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Beaver Gut Microbiome Provides Clues to Plant Material Breakdown


NEW YORK (GenomeWeb) – A Canadian team reporting in PLOS One has started tallying up the bacterial and archaeal representatives present in the gastrointestinal tract of the beaver — a large rodent capable of digesting complex plant materials using hindgut fermentation.

Researchers from Agriculture and Agri-Food Canada relied on 16S ribosomal RNA sequencing to track the bacteria and archaea representatives present in the gastrointestinal tract of the North American beaver, Castor canadensis, using fecal samples and samples from ceacum site in the hindgut where the animals digest and ferment lignocellulose from plant.

From 16S rRNA sequences detected in samples from four adult beavers, the team identified almost 1,500 bacterial species apiece in beaver ceacum and feces, including some that resembled lignocellulose-degrading bugs. One main archaea species — Methanosphaera stadtmanae — prevailed in samples from both sites.

And based on the types of uncharacterized bacteria detected in the samples, the study's authors noted that it is "probably that novel, uncharacterized bacteria with plant cell wall degrading activity play a role in digestion in the beaver [gastrointestinal] tract.

"Further studies that focus on the metabolic activity of these communities and the enzymes they express are needed to provide further details on the enzymatic process that is utilized by the beaver microbiome to facilitate the digestion of lignocellulose," senior author Robert Forster, with Agriculture and Agri-Food Canada's Lethbridge Research and Innovation Centre, and his co-authors wrote.

Within the rodent family, the beaver is notable for its size — second only to capybara from South America — and its ability to produce massive dam structures that can alter the flow of the streams or rivers where they're found, the team noted. In addition to foraging for roots and aquatic plants, the animals are capable of consuming tricky-to-digest materials such as bark and woody plant material, which undergoes digestion and fermentation with the help of hindgut fermentation and microbes in the ceacum.

"Evidence of cellulase [enzyme] activity within the ceacal contents has previously been reported but the source of this activity has not been determined," the researchers wrote.  "Undoubtedly, the ability of the beaver to breakdown lignocellulose can be attributed to the microbiome found in the [gastrointestinal] tract, but the makeup of this community has not been examined."

In an effort to begin characterizing these microbial communities, Forster and colleagues used the Illumina MiSeq to do 16S rRNA sequencing with bacterial or archaeal-specific primers, using ceacum and lower colon fecal samples that had been collected from two male and two female beavers within an hour of death.

Nearly 60 percent of the 1,435 bacterial operational taxonomic units detected in beaver fecal samples belonged to the Firmicutes phylum, while almost 37 percent came from Bacteroidetes.

Although the 1,447 bacterial representatives in the ceacal gut microbiome included similar OTUs to those found in the fecal samples, the team saw shifts in the abundance of the bugs at the two gut sites. In the ceacum, for example, Bacteroidetes bacteria made up more than 49 percent of the OTUs, slightly eclipsing Firmicutes representatives.

At both sites, the researchers identified several other phyla found at far lower abundance, while their family- and OTU-level classifications of the samples uncovered more detailed differences between bacterial representation at each site.

Meanwhile, the team narrowed in on archaea from just three genera in the samples considered, with most reads stemming from M. stadtmanae, a species previously detected in the forestomach of kangaroos and the Sumatran orangutan guts.