Presented at ICG12

Included in metagenomics theme

Altmetric score 6.1 (top 16.9%)

Author: Valerie De Anda
Editor: Scott Edmunds
Research area: bioinformatics
Type:

Open peer-review

Review content is open, signing review is optional.

A new multi-genomic approach for the study of biogeochemical cycles at global scale: the molecular reconstruction of the sulfur cycle


Created on 11th June 2017

Valerie De Anda; Icoquih Zapata-Penasco; Bruno Contreras-Moreira; Augusto Cesar Poot-Hernandez; Luis E. Eguiarte; Valeria Souza;


Despite the great advances in microbial ecology and the explosion of high throughput sequencing, our ability to understand and integrate the global biogeochemical cycles is still limited. Here we propose a novel approach to summarize the complexity of the Sulfur cycle based on the minimum ecosystem concept, the microbial mat model and the relative entropy of protein domains involved in S-metabolism. This methodology produces a single value, called the Sulfur Score (SS), which informs about the specific S-related molecular machinery. After curating an inventory of microorganisms, pathways and genes taking part in this cycle, we benchmark the performance of the SS on a collection of 2,107 non-redundant RefSeq genomes, 900 metagenomes from MG-RAST and 35 metagenomes analyzed for the first time. We find that the SS is able to correctly classify microorganisms known to be involved in the S-cycle, yielding an Area Under the ROC Curve of 0.985. Moreover, when sorting environments the top-scoring metagenomes were hydrothermal vents, microbial mats and deep-sea sediments, among others. This methodology can be generalized to the analysis of other biogeochemical cycles or processes. Provided that an inventory of relevant pathways and microorganisms can be compiled, entropy-based scores could be used to detect environmental patterns and informative samples in multi-genomic scale.

Show more

Review Summary

This paper has 0 completed reviews and 0 reviews in progress.

# Status Date
Daan Speth Completed 27 Jul 2017 View review
Thulani Peter Makh... Completed 28 Jul 2017 View review
Thulani Peter Makh... Completed 18 Sep 2017 View review



Name:
Email: