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Microbiome refers to different communities of microorganisms and their role within a specific environment, considering environmental conditions and interactions with one another in a defined environment. A defined environment could be an entire organism (e.g., a human being) or parts of it (e.g., the gut or the skin).

Microbiomes play an important role in individual health and ecology and in particular in marine mammals the discovery of different microbiomes in gut, skin and nose permitted to analyze their conditions and the condition of the marine environment in which they live.

Gut Microbiome
The access of microbial samples from the gut out of marine mammals is limited because most species are rare, endangered, and deep divers. There are different techniques for sampling the cetacean's gut microbiome. The most common is collecting fecal samples from the environment and taking a probe from the center that is non-contaminated. Besides there are studies from rectal swabs and rare studies from stranded dead or living animals direct from the intestine.

The intestinal microbiome of Cetaceans is a complex ecosystem that plays an important role in the metabolism, health, and immunity of the host. The microbial communities of marine mammals are diverse and distinct from terrestrial mammals, and the community depends on different factors like kind of diet, phylogeny, health, and age.

As the microbiome is involved in the decomposition of food, diet is a predominant factor for the microbial community. Different studies have shown that members of Bacteroidetes and Firmicutes are the most abundant phyla of gut microorganisms in animals that are cephalopod predators or zooplankton predators like in short-finned pilot whales and baleen whales. Especially the genus Bacteroides (phyla Bacteroidetes) seems to play a major role in the decomposition of the chitin-rich diet of these species and were also found in the gut microbiome of baleen whales.

In toothed cetacean species which food consumption is mainly piscivore the most abundant phyla are Firmicutes, Fusobacteria, and Proteobacteria. Proteobacteria are classified as a minor important group for marine mammals that consume cephalopods and zooplankton but are highly abundant in piscivorous predators like bottlenose dolphins, East Asian finless porpoises, and belugas. These findings could mirror the different dietary niches of these species.

Besides the dietary also the age seems to determine the differences in the microbial community between cetaceans. Maron et al. have shown that the microbial community is changing in right whale caves during their development. Interestingly the genera Bilophila, Peptococcus, and Treponema are more abundant in older calves. The higher abundance of Bilophila might be a response to the greater milk intake of the older calves.

The microbiome of the respiratory system
The cetaceans are in danger because they are affected by multiple stress factors, especially of an anthropogenic nature, which make them more vulnerable to various diseases. These animals have been noted to show high susceptibility to airway infections, but very little is known about their respiratory microbiome. Therefore, the sampling of the exhaled breath or "blow" of the cetaceans can provide an assessment of the state of health. Blow is composed of a mixture of microorganisms and organic material, including lipids, proteins and cellular debris derived from the linings of the airways which, when released into the relatively cooler outdoor air, condense to form a visible mass of vapor, which can be collected. There are various methods for collecting exhaled breath samples, one of the most recent is through the use of aerial drones. This method provides a safer, quieter, and less invasive alternative and often a cost-effective option for monitoring fauna and flora. Once obtained, the blow samples are taken to the laboratory and we proceed with the amplification and sequencing of the respiratory tract microbiota. The use of aerial drones has been more successful with large cetaceans due to slow swim speeds and larger blow sizes.

In all the studies carried out, in addition to exhaled breath samples, seawater and air samples were collected to more accurately identify the specific microorganisms for exhaled breath.

Through various studies carried out on different cetaceans, among which, Humpback whales (Megaptera novaeangliae) , Blue whale (Balænoptera musculus) , Gray whale (Eschrichtius robustus) , Sperm whale (Physeter macrocephalus) , Killer whale ( Orcinus orca) and bottlenose dolphins (Tursiops truncatus)  , the respiratory microbiome has begun to be defined, i.e., a microbial community formed by a complex diversity of common microorganisms to all the specimens examined. These are very recent studies, so knowledge is very limited, only some microorganisms are known while others have not yet been identified and little is known about their functional role within these animals. Overall, the most common bacteria identified at the phylum level included Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes.

Among the Proteobacteria, bacteria belonging to the families Brucellaceae and Enterobacteriaceae and to the genera Candidatus Pelagibacter, Acidovorax, Cardiobacterium, Pseudomonas, Burkholderia, Psychrobacter and some Deltaproteobacteria and Epsilonproteobacteria have been recognized.

Among the Firmicutes, bacteria belonging to the Clostridia and Erysipelotrichia classes and to the genera Anoxybacillus, Paenibacillus and Leptotrichia have been recognized. Bacteria belonging to the Acidimicrobiia class, to the Microbacteriaceae family, and to the genera Corynebacterium, Mycobacterium and Propionibacterium (Cutibacterium), have been recognized among the Actinobacteria

Among the Bacteroidetes, bacteria belonging to the genus Tenacibaculum have been recognized.

To these are added bacteria belonging to the phylum Fusobacteria and Mollicutes.

Finally, potential respiratory pathogens were also detected, such as Balneatrix (proteobacteria) and a range of Gram-positive Clostridia and Bacilli, such as Staphylococcus and Streptococcus (both firmicutes).

Furthermore, one of the most common bacteria in the various cetacean species is the Haemophilus bacterium. These are opportunistic gram-negative coccobacilli, also found in the respiratory tract of humans and other animals, which tend to colonize but without causing the onset of infection. But during periods of immunosuppression these organisms can cause damage by generating meningitis and pneumonia.

Some samples of killer whale blows were subjected to sensitivity tests, which revealed the presence of both gram-positive and gram-negative bacteria resistant to multiple antibodies such as erythromycin, lincomycin, penicillin and ampicillin.

In addition to bacteria, some viruses have also been identified in whale exhaled breath. Among the most abundant bacteriophages were the Siphoviridae and Myoviridae, while among the viral families there were small single-stranded DNA viruses (ss), in particular the Circoviridae, members of the Parvoviridae and a family of RNA viruses, the Tombusviridae. To conclude the persistence of these central members, which make up the respiratory microbiome, in apparently healthy individuals suggests that they may be indicative of a healthy, uninfected lung system, and their presence or absence could be informative for cetacean health monitoring. In fact, in exhaled breath samples, of some specimens, a low number of cores and a lower biodiversity than that previously listed were found. An explanation for this phenomenon could be that the samples in question were collected from animals following migration and therefore the depletion of the microbiota may reflect a compromised state of health due to the consequences of migration.