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

Lianmin Chen, Valerie Collij, Martin Jaeger, Inge C. L. van den Munckhof, Arnau Vich Vila, Alexander Kurilshikov, Ranko Gacesa, Trishla Sinha, Marije Oosting, Leo A. B. Joosten, Joost H. W. Rutten, Niels P. Riksen, Ramnik J. Xavier, Folkert Kuipers, Cisca Wijmenga, Alexandra Zhernakova, Mihai G. Netea, Rinse K. Weersma and Jingyuan Fu ()
Additional contact information
Lianmin Chen: University Medical Center Groningen
Valerie Collij: University Medical Center Groningen
Martin Jaeger: Radboud University Medical Center
Inge C. L. van den Munckhof: Radboud University Medical Center
Arnau Vich Vila: University Medical Center Groningen
Alexander Kurilshikov: University Medical Center Groningen
Ranko Gacesa: University Medical Center Groningen
Trishla Sinha: University Medical Center Groningen
Marije Oosting: Radboud University Medical Center
Leo A. B. Joosten: Radboud University Medical Center
Joost H. W. Rutten: Radboud University Medical Center
Niels P. Riksen: Radboud University Medical Center
Ramnik J. Xavier: Massachusetts General Hospital
Folkert Kuipers: University Medical Center Groningen
Cisca Wijmenga: University Medical Center Groningen
Alexandra Zhernakova: University Medical Center Groningen
Mihai G. Netea: Radboud University Medical Center
Rinse K. Weersma: University Medical Center Groningen
Jingyuan Fu: University Medical Center Groningen

Nature Communications, 2020, vol. 11, issue 1, 1-12

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-17840-y

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