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Research

Reading the genomes of bacteria’s natural predators

Our research started with SEA-PHAGES genome annotation. It now covers antimicrobial resistance, cancer transcriptomics and metagenomics, with all analysis carried out computationally by undergraduates.

Why phages?

An answer to antimicrobial resistance

Bacteriophages are viruses that infect and kill bacteria. As drug-resistant infections spread, phages and the enzymes they make offer a promising alternative to antibiotics.

Each IBRT cohort works through a genome in detail. Members call genes, check start sites, assign functions and compare the genome with related phages. The finished, quality-checked annotations go to the NCBI GenBank and the HHMI-curated Actinobacteriophage Database, where they stay as a permanent contribution to science.

“The fact that you have been able to submit isolates to the GenBank means that it will always be in that database forever… I will say that is the greatest achievement.” Prof. O.G. Ademowo

A framed IBRT poster on computational analysis of a Gordonia bacteriophage on the department wall
Three IBRT research posters hang on the walls of the BMLS department building
Phage genome library

Eight genomes, permanently on record

Every phage below was annotated by IBRT undergraduates under faculty supervision through the SEA-PHAGES programme.

Idaho
Actinobacteriophage
Accession
MK757448
Annotated
2019
Team
Pioneer cohort (2k18)
Dothraki
Actinobacteriophage
Accession
MT451985
Annotated
2020
Team
Second cohort (2k19)
Sedona
Gordonia phage · Cluster DE1
Accession
MW822146
Annotated
2021
Team
Third cohort (2k20)
Phishy
Actinobacteriophage
Accession
MW862986
Annotated
2021
Team
Third cohort (2k20)
Gretchen
Microbacterium phage
Accession
NCBI submitted
Annotated
2021
Team
Third cohort (2k20)
Popper
Arthrobacter phage
Accession
NCBI submitted
Annotated
2021
Team
Third cohort (2k20)
Bianmat
Gordonia phage
Accession
NCBI submitted
Annotated
2022
Team
2022 research year
Salvador
Gordonia phage
Accession
NCBI submitted
Annotated
2022
Team
2022 research year

Tools we use: DNA Master · GeneMarkS · Phamerator · Starterator · BLAST · HHpred · Artemis & the Artemis Comparison Tool · RAST

Research working groups

Four groups, one training model

From Year 2, each member joins one working group and stays with it through to the end of training. There they design and carry out the group’s projects.

Founding group

Bacteriophage Research Group

This is the core SEA-PHAGES work: annotating and comparing actinobacteriophage genomes. Recent projects include Gordonia phages Bianmat and Salvador, and reviews of phage endolysins, depolymerases and anti-CRISPR systems.

  • Complete genome annotation and comparative genomics
  • Phamerator maps and gene-start analysis with Starterator
  • Reviews on phage therapeutics and diagnostics
AMR

Antimicrobial Resistance Group

This group carries out genomic surveillance of Klebsiella pneumoniae from Nigeria, using public genomes from PathogenWatch. It measures how common AMR determinants are, the role of plasmids and mobile genetic elements, and how resistant lineages are related.

  • PathogenWatch, Kleborate, ResFinder and ICEfinder pipelines
  • Comparison against the MGH 78578 reference strain
  • Manuscripts on hypervirulent, hypermucoid blood isolates
Cancer

Cancer & Transcriptomics Group

This group trains members in RNA-sequencing analysis, from the genetic basis of oncogenesis to running full transcriptomic pipelines on Galaxy and BioJupies.

  • Modules on FASTA/FASTQ, SAM/BAM and quality scores
  • Differential expression and MultiQC reporting
  • 2022 study on CAR T-cells targeting EpCAM
Metagenomics

Metagenomics Group

This group maps prophages and antibiotic-resistance genes (ARGs) in gut metagenomes from non-human primates. It looks at which antibiotic classes those ARGs act against.

  • Prophage detection with PHASTER
  • Functional resistome profiling with ResFinderFG
  • Data drawn from the Ibadan Enterovirus Project and ENA
Affiliate projects

Our model, beyond our team

The Phage Leaders Forum oversees projects that take IBRT’s training approach to other departments.

Ibadan Enterovirus Project

This metagenomics project with the Department of Virology began in June 2021. Members analyse viral metagenomes from non-human primates. The work runs from assembly quality checks through to identifying phage sequences, resistome profiling and preparing manuscripts.

KBase · vConTACT · QUAST · VirSorter2 · CheckV · RASTk · MetaPhinder · PHACTS · ResFinder · VirulenceFinder

BAMSSA Research Hub

This is the flagship research programme of the Faculty of Basic Medical Sciences Student Association, and the first of its kind in any faculty at UI. IBRT designs and teaches its training in basic research, computational studies, AMR and cancer research. Students from Biochemistry, Physiology and BMLS take part.

Have a dataset, a question or a collaboration in mind?

We welcome research partnerships with laboratories, consortia and industry that share our interest in phages and AMR.

Talk to us Our publications