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Mining traits for the enrichment and isolation of not-yet-cultured populations
BACKGROUND: The lack of pure cultures limits our understanding into 99% of bacteria. Proper interpretation of the genetic and the transcriptional datasets can reveal clues for the enrichment and even isolation of the not-yet-cultured populations. Unraveling such information requires a proper mining...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6593511/ https://www.ncbi.nlm.nih.gov/pubmed/31238973 http://dx.doi.org/10.1186/s40168-019-0708-4 |
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author | Zhang, An-Ni Mao, Yanping Wang, Yubo Zhang, Tong |
author_facet | Zhang, An-Ni Mao, Yanping Wang, Yubo Zhang, Tong |
author_sort | Zhang, An-Ni |
collection | PubMed |
description | BACKGROUND: The lack of pure cultures limits our understanding into 99% of bacteria. Proper interpretation of the genetic and the transcriptional datasets can reveal clues for the enrichment and even isolation of the not-yet-cultured populations. Unraveling such information requires a proper mining method. RESULTS: Here, we present a method to infer the hidden traits for the enrichment of not-yet-cultured populations. We demonstrate this method using Candidatus Accumulibacter. Our method constructs a whole picture of the carbon, electron, and energy flows in the not-yet-cultured populations from the genomic datasets. Then, it decodes the coordination across three flows from the transcriptional datasets. Based on it, our method diagnoses the status of the not-yet-cultured populations and provides strategy to optimize the enrichment systems. CONCLUSION: Our method could shed light to the exploration into the bacterial dark matter in the environments. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s40168-019-0708-4) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6593511 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-65935112019-07-09 Mining traits for the enrichment and isolation of not-yet-cultured populations Zhang, An-Ni Mao, Yanping Wang, Yubo Zhang, Tong Microbiome Research BACKGROUND: The lack of pure cultures limits our understanding into 99% of bacteria. Proper interpretation of the genetic and the transcriptional datasets can reveal clues for the enrichment and even isolation of the not-yet-cultured populations. Unraveling such information requires a proper mining method. RESULTS: Here, we present a method to infer the hidden traits for the enrichment of not-yet-cultured populations. We demonstrate this method using Candidatus Accumulibacter. Our method constructs a whole picture of the carbon, electron, and energy flows in the not-yet-cultured populations from the genomic datasets. Then, it decodes the coordination across three flows from the transcriptional datasets. Based on it, our method diagnoses the status of the not-yet-cultured populations and provides strategy to optimize the enrichment systems. CONCLUSION: Our method could shed light to the exploration into the bacterial dark matter in the environments. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s40168-019-0708-4) contains supplementary material, which is available to authorized users. BioMed Central 2019-06-25 /pmc/articles/PMC6593511/ /pubmed/31238973 http://dx.doi.org/10.1186/s40168-019-0708-4 Text en © The Author(s). 2019 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 Zhang, An-Ni Mao, Yanping Wang, Yubo Zhang, Tong Mining traits for the enrichment and isolation of not-yet-cultured populations |
title | Mining traits for the enrichment and isolation of not-yet-cultured populations |
title_full | Mining traits for the enrichment and isolation of not-yet-cultured populations |
title_fullStr | Mining traits for the enrichment and isolation of not-yet-cultured populations |
title_full_unstemmed | Mining traits for the enrichment and isolation of not-yet-cultured populations |
title_short | Mining traits for the enrichment and isolation of not-yet-cultured populations |
title_sort | mining traits for the enrichment and isolation of not-yet-cultured populations |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6593511/ https://www.ncbi.nlm.nih.gov/pubmed/31238973 http://dx.doi.org/10.1186/s40168-019-0708-4 |
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