Combined metagenomic and phenomic approaches identify a novel salt tolerance gene from the human gut microbiome

Culligan, Eamonn P., Marchesi, Julian Roberto ORCID: https://orcid.org/0000-0002-7994-5239, Hill, Colin and Sleator, Roy D. 2014. Combined metagenomic and phenomic approaches identify a novel salt tolerance gene from the human gut microbiome. Frontiers in Microbiology 5 , 189. 10.3389/fmicb.2014.00189

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Abstract

In the current study, a number of salt-tolerant clones previously isolated from a human gut metagenomic library were screened using Phenotype MicroArray (PM) technology to assess their functional capacity. PM's can be used to study gene function, pathogenicity, metabolic capacity and identify drug targets using a series of specialized microtitre plate assays, where each well of the microtitre plate contains a different set of conditions and tests a different phenotype. Cellular respiration is monitored colorimetrically by the reduction of a tetrazolium dye. One clone, SMG 9, was found to be positive for utilization/transport of L-carnitine (a well-characterized osmoprotectant) in the presence of 6% w/v sodium chloride (NaCl). Subsequent experiments revealed a significant growth advantage in minimal media containing NaCl and L-carnitine. Fosmid sequencing revealed putative candidate genes responsible for the phenotype. Subsequent cloning of two genes did not replicate the L-carnitine-associated phenotype, although one of the genes, a σ54-dependent transcriptional regulator, did confer salt tolerance to Escherichia coli when expressed in isolation. The original clone, SMG 9, was subsequently found to have lost the original observed phenotype upon further investigation. Nevertheless, this study demonstrates the usefulness of a phenomic approach to assign a functional role to metagenome-derived clones.

Item Type:	Article
Date Type:	Published Online
Status:	Published
Schools:	Biosciences Systems Immunity Research Institute (SIURI)
Subjects:	Q Science > Q Science (General)
Uncontrolled Keywords:	Metagenomics; functional metagenomics; gut microbiome; microbiota; salt tolerance; BIOLOG; phenotype microarray; transcriptional regulator.
Additional Information:	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. This document is protected by copyright and was first published by Frontiers. All rights reserved. It is reproduced with permission
Publisher:	Frontiers Media
ISSN:	1664-302X
Date of First Compliant Deposit:	30 March 2016
Date of Acceptance:	7 April 2014
Last Modified:	09 May 2023 20:58
URI:	https://orca.cardiff.ac.uk/id/eprint/60331

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