Emergent community architecture despite distinct diversity in the global whale shark (Rhincodon typus) epidermal microbiome

Michael P. Doane, Michael B. Reed, Jody McKerral, Laís Farias Oliveira Lima, Megan Morris, Asha Z. Goodman, Shaili Johri, Bhavya Papudeshi, Taylor Dillon, Abigail C. Turnlund, Meredith Peterson, Maria Mora, Rafael de la Parra Venegas, Richard Pillans, Christoph A. Rohner, Simon J. Pierce, Christine G. Legaspi, Gonzalo Araujo, Deni Ramirez-Macias, Robert A. EdwardsElizabeth A. Dinsdale

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Microbiomes confer beneficial physiological traits to their host, but microbial diversity is inherently variable, challenging the relationship between microbes and their contribution to host health. Here, we compare the diversity and architectural complexity of the epidermal microbiome from 74 individual whale sharks (Rhincodon typus) across five aggregations globally to determine if network properties may be more indicative of the microbiome-host relationship. On the premise that microbes are expected to exhibit biogeographic patterns globally and that distantly related microbial groups can perform similar functions, we hypothesized that microbiome co-occurrence patterns would occur independently of diversity trends and that keystone microbes would vary across locations. We found that whale shark aggregation was the most important factor in discriminating taxonomic diversity patterns. Further, microbiome network architecture was similar across all aggregations, with degree distributions matching Erdos–Renyi-type networks. The microbiome-derived networks, however, display modularity indicating a definitive microbiome structure on the epidermis of whale sharks. In addition, whale sharks hosted 35 high-quality metagenome assembled genomes (MAGs) of which 25 were present from all sample locations, termed the abundant ‘core’. Two main MAG groups formed, defined here as Ecogroup 1 and 2, based on the number of genes present in metabolic pathways, suggesting there are at least two important metabolic niches within the whale shark microbiome. Therefore, while variability in microbiome diversity is high, network structure and core taxa are inherent characteristics of the epidermal microbiome in whale sharks. We suggest the host-microbiome and microbe-microbe interactions that drive the self-assembly of the microbiome help support a functionally redundant abundant core and that network characteristics should be considered when linking microbiomes with host health.
Original languageEnglish
Article number12747
Number of pages13
JournalScientific Reports
Issue number1
Publication statusPublished - 7 Aug 2023


  • Biodiversity
  • Community ecology
  • Ecological networks
  • Ecology
  • Microbial ecology


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