xBASE: a bioinformatics resource for the AgriFood bacteriology community
Lead Research Organisation:
University of Birmingham
Department Name: Immunity and Infection - Infection
Abstract
Bacteria play important roles at every stage in the human food chain, from improving the productivity of the soil to infecting the human consumer. The advent of genome sequencing, functional genomics and systems biology brings the promise of unparalleled progress in the bacteriology of the human food chain. However, bacteriologists are drowning in in a sea of data. Hundreds of bacterial genome projects have been completed or are underway. On top of this, we are now threatened with a novel deluge of data from systems biology studies . Unless the average bacteriologist is able to exploit the new flood of genomics data, the whole genomics enterprise risks becoming an expensive molecular stamp-collecting exercise. In recent years, we have met this challenge by providing bacteriologists with a set of user-friendly tools for visualising, analysing and exploiting genome sequence data from bacteria of importance to the human food chain. Our most recent effort is coliBASE, a web site and database dedicated to the comparative genomics of E. coli and related bacteria of relevance in the AgriFood context. As evidence of its success, this site is receiving >1000 visitors a month. In this proposal, we aim to take these facilities into the second decade of the twenty-first century by the development of xBASE, a series of taxon-specific databases, in which we add breadth (by covering a wider range of organisms) and add depth (by adding additional analytical and visualization tools, including new tools to cope with data from bacterial Systems Biology and meta-genomics projects) to our current repertoire.
Technical Summary
Bacteria play important roles at every stage in the human food chain, from improving the productivity of the soil to infecting the human consumer. The era of genomics and systems biology brings the promise of unparalleled progress in the study of bacteria of agricultural importance. However, if the average bacteriologist is unable to exploit the new flood of new sequence and interaction data, the whole genomics enterprise risks becoming expensive molecular stamp-collecting exercise. In recent years, we have met this challenge by providing bacteriologists with user-friendly tools for visualising, analysing and exploiting genome sequence data from bacteria that affect the human food chain. Our most recent effort is coliBASE, a web site and database dedicated to the comparative genomics of E. coli and related bacteria of relevance in the AgriFood context . As evidence of its success, this site is receiving >1000 visitors a month. In this proposal, we aim to sustain these facilities into the second decade of the twenty-first century by the development of xBASE, a series of taxon-specific databases, in which we add breadth (by covering a wider range of organisms) and add depth (by adding additional analytical and visualization tools, including new tools to cope with data from bacterial Systems Biology and meta-genomics projects) to our current repertoire. xBASE will be implemented through the use of a MySQL database running on a Linux cluster, augmented with visualization, graphing and other software
Organisations
Publications
Chan JZ
(2012)
Defining bacterial species in the genomic era: insights from the genus Acinetobacter.
in BMC microbiology
Chaudhuri RR
(2008)
xBASE2: a comprehensive resource for comparative bacterial genomics.
in Nucleic acids research
Halachev MR
(2014)
Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumannii in Birmingham, England.
in Genome medicine
Halachev MR
(2011)
Calculating orthologs in bacteria and Archaea: a divide and conquer approach.
in PloS one
Hornsey M
(2011)
Whole-genome comparison of two Acinetobacter baumannii isolates from a single patient, where resistance developed during tigecycline therapy.
in The Journal of antimicrobial chemotherapy
Lewis T
(2010)
High-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak.
in The Journal of hospital infection
Loman N
(2010)
EntrezAJAX: direct web browser access to the Entrez Programming Utilities
in Source Code for Biology and Medicine
Loman NJ
(2013)
Clonal expansion within pneumococcal serotype 6C after use of seven-valent vaccine.
in PloS one
Loman NJ
(2012)
Performance comparison of benchtop high-throughput sequencing platforms.
in Nature biotechnology
Loman NJ
(2015)
Twenty years of bacterial genome sequencing.
in Nature reviews. Microbiology
Pallen MJ
(2014)
Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections.
in Parasitology
Pallen MJ
(2013)
Reply to Updating benchtop sequencing performance comparison.
in Nature biotechnology
Pallen MJ
(2010)
High-throughput sequencing and clinical microbiology: progress, opportunities and challenges.
in Current opinion in microbiology
Quick J
(2014)
Draft Genome Sequence of Elizabethkingia meningoseptica Isolated from a Traumatic Wound.
in Genome announcements
Rohde H
(2011)
Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4.
in The New England journal of medicine
Webber MA
(2015)
Parallel evolutionary pathways to antibiotic resistance selected by biocide exposure.
in The Journal of antimicrobial chemotherapy
| Description | This was a research infrastructure project that provided the microbiology research community with an online resource that allowed them to analyse bacterial genome sequence data. The post-docs employed on the project often "test-drove" the xBASE facilities in collaborative research projects, including highly impactful analyses of the 2011 German E. coli outbreak. |
| Exploitation Route | This project has been superceded by the BBSRC Enterobase project, which provides much of the same capability |
| Sectors | Healthcare |