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The Organelle in the Room: Under-annotated Mitochondrial Reads Bias Coral Microbiome Analysis

View ORCID ProfileDylan Sonett, View ORCID ProfileTanya Brown, View ORCID ProfileJohan Bengtsson-Palme, View ORCID ProfileJacqueline L. Padilla-Gamiño, View ORCID ProfileJesse R. Zaneveld
doi: https://doi.org/10.1101/2021.02.23.431501
Dylan Sonett
1Division of Biological Sciences, School of STEM, University of Washington Bothell, Bothell, WA, USA
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Tanya Brown
1Division of Biological Sciences, School of STEM, University of Washington Bothell, Bothell, WA, USA
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Johan Bengtsson-Palme
2Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sweden
3Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Sweden
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Jacqueline L. Padilla-Gamiño
4School of Aquatic and Fisheries Sciences, University of Washington, Seattle, WA, USA
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Jesse R. Zaneveld
1Division of Biological Sciences, School of STEM, University of Washington Bothell, Bothell, WA, USA
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  • For correspondence: zaneveld@uw.edu
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Abstract

The microbiomes of tropical corals are actively studied using 16S rRNA gene amplicons to understand microbial roles in coral health, metabolism, and disease resistance. However, primers targeting bacterial and archaeal 16S rRNA genes may also amplify organelle rRNA genes from the coral, associated microbial eukaryotes, and encrusting organisms. In this manuscript, we demonstrate that standard workflows for annotating microbial taxonomy severely under-annotate mitochondrial sequences in 1272 coral microbiomes from the Earth Microbiome Project. This issue prevents annotation of >95% of reads in some samples and persists when using either Greengenes or SILVA taxonomies. Worse, mitochondrial under-annotation varies between species and across anatomy, biasing comparisons of α- and β-diversity. By supplementing existing taxonomies with diverse mitochondrial rRNA sequences, we resolve ~97% of unique unclassified sequences as mitochondrial, without increasing misannotation in mock communities. We recommend using these extended taxonomies for coral microbiome analysis and encourage vigilance regarding similar issues in other hosts.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/zaneveld/GCMP_Global_Disease/tree/master/analysis/organelle_removal

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted February 24, 2021.
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The Organelle in the Room: Under-annotated Mitochondrial Reads Bias Coral Microbiome Analysis
Dylan Sonett, Tanya Brown, Johan Bengtsson-Palme, Jacqueline L. Padilla-Gamiño, Jesse R. Zaneveld
bioRxiv 2021.02.23.431501; doi: https://doi.org/10.1101/2021.02.23.431501
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The Organelle in the Room: Under-annotated Mitochondrial Reads Bias Coral Microbiome Analysis
Dylan Sonett, Tanya Brown, Johan Bengtsson-Palme, Jacqueline L. Padilla-Gamiño, Jesse R. Zaneveld
bioRxiv 2021.02.23.431501; doi: https://doi.org/10.1101/2021.02.23.431501

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