Biology subjects

Mullany, P.

Publications and source records attributed to Mullany, P..

5 recordsLinked to original sources

bioRxiv2022

PaliDIS: A tool for fast discovery of novel insertion sequences

The diversity of microbial insertion sequences, crucial mobile genetic elements in generating diversity in microbial genomes, needs to be better represented in current microbial databases. Identification of these sequences in microbiome communities presents some significant problems that have led to their underrepresentation. Here, we present a bioinformatics pipeline called Palidis that recognises insertion sequences in metagenomic sequence data rapidly by identifying inverted terminal repeat regions from mixed microbial community genomes. Applying Palidis to 264 human metagenomes identifies 879 unique insertion sequences, with 519 being novel and not previously characterised. Querying this catalogue against a large database of isolate genomes reveals evidence of horizontal gene transfer events across bacterial classes. We will continue to apply this tool more widely, building the Insertion Sequence Catalogue, a valuable resource for researchers wishing to query their microbial genomes for insertion sequences. Data SummaryO_LIPalidis is available here: github.com/blue-moon22/palidis C_LIO_LIThe Insertion Sequence Catalogue is available to download here: https://github.com/blue-moon22/ISC C_LIO_LIThe raw reads from the Human Microbiome Project can be retrieved using the download links provided in Supplementary Data 1 C_LIO_LIThe analysis for this paper is available here: github.com/blue-moon22/palidis_paper_analysis C_LIO_LIThe output of Palidis that was run on these reads is available in Supplementary Data 2 C_LI Impact StatementInsertion sequences are a class of transposable element that play an important role in the dissemination of antimicrobial resistance genes. However, it is challenging to completely characterise the transmission dynamics of insertion sequences and their precise contribution to the spread of antimicrobial resistance. The main reasons for this are that it is impossible to identify all insertion sequences based on limited reference databases and that de novo computational methods are ill-equipped to make fast or accurate predictions based on incomplete genomic assemblies. Palidis generates a larger, more comprehensive catalogue of insertion sequences based on a fast algorithm harnessing genomic diversity in mixed microbial communities. This catalogue will enable genomic epidemiologists and researchers to annotate genomes for insertion sequences more extensively and advance knowledge of how insertion sequences contribute to bacterial evolution in general and antimicrobial resistance spread across microbial lineages in particular. This will be useful for genomic surveillance, and for development of microbiome engineering strategies targeting inactivation or removal of important transposable elements carrying antimicrobial resistance genes.

genomics↗

bioRxiv2020

The human oral phageome is highly diverse and rich in jumbo phages

Until recently, the contribution of bacteriophages to the composition and function of the human microbiome has been largely overlooked. Recent developments in discovering novel bacteriophages from human metagenomes have been mostly focused on the gut. Here we profile and compare the phageome of 633 human oral sites and 221 paired gut phageomes acquired from countries worldwide. Phageome profiles are specific to oral sites and the gut across individuals, with the largest separation between the oral cavity and the gut. The differences in phage genotypes is bolstered by distinct phage host compositions between these sites. The greatest diversity of phages is found on the tongue and in dental plaque. Notably, 37 unique circular jumbo phage genomes were identified in oral sites, particularly on the dorsum of the tongue, whilst none were found in the gut. Oral sites provide conducive environments, such as robust biofilms, that can harbour genetically diverse phages.Competing Interest StatementThe authors have declared no competing interest.View Full Text

genomics↗

bioRxiv2020

Integron Gene Cassettes Harboring Novel Variants of D-Alanine-D-Alanine Ligase Confer High-level Resistance to D-Cycloserine

During a PCR-based screen of antibiotic resistance genes (ARGs) associated with integrons in saliva-derived metagenomic DNA of healthy human volunteers, two novel variants of genes encoding a D-alanine-D-alanine ligase (ddl6 and ddl7) located within gene cassettes in the first position of a reverse integron were identified. Treponema denticola was identified as the likely host of the ddl cassettes. Both ddl6 and ddl7 conferred high level resistance to D-cycloserine when expressed in Escherichia coli with ddl7 conferring four-fold higher resistance to D-cycloserine compared to ddl6. A SNP was found to be responsible for this difference in resistance phenotype between both ddl variants. Molecular dynamics simulations were used to explain the mechanism of this phenotypic change at the atomic scale. A hypothesis for the evolutionary selection of ddl containing integron gene cassettes is proposed, based on molecular docking of plant metabolites within the ATP and D-cycloserine binding pockets of Ddl. Significance StatementThe drivers of antimicrobial resistance are varied and numerous. One such hypothesis is that compounds not normally considered to be antibiotics may be able to select for genes that can provide resistance to conventional antibiotics. Here we provide evidence that dietary flavonoids are likely to provide the selective pressure for two novel variants of the ddl gene, encoding D-alanine-D-alanine ligases, to be maintained as the first gene cassette of a reverse integron detectable in the human oral cavities from both the UK and Bangladesh. We show that Ddl is functional, able to confer resistance to D-cycloserine and that the dietary flavonoids quercetin and apigenin are likely able to compete with both ATP and D-cycloserine within their Ddl binding sites.

microbiology↗

bioRxiv2019

Abundance and diversity of resistomes differ between healthy human oral cavities and gut

The global threat of the \"antimicrobial resistance apocalypse\" that has arisen in recent years has driven the use of high-throughput sequencing techniques to monitor the profile of resistance genes, known as the \"resistome\", in microbial populations. The human oral cavity contains a poorly explored reservoir of these genes, and little is known about their abundance and diversity, or how their profile compares with antimicrobial resistance genes in the gut. Here we analyse the resistome profiles of 788 oral cavities worldwide and compare these profiles with paired stool samples from shotgun metagenomic data. We find country and body site-specific differences in the prevalence of antimicrobial resistance genes, classes and mechanisms in oral and stool samples. However, the abundance of these antimicrobial resistance classes do not correlate with antibiotic prescription rates. A greater similarity was found in interpersonal resistomes between the same body sites than intrapersonal resistomes across different body sites. Between individuals, the oral cavity contains the highest and lowest abundances of specific antimicrobial resistance genes, but a lower diversity of resistance genes compared to the gut, which is likely influenced by differences in microbial composition and exposure to antimicrobial selection pressures. Co-occurrence analysis shows contrasting ARG-species associations between saliva and stool samples. This is the first study to date that characterises the oral cavity resistome worldwide, identifying its distinctive signatures compared to the gut.Maintenance and persistence of antimicrobial resistance is likely to vary across different body sites. Thus, we highlight the importance of characterising the resistome across body sites to uncover the antimicrobial resistance potential in the human body.

microbiology↗

bioRxiv2018

Promoter activity of ORF-less gene cassettes isolated from the oral metagenome

Integrons are genetic elements consisting of a functional platform for recombination and expression of gene cassettes (GCs). GCs usually carry promoter-less open reading frames (ORFs), encoding proteins with various functions including antibiotic resistance. The transcription of GCs relies mainly on a cassette promoter (PC), located upstream of an array of GCs. Some integron GCs, called ORF-less GCs, contain no identifiable ORF with a small number shown to be involved in antisense mRNA mediated gene regulation.\n\nIn this study, promoter sequences were identified, using in silico analysis, within GCs PCR amplified from the oral metagenome. The promoter activity of ORF-less GCs was verified by cloning them upstream of a gusA reporter, proving they can function as a promoter, presumably allowing bacteria to adapt to multiple stresses within the complex physico-chemical environment of the human oral cavity. A bi-directional promoter detection system was also developed allowing direct identification of clones with promoter-containing GCs on agar plates. Novel promoter-containing GCs were identified from the human oral metagenomic DNA using this construct, called pBiDiPD.\n\nThis is the first demonstration and detection of promoter activity of ORF-less GCs and the development of an agar plate-based detection system will enable similar studies in other environments.

microbiology↗