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Functional Environmental Microbiology Research Group:

Current Projects:

Dr Florence Abram: Functional Environmental Microbiology Principal Investigator:

Florence Abram florence.abram@nuigalway.ie IRIS Page Google Scholar Twitter LinkedIn

Kevin McDonnell - IRC funded PhD - co-supervised by Dr Enda Howley (NUIG

This project explores innovative machine learning approaches for improving de novo protein identification from tandem mass spectrometry (MS/MS) data. First, Kevin conducted a thorough evaluation of existing de novo models, that he is currently using to benchmark his own. He is also compiling a practitioner guide to report on a deep analysis of MS/MS data with an emphasis on distinguishing the signal from the noise.

Gaurav Chugh - Hardiman Fellow - co-supervised by Prof Conor O’Byrne (NUIG)

This project focuses on microbial responses to emerging contaminants, including PFOA, a man-made perfluorinated carboxylic acid widely used in industry. Gaurav has performed a series of phenotypic characterisations of E. coli upon exposure of PFOA and octanoic acid, a non-fluorinated C8 compound used for comparative purposes. He is currently investigating E. coli’s molecular mechanisms underpinning specific phenotypes with transcriptomics combined with in vitro evolution.

Sorcha Kelly - Walsh Fellow - co-supervised by Fiona Brennan (Teagasc) and Eric Paterson (JHI)

This project examines the links between microbially mediated soil organic matter turnover and nitrogen availability in agricultural soils. Sorcha has investigated the impact of soil management practices on nitrogen mineralisation. She has also used stable isotope probing to quantify biogeochemical process rates in soil as a function of plant-derived inputs. She is currently characterising the microbial communities driving these processes by 16S and 18S rRNA profiling.

Niranjana Rose Edwin - Walsh Fellow (VistaMilk) - co-supervised by Orla O’Sullivan and Fiona Brennan (Teagasc)

This project aims to explore Irish soils as a reservoir for antimicrobial resistance (AMR) using metagenomics. Soil can act as a potential entry route for AMR into the food chain and as such investigating the prevalence of AMR genes in soil microbiomes is critical to our ability to risk assess and protect the food chain. Rose will analyse metagenomic datasets from an extensive collection comprising over 130 soil samples. She will evaluate existing tools and develop novel ones for the identification of AMR genes from soil metagenomic datasets. She will also recover metagenome-assembled-genomes and construct a soil microbiome database. Finally she will use the available extensive soil metadata to statistically put in context and interpret her findings.