Variation in the hindgut microbial communities of the Florida manatee,Trichechus manatus latirostrisover winter in Crystal River, Florida

Abstract

The Florida manatee, Trichechus manatus latirostris, is a hindgut-fermenting herbivore. In winter, manatees migrate to warm water overwintering sites where they undergo dietary shifts and may suffer from cold-induced stress. Given these seasonally induced changes in diet, the present study aimed to examine variation in the hindgut bacterial communities of wild manatees overwintering at Crystal River, west Florida. Faeces were sampled from 36 manatees of known sex and body size in early winter when manatees were newly arrived and then in mid-winter and late winter when diet had probably changed and environmental stress may have increased. Concentrations of faecal cortisol metabolite, an indicator of a stress response, were measured by enzyme immunoassay. Using 454-pyrosequencing, 2027 bacterial operational taxonomic units were identified in manatee faeces following amplicon pyrosequencing of the 16S rRNA gene V3/V4 region. Classified sequences were assigned to eight previously described bacterial phyla; only 0.36% of sequences could not be classified to phylum level. Five core phyla were identified in all samples. The majority (96.8%) of sequences were classified as Firmicutes (77.3 ± 11.1% of total sequences) or Bacteroidetes (19.5 ± 10.6%). Alpha-diversity measures trended towards higher diversity of hindgut microbiota in manatees in mid-winter compared to early and late winter. Beta-diversity measures, analysed through PERMANOVA, also indicated significant differences in bacterial communities based on the season.

The effect of diet on the gastrointestinal microbiome of juvenile rehabilitating green turtles (Chelonia mydas)

“…In sea turtles, the most common sample types are feces and cloacal swabs; thus our results are comparable to other studies [10][11][12][13]. Our results show that regardless of diet, the fecal bacterial phyla of green turtles consists primarily of Firmicutes and Bacteroidetes, a feature that appears to be conserved across many vertebrate taxa, including other marine herbivores and green turtles elsewhere [11,13,[31][32][33][34]. Principle coordinate analysis, however, revealed a clear difference in the community composition at admission compared to mid-rehabilitation and recovery, following the change in diet from primarily seafood to primarily vegetables.…”

“…The relative abundance of Firmicutes at admission is similar to what has been found in other free-ranging hindgut fermenters, and likely reflects the important role of this phyla in metabolizing seagrass and algae consumed by free-ranging green turtles [32][33][34]. Herbivorous marine iguanas (Amblyrhynchus cristatus) of the Galapagos Islands that have adapted to feed on macrophytic algae also have a microbiome composed predominately of Firmicutes (75.1%) and Bacteroidetes (8.2%) [33].…”

“…Much like green turtles, dugongs (Dugong dugon) are specialist marine herbivores that feed on seagrass, and their fecal bacteria phyla are also primarily Firmicutes (75.6%) and Bacteroidetes (19.9%) [34]. Florida manatees (Trichechus manatus latirostris), another hindgut fermenter but more of a generalist herbivore, also have a microbiome dominated by Firmicutes (77.3%) and Bacteroidetes (19.5%) [32]. Ahasan et al (2017) found that the cloacal microbiome of healthy, wild-captured green turtles in Australia was primarily Firmicutes (>60%) and Bacteroidetes (>27%), while the dominant phyla in stranded turtles were Proteobacteria (47.6%), followed by Bacteroidetes (19.0%), Firmicutes (18.7%) and Fusobacteria (13.6%) [11].…”

Internal parasites of the two subspecies of the West Indian manatee Trichechus manatus

“…During live-capture health assessments completed in the winter in Crystal River, Florida, by the US Geological Survey (USGS), manatees of all age classes were captured, and defecated feces (n = 11) were collected during beach examination (Bonde et al 2012, Merson et al 2014.…”

Peer Review #2 of "A survey of the sperm whale (Physeter catodon) commensal microbiome (v0.2)"

“…C. Bierlich 2018). The composition of the gut microbiomes of marine mammals have also been extensively studied, focusing on the putative functionality of these symbiotic communities, differences between marine mammals, and correlationship between marine mammals' diet and evolution (Bik 2016;Erwin 2017;Merson 2014;Nelson 2013;Sanders 2015). As far as diseases in marine mammals have been concerned, few studies have been conducted on the health impact of bacteria and viruses on marine mammals, which might be limited due to the difficulties in sample collection and the opportunistic nature of stranding events (Godoy-Vitorino 2017; Van Bressem 2014).…”