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Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing

BACKGROUND: The pure culture of prokaryotes remains essential to elucidating the role of these organisms. Scientists have reasoned that hard to cultivate microorganisms might grow in pure culture if provided with the chemical components of their natural environment. However, most microbial species i...

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Autores principales: Mu, Da-Shuai, Liang, Qi-Yun, Wang, Xiao-Man, Lu, De-Chen, Shi, Ming-Jing, Chen, Guan-Jun, Du, Zong-Jun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6307301/
https://www.ncbi.nlm.nih.gov/pubmed/30587241
http://dx.doi.org/10.1186/s40168-018-0613-2
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author Mu, Da-Shuai
Liang, Qi-Yun
Wang, Xiao-Man
Lu, De-Chen
Shi, Ming-Jing
Chen, Guan-Jun
Du, Zong-Jun
author_facet Mu, Da-Shuai
Liang, Qi-Yun
Wang, Xiao-Man
Lu, De-Chen
Shi, Ming-Jing
Chen, Guan-Jun
Du, Zong-Jun
author_sort Mu, Da-Shuai
collection PubMed
description BACKGROUND: The pure culture of prokaryotes remains essential to elucidating the role of these organisms. Scientists have reasoned that hard to cultivate microorganisms might grow in pure culture if provided with the chemical components of their natural environment. However, most microbial species in the biosphere that would otherwise be “culturable” may fail to grow because of their growth state in nature, such as dormancy. That means even if scientist would provide microorganisms with the natural environment, such dormant microorganisms probably still remain in a dormant state. RESULTS: We constructed an enrichment culture system for high-efficiency isolation of uncultured strains from marine sediment. Degree of enrichment analysis, dormant and active taxa calculation, viable but non-culturable bacteria resuscitation analysis, combined with metatranscriptomic and comparative genomic analyses of the interactions between microbial communications during enrichment culture showed that the so-called enrichment method could culture the “uncultured” not only through enriching the abundance of “uncultured,” but also through the resuscitation mechanism. In addition, the enrichment culture was a complicated mixed culture system, which contains the competition, cooperation, or coordination among bacterial communities, compared with pure cultures. CONCLUSIONS: Considering that cultivation techniques must evolve further—from axenic to mixed cultures—for us to fully understand the microbial world, we should redevelop an understanding of the classic enrichment culture method. Enrichment culture methods can be developed and used to construct a model for analyzing mixed cultures and exploring microbial dark matter. This study provides a new train of thought to mining marine microbial dark matter based on mixed cultures. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s40168-018-0613-2) contains supplementary material, which is available to authorized users.
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spelling pubmed-63073012019-01-02 Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing Mu, Da-Shuai Liang, Qi-Yun Wang, Xiao-Man Lu, De-Chen Shi, Ming-Jing Chen, Guan-Jun Du, Zong-Jun Microbiome Research BACKGROUND: The pure culture of prokaryotes remains essential to elucidating the role of these organisms. Scientists have reasoned that hard to cultivate microorganisms might grow in pure culture if provided with the chemical components of their natural environment. However, most microbial species in the biosphere that would otherwise be “culturable” may fail to grow because of their growth state in nature, such as dormancy. That means even if scientist would provide microorganisms with the natural environment, such dormant microorganisms probably still remain in a dormant state. RESULTS: We constructed an enrichment culture system for high-efficiency isolation of uncultured strains from marine sediment. Degree of enrichment analysis, dormant and active taxa calculation, viable but non-culturable bacteria resuscitation analysis, combined with metatranscriptomic and comparative genomic analyses of the interactions between microbial communications during enrichment culture showed that the so-called enrichment method could culture the “uncultured” not only through enriching the abundance of “uncultured,” but also through the resuscitation mechanism. In addition, the enrichment culture was a complicated mixed culture system, which contains the competition, cooperation, or coordination among bacterial communities, compared with pure cultures. CONCLUSIONS: Considering that cultivation techniques must evolve further—from axenic to mixed cultures—for us to fully understand the microbial world, we should redevelop an understanding of the classic enrichment culture method. Enrichment culture methods can be developed and used to construct a model for analyzing mixed cultures and exploring microbial dark matter. This study provides a new train of thought to mining marine microbial dark matter based on mixed cultures. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s40168-018-0613-2) contains supplementary material, which is available to authorized users. BioMed Central 2018-12-26 /pmc/articles/PMC6307301/ /pubmed/30587241 http://dx.doi.org/10.1186/s40168-018-0613-2 Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Mu, Da-Shuai
Liang, Qi-Yun
Wang, Xiao-Man
Lu, De-Chen
Shi, Ming-Jing
Chen, Guan-Jun
Du, Zong-Jun
Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing
title Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing
title_full Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing
title_fullStr Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing
title_full_unstemmed Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing
title_short Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing
title_sort metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6307301/
https://www.ncbi.nlm.nih.gov/pubmed/30587241
http://dx.doi.org/10.1186/s40168-018-0613-2
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