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Mapping potential pathogen profiling in cetacean blow: comparative insights from sequencing technologies.

Johann Frederick Jaitner1,2, Nicola Gambardella1, Luís Afonso1,3

  • 1CIIMAR/CIMAR LA, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, 4450-208, Matosinhos, Portugal.

Microbial Genomics
|July 8, 2026
PubMed
Summary

Exhaled breath condensate (EBC) analysis reveals distinct respiratory microbiomes in cetaceans. Long-read sequencing offers a more comprehensive view of microbial communities and potential pathogens in marine mammals.

Keywords:
Delphinus delphisGlobicephala macrorhynchusblow samplingexhale breath condensatemetabarcodingpathogen detection

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Area of Science:

  • Marine Mammal Health
  • Microbiome Research
  • Genomic Sequencing Technologies

Background:

  • Cetaceans are vital to marine ecosystems and serve as indicators of environmental health.
  • Assessing cetacean health is crucial for effective marine conservation efforts.
  • Understanding the respiratory microbiome can provide insights into marine mammal health.

Purpose of the Study:

  • To characterize the prokaryotic communities in cetacean exhaled breath condensate (EBC) using 16S rRNA gene sequencing.
  • To compare the efficacy of short-read (Illumina) and long-read (PacBio) sequencing platforms for microbiome analysis.
  • To identify potential pathogenic bacteria within the cetacean respiratory tract.

Main Methods:

  • Collected EBC samples from cetaceans.
  • Employed 16S rRNA gene sequencing on both Illumina and PacBio platforms.
  • Utilized the Multiple Bacterial Pathogen Detection (MBPD) database to identify putative pathogens.

Main Results:

  • PacBio sequencing yielded significantly more amplicon sequence variants (ASVs) and identified more potential pathogens than Illumina.
  • PacBio data revealed higher alpha diversity and meaningful beta diversity clustering correlated with sample metadata.
  • Distinct EBC microbial signatures were found for pilot whales (Globicephala macrorhynchus) and common dolphins (Delphinus delphis), differing from seawater microbiota.

Conclusions:

  • Exhaled breath condensate (EBC) is a non-invasive and valuable tool for respiratory microbiome analysis in marine mammals.
  • Long-read sequencing (PacBio) provides a more comprehensive characterization of cetacean respiratory microbiomes compared to short-read sequencing.
  • This study establishes a baseline for respiratory microbiota in Delphinus delphis, aiding future health and pathogen monitoring in free-ranging cetaceans.