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

Authors

Eamon Culligan, Alimentary Pharmabiotic Centre, Biosciences Institute, University College Cork, Cork, Ireland
Julian R. Marchesi, Alimentary Pharmabiotic Centre, Biosciences Institute, University College Cork, Cork, Ireland, Cardiff School of Biosciences, Cardiff University, Cardiff, UK, Department of Surgery and Cancer, Centre for Digestive and Gut Health, Imperial College London, London, UK
Colin Hill, Alimentary Pharmabiotic Centre; University College Cork; Cork, Ireland
Roy D. Sleator, Alimentary Pharmabiotic Centre; University College Cork; Cork, Ireland; Department of Biological Sciences; Cork Institute of Technology; Cork, Ireland.

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.

Disciplines

Biology | Cell Biology | Genetics and Genomics | Genomics | Human and Clinical Nutrition | Microbiology | Molecular, Genetic, and Biochemical Nutrition | Molecular Genetics

DOI

10.3389/fmicb.2014.00189

Full Publication Date

April 2014

Publication Details

Frontiers in Microbiology

Publisher

Frontiers Media

Funder Name 1

Science Foundation Ireland

Award Number 1

07/CE/B1368

Resource Type

journal article

Access Rights

open access

License Condition

This work is licensed under a Creative Commons Attribution 4.0 International License.

Alternative Identifier

https://www.frontiersin.org/articles/10.3389/fmicb.2014.00189/full

Recommended Citation

Culligan EP, Marchesi JR, Hill C and Sleator RD (2014) Combined metagenomic and phenomic approaches identify a novel salt tolerance gene from the human gut microbiome. Front. Microbiol. 5:189. doi: 10.3389/fmicb.2014.00189