Skip to the content

Using “omics” and integrated multi-omits approaches to guide probiotic selection to mitigate chytridiomycosis and other emerging infectious diseases

Rebollar, EA, Antwis, RE, Becker, MH, Belden, LK, Bletz, MC, Brucker, RM, Harrison, XA, Hughey, MC, Kueneman, JG, Loudon, AH, McKenzie, V, Medina, D, Minbiole, KPC, Rollins-Smith, LA, Walke, JB, Weiss, S, Woodhams, DC and Harris, RN 2016, 'Using “omics” and integrated multi-omits approaches to guide probiotic selection to mitigate chytridiomycosis and other emerging infectious diseases' , Frontiers in Microbiology, 7 (68) .

[img]
Preview
PDF - Published Version
Available under License Creative Commons Attribution.

Download (3MB) | Preview
[img]
Preview
PDF - Accepted Version
Available under License Creative Commons Attribution.

Download (610kB) | Preview
[img] Microsoft Word - Accepted Version
Restricted to Repository staff only
Available under License Creative Commons Attribution.

Download (741kB) | Request a copy
Access Information: This Document is Protected by copyright and was first published by Frontiers. All rights reserved. It is reproduced with permission.

Abstract

Emerging infectious diseases in wildlife are responsible for massive population declines. In amphibians, chytridiomycosis caused by Batrachochytrium dendrobatidis, Bd, has severely affected many amphibian populations and species around the world. One promising management strategy is probiotic bioaugmentation of antifungal bacteria on amphibian skin. In vivo experimental trials using bioaugmentation strategies have had mixed results, and therefore a more informed strategy is needed to select successful probiotic candidates. Metagenomic, transcriptomic, and metabolomic methods, colloquially called “omics,” are approaches that can better inform probiotic selection and optimize selection protocols. The integration of multiple omic data using bioinformatic and statistical tools and in silico models that link bacterial community structure with bacterial defensive function can allow the identification of species involved in pathogen inhibition. We recommend using 16S rRNA gene amplicon sequencing and methods such as indicator species analysis, the Kolmogorov–Smirnov Measure, and co-occurrence networks to identify bacteria that are associated with pathogen resistance in field surveys and experimental trials. In addition to 16S amplicon sequencing, we recommend approaches that give insight into symbiont function such as shotgun metagenomics, metatranscriptomics, or metabolomics to maximize the probability of finding effective probiotic candidates, which can then be isolated in culture and tested in persistence and clinical trials. An effective mitigation strategy to ameliorate chytridiomycosis and other emerging infectious diseases is necessary; the advancement of omic methods and the integration of multiple omic data provide a promising avenue toward conservation of imperiled species.

Item Type: Article
Schools: Schools > School of Environment and Life Sciences > Ecosystems and Environment Research Centre
Journal or Publication Title: Frontiers in Microbiology
Publisher: Frontiers Media
ISSN: 1664-302X
Related URLs:
Funders: North-West University
Depositing User: Dr Rachael Antwis
Date Deposited: 07 Mar 2016 14:42
Last Modified: 18 Apr 2016 12:40
URI: http://usir.salford.ac.uk/id/eprint/38077

Actions (login required)

Edit record (repository staff only) Edit record (repository staff only)

Downloads

Downloads per month over past year