Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

Alexandra Zhernakova; Alexander Kurilshikov; Marc Jan Bonder; Ettje F. Tigchelaar; Melanie Schirmer; Tommi Vatanen; Zlatan Mujagic; Arnau Vich Vila; Gwen Falony; Sara Vieira-Silva; Jun Wang; Floris Imhann; Eelke Brandsma; Soesma A. Jankipersadsing; Marie Joossens; Maria Carmen Cenit; Patrick Deelen; Morris A. Swertz; Rinse K. Weersma; Edith J. M. Feskens; Mihai G. Netea; Dirk Gevers; Daisy Jonkers; Lude Franke; Yurii S. Aulchenko; Curtis Huttenhower; Jeroen Raes; Marten H. Hofker; Ramnik J. Xavier; Cisca Wijmenga; Jingyuan Fu

doi:10.1126/science.aad3369

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

Alexandra Zhernakova^*, Alexander Kurilshikov, Marc Jan Bonder, Ettje F. Tigchelaar, Melanie Schirmer, Tommi Vatanen, Zlatan Mujagic, Arnau Vich Vila, Gwen Falony, Sara Vieira-Silva, Jun Wang, Floris Imhann, Eelke Brandsma, Soesma A. Jankipersadsing, Marie Joossens, Maria Carmen Cenit, Patrick Deelen, Morris A. Swertz, Rinse K. Weersma, Edith J. M. FeskensMihai G. Netea, Dirk Gevers, Daisy Jonkers, Lude Franke, Yurii S. Aulchenko, Curtis Huttenhower, Jeroen Raes, Marten H. Hofker, Ramnik J. Xavier, Cisca Wijmenga^*, Jingyuan Fu^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

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.

Original language	English
Pages (from-to)	565-569
Journal	Science
Volume	352
Issue number	6285
DOIs	https://doi.org/10.1126/science.aad3369
Publication status	Published - 29 Apr 2016

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10.1126/science.aad3369

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Zhernakova, A., Kurilshikov, A., Bonder, M. J., Tigchelaar, E. F., Schirmer, M., Vatanen, T., Mujagic, Z., Vila, A. V., Falony, G., Vieira-Silva, S., Wang, J., Imhann, F., Brandsma, E., Jankipersadsing, S. A., Joossens, M., Cenit, M. C., Deelen, P., Swertz, M. A., Weersma, R. K., ... Fu, J. (2016). Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science, 352(6285), 565-569. https://doi.org/10.1126/science.aad3369

@article{0562bd66788548d8a5621ef51c0812b1,

title = "Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity",

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.",

author = "Alexandra Zhernakova and Alexander Kurilshikov and Bonder, {Marc Jan} and Tigchelaar, {Ettje F.} and Melanie Schirmer and Tommi Vatanen and Zlatan Mujagic and Vila, {Arnau Vich} and Gwen Falony and Sara Vieira-Silva and Jun Wang and Floris Imhann and Eelke Brandsma and Jankipersadsing, {Soesma A.} and Marie Joossens and Cenit, {Maria Carmen} and Patrick Deelen and Swertz, {Morris A.} and Weersma, {Rinse K.} and Feskens, {Edith J. M.} and Netea, {Mihai G.} and Dirk Gevers and Daisy Jonkers and Lude Franke and Aulchenko, {Yurii S.} and Curtis Huttenhower and Jeroen Raes and Hofker, {Marten H.} and Xavier, {Ramnik J.} and Cisca Wijmenga and Jingyuan Fu",

year = "2016",

month = apr,

day = "29",

doi = "10.1126/science.aad3369",

language = "English",

volume = "352",

pages = "565--569",

journal = "Science",

issn = "0036-8075",

publisher = "American Association for the Advancement of Science",

number = "6285",

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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 2016, 'Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity', Science, vol. 352, no. 6285, pp. 565-569. https://doi.org/10.1126/science.aad3369

TY - JOUR

T1 - Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

AU - Zhernakova, Alexandra

AU - Kurilshikov, Alexander

AU - Bonder, Marc Jan

AU - Tigchelaar, Ettje F.

AU - Schirmer, Melanie

AU - Vatanen, Tommi

AU - Mujagic, Zlatan

AU - Vila, Arnau Vich

AU - Falony, Gwen

AU - Vieira-Silva, Sara

AU - Wang, Jun

AU - Imhann, Floris

AU - Brandsma, Eelke

AU - Jankipersadsing, Soesma A.

AU - Joossens, Marie

AU - Cenit, Maria Carmen

AU - Deelen, Patrick

AU - Swertz, Morris A.

AU - Weersma, Rinse K.

AU - Feskens, Edith J. M.

AU - Netea, Mihai G.

AU - Gevers, Dirk

AU - Jonkers, Daisy

AU - Franke, Lude

AU - Aulchenko, Yurii S.

AU - Huttenhower, Curtis

AU - Raes, Jeroen

AU - Hofker, Marten H.

AU - Xavier, Ramnik J.

AU - Wijmenga, Cisca

AU - Fu, Jingyuan

PY - 2016/4/29

Y1 - 2016/4/29

N2 - 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.

AB - 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.

U2 - 10.1126/science.aad3369

DO - 10.1126/science.aad3369

M3 - Article

SN - 0036-8075

VL - 352

SP - 565

EP - 569

JO - Science

JF - Science

IS - 6285

ER -