Extending Seqenv: a taxa-centric approach to environmental annotations of 16S rDNA sequences

Ijaz, A. Z., Jeffries, T. C., Ijaz, U. Z. , Hamonts, K. and SinghIjaz, B. K. (2017) Extending Seqenv: a taxa-centric approach to environmental annotations of 16S rDNA sequences. PeerJ, 5, e3827. (doi:10.7717/peerj.3827) (PMID:29038749) (PMCID:PMC5639872)

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Abstract

Understanding how the environment selects a given taxon and the diversity patterns that emerge as a result of environmental filtering can dramatically improve our ability to analyse any environment in depth as well as advancing our knowledge on how the response of different taxa can impact each other and ecosystem functions. Most of the work investigating microbial biogeography has been site-specific, and logical environmental factors, rather than geographical location, may be more influential on microbial diversity. SEQenv, a novel pipeline aiming to provide environmental annotations of sequences emerged to provide a consistent description of the environmental niches using the ENVO ontology. While the pipeline provides a list of environmental terms on the basis of sample datasets and, therefore, the annotations obtained are at the dataset level, it lacks a taxa centric approach to environmental annotation. The work here describes an extension developed to enhance the SEQenv pipeline, which provided the means to directly generate environmental annotations for taxa under different contexts. 16S rDNA amplicon datasets belonging to distinct biomes were selected to illustrate the applicability of the extended SEQenv pipeline. A literature survey of the results demonstrates the immense importance of sequence level environmental annotations by illustrating the distribution of both taxa across environments as well as the various environmental sources of a specific taxon. Significantly enhancing the SEQenv pipeline in the process, this information would be valuable to any biologist seeking to understand the various taxa present in the habitat and the environment they originated from, enabling a more thorough analysis of which lineages are abundant in certain habitats and the recovery of patterns in taxon distribution across different habitats and environmental gradients.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Ijaz, Dr Umer
Authors: Ijaz, A. Z., Jeffries, T. C., Ijaz, U. Z., Hamonts, K., and SinghIjaz, B. K.
College/School:College of Science and Engineering > School of Engineering > Infrastructure and Environment
Journal Name:PeerJ
Publisher:PeerJ
ISSN:2167-8359
ISSN (Online):2167-8359
Copyright Holders:Copyright © 2017 Ijaz et al.
First Published:First published in PeerJ 5: e3827
Publisher Policy:Reproduced under a Creative Commons license

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
652772Understanding microbial community through in situ environmental 'omic data synthesisUmer Zeeshan IjazNatural Environment Research Council (NERC)NE/L011956/1ENG - ENGINEERING INFRASTRUCTURE & ENVIR

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