scholarly journals Genotyping of evolving prokaryotic populations

2016 ◽  
Author(s):  
Markus Zojer ◽  
Lisa N Schuster ◽  
Frederik Schulz ◽  
Alexander Pfundner ◽  
Matthias Horn ◽  
...  
Keyword(s):  
Experimental Evolution ◽  
Bacterial Species ◽  
Clinical Diagnostics ◽  
Structural Variations ◽  
Natural Habitats ◽  
Reliable Prediction ◽  
Low Frequencies ◽  
Bacterial Populations ◽  
Sequencing Errors ◽  
Genomic Environment

Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments, clinical diagnostics and occurs as micro-diversity of natural habitats. The challenge for genome research is to accurately capture this heterogeneity with the currently used short sequencing reads. Recent advances in NGS technologies improved the speed and coverage and thus allowed for deep sequencing of bacterial populations. This facilitates the quantitative assessment of genomic heterogeneity, including low frequent alleles or haplotypes. However, false positive variant predictions due to sequencing errors and mapping artifacts of short reads need to be prevented. We therefore created VarCap, a workflow for the reliable prediction of different types of variants even at low frequencies. In order to predict SNPs, indels and structural variations, we evaluated the sensitivity and accuracy of different software tools using synthetic read data. The results suggested that the best sensitivity could be reached by a combination of different tools. We identified possible reasons for false predictions and used this knowledge to improve the accuracy by post-filtering the predicted variants according to properties such as frequency, coverage, genomic environment/localization and co-localization with other variants. This resulted in the reliable prediction of variants above a minimum relative abundance of 2%. VarCap is designed for being routinely used within experimental evolution experiments or for clinical diagnostics. The detected variants are reported as frequencies within a vcf file and as a graphical overview of the distribution of the different variant/allele/haplotype frequencies. The source code of VarCap is available at https://github.com/ma2o/VarCap. In order to provide this workflow to a broad community, we implemeted VarCap on a Galaxy webserver (Afgan et al. 2016) , which is accessible at http://galaxy.csb.univie.ac.at.

scholarly journals Genotyping of evolving prokaryotic populations

2016 ◽  
Author(s):  
Markus Zojer ◽  
Lisa N Schuster ◽  
Frederik Schulz ◽  
Alexander Pfundner ◽  
Matthias Horn ◽  
...  
Keyword(s):  
Experimental Evolution ◽  
Bacterial Species ◽  
Clinical Diagnostics ◽  
Structural Variations ◽  
Natural Habitats ◽  
Reliable Prediction ◽  
Low Frequencies ◽  
Bacterial Populations ◽  
Sequencing Errors ◽  
Genomic Environment

Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments, clinical diagnostics and occurs as micro-diversity of natural habitats. The challenge for genome research is to accurately capture this heterogeneity with the currently used short sequencing reads. Recent advances in NGS technologies improved the speed and coverage and thus allowed for deep sequencing of bacterial populations. This facilitates the quantitative assessment of genomic heterogeneity, including low frequent alleles or haplotypes. However, false positive variant predictions due to sequencing errors and mapping artifacts of short reads need to be prevented. We therefore created VarCap, a workflow for the reliable prediction of different types of variants even at low frequencies. In order to predict SNPs, indels and structural variations, we evaluated the sensitivity and accuracy of different software tools using synthetic read data. The results suggested that the best sensitivity could be reached by a combination of different tools. We identified possible reasons for false predictions and used this knowledge to improve the accuracy by post-filtering the predicted variants according to properties such as frequency, coverage, genomic environment/localization and co-localization with other variants. This resulted in the reliable prediction of variants above a minimum relative abundance of 2%. VarCap is designed for being routinely used within experimental evolution experiments or for clinical diagnostics. The detected variants are reported as frequencies within a vcf file and as a graphical overview of the distribution of the different variant/allele/haplotype frequencies. The source code of VarCap is available at https://github.com/ma2o/VarCap. In order to provide this workflow to a broad community, we implemeted VarCap on a Galaxy webserver (Afgan et al. 2016) , which is accessible at http://galaxy.csb.univie.ac.at.

scholarly journals Variant profiling of evolving prokaryotic populations

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2997 ◽  
Author(s):  
Markus Zojer ◽  
Lisa N. Schuster ◽  
Frederik Schulz ◽  
Alexander Pfundner ◽  
Matthias Horn ◽  
...  
Keyword(s):  
Experimental Evolution ◽  
Bacterial Species ◽  
Low Frequency ◽  
Clinical Diagnostics ◽  
Structural Variations ◽  
Natural Habitats ◽  
Reliable Prediction ◽  
Low Frequencies ◽  
Bacterial Populations ◽  
Link Type

Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments and clinical diagnostics, and occurs as micro-diversity of natural habitats. The challenge for genome research is to accurately capture this heterogeneity with the currently used short sequencing reads. Recent advances in NGS technologies improved the speed and coverage and thus allowed for deep sequencing of bacterial populations. This facilitates the quantitative assessment of genomic heterogeneity, including low frequency alleles or haplotypes. However, false positive variant predictions due to sequencing errors and mapping artifacts of short reads need to be prevented. We therefore created VarCap, a workflow for the reliable prediction of different types of variants even at low frequencies. In order to predict SNPs, InDels and structural variations, we evaluated the sensitivity and accuracy of different software tools using synthetic read data. The results suggested that the best sensitivity could be reached by a union of different tools, however at the price of increased false positives. We identified possible reasons for false predictions and used this knowledge to improve the accuracy by post-filtering the predicted variants according to properties such as frequency, coverage, genomic environment/localization and co-localization with other variants. We observed that best precision was achieved by using an intersection of at least two tools per variant. This resulted in the reliable prediction of variants above a minimum relative abundance of 2%. VarCap is designed for being routinely used within experimental evolution experiments or for clinical diagnostics. The detected variants are reported as frequencies within a VCF file and as a graphical overview of the distribution of the different variant/allele/haplotype frequencies. The source code of VarCap is available at https://github.com/ma2o/VarCap. In order to provide this workflow to a broad community, we implemeted VarCap on a Galaxy webserver, which is accessible at http://galaxy.csb.univie.ac.at.

scholarly journals Introduction When culturing bacteria in artificial microhabitats, such as in microfluidic devices, microchambers and microreactors, the ecological and microbiological aspects must be considered. In such devices and experiments cells often live in structured environments that from an ecological viewpoint could be considered “patchy” (i.e. with strong spatial heterogeneities and variations in suitability for the cells).1 In such artificial habitats, the formation of a metapopulation, a set of interacting subpopulations, is observed along with a complex population dynamics.2 The ecological aspects are also manifested in the fact that cells compete for resources,3 which sometimes results in unexpected spatial distribution and growth of cells.4 In such biological scenarios, cell-cell communication is important.5 The complexity of the evolved communication mechanisms among prokaryotes can be distinguished by the various chemical signals used by the different bacterial species. Beside the known quorum sensing signaling molecules (homoserine lactones and oligopeptides6,7), bacteria use toxins (antibiotics, bacteriocins8), antimicrobial peptides,9 amino acids,10 exopolysaccharides,11 or metabolic waste products (indole11) as signaling molecules. These chemical signals have distinguishable targets and functions (intra-, or interspecies communication, inter-kingdom signaling), and they have a key role in the communication of bacterial populations in natural habitats. Motile bacteria have the great advantage of being able to explore the heterogeneous environment. By a mechanism called chemotaxis bacteria are able to sense concentration changes of certain chemicals, and swim towards increasing or decreasing concentrations of chemoattractants or chemorepellent molecules, respectively.13,14 It has been shown that signaling and chemotaxis may be coupled, and signaling molecules may act as chemoeffectors.5 Although traditional microbiology techniques enable us to study the interactions of bacterial communities on a large scale (such as co-culturing bacteria on agar plates or in shaken flasks), these traditional tools do not allow us to follow the dynamics and the fundamental mechanisms on single cell level. In the last few decades, the development of microengineering and nanotechnology has revealed new directions in traditional microbiology. Microfluidics has provided excellent tools for studying bacteria in controlled environments.15–18 Here we present experiments performed with microfluidic devices to study the interaction of physically separated but chemically coupled bacterial populations. These populations, growing in microchambers and channels separated by porous membranes, exhibit dynamic spatial rearrangements as a result of secreInteraction of Bacterial Populations in Coupled Microchambers

2014 ◽  
Vol 28 (2) ◽  
pp. 225-231 ◽  
Author(s):  
K. Nagy ◽  
O. Sipos ◽  
É. Gombai ◽  
Á. Kerényi ◽  
S. Valkai ◽  
...  
Keyword(s):  
Large Scale ◽  
Bacterial Species ◽  
Cell Communication ◽  
Microfluidic Devices ◽  
Signaling Molecules ◽  
Chemical Signals ◽  
Natural Habitats ◽  
Bacterial Populations ◽  
Waste Products ◽  
Concentration Changes

On The Necessity to Study Natural Bacterial Populations-The Model of Bacillus Simplex From "Evolution Canyons" I and II, Israel

2006 ◽  
Vol 52 (3-4) ◽  
pp. 527-542 ◽  
Author(s):  
Johannes Sikorski ◽  
Eviatar Nevo
Keyword(s):  
Bacterial Species ◽  
Natural Populations ◽  
Natural Environments ◽  
Natural Habitats ◽  
Bacterial Populations ◽  
Bacillus Simplex ◽  
Evolution Canyon ◽  
Bacterial Systematics ◽  
Taxon Identification ◽  
Insight Into

How do bacteria evolve and speciate in natural environments? How does bacterial evolution relate to bacterial systematics? Exploring these answers is essential because bacteria profoundly impact life in general and, in particular, that of humans. Much insight into bacterial microevolution has come from theoretical and computational studies and from multigenerational laboratory systems ("Experimental Evolution"). These studies, however, do not take into account the diversity of modes of how bacteria can evolve under the complexity of the real world, i.e., nature. We argue, therefore, that for a comprehensive understanding of bacterial microevolution, it is essential to study natural populations. We underline our argument by introducing the Bacillus simplex model from "Evolution Canyon", Israel. This metapopulation splits into different evolutionary lineages that have adapted to the microclimatically different slopes of "Evolution Canyon". It was shown that temperature stress is a major environmental factor driving the B. simplex adaptation and speciation progress. Therefore, this model population has proven highly suitable to study bacterial microevolution in natural habitats. Finally, we discuss the B. simplex intrapopulation divergence of lineages in light of current controversies on bacterial species concepts and taxon identification.

Ice nucleation activity of bacteria isolated from snow compared with organic and inorganic substrates

2008 ◽  
Vol 5 (6) ◽  
pp. 373 ◽  
Author(s):  
Roya Mortazavi ◽  
Christopher T. Hayes ◽  
Parisa A. Ariya
Keyword(s):  
Bacterial Species ◽  
Ice Nucleation ◽  
Detailed Knowledge ◽  
Bacterial Populations ◽  
Inorganic Aerosols ◽  
Ice Nucleators ◽  
Species Population ◽  
Nucleation Activity ◽  
Ice Nucleation Activity ◽  
Snow Samples

Environmental context. Biological ice nucleators have been found to freeze water at very warm temperatures. The potential of bio-aerosols to greatly influence cloud chemistry and microphysics is becoming increasingly apparent, yet detailed knowledge of their actual role in atmospheric processes is lacking. The formation of ice in the atmosphere has significant local, regional and global influence, ranging from precipitation to cloud nucleation and thus climate. Ice nucleation tests on bacteria isolated from snow and laboratory-grown bacteria, in comparison with those of known organic and inorganic aerosols, shed light on this issue. Abstract. Ice nucleation experiments on bacteria isolated from snow as well as grown in the laboratory, in comparison with those of known organic and inorganic aerosols, examined the importance of bio-aerosols on cloud processes. Snow samples were collected from urban and suburban sites in the greater Montreal region in Canada (45°28′N, 73°45′W). Among many snow bacterial isolates, eight types of bacterial species, none belonging to known effective ice nucleators such as Pseudomonas or Erwinia genera, were identified to show an intermediate range of ice nucleation activity (–12.9 ± 1.3°C to –17.5 ± 2.8°C). Comparable results were also obtained for molten snow samples and inorganic suspensions (kaolin and montmorillonite) of buffered water solutions. The presence of organic molecules (oxalic, malonic and succinic acids) had minimal effect (<2°C) on ice nucleation. Considering experimental limitations, and drawing from observation in snow samples of a variety of bacterial populations with variable ice-nucleation ability, a shift in airborne-species population may significantly alter glaciation processes in clouds.

scholarly journals Antimicrobial Activity of Non-steroidal Anti-inflammatory Drugs on Biofilm: Current Evidence and Potential for Drug Repurposing

2021 ◽  
Vol 12 ◽  
Author(s):  
Rodrigo Cuiabano Paes Leme ◽  
Raquel Bandeira da Silva
Keyword(s):  
Bacterial Species ◽  
Drug Repurposing ◽  
Current Evidence ◽  
Pharmacokinetic Studies ◽  
Bacterial Populations ◽  
Human Pharmacokinetic ◽  
Inflammatory Drugs ◽  
Anti Inflammatory

It has been demonstrated that some non-steroidal anti-inflammatory drugs (NSAIDs), like acetylsalicylic acid, diclofenac, and ibuprofen, have anti-biofilm activity in concentrations found in human pharmacokinetic studies, which could fuel an interest in repurposing these well tolerated drugs as adjunctive therapies for biofilm-related infections. Here we sought to review the currently available data on the anti-biofilm activity of NSAIDs and its relevance in a clinical context. We performed a systematic literature review to identify the most commonly tested NSAIDs drugs in the last 5 years, the bacterial species that have demonstrated to be responsive to their actions, and the emergence of resistance to these molecules. We found that most studies investigating NSAIDs’ activity against biofilms were in vitro, and frequently tested non-clinical bacterial isolates, which may not adequately represent the bacterial populations that cause clinically-relevant biofilm-related infections. Furthermore, studies concerning NSAIDs and antibiotic resistance are scarce, with divergent outcomes. Although the potential to use NSAIDs to control biofilm-related infections seems to be an exciting avenue, there is a paucity of studies that tested these drugs using appropriate in vivo models of biofilm infections or in controlled human clinical trials to support their repurposing as anti-biofilm agents.

scholarly journals Stenotrophomonas Nematodicola Sp. Nov., a Novel Intestinal Lifespan-Prolonging Bacterium for Caenorhabditis Elegans That Assists in Host Resistance to Bacillus Nematocida Colonization

2021 ◽  
Author(s):  
Rui Han ◽  
Yu Wang ◽  
Yang Deng ◽  
Yuqin Zhang ◽  
Lin Zhang ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Host Resistance ◽  
Type Strain ◽  
Novel Species ◽  
Bacterial Species ◽  
Intestinal Bacteria ◽  
Phenotypic Characteristics ◽  
Natural Habitats ◽  
Metagenomic Sequence ◽  
C Elegans

Abstract The soil-dwelling opportunistic bacterium Bacillus nematocida B16 shows comparatively strong killing activities against a variety of pathogenic nematodes. A bacterial strain CPCC 101271T, isolated from intestines of C. elegans in natural habitats, was found not only to be probiotics for C. elegans but also assist in resisting pathogen B16 infection. The lifespan of Caenorhabditis elegans fed on strain CPCC 101271T was extended by approximately 40% compared with that of worms fed on Escherichia coli OP50. In addition, the colonization of C. elegans by the pathogenic bacterium B. nematocida B16 was inhibited when it was pre-fed with strain CPCC 101271T. Based on a polyphasic taxonomy study including genotypic, chemotaxonomic and phenotypic characteristics, we propose that strain CPCC 101271T represents a novel bacterial species with the name Stenotrophomonas nematodicola sp. nov. and CPCC 101271T as the type strain. Metagenomic sequence analysis of the intestinal microbiota of C. elegans fed with strain CPCC 101271T and then infected with B16 revealed that pre-feeding with CPCC 101271T improved the diversity of intestinal bacteria, while the community structure varied significantly together with the fluctuation of Stenotrophomonas spp. and Bacillus spp. abundance during competition between strain CPCC 101271T and B16. In conclusion, the nematode microbiota strain CPCC 101271T, a novel species of the genus Stenotrophomonas, assisted in its host resistance to the pathogen Bacillus nematocida colonization, so as to act as an intestinal life span-prolonging for C. elegans.

scholarly journals A Trifecta of New Insights into Ovine Footrot for Infection Drivers, Immune Response and Host Pathogen Interactions.

2021 ◽  
Author(s):  
Adam M. Blanchard ◽  
Ceri E. Staley ◽  
Laurence Shaw ◽  
Sean R Wattegedera ◽  
Christina-Marie Baumbach ◽  
...  
Keyword(s):  
Immune Response ◽  
Type I Collagen ◽  
Global Analysis ◽  
Bacterial Species ◽  
Skin Barrier ◽  
Control Measures ◽  
Skin Barrier Function ◽  
Type I ◽  
Bacterial Populations

Footrot is a polymicrobial infectious disease in sheep causing severe lameness, leading to one of the industry’s biggest welfare problems. The complex aetiology of footrot makes in-situ or in-vitro investigations difficult. Computational methods offer a solution to understanding the bacteria involved, how they may interact with the host and ultimately providing a way to identify targets for future hypotheses driven investigative work. Here we present the first combined global analysis of the bacterial community transcripts together with the host immune response in healthy and diseased ovine feet during a natural polymicrobial infection state using metatranscriptomics. The intra tissue and surface bacterial populations and the most abundant bacterial transcriptome were analysed, demonstrating footrot affected skin has a reduced diversity and increased abundances of, not only the causative bacteria Dichelobacter nodosus , but other species such as Mycoplasma fermentans and Porphyromonas asaccharolytica . Host transcriptomics reveals a suppression of biological processes relating to skin barrier function, vascular functions, and immunosurveillance in unhealthy interdigital skin, supported by histological findings that type I collagen (associated with scar tissue formation) is significantly increased in footrot affected interdigital skin comparted to outwardly healthy skin. Finally, we provide some interesting indications of host and pathogen interactions associated with virulence genes and the host spliceosome which could lead to the identification of future therapeutic targets. Impact Statement Lameness in sheep is a global welfare and economic concern and footrot is the leading cause of lameness, affecting up to 70% of flocks in the U.K. Current methods for control of this disease are labour intensive and account for approximately 65% of antibiotic use in sheep farming, whilst preventative vaccines suffer from poor efficacy due to antigen competition. Our limited understanding of cofounders, such as strain variation and polymicrobial nature of infection mean new efficacious, affordable and scalable control measures are not receiving much attention. Here we examine the surface and intracellular bacterial populations and propose potential interactions with the host. Identification of these key bacterial species involved in the initiation and progression of disease and the host immune mechanisms could help form the basis of new therapies.

scholarly journals Heterogeneous ceramide distributions alter spatially resolved growth of Staphylococcus aureus on human stratum corneum

2018 ◽  
Vol 15 (141) ◽  
pp. 20170848 ◽  
Author(s):  
Joseph M. Cleary ◽  
Zachary W. Lipsky ◽  
Minyoung Kim ◽  
Cláudia N. H. Marques ◽  
Guy K. German
Keyword(s):  
Staphylococcus Aureus ◽  
Stratum Corneum ◽  
Bacterial Growth ◽  
Disease Transmission ◽  
Bacterial Species ◽  
Causal Link ◽  
Bacterial Populations ◽  
Human Stratum Corneum ◽  
Spatially Resolved ◽  
Skin Cleansing

Contemporary studies have revealed dramatic changes in the diversity of bacterial microbiota between healthy and diseased skin. However, the prevailing use of swabs to extract the microorganisms has meant that only population ‘snapshots’ are obtained, and all spatially resolved information of bacterial growth is lost. Here we report on the temporospatial growth of Staphylococcus aureus on the surface of the human stratum corneum (SC); the outermost layer of skin. This bacterial species dominates bacterial populations on skin with atopic dermatitis (AD). We first establish that the distribution of ceramides naturally present in the SC is heterogeneous, and correlates with the tissue's structural topography. This distribution subsequently impacts the growth of bacterial biofilms. In the SC retaining healthy ceramide concentrations, biofilms exhibit no spatial preference for growth. By contrast, a depletion of ceramides consistent with reductions known to occur with AD enables S. aureus to use the patterned network of topographical canyons as a conduit for growth. The ability of ceramides to govern bacterial growth is confirmed using a topographical skin canyon analogue coated with the ceramide subcomponent d -sphingosine. Our work appears to explain the causal link between ceramide depletion and increased S. aureus populations that is observed in AD. It may also provide insight into disease transmission as well as improving pre-operative skin cleansing techniques.

Connecting Microbial Population Genetics with Microbial Pathogenesis Engineering Microfluidic Cell Arrays for High-throughput Interrogation of Host-Pathogen Interaction

2011 ◽  
pp. 533-548
Author(s):  
Palaniappan Sethu ◽  
Kalyani Putty ◽  
Yongsheng Lian ◽  
Awdhesh Kalia
Keyword(s):  
High Throughput ◽  
Bacterial Species ◽  
Human Cells ◽  
Bacterial Strains ◽  
Cell Array ◽  
Bacterial Populations ◽  
Host Pathogen Interaction ◽  
Gradient Generator ◽  
Molecular Events ◽  
Host Pathogen

A bacterial species typically includes heterogeneous collections of genetically diverse isolates. How genetic diversity within bacterial populations influences the clinical outcome of infection remains mostly indeterminate. In part, this is due to a lack of technologies that can enable contemporaneous systems-level interrogation of host-pathogen interaction using multiple, genetically diverse bacterial strains. This chapter presents a prototype microfluidic cell array (MCA) that allows simultaneous elucidation of molecular events during infection of human cells in a semi-automated fashion. It shows that infection of human cells with up to sixteen genetically diverse bacterial isolates can be studied simultaneously. The versatility of MCAs is enhanced by incorporation of a gradient generator that allows interrogation of host-pathogen interaction under four different concentrations of any given environmental variable at the same time. Availability of high throughput MCAs should foster studies that can determine how differences in bacterial gene pools and concentration-dependent environmental variables affect the outcome of host-pathogen interaction.

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