Functional Characterisation of Bile Metagenome: Study of Metagenomic Dark Matter

Gallbladder metagenome involves a wide range of unidentified sequences comprising the so-called metagenomic dark matter. Therefore, this study aimed to characterise three gallbladder metagenomes and a fosmid library with an emphasis on metagenomic dark matter fraction. For this purpose, a novel data...

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Autores principales:	Carlos Sabater, Natalia Molinero, Manuel Ferrer, Carmen María García Bernardo, Susana Delgado, Abelardo Margolles
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	bile microbiome metagenomic dark matter multidrug resistance molecular docking molecular dynamics Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/5ff01d01aa864983be37c90d3979d6f0
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spelling	oai:doaj.org-article:5ff01d01aa864983be37c90d3979d6f02021-11-25T18:24:11ZFunctional Characterisation of Bile Metagenome: Study of Metagenomic Dark Matter10.3390/microorganisms91122012076-2607https://doaj.org/article/5ff01d01aa864983be37c90d3979d6f02021-10-01T00:00:00Zhttps://www.mdpi.com/2076-2607/9/11/2201https://doaj.org/toc/2076-2607Gallbladder metagenome involves a wide range of unidentified sequences comprising the so-called metagenomic dark matter. Therefore, this study aimed to characterise three gallbladder metagenomes and a fosmid library with an emphasis on metagenomic dark matter fraction. For this purpose, a novel data analysis strategy based on the combination of remote homology and molecular modelling has been proposed. According to the results obtained, several protein functional domains were annotated in the metagenomic dark matter fraction including acetyltransferases, outer membrane transporter proteins, membrane assembly factors, DNA repair and recombination proteins and response regulator phosphatases. In addition, one deacetylase involved in mycothiol biosynthesis was found in the metagenomic dark matter fraction of the fosmid library. This enzyme may exert a protective effect in Actinobacteria against bile components exposure, in agreement with the presence of multiple antibiotic and multidrug resistance genes. Potential mechanisms of action of this novel deacetylase were elucidated by molecular simulations, highlighting the role of histidine and aspartic acid residues. Computational pipelines presented in this work may be of special interest to discover novel microbial enzymes which had not been previously characterised.Carlos SabaterNatalia MolineroManuel FerrerCarmen María García BernardoSusana DelgadoAbelardo MargollesMDPI AGarticlebile microbiomemetagenomic dark mattermultidrug resistancemolecular dockingmolecular dynamicsBiology (General)QH301-705.5ENMicroorganisms, Vol 9, Iss 2201, p 2201 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	bile microbiome metagenomic dark matter multidrug resistance molecular docking molecular dynamics Biology (General) QH301-705.5
spellingShingle	bile microbiome metagenomic dark matter multidrug resistance molecular docking molecular dynamics Biology (General) QH301-705.5 Carlos Sabater Natalia Molinero Manuel Ferrer Carmen María García Bernardo Susana Delgado Abelardo Margolles Functional Characterisation of Bile Metagenome: Study of Metagenomic Dark Matter
description	Gallbladder metagenome involves a wide range of unidentified sequences comprising the so-called metagenomic dark matter. Therefore, this study aimed to characterise three gallbladder metagenomes and a fosmid library with an emphasis on metagenomic dark matter fraction. For this purpose, a novel data analysis strategy based on the combination of remote homology and molecular modelling has been proposed. According to the results obtained, several protein functional domains were annotated in the metagenomic dark matter fraction including acetyltransferases, outer membrane transporter proteins, membrane assembly factors, DNA repair and recombination proteins and response regulator phosphatases. In addition, one deacetylase involved in mycothiol biosynthesis was found in the metagenomic dark matter fraction of the fosmid library. This enzyme may exert a protective effect in Actinobacteria against bile components exposure, in agreement with the presence of multiple antibiotic and multidrug resistance genes. Potential mechanisms of action of this novel deacetylase were elucidated by molecular simulations, highlighting the role of histidine and aspartic acid residues. Computational pipelines presented in this work may be of special interest to discover novel microbial enzymes which had not been previously characterised.
format	article
author	Carlos Sabater Natalia Molinero Manuel Ferrer Carmen María García Bernardo Susana Delgado Abelardo Margolles
author_facet	Carlos Sabater Natalia Molinero Manuel Ferrer Carmen María García Bernardo Susana Delgado Abelardo Margolles
author_sort	Carlos Sabater
title	Functional Characterisation of Bile Metagenome: Study of Metagenomic Dark Matter
title_short	Functional Characterisation of Bile Metagenome: Study of Metagenomic Dark Matter
title_full	Functional Characterisation of Bile Metagenome: Study of Metagenomic Dark Matter
title_fullStr	Functional Characterisation of Bile Metagenome: Study of Metagenomic Dark Matter
title_full_unstemmed	Functional Characterisation of Bile Metagenome: Study of Metagenomic Dark Matter
title_sort	functional characterisation of bile metagenome: study of metagenomic dark matter
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/5ff01d01aa864983be37c90d3979d6f0
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Functional Characterisation of Bile Metagenome: Study of Metagenomic Dark Matter

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