Different Groups of Novel Bacteroidetes Dominate the Gut Microbial Community of Wild Manatees (Trichechus manatus) from Belize and Florida (USA) revealed by 454-pyrosequencing

Manatees and dugongs (Order Sirenia) are the only known herbivorous aquatic mammals. They are hindgut fermenters with high cellulose digestion efficiency, which may be attributable to resident gut microorganisms. To understand the composition of gut microbial communities of manatees as well as the impact of geographic location, a comparative study between wild manatees (T. manatus) at Florida and Belize was carried out. Fecal bacterial and archaeal (methanogenic) communities were analyzed by barcoded pyrosequencing and cloning of 16S rRNA genes, respectively. Bacteroidetes (63.5±9.5%) rather than Firmicutes (32.3±8.5%) were found to be the most predominant bacteria in all manatees. In total, 4543 OTUs were observed across these manatees; 290 OTUs, mainly belonging to the Bacteroidetes phylum, were unclassifiable at class level while 92 of the OTUs had low similarity (<90%) with any yet known 16S rRNA gene sequences. Principal component analysis of T-RFLP, DGGE and pyrosequencing results showed that gut bacterial communities of these two groups of manatees were clearly different. The methanogenic communities of these two groups were also significantly different (P=0.001), being dominated by different species of Methanobrevibacter. Rarefaction analysis revealed that the bacterial diversity of Belize manatees (BMs) was consistently lower than that of Florida manatees (FMs). These results demonstrate that manatees harbor unique gut bacterial populations that are shaped by the endangered host species and likely contribute to their efficient digestion and utilization of aquatic herbage.