Research group

Quince Group

Driving progress in how we study microbial communities

Chris Quince

High-Resolution Microbiomics Group Leader

Group activities.

The High-resolution Microbiomics group focuses on both theoretical and experimental methods for microbial community analysis.

Combining statistical bioinformatics with technological developments in sequencing and ‘omics data generation to resolve both the microbes present in a community and their functional roles and interactions. Current areas of focus include strain resolution from metagenomes, integration of metabolomics and metagenomics, and mathematical models of community assembly. These methods are applied to both simple bench-top experiments with microbial communities and large scale 'omics studies. These studies span a range of environments from host-associated to biotechnology applications.

Our Group works across both the Earlham Institute and Quadram Institute. Anyone interested in undertaking a PhD or Postdoctoral role in the Quince Group is encouraged to get in touch: christopher.quince@earlham.ac.uk.

For the latest vacancies, click here.

Methods development

Algorithms developed by our group have been incorporated into a number of bioinformatics pipelines for metagenomics maintained by ourselves and others. These include CONCOCT for metagenome binning - https://github.com/BinPro/CONCOCT, STRONG for strain resolution on assembly graphs - https://github.com/chrisquince/STRONG, and MetaHood - https://github.com/Sebastien-Raguideau/Metahood, which is an integrated metagenome analysis pipeline. We are currently working on the following novel methods:

Strain genomes from metagenome time series: we have developed algorithms for strain resolved metagenomics from short-read assembly graphs, we will utilise these methods in the future to incorporate long-reads and allow complete genome-resolved metagenomics
Experimental methods development: we are researching better extraction protocols for long reads and novel library strategies that can link plasmids to genomes such as Meta-HiC
Novel methods for multi-omics analysis: additional sources of ‘omics data can provide insights on the functional roles of community members. We are working on novel algorithms that integrate metagenomics with metabolomics to enable metabolome changes to be assigned to either the host or microbiome
Mathematical models for microbial community assembly: modelling of microbial communities has lagged behind data generation. We are developing a synthesis of statistical and dynamical models of microbial community assembly incorporating both niche-and neutral effects

Applications

Our existing pipelines and these novel methods will be applied to a wide range of systems including:

Bench-top experiments: we use simple mesocosms to explore changes in microbial communities in a controlled fashion, for instance subjecting sediments to sub-lethal levels of antibiotics (collaboration with Prof Wellington - U. of Warwick), or perturbing synthetic human microbiomes in artificial colons (collaboration with the QIB)
Treatments for pediatric Crohn’s disease: through a long-standing collaboration with Dr Gerasimidis at the University of Glasgow we are involved in the analysis of clinical trials of both therapeutic and ordinary food diets for the treatment of Crohn’s disease. Through integrated analysis of the metagenome and metabolome we aim to gain a mechanistic understanding of dietary action through modulation of the microbiome
AMR in the environment and human gut: we have developed a complete AMR metagenome analysis pipeline that has been applied to a large-scale analyses of antimicrobial resistance genes both in the River Thames and human gut microbiomes
Anaerobic digesters: this biotechnology converts organic waste to methane containing biogas that can then be used for heat and power. This conversion is performed by a complex microbial community, we have resolved thousands of microbial genomes from UK industrial AD reactors that we are now using to better understand the waste conversion process
Gastroenteritic pathogens: we head a large-scale GCRF-funded international consortium to determine the principle reservoirs of non-viral gastroenteritis in Pakistan

Projects

Team

Publications

Quince Group

Chris Quince

Group activities.

Projects.

GastroPak: Understanding and preventing the spread of non-viral gastroenteritis in Pakistan.

Methods to detect hidden diversity

Characterising gene function, biosynthetic pathways, and variation in agri/aquacultural traits

Linking fine-scale microbial diversity to ecosystem functions

Team members.

Chris Quince

Sébastien Raguideau

Rob James

Georgina Alabone

Başak Bahcivanci

Daniel Gómez Pérez

Ricardo Valencia Albornoz

Tulay Ugurlu

Lauren Messer

Haitao Han

Arkajyoti Banerjee

Publications.

Comparative genomic analysis of a metagenome-assembled genome reveals distinctive symbiotic traits in a Mucoromycotina fine root endophyte arbuscular mycorrhizal fungus

Inferring antibiotic resistance selection in the environment can be confounded by correlations between resistance genes and unrelated functional traits

The invisible threats of sunscreen as a plastic co-pollutant: Impact of a common organic UV filter on biofilm formation and metabolic function in the nascent marine plastisphere

Exploiting microplastics and the plastisphere for the surveillance of human pathogenic bacteria discharged into surface waters in wastewater effluent

Monitoring of bacterial and potentially toxic elements contamination in the Rawal Lake tributaries and filtration plant

Rapid Assembly and Functional Differentiation of the Soil Surface Microbiome in Temperate Agricultural soil

Integrating natural language processing and genome analysis enables accurate bacterial phenotype prediction

Optimisation of surfactin yield in Bacillus using data-efficient active learning and high-throughput mass spectrometry

Comparative genomic analysis of a metagenome-assembled genome reveals distinctive symbiotic traits in a Mucoromycotina fine root endophyte arbuscular mycorrhizal fungus

Design and Synthesis of Triazine-Based Hydrogel for Combined Targeted Doxorubicin Delivery and PI3K Inhibition

A closer look at plastic colonisation: Prokaryotic dynamics in established versus newly synthesised marine plastispheres and their planktonic state

Soil Metagenome PacBio V2 v2

Soil Metagenome ONT v1

Dose-dependent effects of enteral nutrition on the faecal microbiota and short chain fatty acids

Macroevolutionary Dynamics in Micro-organisms: Generalists Give Rise to Specialists Across Biomes in the Ubiquitous Bacterial Phylum Myxococcota

A genome-centric view of the role of the Acropora kenti microbiome in coral health and resilience

Gut metabolome and microbiota signatures predict response to treatment with exclusive enteral nutrition in a prospective study in children with active Crohn’s disease

Optimisation of surfactin yield inBacillususing active learning and high-throughput mass spectrometry

A marine heatwave drives significant shifts in pelagic microbiology

High-quality metagenome assembly from long accurate reads with metaMDBG

Nature’s Protectors: A Biofilm Perspective on Bacterial Disease Control in Plants

Adaptive radiations in natural populations of prokaryotes: innovation is key

The microbiome of the branching coral Acropora kenti

Enterosignatures define common bacterial guilds in the human gut microbiome

The primary molecular influences of marine plastisphere formation and function: Novel insights into organism -organism and -co-pollutant interactions

Antigen-driven colonic inflammation is associated with development of dysplasia in primary sclerosing cholangitis

Proteins released into the plant apoplast by the obligate parasitic protist Albugo selectively repress phyllosphere‐associated bacteria

Metabolic independence drives gut microbial colonization and resilience in health and disease

Transient Suppression of Bacterial Populations Associated with Gut Health is Critical in Success of Exclusive Enteral Nutrition for Children with Crohn’s Disease

Population-level impacts of antibiotic usage on the human gut microbiome

Cell specialization in cyanobacterial biofilm development revealed by expression of a cell-surface and extracellular matrix protein

Niche formation and metabolic interactions result in stable diversity in a spatially structured cyanobacterial community

Functional responses of key marine bacteria to environmental change – toward genetic counselling for coastal waters

Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere

Priorities to inform research on marine plastic pollution in Southeast Asia

Single-cell genomics reveals population structures from in vitro evolutionary studies of Salmonella

Analysis of pit latrine microbiota reveals depth-related variation in composition, and key parameters and taxa associated with latrine fill-up rate

Stimulation of Distinct Rhizosphere Bacteria Drives Phosphorus and Nitrogen Mineralization in Oilseed Rape under Field Conditions

Cell specialization in cyanobacterial biofilm development revealed by expression of a cell-surface and extracellular matrix protein

Systematic review of donor and recipient predictive biomarkers of response to faecal microbiota transplantation in patients with ulcerative colitis

Proteins released into the plant apoplast by the obligate parasitic protist Albugo selectively repress phyllosphere-associated bacteria

Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere

Biogeographical and seasonal dynamics of the marine Roseobacter community and ecological links to DMSP-producing phytoplankton

Meta-exoproteomics identifies active plant-microbe interactions operating in the rhizosphere

Impact of sulfamethoxazole on a riverine microbiome

Rhodococcus comparative genomics reveals a phylogenomic-dependent non-ribosomal peptide synthetase distribution: insights into biosynthetic gene cluster connection to an orphan metabolite

STRONG: metagenomics strain resolution on assembly graphs

Strainberry: automated strain separation in low-complexity metagenomes using long reads

Swarm v3: towards tera-scale amplicon clustering

Novel microbial syntrophies identified by longitudinal metagenomics

Predicting Lifestyle from Positive Selection Data and Genome Properties in Oomycetes

An Integrative Bioinformatic Analysis for Keratinase Detection in Marine-Derived Streptomyces

Metabolic independence drives gut microbial colonization and resilience in health and disease

Temperate southern Australian coastal waters are characterised by surprisingly high rates of nitrogen fixation and diversity of diazotrophs

Automated strain separation in low-complexity metagenomes using long reads

Predicting lifestyle and host from positive selection data and genome properties in oomycetes

Amyloid Proteins in Plant-Associated Microbial Communities

Gene duplication drives genome expansion in a major lineage of Thaumarchaeota

Microbial tropicalization driven by a strengthening western ocean boundary current