I finished my PhD at the University of Warwick, UK, in Biological Sciences (microbial ecology) in October 2019 and have since held several different postdoctoral research fellow positions, primarily in the Langille Lab at Dalhousie University. Between January 2021 and December 2022, I was supported by an I3V-DMRF Dr. David H. Hubel postdoctoral fellowship and in January 2023 and again in April 2024 I was awarded a Mitacs Accelerate fellowship to work jointly between the Langille Lab and the Crosbie Lab at SickKids, Toronto.

My research interests lie in understanding the roles that microbial communities play in human and ecosystem health. This includes specific interests in: (i) evaluating the association between the microbiome and human health and disease; (ii) assessing and benchmarking the methods that we use to study microbial systems; (iii) interactions between microbial community members and how the undulations between cooperation and competition drive microbial community organisation and niche specialisation; (iv) isolating and characterising bacterial strains that are potentially able to remediate human or ecosystem health threats; and (v) understanding the evolution of mechanisms for microbial growth and persistence.

KEY SKILLS

  • Excellent written and oral communication skills, demonstrated by multiple first-author publications in peer-reviewed journals, invited conference/seminar presentations, and success in obtaining fellowships, scholarships & grants
  • Experience teaching and organizing bioinformatics workshops hosted through the Canadian Bioinformatics Workshops, IMPACTT (University of Calgary), and others at Dalhousie University run on Amazon Web Services (AWS) and Digital Research Alliance of Canada (AllianceCan) servers
  • Proficiency using multiple coding languages (Python, R, Bash) for bioinformatic analyses (both locally and cloud-based), using RStudio for tracking code used, and Github for version control and hosting tutorials

Specific skills

  • Programming languages:
    • Python (proficient)
    • R (intermediate)
    • Bash (intermediate)
    • Java (familiar)
    • Matlab (familiar)
  • Microbiome genomic analyses: development and use of analysis pipelines/scripts for:
    • Amplicon sequencing (QIIME2, Mothur and R)
    • Shotgun metagenome sequencing (taxonomic/functional read- and Metagenome Assembled Genome-based analyses using multiple tools) (e.g. HUMAnN 2/3, MMSeqs, Kraken 2, Anvi’o, MetaSPADES, MetaQUAST, PathoFact, CARD RGI)
    • Individual microbial genomes (e.g. Prokka, KEGG KOALA, Conserved Domain Searches, and CheckM)
  • Contribution to software/tools: development of existing (BioPython, PICRUSt2, QIIME2) and novel (Genome Checker) tools and databases and providing support to users of tools (Microbiome Helper, PICRUSt)
  • Miscellaneous bioinformatics:
    • Use of high-performance clusters
    • Batch job submission using cloud servers
    • Management of Amazon Web Services Instances
    • Version control using Github
    • Management of workflows/ scripts with RStudio/R notebooks
    • Proteomic and metabolomic data analysis using platform-specific programs
    • Computational models of microbial growth using Matlab/Java (iDynoMiCS)
  • Wet-lab:
    • Molecular biology techniques including Illumina MiSeq library preparation, DNA/RNA extraction, qRT-PCR, proteomic sample preparation including SDS-PAGE and Trypsin In-Gel Proteolysis; microbiological culturing/isolations/aseptic techniques
    • Microscopy including transmission electron & fluorescent
    • Analytical chemistry including spectroscopy (FTIR & Raman) and HPLC-Mass Spectrometry

ACCOMPLISHMENTS

  • 14 peer-reviewed journal articles (eight first-author; link to Google Scholar, H-index: 12)
  • 11 invited oral presentations at conferences and seminars, two invited panel discussions, 15 oral presentations, and five poster presentations at national and international conferences
  • Translational articles written on microbes colonizing oceanic plastics for the Society for Applied Microbiology, Microbiology Society, and Biological Sciences Review (magazine for 16–18-year-old Biology students)
  • Successful scholarship/fellowship awards for:
    • British Biological Sciences Research Council PhD Scholarship (2015-2019, ~£88,000/$155,000)
    • The Association of Commonwealth Universities Blue Charter Postdoctoral Fellowship (six months 2019-2020, £18,000/$32,000) – one of only ten awardees across the Commonwealth
    • I3V-DMRF (Inflammation, Infectious Diseases, Immunology and Vaccinology-Dalhousie Medical Research Foundation) Dr. David H. Hubel 2021 Postdoctoral Fellowship Award (2021-2022, $80,000)
    • Two Mitacs Postdoctoral Fellowship awards for work in collaboration with SickKids/University of Toronto (2023-2024 and 2024-2025, $60,000 and $90,000, respectively)
    • Travel grants from the International Society for Microbial Ecology (2024), Microbiology Society (2017 and 2019) and Federation of European Microbiological Societies (2018).
  • Assisted in writing grant applications within the Langille Lab (postdoc) and Christie-Oleza Lab (PhD student)
  • Senior Gray-Doolittle Award for Research Excellence (2021)
  • Faculty of Science, Engineering and Medicine Thesis Prize Winner for School of Life Sciences (2020)
  • Warwick School of Life Sciences Prize for best seminar presentation (2019)
  • Inclusion on Dean’s List for School of Marine Science and Engineering (2011, 2012 & 2013)

CURRENT POSITION

05/2020 - present
Department of Pharmacology, Dalhousie University, Nova Scotia, Canada
Principal Investigator: Dr. Morgan Langille

I am involved with several projects, but the over-arching themes of these projects are to gain an understanding of the role that the microbiome plays in the health and disease of humans. This has included analyses of: (i) the microbiome of COVID-19 testing swabs; (ii) the blood microbiomes in a large cohort of healthy Canadians (collaboration with the Personal Genome Project Canada); (iii) the saliva microbiomes of Atlantic Canadians with inflammatory bowel disease (collaboration with Atlantic Partnership for Tomorrow’s Health); (iv) the saliva microbiomes of children and adolescents with a range of mental health diagnoses and traits.

SELECTED OTHER POSITIONS

Postdoctoral Research Fellow

10/2019 - 04/2020
School for Resources and Environmental Studies, Dalhousie University
Principal Investigator: Dr. Tony Walker
Conceptualized and conducted the first meta-analysis of ~50 studies that used amplicon sequencing to characterize the “plastisphere” (microbes colonizing plastics in the environment)

Instructor for Canadian Bioinformatics Workshops (CBW)

05/2024
Design and delivery of Beginner and Advanced Microbiome Workshops held at Memorial University
Overall design of curriculum and content for all modules, overseeing design of labs by TA’s and specific design of Beginner (Module 1: Introduction to sequencing data analysis and Module 4: Functional prediction and additional analyses) and Advanced (Module 2: Metagenomic assembly and binning and Module 3: Metagenomic functional annotation) labs
Delivery of lectures in both Beginner (Module 2: Marker gene profiling) and Advanced (Module 3: Metagenomic functional annotation) courses

Sole Instructor for ICG Bioinformatics Workshop

07/2024
Institute for Comparative Genomics, Dalhousie University
Content of the workshop was mainly the same as the Beginner and Advanced Microbiome Workshops, above, but all lectures and labs were delivered by me
Setup of AWS Instances for all workshop participants, including install of all programs needed for analyses & RStudio server as well as launching of accounts/instances for participants and organizing/logistics of workshop

Other roles

  • Contribution to Microbiome Helper (Github dedicated to microbiome analysis tutorials/workflows)
  • Instructor/TA for other bioinformatics workshops: CBW-IMPACTT (University of Calgary, 07/2023, AWS), ICG (05/2023, AllianceCanada), IMPACTT (University of Calgary, 05/2022 & McGill University, 12/2022, AWS)
  • Demonstrator (TA) for undergraduate quantitative skills & statistics module (University of Warwick, 2017-2019)
  • Institute for Comparative Genomics (Dalhousie University) seminar and social media coordinator (2022-2024)

EDUCATION

PhD Biological Sciences

2015 - 2019
School of Life Sciences, University of Warwick, UK
Faculty of Science, Engineering and Medicine Thesis Prize Winner for School of Life Sciences

Thesis (July 2016-Sep 2019): Food or just a free ride? Exploring marine microbial community dynamics on natural and synthetic polymers Supervisors: Dr. Joseph Christie-Oleza (University of the Balearic Islands, Spain) and Prof. Matthew Gibson (University of Manchester, UK)
Chapter 1: Understanding microbial community dynamics to improve optimal microbiome selection
Chapter 2: A multi-OMIC study of biodegradation and microbial community succession within the PET Plastisphere
Chapter 3: Plasticizer degradation by marine bacterial isolates: a proteogenomic and metabolomic characterization

Training year (Sep 2015-July 2016):
Classes: Computer programming (R/Matlab), Statistics, High sensitivity detection of biomolecules in complex fluids (at University Hospital Coventry & Warwickshire), Chromatography, DNA sequence compilation and analysis, Protein Structure, Reverse Genetics, Shotgun Proteomics and Fluorescence Activated Cell Sorting.
Rotation project (3 months): Aging of bacteria in biofilms, using an individual-based model to study growth. Supervised by Dr. Jan-Ulrich Kreft, University of Birmingham, UK.
Professional internship (3 months): Waste Services at Coventry City Council

BSc Marine Biology (First Class, Hons.)

2010 - 2013
University of Plymouth, UK

Third year honors project: Acute toxicity of DDT sorbed to uPVC plastic particles using Cytochrome P450 1A1 (Cyp1a) gene expression analysis in larval zebrafish
Supervisors: Prof. Theodore Henry (Heriot-Watt University, UK) and Prof. Richard Thompson OBE FRS (University of Plymouth, UK)

SCHOLARSHIPS/FELLOWSHIPS

2024-2025 Mitacs: Partial salary support for 18 months of research in the Dalhousie Faculty of Medicine and at SickKids in Toronto
2023-2024 Mitacs: Partial salary support for 18 months of research in the Dalhousie Faculty of Medicine and at SickKids in Toronto
2021-2022 I3V-DMRF (Inflammation, Infectious Diseases, Immunology and Vaccinology-Dalhousie Medical Research Foundation) Dr. David H. Hubel 2021 Postdoctoral Fellowship Award: Partial salary support for two years of research in the Dalhousie Faculty of Medicine.
2019-2020 The Association of Commonwealth Universities Blue Charter Fellowship: Funding (salary, travel and consumables) for six months of research at Dalhousie University, Canada; one of ten awardees across all Commonwealth countries.
2015-2019 Midlands Integrative Biosciences Training Partnership (MIBTP) doctoral training program scholarship: Competitive PhD scholarship for British Biological Sciences Research Council (BBSRC) and MIBTP-funded Doctoral Training Partnership between the Universities of Warwick, Birmingham and Leicester. Funding included annually a stipend of ~£14,000 ($26,000), a research allowance of £4,000 ($7,000) and tuition fees of ~£4,000 ($7,000).

PRIZES

2021 Senior Gray-Doolittle Award for Research Excellence (Postdoc) Awarded for contributions to Wright et al. (2021) “Food or just a free ride? A meta-analysis reveals the global diversity of the Plastisphere”

2020 Faculty of Science, Engineering and Medicine Thesis Prize Winner for School of Life Sciences Of PhD theses completed in 2019-2020 in the School of Life Sciences, University of Warwick, UK.

2019 Warwick School of Life Sciences Prize for best seminar presentation Voted for by staff as best presentation of final year PhD student oral presentations at the Warwick School of Life Sciences postgraduate symposium.

2011, 2012 & 2013 Inclusion on Dean’s List for School of Marine Science and Engineering In recognition of exemplary academic performance during all years of BSc Marine Biology degree.

CONFERENCE & INVITED SEMINAR PRESENTATIONS

06/2024 Having IMPACTT 4: Advancing Microbiome Research Symposium (Canmore, AB, Canada)
Reducing false-positive taxa in metagenomes by coverage validation of reference genomes

02/2024 IMMSA Bioinformatics “Year Of Data Reuse” (Webinar Series)
From defaults to databases: simulated samples vs the real world

11/2023 Canadian Cancer Research Conference (Halifax, NS, Canada)
Linking tumour, blood and oral microbiomes with cancer outcomes

05/2023 OpenPlastic Symposium (Kingston, ON, Canada)
Elucidating the functional capacity of the aquatic plastisphere

10/2021 How polluting is plastic? (Microbiology Society and Royal Society of Chemistry webinar)
Biodegradation and microbial dynamics within the PET plastisphere (15 min virtual presentation)

10/2021 MIPLACE seminar series (Imperial College London, UK)
Food or just a free ride? Elucidating the functional capacity of the aquatic plastisphere (1 hr virtual presentation)

04/2021 Webinar Series on Plastic Pollution and Plastisphere (Nanyang Technological University, Singapore)
Food or a just free ride? Elucidating the role of the plastisphere in marine plastic degradation (1 hr virtual presentation)

04/2021 ACS Spring 2021 (Virtual conference and panel discussion)
Food or a just free ride? Elucidating the role of the plastisphere in marine plastic degradation (30 min virtual presentation)

12/2020 MicroSeminar (Virtual Microbiology Seminar Series)
Food or just a free ride? Elucidating the role of the Plastisphere in marine plastic degradation (1 hr virtual presentation; available online here)

03/2019 Plastic Pollution: Individual responsibility or beyond our control? (University of Birmingham, UK)
Panel discussion

03/2017 Warwick Manufacturing Group Seminar Series (University of Warwick, UK)
Plastic oceans – can microbes clean up our mess? (1 hr presentation)

04/2013 University of the Third Age (Plymouth, UK)
1 hr presentation to retired academics on the sources and impacts of marine microplastics

OTHER CONFERENCE PRESENTATIONS

08/2024 ISME19 (Cape Town, South Africa)

  1. Reducing false-positive taxa in metagenomes by coverage validation of reference genomes (Oral presentation)
  2. Linking the oral microbiome with child and adolescent mental health (Poster presentation)

06/2024 Precision Child and Youth Mental Health (Ottawa, ON, Canada)
Linking the oral microbiome with child and adolescent mental health (Oral presentation)

07/2023 Having IMPACTT 3: Advancing Microbiome Research (Canmore, AB, Canada)
Linking the oral microbiome with child and adolescent mental health (Poster presentation)

06/2023 72nd Annual Conference of the Canadian Society of Microbiologists (Halifax, NS, Canada)
Linking the oral microbiome with child and adolescent mental health (Oral presentation)

10/2022 Cold Spring Harbor Laboratory Microbiome Meeting (Long Island, NY, USA)
Exploring compositional changes and microbial biomarkers of Inflammatory bowel disease in the saliva microbiome (Poster presentation)

06/2022 Having IMPACTT 2: Advancing Microbiome Research (Canmore, AB, Canada)
From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools in low microbial biomass samples (Oral presentation)

06/2021 Having IMPACTT: Advancing Microbiome Research Symposium (Virtual conference)
Utilising human genome sequencing data to investigate the blood microbiome: Choice of analysis methods drastically affect taxonomic profiling (Poster presentation)

10/2020 Cold Spring Harbour Laboratory Virtual Microbiome Meeting
Choice of classification tool and taxonomic database drastically affect taxonomic profiling of human blood metagenomes (Poster and flash oral presentation)

04/2019 Microbiology Society Annual Conference 2019 (Belfast, UK)

  1. Food or a free ride? The ability of a marine microbial community to degrade plastics (Oral presentation)
  2. Bacterial coping mechanisms for aging: using an individual-based model to study aging in biofilms (Oral presentation)

03/2019 Warwick School of Life Sciences Postgraduate Symposium (Warwick, UK)
Food or a free ride? The ability of a marine microbial community to degrade plastics (Oral presentation; prize for best seminar presentation)

12/2018 Molecular Microbial Ecology Group 2018 (Swansea, UK)
Food or a free ride? The ability of a marine microbial community to degrade plastics (Oral presentation)

11/2018 MICRO2018 Fate and Impact of Microplastics (Lanzarote, Spain)
Can a microbial community biodegrade poly(ethylene terephthalate) (PET)? (Oral presentation)

05/2018 15th Marine Biological Association Postgraduate Conference 2018 (Plymouth, UK)
Artificial ecosystem selection for marine polymer degradation (Oral presentation)

03/2018 6th International Marine Debris Conference (San Diego, USA)
Artificial ecosystem selection for marine polymer degradation (Oral presentation)

12/2017 Molecular Microbial Ecology Group (Warwick, UK)
Artificial ecosystem selection for marine polymer degradation (Oral presentation)

04/2017 Microbiology Society Annual Conference (Edinburgh, UK)
Is repair better than segregation of damage for aging cells in a biofilm? (Poster and flash oral presentation)

12/2016 ISCB Computational and Molecular Biology Symposium (Dublin, Ireland)
Aging of biofilms using a single-cell growth model (Oral presentation)

09/2013 ERIC and SETAC joint annual meeting (Plymouth, UK)
Acute toxicity of DDT and expression of Cytochrome P450 1A1 (CYP1A1) gene transcripts in larval zebrafish (Poster presentation)

OTHER ACADEMIC ACTIVITIES

2020 - present Peer-reviewer for multiple Q1 journals and grants: Microbiome (1), Environmental Microbiology (3), Environmental Science and Technology Letters (1), Journal of Hazardous Materials (2), Marine Pollution Bulletin (3), Environment International (1), Environmental Pollution (1), mSystems (2), PeerJ (2), Environmental Science and Technology (2), MicrobiologyOpen (1), Applied & Environmental Microbiology (1), Genome Biology (1), Environmental Microbiome (2), Environmental Science: Processes & Impacts (1), Frontiers in Microbiology and Symbiosis (1)
2022 - present Vice-President of Dalhousie Postdoctoral Society
2022 - 2024 Institute for Comparative Genomics (ICG), Dalhousie University, seminar series coordinator
2022 - 2023 72nd Annual Conference of the Canadian Society of Microbiologists organizing committee
2021 - 2024 Public Service Alliance of Canada Dalhousie Postdoc collective agreement bargaining team
2018 - 2019 School of Life Sciences symposium organizing committee
2018 - 2019 Staff-student liaison committee, University of Warwick, UK

OUTREACH

08/2021 Interviewed for The Guardian article “Welcome to the ‘plastisphere’: the synthetic ecosystem evolving at sea” (link to article)
11/2020 Radio interview with Portia Clark on CBC (Canadian Broadcasting Corporation) Information Morning Nova Scotia (link to interview)
11/2020 “The bacterial colonisers of plastics – food or just a free ride?”: Nature Microbiology behind the paper blog post based on the “Food or just a free ride? A meta-analysis reveals the global diversity of the Plastisphere” publication (link to blog post)
07/2020 Participated in video on plastic pollution produced by the Blue Charter (Association of Commonwealth Universities for World Ocean Day 2020 (link to video)
04/2019 Sponsored cycle to Belfast (total 500 km) for Microbiology Society Annual Conference 2019 (Blog post written for the Microbiology Society: Annual conference 2019: the road to Belfast) in order to raise awareness of the climate impact of conference travel
2017 Oceans public science evening open science evening event held at the University of Warwick
2016 - 2019 Science Technology Engineering and Maths (STEM) ambassador
2011 - 2014 Surfers Against Sewage charity area representative (organizing and attending beach cleans)
2012 Plymouth marine city showcase volunteer representative for Plymouth University - educating adults and children on what microplastics are, the associated problems with their use and design and implementation of interactive activities.