Rapid prototyping for quantifying belief weights of competing hypotheses about emergent diseases

Robertson, Ellen P.; Walsh, Daniel P.; Martin, Julien; Work, Thierry M.; Kellogg, Christina A.; Evans, James S.; Barker, Victoria; Hawthorn, Aine; Aeby, Greta S.; Paul, Valerie J.; Walker, Brian K.; Kiryu, Yasunari; Woodley, Cheryl M.; Meyer, Julie; Rosales, Stephanie M.; Studivan, Michael S.; Moore, J. F.; Brandt, Marilyn E.; Bruckner, Andrew W.

doi:10.1016/j.jenvman.2023.117668

Cited by 1 publication

(2 citation statements)

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“…Some work has suggested that the etiology of SCTLD has been hypothesized to be viral (Robertson et al . 2023), and gene expression data show that there is an increase in coral viral immune response in corals with SCTLD (Beavers et al .…”

Section: Discussionmentioning

confidence: 99%

“…Therefore, while matches to different Vibrio species and their potential role in SCTLD may offer some insights, a more robust interpretation is to consider the implications of disease association by Vibrio at the genus level. Some work has suggested that the etiology of SCTLD has been hypothesized to be viral (Robertson et al 2023), and gene expression data show that there is an increase in coral viral immune response in corals with SCTLD (Beavers et al 2023). Researchers have explored the potential role of RNA viruses in SCTLD, but no RNA viruses have been found enriched in corals with SCTLD (Veglia et al 2022) and these viruses are likely ubiquitous in corals without any potential relationship to SCTLD (Howe-Kerr et al 2023).…”

Section: Discussionmentioning

confidence: 99%

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Novel metagenomics analysis of stony coral tissue loss disease

Heinz,

Lu,

Huebner

et al. 2024

Preprint

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Stony coral tissue loss disease (SCTLD) has devastated coral reefs off the coast of Florida and continues to spread throughout the Caribbean. Although a number of bacterial taxa have consistently been associated with SCTLD, no pathogen has been definitively implicated in the etiology of SCTLD. Previous studies have predominantly focused on the prokaryotic community through 16S rRNA sequencing of healthy and infected tissues. Here, we provide a different analytical approach by applying a bioinformatics pipeline to publicly available whole genome sequencing samples of SCTLD lesions and healthy tissues from four stony coral species. To compensate for the lack of coral reference genomes, we used data from apparently healthy coral samples to approximate a host genome and healthy microbiome reference. The healthy reference reads were then used to filter the reads from diseased lesion tissue samples, and the remaining data were taxonomically classified at the DNA and protein levels. For DNA classifications, we used a pathogen identification protocol originally designed to identify pathogens in human tissue samples, and for protein classifications, we used a fast protein sequence aligner. Although these data were previously analyzed, our approach revealed unique patterns that were not identified in the previous work. We found a relatively high abundance of theVibriogenus across diseased samples as well as a number of enrichedVibriophages that further support the presence of this genus in diseased samples, suggesting that a member of theVibriogenus may be involved in the visual lesion formation stage of SCTLD.Article SummaryStudies of stony coral tissue loss disease (SCTLD), a devastating coral disease, have primary used 16S rRNA sequencing approaches to identify putative pathogens. This study applied human tissue pathogen identification protocols to SCTLD whole genome DNA samples. A k-mer based filtering method for diseased samples was utilized to compensate for the lack of host reference genomes. DNA and protein level classifications revealed a relatively abundant member of theVibriogenus associated with SCTLD across four stony coral species.

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Section: Discussionmentioning

confidence: 99%