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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..

Determining management strategies to control ash dieback disease through molecular and environmental interactions (2023)
Thesis
Raykova, A. (2023). Determining management strategies to control ash dieback disease through molecular and environmental interactions. (Thesis). University of Salford

Forest trees have been increasingly threatened by invasive pathogens, endangering associated biodiversity, and reducing ecosystems. Such an alien pathogen, Hymenoscyphus fraxineus, has had considerable impacts on the common ash tree (Fraxinus exce... Read More about Determining management strategies to control ash dieback disease through molecular and environmental interactions.

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.

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
Monahan, T., Baker, J. A., Krabben, P., Davies, E. T., Jenkinson, E. R., Goodhead, I. B., …Shepherd, M. (2021). Deletion of glyceraldehyde-3-phosphate dehydrogenase (gapN) in Clostridium saccharoperbutylacetonicum N1-4(HMT) using CLEAVE™ increases the ATP pool and accelerates solvent production. Microbial Biotechnology, 15(5), 1574-1585. https://doi.org/10.1111/1751-7915.13990

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.

Characterising the bacterial microbiota of Phlebotomus and Glossina insects : vectors of parasitic diseases (2021)
Thesis
Pescod, P. (2021). Characterising the bacterial microbiota of Phlebotomus and Glossina insects : vectors of parasitic diseases. (Thesis). University of Salford

As the technology used to examine bacteria using culture-independent methods has advanced, so too has our knowledge of the bacterial microbiome of insect vectors and its effect on the pathogens they carry. Trypanosomiasis and leishmaniasis are neglec... Read More about Characterising the bacterial microbiota of Phlebotomus and Glossina insects : vectors of parasitic diseases.

Investigation of de-novo copy number variants in patients with Autism Spectrum Disorder in Vietnam (2021)
Thesis
Bui, H. Investigation of de-novo copy number variants in patients with Autism Spectrum Disorder in Vietnam. (Thesis). University of Salford

Autism spectrum disorder (ASD) is a neurodevelopmental disorder with a prevalence of approximately 1% children worldwide. ASD is characterized by deficits in social communication and interaction and the presence of restricted interests and repetitive... Read More about Investigation of de-novo copy number variants in patients with Autism Spectrum Disorder in Vietnam.

Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome (2021)
Journal Article
Harrison, X., McDevitt, A., Dunn, J., Grifftihs, S., Benvenuto, C., Birtles, R., …Antwis, R. (2021). Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome. Proceedings of the Royal Society B: Biological Sciences, 288(1957), 20210552. https://doi.org/10.1098/rspb.2021.0552

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
Ackers-Johnson, G., Kibombo, D., Kusiima, B., Nsubuga, M., Kigozi, E., Kajumbula, H., …James, C. (2021). Antibiotic resistance profiles and population structure of disease-associated Staphylococcus aureus infecting patients in Fort Portal Regional Referral Hospital, Western Uganda. Microbiology, 167(5), 001000. https://doi.org/10.1099/mic.0.001000

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
Ribiero, C., Rahman, L., Holmes, L., Woody, A., Webster, C., Monaghan, T., …Shepherd, M. (2021). Nitric oxide (NO) elicits aminoglycoside tolerance in Escherichia coli but antibiotic resistance gene carriage and NO sensitivity have not co-evolved. Archives of Microbiology, 203(5), 2541-2550. https://doi.org/10.1007/s00203-021-02245-2

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.

Proinflammatory cytokines as mediators of phenotypic change in bacteria implicated in ventilator-associated pneumonia (2021)
Thesis
Tompsett, A. Proinflammatory cytokines as mediators of phenotypic change in bacteria implicated in ventilator-associated pneumonia. (Thesis). University of Salford

Ventilator-associated pneumonia (VAP) is a common hospital-acquired infection in intensive care. VAP is associated with increased hospital stay, healthcare costs, and high mortality. VAP is difficult to diagnose and manage appropriately, leading to w... Read More about Proinflammatory cytokines as mediators of phenotypic change in bacteria implicated in ventilator-associated pneumonia.

Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome (2021)
Other
Harrison, X., McDevitt, A., Dunn, J., Griffiths, S., Benvenuto, C., Birtles, R., …Antwis, R. (2021). Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome

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.

Validation of FASTFISH-ID : a new commercial platform for rapid fish species authentication via universal closed-tube barcoding (2021)
Journal Article
Naaum, A., Cusa, M., Singh, M., Bleicher, Z., Elliott, C., Goodhead, I., …Sanchez, J. (2021). Validation of FASTFISH-ID : a new commercial platform for rapid fish species authentication via universal closed-tube barcoding. Food Research International, 141, 110035. https://doi.org/10.1016/j.foodres.2020.110035

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
Goodhead, I., Blow, F., Brownridge, P., Hughes, M., Kenny, J., Krishna, R., …Darby, A. (2020). Large-scale and significant expression from pseudogenes in Sodalis glossinidius – a facultative bacterial endosymbiont. Microbial Genomics, 6(1), https://doi.org/10.1099/mgen.0.000285

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.

Functional genomics of a symbiotic community : shared traits in the olive fruit fly gut microbiota (2019)
Journal Article
Blow, F., Gioti, A., Goodhead, I., Kalyva, M., Kampouraki, A., Vontas, J., & Darby, A. (2020). Functional genomics of a symbiotic community : shared traits in the olive fruit fly gut microbiota. Genome Biology and Evolution, 12(2), 3778-3791. https://doi.org/10.1093/gbe/evz258

The olive fruit fly Bactrocera oleae is a major pest of olives worldwide and houses a specialized gut microbiota dominated by the obligate symbiont “Candidatus Erwinia dacicola”. Ca. E. dacicola is thought to supplement dietary nitrogen to the host,... Read More about Functional genomics of a symbiotic community : shared traits in the olive fruit fly gut microbiota.

Complex associations between cross-kingdom microbial endophytes and host genotype in ash dieback disease dynamics (2019)
Journal Article
Griffiths, S., Galambao, M., Rowntree, J., Goodhead, I., Hall, J., O'Brien, D., …Antwis, R. (2020). Complex associations between cross-kingdom microbial endophytes and host genotype in ash dieback disease dynamics. Journal of Ecology, 108(1), 291-309. https://doi.org/10.1111/1365-2745.13302

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.

Establishing Sodalis species as a laboratory model of endosymbionts (2019)
Thesis
Markham, T. Establishing Sodalis species as a laboratory model of endosymbionts. (Dissertation). University of Salford

Symbiosis is defined as the close and long relationship between two organisms. Establishment of new symbioses, or redefining relationships underpins much of the ecological diversity found in the natural world. Microbial symbionts, being some of the... Read More about Establishing Sodalis species as a laboratory model of endosymbionts.

Evolutionary trade-offs associated with loss of PmrB function in host-adapted Pseudomonas aeruginosa (2018)
Journal Article
Bricio-Moreno, L., Sheridan, V., Goodhead, I., Armstrong, S., Wong, J., Waters, E., …Neill, D. (2018). Evolutionary trade-offs associated with loss of PmrB function in host-adapted Pseudomonas aeruginosa. Nature communications, 9, 2635. https://doi.org/10.1038/s41467-018-04996-x

Pseudomonas aeruginosa colonises the upper airway of cystic fibrosis (CF) patients, providing a reservoir of host-adapted genotypes that subsequently establish chronic lung infection. We previously experimentally-evolved P. aeruginosa in a murine mod... Read More about Evolutionary trade-offs associated with loss of PmrB function in host-adapted Pseudomonas aeruginosa.

Campylobacter jejuni transcriptome changes during loss of culturability in water (2017)
Journal Article
Bronowski, C., Mustafa, K., Goodhead, I., James, C., Nelson, C., Lucaci, A., …Winstanley, C. (2017). Campylobacter jejuni transcriptome changes during loss of culturability in water. PLoS ONE, 12(11), e0188936. https://doi.org/10.1371/journal.pone.0188936

Background: Water serves as a potential reservoir for Campylobacter, the leading cause of bacterial gastroenteritis in humans. However, little is understood about the mechanisms underlying variations in survival characteristics between different st... Read More about Campylobacter jejuni transcriptome changes during loss of culturability in water.

Challenging the Wigglesworthia, Sodalis, Wolbachia symbiosis dogma in tsetse flies : Spiroplasma is present in both laboratory and natural populations (2017)
Journal Article
Doudoumis, V., Blow, F., Saridaki, A., Augustinos, A., Dyer, N., Goodhead, I., …Tsiamis, G. (2017). Challenging the Wigglesworthia, Sodalis, Wolbachia symbiosis dogma in tsetse flies : Spiroplasma is present in both laboratory and natural populations. Scientific reports, 7(4699), https://doi.org/10.1038/s41598-017-04740-3

Profiling of wild and laboratory tsetse populations using 16S rRNA gene amplicon sequencing allowed us to examine whether the “Wigglesworthia-Sodalis-Wolbachia dogma” operates across species and populations. The most abundant taxa, in wild and labora... Read More about Challenging the Wigglesworthia, Sodalis, Wolbachia symbiosis dogma in tsetse flies : Spiroplasma is present in both laboratory and natural populations.

50 important research questions in microbial ecology (2017)
Journal Article
Antwis, R., Griffiths, S., Harrison, X., Aranega-Bou, P., Arce, A., Bettridge, A., …Sutherland, W. (2017). 50 important research questions in microbial ecology. FEMS Microbiology Ecology, 93(5), https://doi.org/10.1093/femsec/fix044

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... Read More about 50 important research questions in microbial ecology.

A simple procedure for directly obtaining haplotype sequences of diploid genomes (2015)
Journal Article
Noyes, H., Daly, D., Goodhead, I., Kay, S., Kemp, S., Kenny, J., …Hall, N. (2015). A simple procedure for directly obtaining haplotype sequences of diploid genomes. BMC Genomics, 16(1), 642. https://doi.org/10.1186/s12864-015-1818-4

Background Almost all genome sequencing projects neglect the fact that diploid organisms contain two genome copies and consequently what is published is a composite of the two. This means that the relationship between alternate alleles at two or... Read More about A simple procedure for directly obtaining haplotype sequences of diploid genomes.

ApiAP2 factors as candidate regulators of stochastic commitment to merozoite production in Theileria annulata (2015)
Journal Article
Pieszko, M., Weir, W., Goodhead, I., Kinnaird, J., & Shiels, B. (2015). ApiAP2 factors as candidate regulators of stochastic commitment to merozoite production in Theileria annulata. PLoS Neglected Tropical Diseases, 9(8), 1-26. https://doi.org/10.1371/journal.pntd.0003933

The ability of vector-borne Apicomplexan parasites (Babesia, Plasmodium and Theileria) to change from one life-cycle stage to the next is critical for establishment of infection and transmission to new hosts. Stage differentiation steps of both Plasm... Read More about ApiAP2 factors as candidate regulators of stochastic commitment to merozoite production in Theileria annulata.

Taking the pseudo out of pseudogenes (2014)
Journal Article
Goodhead, I., & Darby, A. (2015). Taking the pseudo out of pseudogenes. Current Opinion in Microbiology, 23, 102-109. https://doi.org/10.1016/j.mib.2014.11.012

Pseudogenes are defined as fragments of once-functional genes that have been silenced by one or more nonsense, frameshift or missense mutations. Despite continuing increases in the speed of sequencing and annotating bacterial genomes, the identificat... Read More about Taking the pseudo out of pseudogenes.

Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes (2014)
Journal Article
IIott, N., Heward, J., Roux, B., Tsitsiou, E., Fenwick, P., Lenzi, L., …Lindsay, M. (2014). Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes. Nature communications, 5, 3979-3979. https://doi.org/10.1038/ncomms4979

Early reports indicate that long non-coding RNAs (lncRNAs) are novel regulators of biological responses. However, their role in the human innate immune response, which provides the initial defence against infection, is largely unexplored. To address... Read More about Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes.

Whole-Genome sequencing of Trypanosoma brucei reveals introgression between subspecies that is associated with virulence (2013)
Journal Article
Goodhead, I., Capewell, P., Bailey, J., Beament, T., Chance, M., Kay, S., …Noyes, H. (2013). Whole-Genome sequencing of Trypanosoma brucei reveals introgression between subspecies that is associated with virulence. mBio, 4(4), e00197. https://doi.org/10.1128/mBio.00197-13

Human African trypanosomiasis is caused by two subspecies of Trypanosoma brucei. Trypanosoma brucei rhodesiense is found in East Africa and frequently causes acute disease, while Trypanosoma brucei gambiense is found in West Africa and is associated... Read More about Whole-Genome sequencing of Trypanosoma brucei reveals introgression between subspecies that is associated with virulence.

Insights into hominid evolution from the gorilla genome sequence (2012)
Journal Article
Scally, A., Dutheil, J., Hillier, L., Jordan, G., Goodhead, I., Herrero, J., …Marques-Bonet, T. (2012). Insights into hominid evolution from the gorilla genome sequence. Nature, 483(7388), 169-175. https://doi.org/10.1038/nature10842

Gorillas are humans’ closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla,and compare... Read More about Insights into hominid evolution from the gorilla genome sequence.

A comprehensive genetic analysis of candidate genes regulating response to Trypanosoma congolense infection in mice (2010)
Journal Article
Goodhead, I., Archibald, A., Amwayi, P., Brass, A., Gibson, J., Hall, N., …Kemp, S. (2010). A comprehensive genetic analysis of candidate genes regulating response to Trypanosoma congolense infection in mice. PLoS Neglected Tropical Diseases, 4(11), e880-e880. https://doi.org/10.1371/journal.pntd.0000880

African trypanosomes are protozoan parasites that cause “sleeping sickness” in humans and a similar disease in livestock. Trypanosomes also infect laboratory mice and three major quantitative trait loci (QTL) that regulate survival time after infecti... Read More about A comprehensive genetic analysis of candidate genes regulating response to Trypanosoma congolense infection in mice.

How do temperate bacteriophages affect the fitness of Pseudomonas aeruginosa?
Presentation / Conference
Plahe, G., Alison, H., Goodhead, I., & James, C. How do temperate bacteriophages affect the fitness of Pseudomonas aeruginosa?. Poster presented at Microbiology Society Annual Conference 2020, Edinburgh, UK

The Liverpool Epidemic Strain(LES) of Pseudomonas aeruginosa is a key opportunistic bacterium and a major cause of mortality and morbidity in cystic fibrosis (CF) patients. It has been established to carry distinctive prophages within its genome, pro... Read More about How do temperate bacteriophages affect the fitness of Pseudomonas aeruginosa?.