Metagenomics & Meta-transcriptomics
Reading whole microbial communities — who is there, and what are they doing — from soils, water and the built environment.
01School of Biological Sciences, University of Reading
Dr Soon Gweon
Associate Professor in Applied Genomics & Bioinformatics
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Bioinformatics-led research on the hidden world of microbes.
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Hyun Soon Gweon
// about
Hi, I'm Soon.
I am an Associate Professor at the School of Biological Sciences, University of Reading (2017–present). I read Genetics at the University of Nottingham and Bioinformatics (Structural Biology) at the University of Cambridge. Before Reading, I spent several years at the UK Centre for Ecology & Hydrology (2011–2017).
My research sits at the interface of molecular ecology, applied genomics and bioinformatics. I combine computational analysis with molecular techniques to ask — and answer — questions about the microbial world.
My group studies the abundance, diversity, activity and interactions of microbes across ecosystems — from soils and rivers to hospital sink drains — using metagenomics, metabarcoding and genomics, backed by dedicated HPC infrastructure.
Genetics Univ. of Nottingham
Bioinformatics Univ. of Cambridge
UKCEH 2011–2017
Univ. of Reading 2017–present
// research
What we work on
We are a bioinformatics-led lab working to understand the abundance, diversity, activity and interactions of microbes across a wide range of ecosystems — combining cutting-edge sequencing, state-of-the-art molecular biology, and big-data analysis on dedicated HPC.
Antimicrobial Resistance
Tracking the emergence, dissemination and persistence of AMR along the wastewater–river continuum and in clinical settings.
02Microbes of the Built Environment
Hospital and campus sink drains as hotspots for microbial communities and resistant pathogens.
03Soil & Freshwater Microbial Ecology
How land use, pH, nutrients and disturbance shape bacterial and fungal communities and the functions they drive.
04Tool & Algorithm Development
Building open, reproducible bioinformatics pipelines that the wider community can pick up and run.
05eDNA & Biomonitoring
Environmental DNA and citizen-science approaches for national-scale, long-term biodiversity monitoring.
06// people
The team
Current doctoral researchers driving the lab's work forward.
AC
Ana Carolina Yamakawa
PhD (2022–present)
AD
Ashinsa de Silva Wijeyeratne
PhD (2022–present)
OJ
Oliver J Hasimuna
PhD (2023–present)
CS
Calum S McKinney
PhD (2025–present)
Past members & students 21 ↓
- Zoe Withey · PhD · (2019–2024)
- Lucy Bates · MSc · (2020–2021)
- Alex Stormer · MSc · (2020–2021)
- Emily Wright · UROP · (2022–2023)
- Marcello Beltrami · Undergraduate · (2022–2023)
- Phoebe French · Undergraduate · (2022–2023)
- Jasper Almond · Undergraduate · (2022–2023)
- James Bussingham · Undergraduate · (2022–2023)
- Alex Thomas · Undergraduate · (2022–2023)
- Naomi Jenkins Martinez · Undergraduate · (2021–2022)
- Elsie Fell · Undergraduate · (2021–2022)
- Alisha Awan · Undergraduate · (2021–2022)
- Naol Duguma · Undergraduate · (2021–2022)
- Ed Neary · Undergraduate · (2021–2022)
- Elin Smith · Undergraduate · (2021–2022)
- Jack Lindsell · Undergraduate · (2020–2021)
- Lucy Wells · Undergraduate · (2019–2020)
- Laura O’Gallagher · Undergraduate · (2019–2020)
- Max Long · Undergraduate · (2019–2020)
- Kai Smith · Undergraduate · (2019–2020)
- Kieren Mundy · Undergraduate · (2019–2020)
// publications
Selected & recent work
Auto-synced from Google Scholar · 2026-07-31- 2026 Biofilm removal in hospital sink drains drives unintended surges in antibiotic resistance npj Antimicrobials and Resistance 5 cites
- 2026 Unlocking river biofilm microbial diversity: a comparative analysis of sequencing technologies Molecular Ecology Resources 2 cites
- 2026 Heavy Metal Contamination in Two Tilapia Species (Oreochromis macrochir and Coptodon rendalli) From the Kabompo River, Zambia Aquaculture, Fish and Fisheries 1 cites
- 2026 Molecular detection of honeybee pathogens in honey from a UK citizen science program Journal of Microbiological Methods 1 cites
- 2026 Taxonomic filtering accompanies functional expansion during long-term soil restoration The ISME Journal 1 cites
- 2026 Antimicrobial resistance as a signature of soil restoration across a 143-year chronosequence bioRxiv, 2026.06. 02.729492 0 cites
- 2026 Using honeybees for national scale long-term eDNA biomonitoring. Plos one 0 cites
- 2026 Redclaw crayfish: challenge or resource? Voices of fishers in Zambia Aquatic Conservation: Marine and Freshwater Ecosystems 0 cites
- 2025 Evaluating the effectiveness of sodium hypochlorite for genomic DNA decontamination Environmental DNA 7 cites
- 2025 Heavy metal contamination and ecological risk in Kabompo River, Northwestern Zambia Environmental Pollutants and Bioavailability 4 cites
- 2025 Deciphering Landscape‐Scale Plant Cover and Biodiversity From Soil eDNA Environmental DNA 3 cites
- 2024 A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses Molecular ecology resources 102 cites
- 2024 Dissemination and persistence of antimicrobial resistance (AMR) along the wastewater-river continuum Water research 45 cites
- 2024 Longitudinal bacterial community dynamics and sodium hypochlorite intervention in a newly built university building Science of the Total Environment 4 cites
- 2023 Mycobial community assemblages in sink drains across a university campus Environmental DNA 3 cites
- 2023 Microbial diversity and antimicrobial resistance in faecal samples from acute medical patients assessed through metagenomic sequencing Plos one 2 cites
- 2022 Accumulation of nylon microplastics and polybrominated diphenyl ethers and effects on gut microbial community of Chironomus sancticaroli Science of the Total Environment 34 cites
- 2022 Sedimentary DNA records long‐term changes in a lake bacterial community in response to varying nutrient availability Environmental DNA 23 cites
- 2022 Citizen science monitoring reveals links between honeybee health, pesticide exposure and seasonal availability of floral resources Scientific Reports 20 cites
- 2022 Environmental factors and host genetic variation shape the fungal endophyte communities within needles of Scots pine (Pinus sylvestris) Fungal Ecology 18 cites
- 2022 The interactions and hierarchical effects of long‐term agricultural stressors on soil bacterial communities Environmental microbiology reports 8 cites
- 2021 Contrasting community assembly processes structure lotic bacteria metacommunities along the river continuum Environmental Microbiology 204 cites
- 2021 Interacting effects of land use type, microbes and plant traits on soil aggregate stability Soil Biology and Biochemistry 105 cites
- 2021 Niche and local geography shape the pangenome of wastewater-and livestock-associated Enterobacteriaceae Science advances 103 cites
- 2021 A genomic epidemiological study shows that prevalence of antimicrobial resistance in Enterobacterales is associated with the livestock host, as well as Microbial Genomics 65 cites
- 2021 Genomic network analysis of environmental and livestock F-type plasmid populations The ISME journal 53 cites
- 2021 Population-level faecal metagenomic profiling as a tool to predict antimicrobial resistance in Enterobacterales isolates causing invasive infections EClinicalMedicine 26 cites
- 2021 Equine grass sickness (a multiple systems neuropathy) is associated with alterations in the gastrointestinal mycobiome Animal Microbiome 21 cites
- 2021 Characterization of communal sink drain communities of a university campus Environmental DNA 18 cites
- 2021 Bacterial communities in larger islands have reduced temporal turnover The ISME Journal 17 cites
- 2021 Neonicotinoid use on cereals and sugar beet is linked to continued low exposure risk in honeybees Agriculture, Ecosystems & Environment 17 cites
- 2021 Integration of DNA extraction, metabarcoding and an informatics pipeline to underpin a national citizen science honey monitoring scheme MethodsX 15 cites
- 2021 Gut and faecal bacterial community of the terrestrial isopod Porcellionides pruinosus: potential use for monitoring exposure scenarios Ecotoxicology 9 cites
- 2020 Genomic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients Microbial genomics 79 cites
- 2020 Accumulation of polybrominated diphenyl ethers and microbiome response in the great pond snail Lymnaea stagnalis with exposure to nylon (polyamide) microplastics Ecotoxicology and Environmental Safety 58 cites
- 2020 Rhizosphere bacteria are more strongly related to plant root traits than fungi in temperate montane forests Plant and Soil 51 cites
- 2020 Nutrients influence the dynamics of Klebsiella pneumoniae carbapenemase producing enterobacterales in transplanted hospital sinks Water research 43 cites
- 2020 The unintended consequences of a surge in antibiotic resistance when removing wastewater drain biofilm bioRxiv, 2020.11. 06.372326 6 cites
- 2020 Metrics for public health perspective surveillance of bacterial antibiotic resistance in low-and middle-income countries Biorxiv 4 cites
- 2020 Multi-omic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients bioRxiv, 2020.02. 19.952366 2 cites
- 2019 The pH optimum of soil exoenzymes adapt to long term changes in soil pH Soil Biology and Biochemistry 193 cites
- 2019 The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples Environmental Microbiome 149 cites
- 2019 Genetic, epigenetic and microbiome characterisation of an earthworm species (Octolasion lacteum) along a radiation exposure gradient at Chernobyl Environmental Pollution 27 cites
- 2019 Beyond taxonomic identification: integration of ecological responses to a soil bacterial 16S rRNA gene database bioRxiv 23 cites
- 2019 Environmental and host filtering of ectomycorrhizal fungi at large scales S van der Linde, LM Suz, D Orme, F Cox, H Andreae, E Asi, B Atkinson, ... 0 cites
- 2018 Soil bacterial networks are less stable under drought than fungal networks Nature communications 2,153 cites
- 2018 Land use driven change in soil pH affects microbial carbon cycling processes Nature communications 1,040 cites
- 2018 Environment and host as large-scale controls of ectomycorrhizal fungi Nature 506 cites
- 2018 Soil microbial diversity in open and closed forest patches along a soil temperature gradient Annual Meeting" Soil Biodiversity and european woody agroecosystems. COST … 0 cites
- 2018 Author Correction: Environment and host as large-scale controls of ectomycorrhizal fungi Nature 0 cites
- 2017 Environmental metabarcoding reveals contrasting belowground and aboveground fungal communities from poplar at a Hg phytomanagement site Microbial Ecology 61 cites
- 2017 Helminth burden and ecological factors associated with alterations in wild host gastrointestinal microbiota The ISME journal 50 cites
- 2017 Assessment of the bimodality in the distribution of bacterial genome sizes The ISME Journal 12 cites
- 2017 Microbial communities from poplar at a Hg phytomanagement site 14th International Conference on the Biogeochemistry of Trace Elements (ICOBTE) 0 cites
- 2016 Soil pH effects on the interactions between dissolved zinc, non-nano-and nano-ZnO with soil bacterial communities Environmental Science and Pollution Research 114 cites
- 2016 Mapping and validating predictions of soil bacterial biodiversity using European and national scale datasets Applied Soil Ecology 94 cites
- 2016 Sequence and organization of the complete mitochondrial genome of the blackfly Simulium variegatum (Diptera: Simuliidae) Mitochondrial DNA Part B 9 cites
- 2015 PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the I llumina sequencing platform Methods in ecology and evolution 417 cites
- 2015 Catchment-scale biogeography of riverine bacterioplankton The ISME journal 296 cites
- 2015 Rearing and foraging affects bumblebee (Bombus terrestris) gut microbiota Environmental Microbiology Reports 23 cites
- 2015 Monitoring soil biodiversity in nature reserves in England-a role for metabarcoding First Global Soil Biodiversity Conference 0 cites
- 2012 Bio-Linux as a tool for bioinformatics training 2012 IEEE 12th International Conference on Bioinformatics & Bioengineering … 1 cites
- 2010 PIPITS: An automated pipeline for analyses of fungal ITS sequences from the Illumina sequencing platform HS Gweon, A Oliver, J Taylor, T Booth, M Gibbs, DS Read, RI Griffiths, ... 1 cites
- 2004 Organisation of the pantothenate (vitamin B5) biosynthesis pathway in higher plants The Plant Journal 99 cites
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// join us
Work with us
We are always looking for talented, motivated researchers interested in questions of mutual interest. Get in touch — even when no funded post is advertised, we are happy to support fellowship and funding applications.
Postdoctoral Researchers
Funded positions are posted here when available. We are also happy to discuss and co-develop fellowship or grant proposals. See this list of potential funding schemes.
PhD Students
We welcome PhD students working on molecular & microbial ecology, eDNA, AMR, metagenomics and related areas. The application cycle typically opens in October and closes in December (details). Please contact us with a CV and a short research statement.
Interns & Research Assistants
We welcome motivated graduate students able to commit six months or more, and a limited number of undergraduates over vacations — we encourage applying to the UROP programme or external schemes. Get in touch for an informal chat first.
// contact
Get in touch
h.s.gweon [at] reading.ac.uk ↗
Health and Life Sciences Building, University of Reading, Whiteknights, Reading RG6 6EX, UK