Microbiome Dynamics in Marine Mammals

Marine mammals host complex and dynamic microbial communities across multiple body sites, including the gut, skin and respiratory tract. These microbiomes are shaped by host phylogeny, diet and habitat, yet remain distinct from both terrestrial mammal microbiomes and surrounding seawater. Gut communities facilitate digestion of specialised diets—ranging from chitinous zooplankton to lipid-rich prey—and contribute to nutrient cycling in ocean ecosystems. Skin and respiratory microbiota offer non-invasive windows into health status, with core assemblages that may signal stress or disease. Temporal and geographic factors, social interactions and rehabilitative care further influence community composition. Understanding these dynamics offers novel insights into marine mammal physiology, conservation strategies and the broader role of marine vertebrates in biogeochemical processes.

Research from Nature Portfolio

Recent studies have characterised the biogeography and functional capacity of marine mammal microbiomes. Analyses of dolphins and sea lions revealed highly diverse, body-site specific bacterial assemblages, with over two-thirds of near-full-length 16S sequences in dolphins unrepresented in existing databases, underscoring extensive microbial novelty shaped by host ecology and diet. Investigations of baleen whale gut microbiota demonstrated surprising parallels with terrestrial herbivores in fermentative pathways, despite an animal-derived diet, alongside protein catabolism functions more typical of carnivores, highlighting the combined influence of evolutionary history and feeding strategy. Work on pygmy and dwarf sperm whales uncovered gut communities dominated by fermentative and sulfate-respiring taxa, with distinct compositions even between closely related host species, emphasising host identity as a key driver of microbiome structure.

Microbiome Dynamics in Marine Mammals publication trend

The graph below shows the total number of articles in microbiome dynamics in marine mammals across all publications each year (not limited to Nature Index journals).

Technical terms

Microbiome: Collection of microorganisms and their genetic material within a defined environment.

Core microbiome: Set of microbial taxa consistently found across multiple individuals or sites.

Lipidome: Complete lipid profile within a biological system, often analysed alongside microbial communities.

Exhaled breath condensate: Respiratory secretion collected from whale blow for microbiome analysis.

16S ribosomal RNA gene sequencing: Technique for profiling bacterial communities by analysing a conserved marker gene.

Metagenomics: Culture-independent sequencing approach to characterise all genetic material in an environmental sample.

References

1. Fecal and skin microbiota of two rescued Mediterranean monk seal pups during rehabilitation. Microbiology Spectrum (2023).
2. Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea. Nature Communications (2016).
3. Coordinated transformation of the gut microbiome and lipidome of bowhead whales provides novel insights into digestion. The ISME Journal: Multidisciplinary Journal of Microbial Ecology (2019).
4. Extensive Core Microbiome in Drone-Captured Whale Blow Supports a Framework for Health Monitoring. mSystems (2017).
5. Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores. Nature Communications (2015).
6. High diversity and unique composition of gut microbiomes in pygmy (Kogia breviceps) and dwarf (K. sima) sperm whales. Scientific Reports (2017).