ORCID Profile
0000-0002-3110-9442
Current Organisations
University of South Australia
,
University of Salford
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Publisher: Oxford University Press (OUP)
Date: 03-04-2017
Abstract: Microbial ecology provides insights into the ecological and evolutionary dynamics of microbial communities underpinning every ecosystem on Earth. Microbial communities can now be investigated in unprecedented detail, although there is still a wealth of open questions to be tackled. Here we identify 50 research questions of fundamental importance to the science or application of microbial ecology, with the intention of summarising the field and bringing focus to new research avenues. Questions are categorised into seven themes: host-microbiome interactions health and infectious diseases human health and food security microbial ecology in a changing world environmental processes functional ersity and evolutionary processes. Many questions recognise that microbes provide an extraordinary array of functional ersity that can be harnessed to solve real-world problems. Our limited knowledge of spatial and temporal variation in microbial ersity and function is also reflected, as is the need to integrate micro- and macro-ecological concepts, and knowledge derived from studies with humans and other erse organisms. Although not exhaustive, the questions presented are intended to stimulate discussion and provide focus for researchers, funders and policy makers, informing the future research agenda in microbial ecology.
Publisher: Springer Science and Business Media LLC
Date: 06-3011
DOI: 10.1038/NATURE10842
Publisher: ACM
Date: 30-04-2023
Publisher: Wiley
Date: 11-2007
Publisher: Cold Spring Harbor Laboratory
Date: 10-04-2008
Abstract: Mycobacterium marinum , a ubiquitous pathogen of fish and hibia, is a near relative of Mycobacterium tuberculosis , the etiologic agent of tuberculosis in humans. The genome of the M strain of M. marinum comprises a 6,636,827-bp circular chromosome with 5424 CDS, 10 prophages, and a 23-kb mercury-resistance plasmid. Prominent features are the very large number of genes (57) encoding polyketide synthases (PKSs) and nonribosomal peptide synthases (NRPSs) and the most extensive repertoire yet reported of the mycobacteria-restricted PE and PPE proteins, and related-ESX secretion systems. Some of the NRPS genes comprise a novel family and seem to have been acquired horizontally. M. marinum is used widely as a model organism to study M. tuberculosis pathogenesis, and genome comparisons confirmed the close genetic relationship between these two species, as they share 3000 orthologs with an average amino acid identity of 85%. Comparisons with the more distantly related Mycobacterium avium subspecies paratuberculosis and Mycobacterium smegmatis reveal how an ancestral generalist mycobacterium evolved into M. tuberculosis and M. marinum . M. tuberculosis has undergone genome downsizing and extensive lateral gene transfer to become a specialized pathogen of humans and other primates without retaining an environmental niche. M. marinum has maintained a large genome so as to retain the capacity for environmental survival while becoming a broad host range pathogen that produces disease strikingly similar to M. tuberculosis . The work described herein provides a foundation for using M. marinum to better understand the determinants of pathogenesis of tuberculosis.
Publisher: Springer Science and Business Media LLC
Date: 27-07-2008
DOI: 10.1038/NG.195
Publisher: Public Library of Science (PLoS)
Date: 09-11-2010
Publisher: Association for Computing Machinery (ACM)
Date: 28-12-2022
DOI: 10.1145/3546912
Abstract: Much of today’s data are represented as graphs, ranging from social networks to bibliographic citations. Nodes in such graphs correspond to records that generally represent entities, while edges represent relationships between these entities. Both nodes and edges in a graph can have attributes that characterize the entities and their relationships. Relationships are either explicitly known (like friends in a social network), or they are inferred using link prediction (such as two babies are siblings because they have the same mother). Any graph representing real-world data likely contains nodes and edges that are abnormal, and identifying these can be important for outlier detection in applications ranging from crime and fraud detection to viral marketing. We propose a novel approach to the unsupervised detection of abnormal nodes and edges in graphs. We first characterize nodes and edges using a set of features, and then employ a one-class classifier to identify abnormal nodes and edges. We extract patterns of features from these abnormal nodes and edges, and apply clustering to identify groups of patterns with similar characteristics. We finally visualize these abnormal patterns to show co-occurrences of features and relationships between those features that mostly influence the abnormality of nodes and edges. We evaluate our approach on datasets from erse domains, including historical birth certificates, COVID patient records, e-mails, books, and movies. This evaluation demonstrates that our approach is well suited to identify both abnormal nodes and edges in graphs in an unsupervised way, and it can outperform several baseline anomaly detection techniques.
Publisher: IEEE
Date: 12-2018
Publisher: ACM
Date: 06-12-2021
Publisher: IEEE
Date: 12-2021
Publisher: Springer Science and Business Media LLC
Date: 07-03-2021
DOI: 10.1007/S00203-021-02245-2
Abstract: The spread of multidrug-resistance in Gram-negative bacterial pathogens presents a major clinical challenge, and new approaches are required to combat these organisms. Nitric oxide (NO) is a well-known antimicrobial that is produced by the immune system in response to infection, and numerous studies have demonstrated that NO is a respiratory inhibitor with both bacteriostatic and bactericidal properties. However, given that loss of aerobic respiratory complexes is known to diminish antibiotic efficacy, it was hypothesised that the potent respiratory inhibitor NO would elicit similar effects. Indeed, the current work demonstrates that pre-exposure to NO-releasers elicits a tenfold increase in IC 50 for gentamicin against pathogenic E. coli (i.e. a huge decrease in lethality). It was therefore hypothesised that hyper-sensitivity to NO may have arisen in bacterial pathogens and that this trait could promote the acquisition of antibiotic-resistance mechanisms through enabling cells to persist in the presence of toxic levels of antibiotic. To test this hypothesis, genomics and microbiological approaches were used to screen a collection of E. coli clinical isolates for antibiotic susceptibility and NO tolerance, although the data did not support a correlation between increased carriage of antibiotic resistance genes and NO tolerance. However, the current work has important implications for how antibiotic susceptibility might be measured in future (i.e. ± NO) and underlines the evolutionary advantage for bacterial pathogens to maintain tolerance to toxic levels of NO.
Publisher: IEEE
Date: 12-2018
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Ian Goodhead.