Publication

Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity

Chen, L., Collij, V., Jaeger, M., van den Munckhof, I. C. L., Vich Vila, A., Kurilshikov, A., Gacesa, R., Sinha, T., Oosting, M., Joosten, L. A. B., Rutten, J. H. W., Riksen, N. P., Xavier, R. J., Kuipers, F., Wijmenga, C., Zhernakova, A., Netea, M. G., Weersma, R. K. & Fu, J., 11-Aug-2020, In : Nature Communications. 11, 1, p. 4018 12 p., 4018.

Research output: Contribution to journalArticleAcademicpeer-review

APA

Chen, L., Collij, V., Jaeger, M., van den Munckhof, I. C. L., Vich Vila, A., Kurilshikov, A., Gacesa, R., Sinha, T., Oosting, M., Joosten, L. A. B., Rutten, J. H. W., Riksen, N. P., Xavier, R. J., Kuipers, F., Wijmenga, C., Zhernakova, A., Netea, M. G., Weersma, R. K., & Fu, J. (2020). Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity. Nature Communications, 11(1), 4018. [4018]. https://doi.org/10.1038/s41467-020-17840-y

Author

Chen, Lianmin ; Collij, Valerie ; Jaeger, Martin ; van den Munckhof, Inge C. L. ; Vich Vila, Arnau ; Kurilshikov, Alexander ; Gacesa, Ranko ; Sinha, Trishla ; Oosting, Marije ; Joosten, Leo A. B. ; Rutten, Joost H. W. ; Riksen, Niels P. ; Xavier, Ramnik J. ; Kuipers, Folkert ; Wijmenga, Cisca ; Zhernakova, Alexandra ; Netea, Mihai G. ; Weersma, Rinse K. ; Fu, Jingyuan. / Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity. In: Nature Communications. 2020 ; Vol. 11, No. 1. pp. 4018.

Harvard

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 2020, 'Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity', Nature Communications, vol. 11, no. 1, 4018, pp. 4018. https://doi.org/10.1038/s41467-020-17840-y

Standard

Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity. / Chen, Lianmin; Collij, Valerie; Jaeger, Martin; van den Munckhof, Inge C. L.; Vich Vila, Arnau; Kurilshikov, Alexander; Gacesa, Ranko; Sinha, Trishla; Oosting, Marije; Joosten, Leo A. B.; Rutten, Joost H. W.; Riksen, Niels P.; Xavier, Ramnik J.; Kuipers, Folkert; Wijmenga, Cisca; Zhernakova, Alexandra; Netea, Mihai G.; Weersma, Rinse K.; Fu, Jingyuan.

In: Nature Communications, Vol. 11, No. 1, 4018, 11.08.2020, p. 4018.

Research output: Contribution to journalArticleAcademicpeer-review

Vancouver

Chen L, Collij V, Jaeger M, van den Munckhof ICL, Vich Vila A, Kurilshikov A et al. Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity. Nature Communications. 2020 Aug 11;11(1):4018. 4018. https://doi.org/10.1038/s41467-020-17840-y


BibTeX

@article{0d3c93bbace14af68b693539156cf7d9,
title = "Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity",
abstract = "The gut microbiome is an ecosystem that involves complex interactions. Currently, our knowledge about the role of the gut microbiome in health and disease relies mainly on differential microbial abundance, and little is known about the role of microbial interactions in the context of human disease. Here, we construct and compare microbial co-abundance networks using 2,379 metagenomes from four human cohorts: an inflammatory bowel disease (IBD) cohort, an obese cohort and two population-based cohorts. We find that the strengths of 38.6% of species co-abundances and 64.3% of pathway co-abundances vary significantly between cohorts, with 113 species and 1,050 pathway co-abundances showing IBD-specific effects and 281 pathway co-abundances showing obesity-specific effects. We can also replicate these IBD microbial co-abundances in longitudinal data from the IBD cohort of the integrative human microbiome (iHMP-IBD) project. Our study identifies several key species and pathways in IBD and obesity and provides evidence that altered microbial abundances in disease can influence their co-abundance relationship, which expands our current knowledge regarding microbial dysbiosis in disease.",
author = "Lianmin Chen and Valerie Collij and Martin Jaeger and {van den Munckhof}, {Inge C. L.} and {Vich Vila}, Arnau and Alexander Kurilshikov and Ranko Gacesa and Trishla Sinha and Marije Oosting and Joosten, {Leo A. B.} and Rutten, {Joost H. W.} and Riksen, {Niels P.} and Xavier, {Ramnik J.} and Folkert Kuipers and Cisca Wijmenga and Alexandra Zhernakova and Netea, {Mihai G.} and Weersma, {Rinse K.} and Jingyuan Fu",
year = "2020",
month = aug,
day = "11",
doi = "10.1038/s41467-020-17840-y",
language = "English",
volume = "11",
pages = "4018",
journal = "Nature Communications",
issn = "2041-1723",
publisher = "Nature Publishing Group",
number = "1",

}

RIS

TY - JOUR

T1 - Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity

AU - Chen, Lianmin

AU - Collij, Valerie

AU - Jaeger, Martin

AU - van den Munckhof, Inge C. L.

AU - Vich Vila, Arnau

AU - Kurilshikov, Alexander

AU - Gacesa, Ranko

AU - Sinha, Trishla

AU - Oosting, Marije

AU - Joosten, Leo A. B.

AU - Rutten, Joost H. W.

AU - Riksen, Niels P.

AU - Xavier, Ramnik J.

AU - Kuipers, Folkert

AU - Wijmenga, Cisca

AU - Zhernakova, Alexandra

AU - Netea, Mihai G.

AU - Weersma, Rinse K.

AU - Fu, Jingyuan

PY - 2020/8/11

Y1 - 2020/8/11

N2 - The gut microbiome is an ecosystem that involves complex interactions. Currently, our knowledge about the role of the gut microbiome in health and disease relies mainly on differential microbial abundance, and little is known about the role of microbial interactions in the context of human disease. Here, we construct and compare microbial co-abundance networks using 2,379 metagenomes from four human cohorts: an inflammatory bowel disease (IBD) cohort, an obese cohort and two population-based cohorts. We find that the strengths of 38.6% of species co-abundances and 64.3% of pathway co-abundances vary significantly between cohorts, with 113 species and 1,050 pathway co-abundances showing IBD-specific effects and 281 pathway co-abundances showing obesity-specific effects. We can also replicate these IBD microbial co-abundances in longitudinal data from the IBD cohort of the integrative human microbiome (iHMP-IBD) project. Our study identifies several key species and pathways in IBD and obesity and provides evidence that altered microbial abundances in disease can influence their co-abundance relationship, which expands our current knowledge regarding microbial dysbiosis in disease.

AB - The gut microbiome is an ecosystem that involves complex interactions. Currently, our knowledge about the role of the gut microbiome in health and disease relies mainly on differential microbial abundance, and little is known about the role of microbial interactions in the context of human disease. Here, we construct and compare microbial co-abundance networks using 2,379 metagenomes from four human cohorts: an inflammatory bowel disease (IBD) cohort, an obese cohort and two population-based cohorts. We find that the strengths of 38.6% of species co-abundances and 64.3% of pathway co-abundances vary significantly between cohorts, with 113 species and 1,050 pathway co-abundances showing IBD-specific effects and 281 pathway co-abundances showing obesity-specific effects. We can also replicate these IBD microbial co-abundances in longitudinal data from the IBD cohort of the integrative human microbiome (iHMP-IBD) project. Our study identifies several key species and pathways in IBD and obesity and provides evidence that altered microbial abundances in disease can influence their co-abundance relationship, which expands our current knowledge regarding microbial dysbiosis in disease.

U2 - 10.1038/s41467-020-17840-y

DO - 10.1038/s41467-020-17840-y

M3 - Article

C2 - 32782301

VL - 11

SP - 4018

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

IS - 1

M1 - 4018

ER -

ID: 131167972