All Outputs (26)

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..

Identification of constrained sequence elements across 239 primate genomes. (2023)
Journal Article
Kuderna, L. F., Ulirsch, J. C., Rashid, S., Ameen, M., Sundaram, L., Hickey, G., …Farh, K. K. (2023). Identification of constrained sequence elements across 239 primate genomes. Nature, 36, https://doi.org/10.1038/s41586-023-06798-8

Noncoding DNA is central to our understanding of human gene regulation and complex diseases , and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome . Identifying... Read More about Identification of constrained sequence elements across 239 primate genomes..

The landscape of tolerated genetic variation in humans and primates. (2023)
Journal Article
Gao, H., Hamp, T., Ede, J., Schraiber, J. G., McRae, J., Singer-Berk, M., …Jolly, C. J. (2023). The landscape of tolerated genetic variation in humans and primates. Science, 380(6648), https://doi.org/10.1126/science.abn8197

Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtain... Read More about The landscape of tolerated genetic variation in humans and primates..

A global catalog of whole-genome diversity from 233 primate species. (2023)
Journal Article
Kuderna, L. F. K., Gao, H., Janiak, M. C., Kuhlwilm, M., Orkin, J. D., Bataillon, T., …Jolly, C. J. (2023). A global catalog of whole-genome diversity from 233 primate species. Science, 380(6648), 906-913. https://doi.org/10.1126/science.abn7829

The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into lon... Read More about A global catalog of whole-genome diversity from 233 primate species..

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
Janiak, M. C., Silva, F. E., Beck, R. M. D., de Vries, D., Kuderna, L. F. K., Torosin, N. S., …Boubli, J. P. (2022). Two hundred and five newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates. Molecular Ecology, 31(14), 3888-3902. https://doi.org/10.1111/mec.16554

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
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.

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.

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.

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.

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.

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.