Biology subjects

Yasir, M.

Publications and source records attributed to Yasir, M..

15 recordsLinked to original sources

bioRxiv2026

Unsupervised decomposition of massively parallel TraDIS-Xpress fitness data from Escherichia coli identifies distinct functional and expression modules of antimicrobial resistance determinants

Linking genotype to phenotype is a central goal in biology, one way to do this is using transposon insertion sequencing (TIS) where the fitness impacts of mutations across a genome are assessed in different conditions. Traditional analyses use comparison of each gene response independently in control versus test conditions, so a compendium of hundreds of test conditions returns hundreds of separate ranked gene lists. To unlock the potential information hidden within large data sets, we applied independent component (ICA) analysis to 754 Escherichia coli BW25113 TraDIS-Xpress samples. These samples included a series of antibiotic and other stress condition exposures. ICA is designed to identify hidden structure within complex data and to extract meaningfully linked components. In this analysis each annotated gene was resolved into a gene body and 198 bp 5' and 3' features so that expression effects driven by the transposon's outwards facing promoter enter the matrix separately from gene disruption effects. The decomposition returned 99 components, which we term fxModules, which were defined as containing elements with similar responses across the whole compendium rather than per any individual experiment. Of the 754 stress samples, the antibiotic arm included 110 samples derived from exposure to 14 separate agents at multiple concentrations. Many of these have been highly studied allowing us to explore the accuracy of predicted responsive fxModules. This analysis showed excellent predictive power of the approach and the fxModules responsive to individual drugs typically reproduced known mechanisms at a resolution superior to analysis of single gene sets. For example, exposure to fosfomycin identified responsive fxModules containing genes which are known to be involved in uptake of the drug, cAMP-CRP control and exposure to gentamicin identified oxidative phosphorylation split across three fxModules responding with different magnitudes and directions at different concentrations. This recapitulates recent work studying the landscape of E. coli genes sensitive to this drug with high precision without any prior knowledge of functional annotation. Similarly precise predictions were made for other drugs. Responsive modules also identified novel groups of genes and linkages beyond the boundaries of defined pathways as being responsive to various stresses demonstrating the ability to predict new genotype-phenotype links. Inclusion of the regulatory regions also resolved fxModules which were entirely contributed by promoter regions, for example for chloramphenicol genes responsible for efflux were identified by signals in intergenic control regions, and unidirectional insertions in gene bodies, a signal that a gene level matrix would not be able to predict with accuracy. These data show that ICA decomposition provides an efficient and accurate annotation independent approach to identifying sets of genes with related functional impacts in any given condition in the compendium. The functional modular association of genes also help in predicting gene functions of unknown genes based on the group function. This approach allows rapid identification of novel genotype-phenotype links and unlocks the power of multiple comparisons of transposon mutagenesis data.

microbiology↗

bioRxiv2026

Inactivation of Microorganisms in the Complex Regions of Transvaginal Ultrasound Probes By a UVC-LED Light Based Disinfection System

Endocavity ultrasound transducers, particularly transvaginal ultrasound (TVUS) probes, contain intricate structures such as notches, grooves, lens surfaces, and handle edges that are highly susceptible to microbial contamination yet difficult to disinfect using conventional high-level disinfection (HLD) methods. This study evaluated the efficacy of a novel ultraviolet-C light-emitting diode (UV-C LED) HLD system in eliminating microbial contamination from these complex probe surfaces. Two TVUS probes were sampled from predefined high-risk regions before and after disinfection following clinical use. Probe A was sampled at the top and bottom notches and both sides of the handle, while Probe B was assessed at the lens, edges, and bent groove regions. Microbial contamination was quantified using swab sampling, culture on agar plates, and identification via MALDI-TOF. Environmental sampling of examination and disinfection rooms was also performed. To assess this system robustness, probe sites were repeatedly inoculated with Bacillus subtilis spores and evaluated following UV-C treatment. Before UV-C treatment, contamination rates ranged from 25% to 57% across sampled regions, with microbial loads reaching up to 3.9 log CFU. Identified organisms included Staphylococcus epidermidis, Pseudomonas koreensis, Bacillus cereus, and Propionibacterium spp. Probe sheaths were also predominantly contaminated with Staphylococcus epidermidis., with counts reaching up to 4.3 log CFU, Environmental sampling revealed diverse microbiota, with higher contamination levels in examination rooms compared to disinfection areas. Following 90 seconds of UV-C exposure, no microbial growth was detected on any sampled site, indicating 100% decontamination. Additionally, UV-C treatment achieved >6.7 log reduction of B. subtilis spores across all tested regions. These findings demonstrate that UV-C LED technology provides rapid, effective, and consistent high-level disinfection of complex TVUS probe surfaces, supporting its potential as a rapid and reliable disinfection modality in clinical setting.

microbiology↗

bioRxiv2025

Antimicrobial resistance and comparative genome analysis of high-risk Escherichia coli clones isolated from Egyptian children with diarrhoea.

Escherichia coli is an important human pathogen that is able to cause a variety of infections, which can result in diarrhoea, urinary tract infections, sepsis, and even meningitis, depending on the pathotype of the infecting strain. Like many Gram-negative bacteria, E. coli is becoming increasingly resistant to many frontline antibiotics, including third generation cephalosporins and carbapenems, which are often considered the antibiotics of last resort for these infections. This is particularly the case in Egypt, where multidrug resistance (MDR) E. coli is highly prevalent. However, in spite of this, few Egyptian MDR E. coli strains have been fully characterised by genome sequencing. Here, we present the genome sequences of ten highly MDR E. coli strains, which were isolated from children, who presented with diarrhoea at the Outpatients Clinic of Assiut University Children's Hospital in Assiut, Egypt. We report that they carry multiple antimicrobial resistance genes, which includes extended spectrum {beta}-lactamase genes, as well as blaNDM and blaOXA carbapenemase genes, encoded on IncX3 and potentially IncF plasmids. Many of these stains were also found to be high-risk extra-intestinal pathogenic E. coli (ExPEC) clones, belonging to sequence types ST167, ST410 and ST617. Thus, their presence in the Egyptian paediatric population is particularly worrying, and this highlights the need for increased surveillance of high-priority pathogens in this part of the world.

genomics↗

bioRxiv2025

The metallophore staphylopine is essential for survival of Staphylococcus epidermidis in human synovial fluid

Due to extended life expectancies, prosthetic joint infections are an increasing burden on healthcare institutions worldwide. The most commonly isolated causative agents are staphylococci, though the mechanisms underpinning survival and proliferation in synovial fluid are still not fully understood. In this study, we aimed to identify genes important for survival in synovial fluid using a transposon mutant library and RNAseq. We produced a transposon mutant library, containing approximately 57,000 unique insertion mutants, in Staphylococcus epidermidis strain 846. This library was grown in Muller Hinton broth or processed human synovial fluid samples, and Transposon-directed Insertion Sequencing (TraDIS) was used to identify genes involved in survival in synovial fluid. This identified importance of the his, pur and cnt operons. These genes were also upregulated in both Staphylococcus epidermidis 846 and the model Staphylococcus epidermidis strain RP62A when exposed to human synovial fluid. All these key pathways contribute to production of the metallophore staphylopine. To confirm staphyopine production is essential for survival in synovial fluid, a defined transposon insertion in the gene encoding for staphylopine export (cntE) mutant was used. This demonstrated impaired survival in synovial fluid compared to the wild type. RT-qPCR also showed that cntE was more highly expressed after exposure to infected synovial fluid (where metals will be depleted) than non-infected fluid. In conclusion, TraDIS and RNASeq both identified the importance of staphylopine for survival in human synovial fluid. This suggests an opportunity for exploitation for therapeutic or diagnostic use. Author SummaryStaphylococcus epidermidis is a common cause of prosthetic joint infection, however accurate diagnosis remains difficult. In this work we explored the genetic basis of Staphylococcus epidermidis survival in human synovial fluid using a large transposon mutant library, and identified which genes were differentially expressed upon exposure to the fluid. We found crossover between the datasets, which pointed to the importance of the metal acquisition compound staphylopine. The expression levels of the gene required for staphylopine export were shown to be dependent on the infection status of the individual samples were obtained from. We also found the gene cluster to be conserved in a range of staphylococcal species isolated from cases of prosthetic joint infection. Our work provides a valuable resource in the from of a large transposon mutant library, and provides a greater understanding of the requirements for staphylococcal survival in human synovial fluid, providing potential biomarkers for future diagnostic development.

microbiology↗

bioRxiv2023

Collateral sensitivity increases the efficacy of a rationally designed bacteriophage combination to control Salmonella enterica

The ability of virulent bacteriophages to lyse bacteria influences bacterial evolution, fitness, and population structure. Knowledge of both host susceptibility and resistance factors is crucial for the successful application of bacteriophages as biological control agents in clinical therapy, food processing and agriculture. In this study, we isolated twelve bacteriophages termed SPLA phage which infect the foodborne pathogen Salmonella enterica. To determine phage host range, a diverse collection of Enterobacteriaceae and Salmonella enterica were used and genes involved in infection by six SPLA phages were identified using Salmonella Typhimurium strain ST4/74. Candidate host receptors included lipopolysaccharide, cellulose and BtuB. Lipopolysaccharide was identified as susceptibility factor for phage SPLA1a and mutations in LPS biosynthesis genes spontaneously emerged during culture with S. Typhimurium. Conversely, LPS was a resistance factor for phage SPLA5b that suggested that emergence of LPS mutations in culture with SPLA1a may represent a case of collateral sensitivity to SPLA5b. We show that combination therapy with SPLA1a and SPLA5b was more successful in limiting the emergence of phage resistance compared to monotherapy. Identification of host susceptibility and resistance genes and understanding infection dynamics is critical step in rationale design of phage cocktails against specific bacterial pathogens.

microbiology↗

bioRxiv2023

Mechanisms of action and synergies of a novel lipid IVA biosynthesis inhibitor

The development of novel antimicrobials provides additional treatment options for infectious diseases, including antimicrobial resistant infections. There are many hurdles to antimicrobial development and identifying an antimicrobials mechanism of action is a crucial step in progressing candidate molecules through the drug discovery pipeline. We used the genome wide screening method TraDIS-Xpress to identify genes in two model Gram-negative bacteria that affected sensitivity to three analogues of a novel antimicrobial compound (OPT-2U1). TraDIS-Xpress identified that all three analogues targeted the lipid IVA biosynthetic pathway in E. coli and Salmonella Typhimurium. Specifically, we determined that the antimicrobial target was likely to be LpxD, and validated this by finding a 5 log2-fold increase in the MIC of the OPT-2U1 analogues in E. coli when lpxD was overexpressed. Synergies were identified between OPT-2U1 analogues combined with rifampicin or colistin, to varying strengths, in both E. coli and S. Typhimurium. LPS composition was a likely reason for differences between E. coli and S.Typhimurium, as perturbation of LPS synthesis affected synergy between antibiotics and OPT-2U1 analogues. Finally, genes involved in ATP synthesis and membrane signalling functions were also found to affect the synergy between colistin and OPT-2U1 analogues. TraDIS-Xpress has proven a powerful tool to rapidly assay all genes (and notably, essential genes) within a bacterium for roles in dictating antimicrobial sensitivity. This study has confirmed the predicted target pathway of OPT-2U1 and identified synergies which could be investigated for development of novel antimicrobial formulations. Data SummaryNucleotide sequence data supporting the analysis in this study has been deposited in ArrayExpress under the accession number E-MTAB-13250. The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

molecular biology↗

bioRxiv2023

Tazobactam selects for multidrug resistance

Piperacillin-Tazobactam is a {beta}-lactam/{beta}-lactamase inhibitor combination which is amongst the most prescribed antimicrobials in hospital medicine. Piperacillin is inactivated by commonly carried resistance enzymes, but tazobactam inhibits these allowing successful treatment. The effect of piperacillin on Gram-negative bacteria has been widely studied, but less attention has been paid to the effects of tazobactam. We used a massive transposon mutagenesis approach (TraDIS-Xpress) to determine the genes in Escherichia coli that affect survival when exposed to piperacillin and tazobactam, separately and together. We found significant differences in the selective pressure of the two drugs: a striking finding was that multiple efflux pump families and regulators were essential for survival in the presence of tazobactam, but only one efflux system was beneficial for piperacillin. Additionally, we identified the shikimate kinase AroK as a potential target for tazobactam. This method also found that genes involved in DNA replication and repair reduced E. coli susceptibility to a combination of piperacillin and tazobactam, not seen from either drug treatment alone. Treatment of E. coli and Klebsiella pneumoniae with piperacillin and/or tazobactam selected for mutants with reduced susceptibility, and SNP analyses supported the TraDIS-Xpress findings that tazobactam selects for changes in membrane permeability and maintenance associated with multidrug-resistance. Increased efflux activity is an important foundation of multidrug resistance in human pathogens, therefore the finding that tazobactam can select for this is concerning. These findings could have consequences for antibiotic prescription and should inform the development of future {beta}-lactamase inhibitors to reduce the global increase in multidrug-resistant infections.

molecular biology↗

bioRxiv2022

LoRTIS Software Suite: Transposon mutant analysis using long-read sequencing

To date transposon insertion sequencing (TIS) methodologies have used short-read nucleotide sequencing technology. However, short-read sequences are unlikely to be matched correctly within repeated genomic regions which are longer than the sequence read. This drawback may be overcome using long-read sequencing technology. We have developed a suite of new analysis tools, the "LoRTIS software suite" (LoRTIS-SS), that produce transposon insertion site mapping data for a reference genome using long-read nucleotide sequence data. Long-read nucleotide sequence data can be applied to TIS, this enables the unique mapping of transposon insertion sites within long genomic repeated sequences. Here we present long-read TIS analysis software, LoRTIS-SS, which uses the Snakemake framework to manage the workflow. A docker image is provided, complete with dependencies and ten scripts are included for experiment specific data processing before or after use of the main workflow. The workflow uses long-read nucleotide sequence data such as those generated by the MinION sequencer (Oxford Nanopore Technologies). The unique mapping properties of long-read sequence data were exemplified by reference to the ribosomal RNA genes of Escherichia coli strain BW25113, of which there are 7 copies of [~]4.9 kbases in length that are at least 99% similar. Of reads that matched within rRNA genes, approximately half matched uniquely. The software workflow outputs data compatible with the established Bio-TraDIS analysis toolkit allowing for existing workflows to be easily upgraded to support long-read sequencing.

bioinformatics↗

bioRxiv2021

Efficacy of anti-microbial gel vapours against aerosolised coronavirus, bacteria, and fungi

BackgroundThe urban population spends up to 90% of their time indoors. The indoor environment harbours a diverse microbial population including viruses, bacteria, and fungi. Pathogens present in the indoor environment can be transmitted to humans through aerosols. AimThis study evaluated the efficacy of an antimicrobial gel containing a mix of essential oils against aerosols of bacteria, fungi, and coronavirus. MethodsThe antimicrobial gel was allowed to vapourize inside a glass chamber for 10 or 20 minutes. Microbial aerosols of Escerichia coli, Aspergillus flavus spores or murine hepatitis virus MHV 1, a surrogate of SARS CoV-2 was passed through the gel vapours and then collected on a 6-stage Andersen sampler. The number of viable microbes present in the aerosols collected in the different stages were enumerated and compared to number of viable microbes in control microbial aerosols that were not exposed to the gel vapours. ResultsVaporizing the antimicrobial gel for 10 and 20 minutes resulted in a 48% (p = 0.002 Vs. control) and 53% (p = 0.001 Vs. control) reduction in the number of MHV-1 in the aerosols, respectively. The antimicrobial gel vaporised for 10 minutes, reduced the number of viable E. coli by 51% (p = 0.032 Vs. control) and Aspergillus flavus spores by 72% (p=0.008 Vs. control) in the aerosols. ConclusionsThe antimicrobial gel may be able to reduce aerosol transmission of microbes.

microbiology↗

bioRxiv2020

Massively parallel transposon mutagenesis identifies temporally essential genes for biofilm formation in Escherichia coli

Biofilms complete a life cycle where cells aggregate, grow and produce a structured community before dispersing to seed biofilms in new environments. Progression through this life cycle requires temporally controlled gene expression to maximise fitness at each stage. Previous studies have largely focused on the essential genome for the formation of a mature biofilm, but here we present an insight into the genes involved at different stages of biofilm formation. We used TraDIS-Xpress; a massively parallel transposon mutagenesis approach using transposon-located promoters to assay the impact of disruption or altered expression of all genes in the genome on biofilm formation. We determined temporal differences in the importance of genes in E. coli growing as a biofilm on glass beads after 12, 24 and 48 hours. A selection of genes identified as important were then validated independently by assaying biofilm biomass, aggregation, curli production and adhesion ability of defined mutants. We identified 48 genes that affected biofilm fitness including genes with known roles and those not previously implicated in biofilm formation. Regulation of type 1 fimbriae and motility were important at all time points. Adhesion and motility were important for the early biofilm, whereas matrix production and purine biosynthesis were only important as the biofilm matured. We found strong temporal contributions to biofilm fitness for some genes including some where expression changed between being beneficial or detrimental depending on the stage at which they are expressed, including dksA and dsbA. Novel genes implicated in biofilm formation included zapE and truA involved in cell division, maoP in DNA housekeeping and yigZ and ykgJ of unknown function. This work provides new insights into the requirements for successful biofilm formation through the biofilm life cycle and demonstrates the importance of understanding expression and fitness through time.

molecular biology↗

bioRxiv2019

A genome wide analysis of Escherichia coli responses to fosfomycin using TraDIS-Xpress reveals novel roles for the phosphonate and phosphate transport systems

Fosfomycin is an antibiotic which has seen a revival in use due to its unique mechanism of action and resulting efficacy against isolates resistant to many other antibiotics. Mechanisms of resistance have been elucidated and loss of function mutations within the genes encoding the sugar importers, GlpT and UhpT are commonly selected for by fosfomycin exposure in E. coli. There has however not been a genome wide analysis of the basis for fosfomycin sensitivity reported to date. Here we used TraDIS-Xpress a high-density transposon mutagenesis approach to assay the role of all genes in E. coli in fosfomycin sensitivity. The data confirmed known mechanisms of action and resistance as well as identifying a set of novel loci involved in fosfomycin sensitivity. The assay was able to identify sub domains within genes of importance and also revealed essential genes with roles in fosfomycin sensitivity based on expression changes. Novel genes identified included those involved in glucose metabolism, the phosphonate import and breakdown system, phnC-M and the phosphate importer, pstSACB. The impact of these genes in fosfomycin sensitivity was validated by measuring the susceptibility of defined inactivation mutants. This work reveals a wider set of genes contribute to fosfomycin sensitivity including core sugar metabolism genes and two transport systems previously unrecognised as having a role in fosfomycin sensitivity. The work also suggests new routes by which drugs with a phosphonate moiety may be transported across the inner membrane of Gram-negative bacteria. ImportanceThe emergence and spread of antibiotic resistant bacteria had resulted in increased use of alternative drugs which retain efficacy against isolates resistant to other classes of drugs. One example is fosfomycin; an old drug which has found greatly increased use in recent years. We studied the mechanisms of fosfomycin resistance by applying a genome wide screen based on comparing the fitness of a massive library of transposon mutants in the presence of fosfomycin. This approach identified the previously known mechanisms of resistance but also identified a number of new pathways which contribute to fosfomycin sensitivity including two importer systems. This information advances our knowledge about an increasingly important antibiotic and identifies new potential routes to resistance.

microbiology↗

bioRxiv2019

Mode of action of the antimicrobial peptide Mel4 is independent of Staphylococcus aureus cell membrane permeability

Mel4 is a novel cationic peptide with potent activity against Gram-positive bacteria. The current study examined the anti-staphylococcal mechanism of action of Mel4 and its precursor peptide melimine. The interaction of peptides with lipoteichoic acid (LTA) and with the cytoplasmic membrane using DiSC(3)-5, Sytox green, Syto-9 and PI dyes were studied. Release of ATP and DNA/RNA from cells exposed to the peptides were determined. Bacteriolysis and autolysin-activated cell death were determined by measuring decreases in OD620nm and killing of Micrococcus luteus cells by cell-free media. Both peptides bound to LTA and rapidly dissipated the membrane potential (within 30 seconds) without affecting bacterial viability. Disturbance of the membrane potential was followed by the release of ATP (50% of total cellular ATP) by melimine and by Mel4 (20%) after 2 minutes exposure (p<0.001). Mel4 resulted in staphylococcal cells taking up PI with 3.9% cells predominantly stained after 150 min exposure, whereas melimine showed 34% staining. Unlike melimine, Mel4 did not release DNA/RNA. Cell-free media from Mel4 treated cells hydrolysed peptidoglycan and produced greater zones of inhibition against M. luteus lawn than melimine treated samples. These findings suggest that pore formation is unlikely to be involved in Mel4-mediated membrane destabilization for Staphylococcci, since there was no significant Mel4-induced PI staining and DNA/RNA leakage. It is likely that the S. aureus killing mechanism of Mel4 involves the release of autolysins followed by cell death. Whereas, membrane interaction is the primary bactericidal activity of melimine, which includes membrane depolarisation, pore formation, release of cellular contents leading to cell death.\n\nThis work is original, has not been published and is not being considered for publication elsewhere. Part of this manuscript has been presented as a poster presentation in Gordon Research Conference Italy in 2019. There are no conflicts of interest for any of the authors that could have influenced the results of this work. Prof. Mark Willcox holds the patent the for the melimine peptide.

microbiology↗

bioRxiv2019

A new massively-parallel transposon mutagenesis approach comparing multiple datasets identifies novel mechanisms of action and resistance to triclosan

The mechanisms by which antimicrobials exert inhibitory effects against bacterial cells and by which bacteria display resistance vary under different conditions. Our understanding of the full complement of genes which can influence sensitivity to many antimicrobials is limited and often informed by experiments completed in a small set of exposure conditions. Capturing a broader suite of genes which contribute to survival under antimicrobial stress will improve our understanding of how antimicrobials work and how resistance can evolve. Here, we apply a new version of TraDIS (Transposon Directed Insert Sequencing); a massively parallel transposon mutagenesis approach to identify different responses to the common biocide triclosan across a 125-fold range of concentrations. We have developed a new bioinformatic tool AlbaTraDIS allowing both predictions of the impacts of individual transposon inserts on gene function to be made and comparisons across multiple TraDIS data sets. This new TraDIS approach allows essential genes as well as non-essential genes to be assayed for their contribution to bacterial survival and growth by modulating their expression. Our results demonstrate that different sets of genes are involved in survival following exposure to triclosan under a wide range of concentrations spanning bacteriostatic to bactericidal. The identified genes include those previously reported to have a role in triclosan resistance as well as a new set of genes not previously implicated in triclosan sensitivity. Amongst these novel genes are those involved in barrier function, small molecule uptake and integrity of transcription and translation. These data provide new insights into potential routes of triclosan entry and bactericidal mechanisms of action. Our data also helps to put recent work which has demonstrated the ubiquitous nature of triclosan in people and the built environment into context in terms of how different triclosan exposures may influence evolution of bacteria. We anticipate the approach we show here that allows comparisons across multiple experimental conditions of TraDIS data will be a starting point for future work examining how different drug conditions impact bacterial survival mechanisms.

microbiology↗

bioRxiv2019

AlbaTraDIS: Comparative analysis of large datasets from parallel transposon mutagenesis experiments

BackgroundBacteria have evolved over billions of years to survive in a wide range of environments. Currently, there is an incomplete understanding of the genetic basis for mechanisms underpinning survival in stressful conditions, such as the presence of anti-microbials. Transposon mutagenesis has been proven to be a powerful tool to identify genes and networks which are involved in survival and fitness under a given condition by simultaneously assaying the fitness of millions of mutants, thereby relating genotype to phenotype and contributing to an understanding of bacterial cell biology. A recent refinement of this approach allows the roles of essential genes in conditional stress survival to be inferred by altering their expression. These advancements combined with the rapidly falling costs of sequencing now allows comparisons between multiple experiments to identify commonalities in stress responses to different conditions. This capacity however poses a new challenge for analysis of multiple data sets in conjunction.\n\nResultsTo address this analysis need, we have developed AlbaTraDIS; a software application for rapid large-scale comparative analysis of TraDIS experiments that predicts the impact of transposon insertions on nearby genes. AlbaTraDIS can identify genes which are up or down regulated, or inactivated, between multiple conditions, producing a filtered list of genes for further experimental validation as well as several accompanying data visualisations. We demonstrate the utility of our new approach by applying it to identify genes used by Escherichia coli to survive in a wide range of different concentrations of the biocide Triclosan. AlbaTraDIS automatically identified all well characterised Triclosan resistance genes, including the primary target, fabI. A number of new loci were also implicated in Triclosan resistance and the predicted phenotypes for a selection of these were validated experimentally and results showed high consistency with predictions.\n\nConclusionsAlbaTraDIS provides a simple and rapid method to analyse multiple transposon mutagenesis data sets allowing this technology to be used at large scale. To our knowledge this is the only tool currently available that can perform these tasks. AlbaTraDIS is written in Python 3 and is available under the open source licence GNU GPL 3 from https://github.com/quadram-institute-bioscience/albatradis.

bioinformatics↗

bioRxiv2018

Prokaryotic Diversity from Extreme Environments of Pakistan and its Potential Applications at Regional Levels

Extremophiles, the microorganisms thriving in extreme environments, provide valuable resources for practicing novel biotechnological processes. Pakistan homes a wide spectrum of extreme environments which harbor various biotechnologically significant microorganisms. This review gauges the structural and functional bacterial diversity of several extreme environments, emphasizing their potentials as a source of extremozymes, and in bioleaching, bioremediation, and bioenergy production at regional level. Further, this review highlights a panoramic account of the local natural conservatories of extremophiles. The inadequacies of current fragmental research are discussed with suggestions to quantitatively define the structural and functional diversity of unexplored extreme localities.

microbiology↗