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Abstract The genomes of mitochondria and chloroplasts contain ribosomal RNA (rRNA) genes, reflecting their ancestry as free-living bacteria. These organellar rRNAs are often amplified in microbiome studies of animals and plants. If identified, they can be discarded, merely reducing sequencing depth. However, we identify certain high-abundance organeller RNAs not identified by common pipelines, which may compromise statistical analysis of microbiome structure and diversity. We quantified this by reanalyzing 7459 samples from seven 16S rRNA studies, including microbiomes from 927 unique animal genera. We find that under-annotation of cryptic mitochondrial and chloroplast reads affects multiple of these large-scale cross-species microbiome comparisons, and varies between host species, biasing comparisons. We offer a straightforward solution: supplementing existing taxonomies with diverse organelle rRNA sequences. This resolves up to 97% of unique unclassified sequences in some entire studies as mitochondrial (14% averaged across all studies), without increasing false positive annotations in mitochondria-free mock communities. Improved annotation decreases the proportion of unknown sequences by ≥10-fold in 2262 of 7459 samples (30%), spanning five of seven major studies examined. We recommend leveraging organelle sequence diversity to better identify organelle gene sequences in microbiome studies, and provide code, data resources and tutorials that implement this approach. 

Abstract BackgroundEvolutionary tradeoffs between life-history strategies are important in animal evolution. Because microbes can influence multiple aspects of host physiology, including growth rate and susceptibility to disease or stress, changes in animal-microbial symbioses have the potential to mediate life-history tradeoffs. Scleractinian corals provide a biodiverse, data-rich, and ecologically-relevant host system to explore this idea. ResultsUsing a comparative approach, we tested if coral microbiomes correlate with disease susceptibility across 425 million years of coral evolution by conducting a cross-species coral microbiome survey (the “Global Coral Microbiome Project”) and combining the results with long-term global disease prevalence and coral trait data. Interpreting these data in their phylogenetic context, we show that microbial dominance predicts disease susceptibility, and traced this dominance-disease association to a single putatively beneficial symbiont genus,Endozoicomonas. Endozoicomonasrelative abundance in coral tissue explained 30% of variation in disease susceptibility and 60% of variation in microbiome dominance across 40 coral genera, while also correlating strongly with high growth rates. ConclusionsThese results demonstrate that the evolution ofEndozoicomonassymbiosis in corals correlates with both disease prevalence and growth rate, and suggest a mediating role. Exploration of the mechanistic basis for these findings will be important for our understanding of how microbial symbioses influence animal life-history tradeoffs.