Full-Length 16S rRNA Profiling of the Intestinal Microbiome of a Stranded Humpback Whale Neonate Reveals an Abundant Phocoenobacter/Pasteurella skyensis-Like Signal

Cetacean strandings provide rare opportunities to characterize gastrointestinal microbial communities, particularly in undersampled regions and life stages. However, postmortem microbiome data require cautious interpretation because carcass condition, environmental exposure, sampling delay, and microbial succession can influence bacterial profiles. Here, we used full-length 16S rRNA sequencing to characterize the distal intestinal bacterial community of a stranded male humpback whale (Megaptera novaeangliae) neonate from Bahía de Caráquez, Manabí, Ecuador. Sequencing generated 37,327 high-quality full-length 16S rRNA CCS reads for taxonomic assignment. The bacterial profile was composed of abundant and low-abundance taxa, with the seven most abundant assignments accounting for 65% of the total relative abundance. The most abundant taxonomic assignment was a Phocoenobacter/Pasteurella skyensis-like signal, representing 17% of the total relative abundance, followed by Fusobacterium perfoetens (16%) and Granulicatella balaenopterae (10%). The Phocoenobacter/P. skyensis-like assignment is taxonomically noteworthy because P. skyensis was originally described from Atlantic salmon (Salmo salar) and has recently been reclassified within Phocoenobacter, a genus that also includes marine mammal-associated lineages. Nevertheless, the data should be interpreted as marker-gene-based molecular signals rather than diagnostic evidence of infection or disease. No histopathology, bacterial culture, quantitative PCR, metagenomic sequencing, whole-genome sequencing, or matched environmental sampling was performed; therefore, bacterial viability, tissue invasion, transmission route, phylogeographic origin, and cause of death cannot be inferred. This case highlights the value of full-length 16S rRNA profiling as a complementary tool for molecular surveillance in cetacean stranding investigations and supports broader sampling across stranded cetaceans, marine environments, prey species, and aquaculture-associated settings in the Eastern Tropical Pacific.