Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores

Abstract

Mammals host gut microbiomes of immense physiological consequence, but the determinants of diversity in these communities remain poorly understood. Diet appears to be the dominant factor, but host phylogeny also seems to be an important, if unpredictable, correlate. Here we show that baleen whales, which prey on animals (fish and crustaceans), harbor unique gut microbiomes with surprising parallels in functional capacity and higher level taxonomy to those of terrestrial herbivores. These similarities likely reflect a shared role for fermentative metabolisms despite a shift in primary carbon sources from plant-derived to animal-derived polysaccharides, such as chitin. In contrast, protein catabolism and essential amino acid synthesis pathways in baleen whale microbiomes more closely resemble those of terrestrial carnivores. Our results demonstrate that functional attributes of the microbiome can vary independently even given an animal-derived diet, illustrating how diet and evolutionary history combine to shape microbial diversity in the mammalian gut.

Terrestriality and bacterial transfer: a comparative study of gut microbiomes in sympatric Malagasy mammals

“…As found previously [10][11][12]14], variation in taxonomic composition among wild Malagasy mammals was correlated with both host evolutionary history and diet, depending on the relatedness of the host species. Moreover, shared terrestriality, but not geographic distance between sampling sites, predicted microbiome similarity among distantly related hosts with divergent diets and digestive physiologies.…”

“…Several studies of zoo animals reared on artificial diets have claimed that diet and shared environment have greater impacts on gut microbiome composition than endogenous factors [10][11][12][13][14]. Other studies have focused on closely related mammal species and generally found that host species and their gut microbes exhibit concordant relationships [8,[15][16][17][18], with the gut microbial communities of different host species forming distinct clusters [18][19][20].…”

“…Most of these comparative microbiome surveys have sampled geographically and ecologically distinct captive or wild populations (but see [14,27,28]). However, captivity alters microbiome composition in mammals [12,[29][30][31], and, when animals are compared across geographic regions, host phylogenetic differences may be confounded by differences in local microbial taxa [15,32].…”

Marine Animal Microbiomes: Toward Understanding Host–Microbiome Interactions in a Changing Ocean

“…Several studies have examined the skin (Figure 3H), gut and respiratory microbiomes of diverse marine mammal species, and describe species-specific relationships (Johnson et al, 2009;Apprill et al, 2014;Bik et al, 2016). Connections between the community composition of the microbiome and animal health (Apprill et al, 2014) and diet (Nelson et al, 2013;Sanders et al, 2015) have been made, and more detailed studies are needed to understand these specific connections. While there are very limited resources available for studying host-microbiome interactions in marine mammals, there are some animals in captivity as well as well-studied populations that will heighten investigations of host-microbiome symbiosis and dysbiosis in these sentinel species.…”

Current Advances in Functional Genomics in Aquaculture

“…In terms of assembly, both whole genome shotgun and marker gene guided sequencing have been used on diferent aquatic organisms. The commonly used marker gene in metagenomics analyses is the 16S ribosomal RNA (16S rRNA), which has been widely used to characterize the microbiota of diferent aquatic organisms including rainbow trout [88,89], Atlantic salmon [11,12], turbot (Scophthalmus maximus) [90], lamprey (Lampetra morii) [91] and Baleen whale [92]. Whole genome shotgun sequencing has also been widely used in the study of environmental microbial communities and pathogens infecting diferent aquatic organisms.…”