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Prof Ian Goodhead's Outputs (29)

Understanding the Impact of Temperate Bacteriophages on Their Lysogens Through Transcriptomics. (2024)
Journal Article
Krishnamurthi, R., González-Tortuero, E., Plahe, G., Goodhead, I. B., Fothergill, J. L., James, C. E., & Allison, H. E. (in press). Understanding the Impact of Temperate Bacteriophages on Their Lysogens Through Transcriptomics. Journal of Visualized Experiments, 10.3791/64945. https://doi.org/10.3791/64945

Temperate phages are found integrated as prophages in the majority of bacterial genomes. Some prophages are cryptic and fixed in the bacterial chromosome, but others are active and can be triggered into a replicative form either spontaneously or by e... Read More about Understanding the Impact of Temperate Bacteriophages on Their Lysogens Through Transcriptomics..

Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches (2022)
Journal Article
Beck, R., de Vries, D., Janiak, M., Goodhead, I., & Boubli, J. (2022). Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches. Journal of Human Evolution, 174, https://doi.org/10.1016/j.jhevol.2022.103293

There have been multiple published phylogenetic analyses of platyrrhine primates (New World
monkeys) using both morphological and molecular data, but relatively few that have integrated
both types of data into a total evidence approach. Here, we pr... Read More about Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches.

Two hundred and five newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates (2022)
Journal Article

Mitochondrial DNA remains a cornerstone for molecular ecology, especially for study species from which high-quality tissue samples cannot be easily obtained. Methods using mitochondrial markers are usually reliant on reference databases, but these ar... Read More about Two hundred and five newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates.

Improving phage genome annotation to understand phage biology: the case of Pseudomonas aeruginosa LES prophages (2022)
Journal Article
Gonzalez Tortuero, E., Krishnamurthi, R., Goodhead, I., Allison, H., & James, C. (2022). Improving phage genome annotation to understand phage biology: the case of Pseudomonas aeruginosa LES prophages. Access Microbiology, 4(5), https://doi.org/10.1099/acmi.ac2021.po0318

Pseudomonas aeruginosais an important opportunistic pathogen, causing nosocomial infections. The Liverpool Epidemic Strain (LES), a major cause of mortality and morbidity in cystic fibrosis patients, harbours five prophages associated with increased... Read More about Improving phage genome annotation to understand phage biology: the case of Pseudomonas aeruginosa LES prophages.

Deletion of glyceraldehyde-3-phosphate dehydrogenase (gapN) in Clostridium saccharoperbutylacetonicum N1-4(HMT) using CLEAVE™ increases the ATP pool and accelerates solvent production (2021)
Journal Article

SummaryThe development and advent of mutagenesis tools for solventogenic clostridial species in recent years has allowed for the increased refinement of industrially relevant strains. In this study we have utilised CLEAVE™, a CRISPR/Cas genome editin... Read More about Deletion of glyceraldehyde-3-phosphate dehydrogenase (gapN) in Clostridium saccharoperbutylacetonicum N1-4(HMT) using CLEAVE™ increases the ATP pool and accelerates solvent production.

Comparative analysis of gene prediction tools for viral genome annotation (2021)
Journal Article
Gonzalez-Tortuero, E., Krishnamurthi, R., Allison, H., Goodhead, I., & James, C. Comparative analysis of gene prediction tools for viral genome annotation. https://doi.org/10.1101/2021.12.11.472104. Manuscript submitted for publication

The number of newly available viral genomes and metagenomes has increased exponentially since the development of high throughput sequencing platforms and genome analysis tools. Bioinformatic annotation pipelines are largely based on open reading fram... Read More about Comparative analysis of gene prediction tools for viral genome annotation.

Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome (2021)
Journal Article

Interactions between hosts and their resident microbial communities are a fundamental component of fitness for both agents. Though recent research has highlighted the importance of interactions between animals and their bacterial communities, compara... Read More about Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome.

Antibiotic resistance profiles and population structure of disease-associated Staphylococcus aureus infecting patients in Fort Portal Regional Referral Hospital, Western Uganda (2021)
Journal Article

Tackling antimicrobial resistance (AMR) is particularly challenging in low-resource settings such as Fort Portal Regional Referral Hospital (FPRRH) in Western Uganda. Specific knowledge of local AMR epidemiology is required to inform evidence-based i... Read More about Antibiotic resistance profiles and population structure of disease-associated Staphylococcus aureus infecting patients in Fort Portal Regional Referral Hospital, Western Uganda.

Nitric oxide (NO) elicits aminoglycoside tolerance in Escherichia coli but antibiotic resistance gene carriage and NO sensitivity have not co-evolved (2021)
Journal Article

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 sys... Read More about Nitric oxide (NO) elicits aminoglycoside tolerance in Escherichia coli but antibiotic resistance gene carriage and NO sensitivity have not co-evolved.

Validation of FASTFISH-ID : a new commercial platform for rapid fish species authentication via universal closed-tube barcoding (2021)
Journal Article

Seafood represents up to 20% of animal protein consumption in global food consumption and is a critical dietary and income resource for the world’s population. Currently, over 30% of marine fish stocks are harvested at unsustainable levels, and the i... Read More about Validation of FASTFISH-ID : a new commercial platform for rapid fish species authentication via universal closed-tube barcoding.

Antibiotic resistance profiles and population structure of disease-associated Staphylococcus aureus infecting patients in Fort Portal Regional Referral Hospital, Western Uganda (2020)
Journal Article
Goodhead, I., Ackers, H., Birtles, R., & James, C. (2020). Antibiotic resistance profiles and population structure of disease-associated Staphylococcus aureus infecting patients in Fort Portal Regional Referral Hospital, Western Uganda. bioRxiv, https://doi.org/10.1101/2020.11.20.371203

Tackling antimicrobial resistance (AMR) is particularly challenging in low-resource settings such as Fort Portal Regional Referral Hospital (FPRRH) in Western Uganda. Specific knowledge of local AMR epidemiology is required to inform evidence-based i... Read More about Antibiotic resistance profiles and population structure of disease-associated Staphylococcus aureus infecting patients in Fort Portal Regional Referral Hospital, Western Uganda.

Large-scale and significant expression from pseudogenes in Sodalis glossinidius – a facultative bacterial endosymbiont (2020)
Journal Article

The majority of bacterial genomes have high coding efficiencies, but there are some genomes of intracellular bacteria that have low gene density. The genome of the endosymbiont Sodalis glossinidius contains almost 50 % pseudogenes containing mutation... Read More about Large-scale and significant expression from pseudogenes in Sodalis glossinidius – a facultative bacterial endosymbiont.

Complex associations between cross-kingdom microbial endophytes and host genotype in ash dieback disease dynamics (2019)
Journal Article

Tree pathogens are a major threat to forest ecosystems. Conservation management strategies can exploit natural mechanisms of resistance, such as tree genotype and host‐associated microbial communities. However, fungal and bacterial communities are ra... Read More about Complex associations between cross-kingdom microbial endophytes and host genotype in ash dieback disease dynamics.

Towards a clinically relevant model for investigation of host-microbe interactions in ventilator-associated pneumonia (2019)
Journal Article
Tompsett, A., Ngoc ngo, L., Goodhead, I., Withers, S., & Latimer, J. (2019). Towards a clinically relevant model for investigation of host-microbe interactions in ventilator-associated pneumonia. Access Microbiology, 1(1A), https://doi.org/10.1099/acmi.ac2019.po0422

Ventilator-associated pneumonia (VAP) is amongst the most common healthcare-associated infections worldwide. Current understanding of the underlying mechanisms has focussed on either the microbiological or physiological elements but host-microbe inte... Read More about Towards a clinically relevant model for investigation of host-microbe interactions in ventilator-associated pneumonia.