Next Article in Journal
Next Article in Special Issue
Previous Article in Journal
Previous Article in Special Issue
Int. J. Mol. Sci. 2014, 15(7), 12364-12378; doi:10.3390/ijms150712364
Article

Exploring Neighborhoods in the Metagenome Universe

,
,
 and *
Received: 31 March 2014; in revised form: 23 June 2014 / Accepted: 25 June 2014 / Published: 14 July 2014
(This article belongs to the Special Issue Metagenomics: a Powerful Lens Viewing the Microbial World)
View Full-Text   |   Download PDF [1211 KB, updated 17 July 2014; original version uploaded 14 July 2014]
Abstract: The variety of metagenomes in current databases provides a rapidly growing source of information for comparative studies. However, the quantity and quality of supplementary metadata is still lagging behind. It is therefore important to be able to identify related metagenomes by means of the available sequence data alone. We have studied efficient sequence-based methods for large-scale identification of similar metagenomes within a database retrieval context. In a broad comparison of different profiling methods we found that vector-based distance measures are well-suitable for the detection of metagenomic neighbors. Our evaluation on more than 1700 publicly available metagenomes indicates that for a query metagenome from a particular habitat on average nine out of ten nearest neighbors represent the same habitat category independent of the utilized profiling method or distance measure. While for well-defined labels a neighborhood accuracy of 100% can be achieved, in general the neighbor detection is severely affected by a natural overlap of manually annotated categories. In addition, we present results of a novel visualization method that is able to reflect the similarity of metagenomes in a 2D scatter plot. The visualization method shows a similarly high accuracy in the reduced space as compared with the high-dimensional profile space. Our study suggests that for inspection of metagenome neighborhoods the profiling methods and distance measures can be chosen to provide a convenient interpretation of results in terms of the underlying features. Furthermore, supplementary metadata of metagenome samples in the future needs to comply with readily available ontologies for fine-grained and standardized annotation. To make profile-based k-nearest-neighbor search and the 2D-visualization of the metagenome universe available to the research community, we included the proposed methods in our CoMet-Universe server for comparative metagenome analysis.
Keywords: metagenomics; functional profile; taxonomic profile; metagenome comparison metagenomics; functional profile; taxonomic profile; metagenome comparison
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Export to BibTeX |
EndNote


MDPI and ACS Style

Aßhauer, K.P.; Klingenberg, H.; Lingner, T.; Meinicke, P. Exploring Neighborhoods in the Metagenome Universe. Int. J. Mol. Sci. 2014, 15, 12364-12378.

AMA Style

Aßhauer KP, Klingenberg H, Lingner T, Meinicke P. Exploring Neighborhoods in the Metagenome Universe. International Journal of Molecular Sciences. 2014; 15(7):12364-12378.

Chicago/Turabian Style

Aßhauer, Kathrin P.; Klingenberg, Heiner; Lingner, Thomas; Meinicke, Peter. 2014. "Exploring Neighborhoods in the Metagenome Universe." Int. J. Mol. Sci. 15, no. 7: 12364-12378.


Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert