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The Combination of Functional Metagenomics and an Oil-Fed Enrichment Strategy Revealed the Phylogenetic Diversity of Lipolytic Bacteria Overlooked by the Cultivation-Based Method

Metagenomic screening and conventional cultivation have been used to exploit microbial lipolytic enzymes in nature. We used an indigenous forest soil (NS) and oil-fed enriched soil (OS) as microbial and genetic resources. Thirty-four strains (17 each) of lipolytic bacteria were isolated from the NS...

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Autores principales: Narihiro, Takashi, Suzuki, Aya, Yoshimune, Kazuaki, Hori, Tomoyuki, Hoshino, Tamotsu, Yumoto, Isao, Yokota, Atsushi, Kimura, Nobutada, Kamagata, Yoichi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Japanese Society of Microbial Ecology/The Japanese Society of Soil Microbiology 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103521/
https://www.ncbi.nlm.nih.gov/pubmed/24859309
http://dx.doi.org/10.1264/jsme2.ME14002
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author Narihiro, Takashi
Suzuki, Aya
Yoshimune, Kazuaki
Hori, Tomoyuki
Hoshino, Tamotsu
Yumoto, Isao
Yokota, Atsushi
Kimura, Nobutada
Kamagata, Yoichi
author_facet Narihiro, Takashi
Suzuki, Aya
Yoshimune, Kazuaki
Hori, Tomoyuki
Hoshino, Tamotsu
Yumoto, Isao
Yokota, Atsushi
Kimura, Nobutada
Kamagata, Yoichi
author_sort Narihiro, Takashi
collection PubMed
description Metagenomic screening and conventional cultivation have been used to exploit microbial lipolytic enzymes in nature. We used an indigenous forest soil (NS) and oil-fed enriched soil (OS) as microbial and genetic resources. Thirty-four strains (17 each) of lipolytic bacteria were isolated from the NS and OS microcosms. These isolates were classified into the (sub)phyla Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Actinobacteria, all of which are known to be the main microbial resources of commercially available lipolytic enzymes. Seven and 39 lipolytic enzymes were successfully retrieved from the metagenomic libraries of the NS and OS microcosms, respectively. The screening efficiency (a ratio of positive lipolytic clones to the total number of environmental clones) was markedly higher in the OS microcosm than in the NS microcosm. Moreover, metagenomic clones encoding the lipolytic enzymes associated with Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Armatimonadetes, and Planctomycetes and hitherto-uncultivated microbes were recovered from these libraries. The results of the present study indicate that functional metagenomics can be effectively used to capture as yet undiscovered lipolytic enzymes that have eluded the cultivation-based method, and these combined approaches may be able to provide an overview of lipolytic organisms potentially present in nature.
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spelling pubmed-41035212014-07-24 The Combination of Functional Metagenomics and an Oil-Fed Enrichment Strategy Revealed the Phylogenetic Diversity of Lipolytic Bacteria Overlooked by the Cultivation-Based Method Narihiro, Takashi Suzuki, Aya Yoshimune, Kazuaki Hori, Tomoyuki Hoshino, Tamotsu Yumoto, Isao Yokota, Atsushi Kimura, Nobutada Kamagata, Yoichi Microbes Environ Articles Metagenomic screening and conventional cultivation have been used to exploit microbial lipolytic enzymes in nature. We used an indigenous forest soil (NS) and oil-fed enriched soil (OS) as microbial and genetic resources. Thirty-four strains (17 each) of lipolytic bacteria were isolated from the NS and OS microcosms. These isolates were classified into the (sub)phyla Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Actinobacteria, all of which are known to be the main microbial resources of commercially available lipolytic enzymes. Seven and 39 lipolytic enzymes were successfully retrieved from the metagenomic libraries of the NS and OS microcosms, respectively. The screening efficiency (a ratio of positive lipolytic clones to the total number of environmental clones) was markedly higher in the OS microcosm than in the NS microcosm. Moreover, metagenomic clones encoding the lipolytic enzymes associated with Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Armatimonadetes, and Planctomycetes and hitherto-uncultivated microbes were recovered from these libraries. The results of the present study indicate that functional metagenomics can be effectively used to capture as yet undiscovered lipolytic enzymes that have eluded the cultivation-based method, and these combined approaches may be able to provide an overview of lipolytic organisms potentially present in nature. Japanese Society of Microbial Ecology/The Japanese Society of Soil Microbiology 2014-06 2014-05-23 /pmc/articles/PMC4103521/ /pubmed/24859309 http://dx.doi.org/10.1264/jsme2.ME14002 Text en Copyright 2014 by Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology http://creativecommons.org/licenses/by/3.0 This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Narihiro, Takashi
Suzuki, Aya
Yoshimune, Kazuaki
Hori, Tomoyuki
Hoshino, Tamotsu
Yumoto, Isao
Yokota, Atsushi
Kimura, Nobutada
Kamagata, Yoichi
The Combination of Functional Metagenomics and an Oil-Fed Enrichment Strategy Revealed the Phylogenetic Diversity of Lipolytic Bacteria Overlooked by the Cultivation-Based Method
title The Combination of Functional Metagenomics and an Oil-Fed Enrichment Strategy Revealed the Phylogenetic Diversity of Lipolytic Bacteria Overlooked by the Cultivation-Based Method
title_full The Combination of Functional Metagenomics and an Oil-Fed Enrichment Strategy Revealed the Phylogenetic Diversity of Lipolytic Bacteria Overlooked by the Cultivation-Based Method
title_fullStr The Combination of Functional Metagenomics and an Oil-Fed Enrichment Strategy Revealed the Phylogenetic Diversity of Lipolytic Bacteria Overlooked by the Cultivation-Based Method
title_full_unstemmed The Combination of Functional Metagenomics and an Oil-Fed Enrichment Strategy Revealed the Phylogenetic Diversity of Lipolytic Bacteria Overlooked by the Cultivation-Based Method
title_short The Combination of Functional Metagenomics and an Oil-Fed Enrichment Strategy Revealed the Phylogenetic Diversity of Lipolytic Bacteria Overlooked by the Cultivation-Based Method
title_sort combination of functional metagenomics and an oil-fed enrichment strategy revealed the phylogenetic diversity of lipolytic bacteria overlooked by the cultivation-based method
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103521/
https://www.ncbi.nlm.nih.gov/pubmed/24859309
http://dx.doi.org/10.1264/jsme2.ME14002
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