. Clin Epigenetics 16: 2024 104	0
Age-dependent sex differences in cardiometabolic risk factors. Zhernakova DV, Sinha T, Andreu-Sánchez S, Prins JR, Kurilshikov A, Balder JW, Sanna S, Lifelines Cohort Study, Franke L, Kuivenhoven JA, Zhernakova A, Fu J. Nat Cardiovasc Res 1: 2022 844-854	9
An expanded database and analytical toolkit for identifying bacterial virulence factors and their associations with chronic diseases. Dong W, Fan X, Guo Y, Wang S, Jia S, Lv N, Yuan T, Pan Y, Xue Y, Chen X, Xiong Q, Yang R, Zhao W, Zhu B. Nat Commun 15: 2024 8084	0