High-throughput DNA sequencing of the ruminal bacteria from moose (Alces alces) in Vermont, Alaska, and Norway.

For the second project of my Ph.D., I expanded upon my findings in Vermont moose.  Following the collection of samples from moose in Vermont, I was able to obtain samples from moose in Alaska and Norway, as well.  The Alaskan moose were part of the Moose Research Station herd in Soldotna, Alaska, where they were allowed to roam and graze freely in a large 1 mi sq enclosure.  During sample collection for another project, Dr. John Crouse and Dr. Kimberlee Beckmen, both of the Alaska Department of Fish & Game, were able to intubate the sedated moose and collect rumen digesta samples.

A colleague in Norway, Dr. Monica Sunset, of the University of Tromsø, was able to facilitate sample collection and storage of moose rumen samples from two hunters; Drs. Even Jørgensen and Helge K. Johnsen, of the University of Tromsø.  As mailing rumen samples across country lines is restricted to prevent the potential spread of livestock diseases, it was actually easier to send me to Norway to extract DNA to ship home.  While in Norway, Dr. Sundset taught me how to culture microorganisms anaerobically – without the presence of oxygen.

For this project, we used high-throughput sequencing using the Roche 454 pyrosequencing platform, required me to learn the fine art of bioinformatics.  We were surprised to find that rumen bacterial communities in moose were different for each geographical location.  While we did not identify the diet that moose were eating, we speculated that these differences were driven by slightly different diets at the time points that each location was sampled in.  Plants often become more fibrous and less nutritious as the growing season develops and passes, and this nutritional change in substrate can select for different bacterial communities.  It has since been confirmed by a number of studies that geographic differences exist in the microbiome, driven by changes in site-specific diet, as well as food- and waterbourne microbial influences.


Ishaq, S.L., Wright, A-D.G. 2014. High-throughput DNA sequencing of the ruminal bacteria from moose (Alces alces) in Vermont, Alaska, and Norway. Microbial Ecology, 68(2):185-195. Article

Abstract

In the present study, the rumen bacteria of moose (Alces alces) from three distinct geographic locations were investigated. Moose are large, browsing ruminants in the deer family, which subsist on fibrous, woody browse, and aquatic plants. Subspecies exist which are distinguished by differing body and antler size, and these are somewhat geographically isolated. Seventeen rumen samples were collected from moose in Vermont, Alaska, and Norway, and bacterial 16S ribosomal RNA genes were sequenced using Roche 454 pyrosequencing with titanium chemistry. Overall, 109,643 sequences were generated from the 17 individual samples, revealing 33,622 unique sequences. Members of the phylum Bacteroidetes were dominant in samples from Alaska and Norway, but representatives of the phylum Firmicutes were dominant in samples from Vermont. Within the phylum Bacteroidetes, Prevotellaceae was the dominant family in all three sample locations, most of which belonged to the genus Prevotella. Within the phylum Firmicutes, the family Lachnospiraceae was the most prevalent in all three sample locations. The data set supporting the results of this article is available in the Sequence Read Archive (SRA), available through NCBI [study accession number SRP022590]. Samples clustered by geographic location and by weight and were heterogenous based on gender, location, and weight class (p < 0.05). Location was a stronger factor in determining the core microbiome than either age or weight, but gender did not appear to be a strong factor. There were no shared operational taxonomic units across all 17 samples, which indicates that these moose may have been isolated long enough to preclude a core microbiome among moose. Other potential factors discussed include differences in climate, food quality and availability, gender, and life cycle.

Keywords

Proteobacteria Unique Sequence Firmicutes Bacteroidetes Weight Class 

Ishaq poster FEMS 2013

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Google+ photo

You are commenting using your Google+ account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

w

Connecting to %s