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Identification of Bacterial Specialists in Hosts belonging to Aves, Mammalia, and Pisces
Citation:
Green, H., J. Fisher, S. Huse, M. Slogin, S. McLellan, AND O. Shanks. Identification of Bacterial Specialists in Hosts belonging to Aves, Mammalia, and Pisces. Presented at 114th American Society for Microbiology General Meeting, #1749, Boston, MA, May 17 - 20, 2014.
Impact/Purpose:
To inform the public.
Description:
Only a portion of bacteria found in animal guts are able to establish specific associations within animal hosts. Taxa that have formed these specialized relationships may have played a prominent role in host evolution and may also contribute significantly to current host physiologies. However, outside model organisms we know relatively little about the taxonomic identity of these bacterial specialists or what proportion of animal microbiomes they compose. In application, identification of specialist taxa may also help guide the development of methods to identify sources of aquatic contaminants. By analyzing over 44 million sequence reads collected from birds, mammals, and fish with a new species distribution model typically used in macroecology, we determine the proportion and taxonomic identity of bacterial specialist found within animal hosts. Materials: We analyzed the V6 region of the bacterial rRNA gene from 73 fecal samples using VAMPs (vamps.mbl.edu) and the vegan package in R. To identify specialist bacteria we used a CLAM test which has been previously used to describe tree distribution patterns in Costa Rican rainforests. Results: CLAM tests on 68,424 OTUs resulted in the identification of 14,031 specialists (20.5% of all OTUs and 92.7% of all sequences in the final dataset). Bacteria from a wide taxonomic range were identified as specialists: however, across all animals a high proportion of Lachnospiraceae, Ruminococcaceae, and Bacteroidaceae were identified as specialists relative to all OTUs within those taxa. Conclusion: These results reinforce the assertion that bacteria within Firmicutes and Bacteroidetes may have formed the most ancient relationships with vertebrate hosts and that macroecological models can be helpful for identifying specialists in large diverse microbial datasets that contain sequences with only a single observation. Newly identified specialist taxa identified herein offer significant potential as indicators of specific sources of contaminants and could be targeted for detection in the environment using more sensitive methods.
