Detection of stable community structures within gut microbiota co-occurrence networks from different human populations

Author:

Jackson Matthew A.1,Bonder Marc Jan2,Kuncheva Zhana3,Zierer Jonas14,Fu Jingyuan25,Kurilshikov Alexander2,Wijmenga Cisca26,Zhernakova Alexandra2,Bell Jordana T.1,Spector Tim D.1,Steves Claire J.1

Affiliation:

1. Department of Twin Research & Genetic Epidemiology, King’s College London, London, United Kingdom

2. University Medical Center Groningen, Department of Genetics, University of Groningen, Groningen, Netherlands

3. Department of Mathematics, Imperial College London, London, United Kingdom

4. Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany

5. University Medical Center Groningen, Department of Pediatrics, University of Groningen, Groningen, Netherlands

6. K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway

Abstract

Microbes in the gut microbiome form sub-communities based on shared niche specialisations and specific interactions between individual taxa. The inter-microbial relationships that define these communities can be inferred from the co-occurrence of taxa across multiple samples. Here, we present an approach to identify comparable communities within different gut microbiota co-occurrence networks, and demonstrate its use by comparing the gut microbiota community structures of three geographically diverse populations. We combine gut microbiota profiles from 2,764 British, 1,023 Dutch, and 639 Israeli individuals, derive co-occurrence networks between their operational taxonomic units, and detect comparable communities within them. Comparing populations we find that community structure is significantly more similar between datasets than expected by chance. Mapping communities across the datasets, we also show that communities can have similar associations to host phenotypes in different populations. This study shows that the community structure within the gut microbiota is stable across populations, and describes a novel approach that facilitates comparative community-centric microbiome analyses.

Funder

National Institutes of Health (NIH)

Wellcome Trust; European Community’s Seventh Framework Programme

National Institute for Health Research (NIHR)-funded BioResource

Clinical Research Facility and Biomedical Research Centre

Chronic Disease Research Foundation (CDRF)

Engineering and Physical Sciences Research Council (EPSRC)

Top Institute Food and Nutrition, Wageningen

Netherlands Organization for Scientific Research (NWO)

CardioVa sculair Onderzoek Nederland

ERC-START grant

Rosalind Franklin Fellowship

Publisher

PeerJ

Subject

General Agricultural and Biological Sciences,General Biochemistry, Genetics and Molecular Biology,General Medicine,General Neuroscience

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