Dr Paul Sheridan

Biography

Hi! I am a microbiologist at the University of Aberdeen with specific interests in the metabolism, genomics and evolution of prokaryotic life.

After receiving an undergraduate degree in Microbiology from Trinity College Dublin, I undertook a joint PhD between the Rowett Institute and University College Cork. My PhD research focused on the gut microbiota and the physiology of the strictly anaerobic and butyrate producing Roseburia genus. This work characterised species-specific differences in polysaccharide utilisation within the Roseburia genus and identified the presence of genomic loci dedicated to polysaccharide utilisation that were analogous but distinct from the prototypic PULs of Bacteroidetes.

I then spent three years as a Microbiology Research Fellow at the Rowett institute developing next generation probiotics from the indigenous members of the human gut microbiota. This involved a combination of in vitro and comparative genomic approaches to study the ecophysiology of a wide range of gut bacteria and the development of numerous techniques for high-throughput phenotypic analysis of gut bacteria that work in tandem with their strictly anaerobic nature.

I then spent three years a Microbial Genomics Research Fellow in the School of Biological Sciences, University of Aberdeen. My research involved developing phylogenetic and comparative genomic methods to study evolution and niche adaption, particularly in archaea, and the recovery and analysis of novel genome sequences from ultra-deep and targeted soil metagenomes.

I am now an Interdisciplinary Research Fellow at the University of Aberdeen. This 3-month project is supported by the SBS Windfall Fund. I work with researchers from the School of Biological Sciences and Computing Science Department to investigate the applications of artificial intelligence in genomic analysis. 

My work would not be possible without the help and support of my amazing collaborators from within my own university and from around the world!

Research Overview

My work focuses on the physiology and evolution of bacteria and archaea using a combination of genomic and experimental approaches. I have published over a dozen peer-reviewed papers, including a first author paper in Nature Communications and have had fruitful collaborations with industrial partners, identifying several promising candidates for development as next generation probiotics. I have developed genomic tools in advanced phylogenetics, context-informed metagenomics, genome-resolved metagenomics and probabilistic ancestor reconstruction, which I have utilized in the in the exploration of microbial physiology and ancient genome evolution. 

Current Research

My current research project involves developing phylogenetic and comparative genomic methods to study ancient genome evolution and niche adaptation, particularly in the thaumarchaeotal phylum, and the recovery of novel genome sequences from ultra-deep soil metagenomics.

In this work we identified that the ancient transition of Thaumarchaeota into a terrestrial environments coincided with two large lateral gene transfer events, and that gene duplication of these new gene families was a major driver of genome expansion in terrestrial ammonia oxidizing archaea.

While gene duplication is a well-documented mechanism in eukaryotic evolution, its role in the evolution of archaea had been under-appreciated and this insight significantly improves our understanding of ancient genome evolution and habitat transition in archaea.

Ongoing work:

Genome evolution driving ancient habitat transitions in archaeal phyla with complex evolutionary histories (Thermoplasmatota)

Recovering genomes from microbes of the terrestrial rare biosphere

Physiology and evolution of novel Thaumarchaeota lineages

Context-informed metagenomics

Developing new genomic, phylogenomic and metagenomic tools

Teaching Responsibilities

Reservoirs of Antimicrobial Resistance

These lectures, in collaboration with Dr Karen Scott (Rowett Institute), explore host and environmental reservoirs of antimicrobial resistance genes and examine molecular and bioinformatics approaches to tracking the origins of antimicrobial resistance. 

This includes the topics:

• Global burden of antibiotic resistance
• Reservoirs of antibiotic resistance genes
• Mechanisms of gene transfer between bacteria
• Evolution of novel antibiotic resistance genes

Genomics in Microbial Ecology

These lectures, in collaboration with Dr Ashish Malik (School of Biological Sciences), explore the use of omics techniques in understanding microbial ecosystems and revealing uncultured branches of microbial life.

This includes the topics:

• Metagenomics
• Genome-resolved metagenomics
• Single-cell genomics
• Comparative genomics
• Transcriptomics
• Applications of Omics techniques in Ecology 

Exploring biodiversity with R

This practical course provides students with hands-on experience using R packages to study the biodiversity of microbial ecosystems.

This includes the topics:

• Metrics of biodiversity
• Practical exercises in R
• Discussion

Practical genomics and metagenomics 

This practical course provides postgraduates with hands-on training in genomics and metagenomics over five afternoon sessions

This includes the topics:

• Sequence read QA and cleaning
• Genome assembly
• Reconstructing metagenome assembled genomes (MAGs)
• Classifying and quantifying MAGs
• Metabolic prediction from genomes