Bacterial and Archaeal Diversity in the Gastrointestinal Tract of the North American Beaver (Castor canadensis)

Abstract

The North American Beaver (Castor canadensis) is the second largest living rodent and an iconic symbol of Canada. The beaver is a semi-aquatic browser whose diet consists of lignocellulose from a variety of plants. The beaver is a hindgut fermenter and has an enlarged ceacum that houses a complex microbiome. There have been few studies examining the microbial diversity in gastrointestinal tract of hindgut fermenting herbivores. To examine the bacterial and archaeal communities inhabiting the gastrointestinal tract of the beaver, the microbiome of the ceacum and feaces was examined using culture-independent methods. DNA from the microbial community of the ceacum and feaces of 4 adult beavers was extracted, and the16S rRNA gene was sequenced using either bacterial or archaeal specific primers. A total of 1447 and 1435 unique bacterial OTUs were sequenced from the ceacum and feaces, respectively. On average, the majority of OTUs within the ceacum were classified as Bacteroidetes (49.2%) and Firmicutes (47.6%). The feaces was also dominated by OTUs from Bacteroidetes (36.8%) and Firmicutes (58.9%). The composition of bacterial community was not significantly different among animals. The composition of the ceacal and feacal microbiome differed, but this difference is due to changes in the abundance of closely related OTUs, not because of major differences in the taxonomic composition of the communities. Within these communities, known degraders of lignocellulose were identified. In contrast, to the bacterial microbiome, the archaeal community was dominated by a single species of methanogen, Methanosphaera stadtmanae. The data presented here provide the first insight into the microbial community within the hindgut of the beaver.

Comparative analysis of microbiota along the length of the gastrointestinal tract of two tree squirrel species (Sciurus aberti and S. niger) living in sympatry

“…For example, Abert's squirrel lower GI tracts had higher diversity and abundance of several representatives from the family Prevotellaceae, with five ASVs present in the lower core microbiome (compared with none in fox squirrels), which were all present in higher abundance in Abert's squirrels (one additional representative was at higher abundance in fox squirrels). Prevotella has been repeatedly associated with high-fiber diets in human studies (De Filippo et al, 2010;Schnorr et al, 2014;Yatsunenko et al, 2012) and is also a major constituent of the microbiome of ruminants and other herbivorous mammals (AvguÅ¡tin, Flint, & Whitehead, 1992;Flint, Scott, Duncan, Louis, & Forano, 2012;Gruninger, McAllister, & Forster, 2016;Kohl, Varner, Wilkening, & Dearing, 2018;Li, Li, Beasley, et al, 2016;Li, Li, Yao, et al, 2016). Within the family Lachnospiraceae, the lower GI tract of Abert's squirrels had higher abundance and diversity within the genus Marvinbryantia, with four ASVs represented in the lower core microbiome (compared to one in fox squirrels), all of which were in higher abundance in Abert's squirrels relative to fox squirrels.…”

Metagenomics reveals functional synergy and novel polysaccharide utilization loci in the Castor canadensis fecal microbiome

“…Gruninger and colleagues recently used small subunit ribosomal RNA (SSU rRNA) gene sequencing to profile the microbial community structure of beaver cecum and feces, indicating a typical mammalian hindgut community dominated by Bacteroidetes and Firmicutes [ 18 ]. As a hindgut fermenter, commensal microbes in the lower digestive tract of the beaver are expected to mediate the degradation and fermentation of complex sugars to provide short chain fatty acids that provision host nutrition [ 19 ].…”

A place for host–microbe symbiosis in the comparative physiologist's toolbox

“…Although studies sequencing the bacterial 16S rRNA gene are widely referred to as studying the 'gut microbiota', it is important to note that many other types of organisms (in addition to bacteria) are present in these samples. Alternative primer sets and sequencing approaches are necessary to produce inventories of the archaeal (Gruninger et al, 2016), fungal (Miller et al, 2016b), protozoan (Parfrey et al, 2014) and viral (Minot et al, 2011) communities. Sequencing techniques vary, as can the pipelines used to process the resulting 'operational taxonomic units' (see Glossary) that loosely represent a microbial species (Caporaso et al, 2010;Schloss et al, 2009).…”