Using “Omics” and Integrated Multi-Omics Approaches to Guide Probiotic Selection to Mitigate Chytridiomycosis and Other Emerging Infectious Diseases

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 bioaug...

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Main Authors:	Rebollar, Eria A., Antwis, Rachael E., Becker, Matthew H., Belden, Lisa K., Bletz, Molly C., Brucker, Robert M., Harrison, Xavier A., Hughey, Myra C., Kueneman, Jordan G., Loudon, Andrew H., McKenzie, Valerie, Medina, Daniel, Minbiole, Kevin P. C., Rollins-Smith, Louise A., Walke, Jenifer B., Weiss, Sophie, Woodhams, Douglas C., Harris, Reid N.
Format:	Online
Language:	English
Published:	Frontiers Media S.A. 2016
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735675/

id	pubmed-4735675
recordtype	oai_dc
spelling	pubmed-47356752016-02-11 Using “Omics” and Integrated Multi-Omics Approaches to Guide Probiotic Selection to Mitigate Chytridiomycosis and Other Emerging Infectious Diseases Rebollar, Eria A. Antwis, Rachael E. Becker, Matthew H. Belden, Lisa K. Bletz, Molly C. Brucker, Robert M. Harrison, Xavier A. Hughey, Myra C. Kueneman, Jordan G. Loudon, Andrew H. McKenzie, Valerie Medina, Daniel Minbiole, Kevin P. C. Rollins-Smith, Louise A. Walke, Jenifer B. Weiss, Sophie Woodhams, Douglas C. Harris, Reid N. Microbiology 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. Frontiers Media S.A. 2016-02-02 /pmc/articles/PMC4735675/ /pubmed/26870025 http://dx.doi.org/10.3389/fmicb.2016.00068 Text en Copyright © 2016 Rebollar, Antwis, Becker, Belden, Bletz, Brucker, Harrison, Hughey, Kueneman, Loudon, McKenzie, Medina, Minbiole, Rollins-Smith, Walke, Weiss, Woodhams and Harris. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Rebollar, Eria A. Antwis, Rachael E. Becker, Matthew H. Belden, Lisa K. Bletz, Molly C. Brucker, Robert M. Harrison, Xavier A. Hughey, Myra C. Kueneman, Jordan G. Loudon, Andrew H. McKenzie, Valerie Medina, Daniel Minbiole, Kevin P. C. Rollins-Smith, Louise A. Walke, Jenifer B. Weiss, Sophie Woodhams, Douglas C. Harris, Reid N.
spellingShingle	Rebollar, Eria A. Antwis, Rachael E. Becker, Matthew H. Belden, Lisa K. Bletz, Molly C. Brucker, Robert M. Harrison, Xavier A. Hughey, Myra C. Kueneman, Jordan G. Loudon, Andrew H. McKenzie, Valerie Medina, Daniel Minbiole, Kevin P. C. Rollins-Smith, Louise A. Walke, Jenifer B. Weiss, Sophie Woodhams, Douglas C. Harris, Reid N. Using “Omics” and Integrated Multi-Omics Approaches to Guide Probiotic Selection to Mitigate Chytridiomycosis and Other Emerging Infectious Diseases
author_facet	Rebollar, Eria A. Antwis, Rachael E. Becker, Matthew H. Belden, Lisa K. Bletz, Molly C. Brucker, Robert M. Harrison, Xavier A. Hughey, Myra C. Kueneman, Jordan G. Loudon, Andrew H. McKenzie, Valerie Medina, Daniel Minbiole, Kevin P. C. Rollins-Smith, Louise A. Walke, Jenifer B. Weiss, Sophie Woodhams, Douglas C. Harris, Reid N.
author_sort	Rebollar, Eria A.
title	Using “Omics” and Integrated Multi-Omics Approaches to Guide Probiotic Selection to Mitigate Chytridiomycosis and Other Emerging Infectious Diseases
title_short	Using “Omics” and Integrated Multi-Omics Approaches to Guide Probiotic Selection to Mitigate Chytridiomycosis and Other Emerging Infectious Diseases
title_full	Using “Omics” and Integrated Multi-Omics Approaches to Guide Probiotic Selection to Mitigate Chytridiomycosis and Other Emerging Infectious Diseases
title_fullStr	Using “Omics” and Integrated Multi-Omics Approaches to Guide Probiotic Selection to Mitigate Chytridiomycosis and Other Emerging Infectious Diseases
title_full_unstemmed	Using “Omics” and Integrated Multi-Omics Approaches to Guide Probiotic Selection to Mitigate Chytridiomycosis and Other Emerging Infectious Diseases
title_sort	using “omics” and integrated multi-omics approaches to guide probiotic selection to mitigate chytridiomycosis and other emerging infectious diseases
description	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.
publisher	Frontiers Media S.A.
publishDate	2016
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735675/
_version_	1613531520953221120

Using “Omics” and Integrated Multi-Omics Approaches to Guide Probiotic Selection to Mitigate Chytridiomycosis and Other Emerging Infectious Diseases

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