Environmental AMR & One Health
How antimicrobial resistance evolves and spreads across wastewater, rivers, soils and hosts — with a focus on mobile genetic elements and catchment-scale surveillance.
resistomesmobilomewastewatersource tracking
Molecular Ecology · UKCEH
Reading ecosystems through their genomes
Dr Susheel Bhanu Busi — Head of Molecular Ecology, UK Centre for Ecology & Hydrology
I build molecular observatories that track how microbial life responds to environmental pressure — from glacier-fed streams to farmland soils and wastewater — to deliver evidence for environmental resilience and One Health.
About
Microbial data as operational evidence
I lead molecular ecology at UKCEH, where our group develops high-resolution, genome-resolved approaches to follow environmental microbiomes over time across terrestrial and aquatic systems. We integrate metagenome-assembled genomes, gene catalogues and trait frameworks to build indicators of soil and ecosystem health, and to track antimicrobial resistance as it moves between people, animals and the environment.
Before UKCEH I spent four years at the Luxembourg Centre for Systems Biology with Paul Wilmes, working on the evolution and spread of AMR in a One Health setting and — with Tom Battin's group at EPFL — on the biofilms of high-alpine glacier-fed streams. My PhD at the University of Missouri used multi-omics to understand how gut biofilms and the microbiome shape colon cancer.
Today my focus is on turning microbial data into evidence that regulators, industry and communities can use — partnering with the Environment Agency, Defra, DAERA and academic colleagues across the UK and Europe.
60+
peer-reviewed papers, including Nature, Nature Communications, Nature Microbiology and The ISME Journal
£3M+
active UKRI/NERC research funding as PI or Co-I, including CLEAR-NEAGH (PI)
16
PhD and MSc students mentored, 11 graduated
2
Associate Editor roles — Environmental DNA and Metabarcoding & Metagenomics
Research
What we work on
Four connected threads, all built on genome-resolved, longitudinal views of microbial communities.
Molecular observatories & eDNA
National-scale biomonitoring of rivers and catchments using eDNA, biofilms and long-read sequencing — building indicators regulators can act on.
eDNAriver biofilmsbiomonitoringNanopore/PacBio
Genomic traits & soil health
Linking microbial genomic traits to ecosystem function — from restoration chronosequences to agricultural soils — to develop nutrient-cycling and soil-health indicators.
MAGstrait frameworksrestorationnutrient cycling
Microbiomes under climate change
The genomic and metabolic adaptations of biofilms in glacier-fed streams and other extreme or rapidly changing ecosystems, and what they tell us about resilience.
cryospherebiofilmscross-domain interactionsBGCs
In figures
Research in pictures
Selected figures from open-access papers. Click any figure to enlarge; each links to the full article.
Current funding
Active projects
Research grants I currently lead or contribute to.
PINERC
CLEAR-NEAGH
Catchment-Level Environmental AMR & eDNA Reconnaissance for Lough Neagh.
Co-INERC
P-FASE
Advancing and integrating knowledge and data on PFAS sources, fate and risks for UK environments.
Co-INERC
MICRO-CYCLE
The role of microbial genomic traits in organic matter cycling and molecular composition along the river continuum.
CollaboratorMRC · FNR
PathoBiome
Expansion and validation of microbiome-derived virulence factors (with P. Wilmes & R. Finn).
Publications
Selected & latest work
The full list below updates automatically from my Google Scholar profile.
Nature · 2025
Diversity and biogeography of the bacterial microbiome in glacier-fed streams
Ezzat, Peter, Bourquin, Busi, … Battin Nat. Commun. · 2025National-scale biogeography and function of river and stream bacterial biofilm communities
Thorpe, Busi, Warren, Hunt, Walsh, Read Nat. Commun. · 2022Genomic and metabolic adaptations of biofilms to ecological windows of opportunity in glacier-fed streams
Busi*, Bourquin*, Fodelianakis*, … Battin Nat. Commun. · 2022Evolution of the murine gut resistome following broad-spectrum antibiotic treatment
de Nies*, Busi*, Tsenkova, Halder, Letellier, WilmesLoading publications…
Experience
Career
- FEB 2025 — PRESENT
Head of Molecular Ecology
UK Centre for Ecology & Hydrology · WallingfordStrategic leadership for molecular ecology across UKCEH; delivering molecular observatories for environmental resilience and One Health.
- 2023 — 2025
Molecular Ecologist
UKCEH · Soils & Land Use Science AreaLinking fine-scale microbial diversity to ecosystem function; genome-resolved soil-health indicators.
- 2019 — 2023
Research & Development Specialist
Luxembourg Centre for Systems Biology · University of LuxembourgAMR evolution and spread in a One Health setting; multi-omics of glacier-fed stream biofilms (with EPFL).
- 2013 — 2018
Doctoral Researcher
University of Missouri · Molecular Pathogenesis & TherapeuticsMulti-omics of gut biofilms and the microbiome in a rat model of colon cancer.
- 2009 — 2013
Research Scientist · Operations Manager
Imagilin Technology LLC · MarylandProbiotic R&D and cGMP manufacturing; inventor on a US patent for heat-resistant probiotics.
- 2008 — 2009
AdWords Representative
Google Inc. · Hyderabad
Education
PhD, Molecular Pathogenesis & TherapeuticsUniversity of Missouri, USA · 2018
MS, Biomedical ScienceHood College, USA · 2012
BSc, MicrobiologyMadras Christian College, India · 2008
Selected honours
- Best Oral Presentation (Postdoc), Luxembourg Microbiology Day · 2021
- Outstanding Oral Presentation, EMBO Human Microbiome Symposium · 2019
- Best Poster, Symposium on Aquatic Microbial Ecology (SAME16) · 2019
- AACR Scholar-in-Training Award · 2018
- Mizzou 18 Inaugural Class · 2018
- 3MT: 1st place & People's Choice (MU), People's Choice (MAGS) · 2017–18
Patent
High temperature resistant probiotics for food and feed preparations. US 9,289,008 (2016).
Community
Service, mentoring & code
Editorial
Associate Editor
Environmental DNAMetabarcoding & Metagenomics
Reviewer for
Nature CommunicationsNature MicrobiologyISME JMicrobiomePLOS BiologyWater ResearchmBiomSystemseLifeCell Host & Microbe
Mentoring & teaching
- Supervised 16 PhD and MSc students (11 graduated), including current UKCEH PhD students
- Lecturer, Global Environmental Change in the Anthropocene, University of Luxembourg (2022–)
- Medical Microbiology & Immunology, University of Missouri School of Medicine
- EMBO Laboratory Leadership for Postdocs (2022)
Outreach
- Chercheurs à l'école school outreach, Luxembourg (2019, 2021)
- Nimools alleng, ëmmer mateneen: Living in a microbial world — FNR public-engagement grant (co-PI)
- Judge, Life Sciences Day, University of Missouri
Open-source bioinformatics
@susheelbhanuContact
Let's work together
I'm always happy to talk about collaborations, studentships, fellowships and ways to put microbial data to work for environmental policy.
Maclean Building, Benson Lane
Crowmarsh Gifford, Wallingford
Oxfordshire OX10 8BB, UK
Group news: @ukceh-moleco on Bluesky