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News
Pathogen-host database refocuses on genes
PHI-base provides a comprehensive resource for deeper insights into pathogens and their hosts
January 7, 2025
A new version of the influential Pathogen–Host Interactions Database (PHI-base) has been developed and aims to provide more depth on how genes affect the outcome of interactions between pathogens and their hosts. PHI-base 5 increases the amount of information that can be pulled from peer-reviewed publications about pathogen–host interactions, say researchers, and with information now recorded in standardised way, should make it easier for both humans and machine learning systems to use the data.
PHI-base has been freely available for use by the scientific community for almost 20 years and will surpass 10,000 genes curated in total by mid-2025.
Kim Hammond-Kosack, lead scientist and PHI-base co-founder, says ‘This latest advancement of the precision of the information we are capturing will make PHI-base even more useful for discovery research, disease control, and monitoring for changes in pathogens that are of the most concern’.
The redesigned PHI-base 5 website displays all information about a given pathogen or host gene on a single page (one page per gene), which is intended to make it easier for researchers to explore genes of interest, and to identify findings in the literature that either confirm, or conflict with, existing knowledge. This change also makes it easier for information from PHI-base to be integrated with other biological databases, such as UniProtKB and KnetMiner.
PHI-base 5 allows the curation of information that is either entirely new to the system or delivered in more detail than before. This includes:
- changes to pathogen genes that cause resistance to antibiotics or antifungals;
- changes to host genes that improve the host’s ability to resist infection;
- phenotypes for interactions that are common in plants, such as gene-for-gene interactions; and
- comparisons between the normal phenotype causally linked to a gene to what happens when the gene is mutated or deleted.
‘Within the One Health concept, there is growing recognition of the multiple interconnectedness between crop health, animal health, human health and ecosystem health’ says Professor Martin Broadley, a science director at Rothamsted Research. ‘PHI-base allows researchers to rapidly explore the rules of life underpinning multiple pathogen types. Having this species breadth readily accessible allows exploitable common and species-specific mechanisms to stand out from the crowd.’
Nearly a fifth of the database (17%) focuses on pathogens of rice and wheat – the two most eaten cereal grains – and almost half (45%) focuses on crop species. In the UK and Europe, the overall production stability and economic success of the wheat crop is now under threat from climate change and an increasing diversity of pathogens and pests. PHI-base provides up to date new knowledge on pathogens and interaction phenotypes at various experimental scales. This is being used by researchers to deliver novel types of genetic and other improvements to advance the resilience of the wheat crop.
Full summary of improved features can be found here.
Publication
Contacts
Dr Kim Hammond-Kosack
Molecular Plant Pathologist
ABOUT ROTHAMSTED RESEARCH
Rothamsted Research is the longest-running agricultural research institute in the world. We work from gene to field with a proud history of ground-breaking
discoveries in areas as diverse as crop management, statistical interpretation and soil health. Our founders, in 1843, were the pioneers of modern
agriculture, and we are known for our imaginative science and our collaborative approach to developing innovative farm practice.
Through independent research, we make significant contributions to improving agri-food systems in the UK and internationally, with
economic impact estimated to exceed £3 bn in annual contribution to the UK economy. Our strength lies in our systems approach, which combines strategic research,
interdisciplinary teams and multiple partnerships.
Rothamsted is home to three unique National Bioscience Research Infrastructures which are open to researchers from all over the world:
The Long-Term Experiments,
Rothamsted Insect Survey and the
North Wyke Farm Platform.
We are strategically funded by the Biotechnology and Biological Sciences Research Council (BBSRC), with additional support from other national and
international funding streams, and from industry. We are also supported by the Lawes Agricultural Trust (LAT).
ABOUT BBSRC
The Biotechnology and Biological Sciences Research Council is part of UK Research and Innovation, a non-departmental public body funded by a grant-in-aid
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BBSRC invests to push back the frontiers of biology and deliver a healthy, prosperous and sustainable future. Through our investments, we build and support a vibrant,
dynamic and inclusive community which delivers ground-breaking discoveries and develops bio-based solutions that contribute to tackling global challenges,
such as sustainable food production, climate change, and healthy ageing.
As part of UK Research and Innovation (UKRI), we not only play a pivotal role in fostering connections that enable the UK’s world-class research and innovation system
to flourish – we also have a responsibility to enable the creation of a research culture that is diverse, resilient, and engaged.
BBSRC proudly forges interdisciplinary collaborations where excellent bioscience has a fundamental role. We pioneer approaches that enhance the equality, diversity,
and inclusion of talent by investing in people, infrastructure, technologies, and partnerships on a global scale.
ABOUT LAT
The Lawes Agricultural Trust, established in 1889 by Sir John Bennet Lawes, supports Rothamsted Research’s national and international agricultural science through the provision of land, facilities and funding. LAT, a charitable trust, owns the estates at Harpenden and Broom's Barn, including many of the buildings used by Rothamsted Research. LAT provides an annual research grant to the Director, accommodation for nearly 200 people, and support for fellowships for young scientists from developing countries. LAT also makes capital grants to help modernise facilities at Rothamsted, or invests in new buildings.