The Pacific harbor seal gut microbiota in Mexico: Its relationship with diet and functional inferences

Abstract

Diet is a primary driver of the composition of gut microbiota and is considered one of the main routes of microbial colonization. Prey identification is fundamental for correlating the diet with the presence of particular microbial groups. The present study examined how diet influenced the composition and function of the gut microbiota of the Pacific harbor seal ( Phoca vitulina richardii ) in order to better understand the role of prey consumption in shaping its microbiota. This species is a good indicator of the quality of the local environment due to both its foraging and haul-out site fidelity. DNA was extracted from 20 fecal samples collected from five harbor seal colonies located in Baja California, Mexico. The V4 region of 16S rRNA gene was amplified and sequenced using the Illumina technology. Results showed that the gut microbiota of the harbor seals was dominated by the phyla Firmicutes (37%), Bacteroidetes (26%) and Fusobacteria (26%) and revealed significant differences in its composition among the colonies. Funtional analysis using the PICRUSt software suggests a high number of pathways involved in the basal metabolism, such as those for carbohydrates (22%) and amino acids (20%), and those related to the degradation of persistent environmental pollutants. In addition, a DNA metabarcoding analysis of the same samples, via the amplification and sequencing of the mtRNA 16S and rRNA 18S genes, was used to identify the prey consumed by harbor seals revealing the consumption of prey with mainly demersal habits. Functional redundancy in the seal gut microbiota was observed, irrespective of diet or location. Our results indicate that the frequency of occurrence of specific prey in the harbor seal diet plays an important role in shaping the composition of the gut microbiota of harbor seals by influencing the relative abundance of specific groups of gut microorganisms. A significant relationship was found among diet, gut microbiota composition and OTUs assigned to a particular metabolic pathway.

The role of the gut microbiota in the dietary niche expansion of fishing bats

“…This is supported by observations of higher prevalence of Firmicutes compared to Proteobacteria in salinity gradients [30]. Increased incidence of Firmicutes has also been related to the consumption of the Engraulidae fish [31] that M. vivesi consumes [32], due to their high content of polyunsaturated fatty acids that are known to promote intestinal enrichment of Firmicutes [33]. Furthermore, Photobacterium are ubiquitous in the oceans [34] and often found in symbiotic relationships with fish within the dietary spectrum of M. vivesi [35,36].…”

Gut Microbiomes of Freshwater Mussels (Unionidae) Are Taxonomically and Phylogenetically Variable across Years but Remain Functionally Stable

“…Of the three mussel species that exhibited functional redundancy ( O. unicolor , E. arca , and C. asperata ), each had significant year-to-year variation in the relative abundances of three abundant bacterial families (Fusobacteriaceae, Planctomycetaceae, and Clostridiaceae). Each of these families was also abundant in previously published microbiomes that also exhibited functional redundancy [ 43 , 44 , 45 ]. The apparent functional redundancy may result in increased functional stability and resilience against not only naturally fluctuating conditions but also anthropogenic disturbances [ 46 ].…”

Microbial diversity and structure in the gastrointestinal tracts of two stranded short‐finned pilot whales (Globicephala macrorhynchus) and a pygmy sperm whale (Kogia breviceps)

“…Some researchers have indicated that host habitat, diet, and phylogeny all contribute to variations in the gut microbial composition of marine mammals (Bik et al 2016). Recently, high-throughput sequencing technology has facilitated the study of gut microbiomes in different marine mammals, such as seals (Pacheco-Sandoval et al 2019), sea lions (Lavery et al 2012), and manatees (Merson et al 2014). However, challenges in the sampling of some marine mammals, especially cetaceans, have resulted in limited information on gut microbiome diversity.…”