Related Experiment Video
Updated: Oct 13, 2025
High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
Published on: March 5, 2022
PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions
Martin Urban1, Alayne Cuzick1, James Seager1
1Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden AL5 2JQ, UK.
Abstract:
Since 2005, the Pathogen-Host Interactions Database (PHI-base) has manually curated experimentally verified pathogenicity, virulence and effector genes from fungal, bacterial and protist pathogens, which infect animal, plant, fish, insect and/or fungal hosts. PHI-base (www.phi-base.org) is devoted to the identification and presentation of phenotype information on pathogenicity and effector genes and their host interactions. Specific gene alterations that did not alter the in host interaction phenotype are also presented. PHI-base is invaluable for comparative analyses and for the discovery of candidate targets in medically and agronomically important species for intervention. Version 4.12 (September 2021) contains 4387 references, and provides information on 8411 genes from 279 pathogens, tested on 228 hosts in 18, 190 interactions. This provides a 24% increase in gene content since Version 4.8 (September 2019). Bacterial and fungal pathogens represent the majority of the interaction data, with a 54:46 split of entries, whilst protists, protozoa, nematodes and insects represent 3.6% of entries. Host species consist of approximately 54% plants and 46% others of medical, veterinary and/or environmental importance. PHI-base data is disseminated to UniProtKB, FungiDB and Ensembl Genomes. PHI-base will migrate to a new gene-centric version (version 5.0) in early 2022. This major development is briefly described.
Insights
The Pathogen-Host Interactions Database (PHI-base) manually curates verified pathogenicity, virulence, and effector genes from diverse pathogens and their hosts. This resource aids in comparative analysis and identifying intervention targets in important species.
Area of Science:
- Microbiology
- Genomics
- Bioinformatics
Background:
- The Pathogen-Host Interactions Database (PHI-base) has been a crucial resource since 2005.
- It manually curates experimentally verified data on pathogenicity, virulence, and effector genes.
- PHI-base covers fungal, bacterial, and protist pathogens infecting a wide range of hosts.
Purpose of the Study:
- To present phenotype information on pathogenicity and effector genes and their host interactions.
- To facilitate comparative analyses for discovering candidate intervention targets.
- To provide an updated and expanded dataset of pathogen-host interactions.
Main Methods:
- Manual curation of experimentally verified gene data.
- Inclusion of specific gene alterations affecting host interaction phenotypes.
- Data dissemination to major biological databases like UniProtKB, FungiDB, and Ensembl Genomes.
Main Results:
- Version 4.12 (September 2021) contains 4387 references, information on 8411 genes from 279 pathogens, and 18,190 interactions.
- A 24% increase in gene content since Version 4.8 (September 2019).
- Bacterial and fungal pathogens constitute the majority (54:46 split), with plants as the primary host type (54%).
Conclusions:
- PHI-base is an invaluable resource for understanding pathogen-host interactions.
- It supports the discovery of novel targets for medical and agricultural interventions.
- A forthcoming gene-centric version (5.0) will enhance data accessibility and utility.
