Variant profiling of evolving prokaryotic populations

Genotyping of evolving prokaryotic populations

10.7287/peerj.preprints.2449v1 ◽

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.

Genotyping of evolving prokaryotic populations

10.7287/peerj.preprints.2449 ◽

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.

Horizontal Spread of Rhodococcus equi Macrolide Resistance Plasmid pRErm46 across Environmental Actinobacteria

Applied and Environmental Microbiology ◽

10.1128/aem.00108-20 ◽

2020 ◽

Vol 86 (9) ◽

Author(s):

Sonsiray Álvarez-Narváez ◽

Steeve Giguère ◽

Londa J. Berghaus ◽

Cody Dailey ◽

José A. Vázquez-Boland

Keyword(s):

Bacterial Species ◽

Low Frequency ◽

Rhodococcus Equi ◽

Macrolide Resistance ◽

Conjugative Plasmid ◽

Bacterial Populations ◽

Prolonged Incubation ◽

Content Type ◽

Host Restriction

ABSTRACT Conjugation is one of the main mechanisms involved in the spread and maintenance of antibiotic resistance in bacterial populations. We recently showed that the emerging macrolide resistance in the soilborne equine and zoonotic pathogen Rhodococcus equi is conferred by the erm(46) gene carried on the 87-kb conjugative plasmid pRErm46. Here, we investigated the conjugal transferability of pRErm46 to 14 representative bacteria likely encountered by R. equi in the environmental habitat. In vitro mating experiments demonstrated conjugation to different members of the genus Rhodococcus as well as to Nocardia and Arthrobacter spp. at frequencies ranging from ∼10−2 to 10−6. pRErm46 transfer was also observed in mating experiments in soil and horse manure, albeit at a low frequency and after prolonged incubation at 22 to 30°C (environmental temperatures), not 37°C. All transconjugants were able to transfer pRErm46 back to R. equi. Conjugation could not be detected with Mycobacterium or Corynebacterium spp. or several members of the more distant phylum Firmicutes such as Enterococcus, Streptococcus, or Staphylococcus. Thus, the pRErm46 host range appears to span several actinobacterial orders with certain host restriction within the Corynebacteriales. All bacterial species that acquired pRErm46 expressed increased macrolide resistance with no significant deleterious impact on fitness, except in the case of Rhodococcus rhodnii. Our results indicate that actinobacterial members of the environmental microbiota can both acquire and transmit the R. equi pRErm46 plasmid and thus potentially contribute to the maintenance and spread of erm(46)-mediated macrolide resistance in equine farms. IMPORTANCE This study demonstrates the efficient horizontal transfer of the Rhodococcus equi conjugative plasmid pRErm46, recently identified as the cause of the emerging macrolide resistance among equine isolates of this pathogen, to and from different environmental Actinobacteria, including a variety of rhodococci as well as Nocardia and Arthrobacter spp. The reported data support the notion that environmental microbiotas may act as reservoirs for the endemic maintenance of antimicrobial resistance in an antibiotic pressurized farm habitat.

First look at the giant radio galaxy 3C 236 with LOFAR

Astronomy and Astrophysics ◽

10.1051/0004-6361/201935586 ◽

2019 ◽

Vol 628 ◽

pp. A69 ◽

Cited By ~ 2

Author(s):

A. Shulevski ◽

P. D. Barthel ◽

R. Morganti ◽

J. J. Harwood ◽

M. Brienza ◽

...

Keyword(s):

Spectral Index ◽

Radio Galaxy ◽

Ambient Medium ◽

Low Frequency ◽

Low Frequencies ◽

North West ◽

Link Type ◽

The North ◽

Morphological Differences ◽

Inner Region

We have examined the giant radio galaxy 3C 236 using LOFAR at 143 MHz down to an angular resolution of 7″, in combination with observations at higher frequencies. We used the low frequency data to derive spectral index maps with the highest resolution yet at these low frequencies. We confirm a previous detection of an inner hotspot in the north-west lobe and for the first time observe that the south-east lobe hotspot is in fact a triple hotspot, which may point to an intermittent source activity. Also, the spectral index map of 3C 236 shows that the spectral steepening at the inner region of the northern lobe is prominent at low frequencies. The outer regions of both lobes show spectral flattening, in contrast with previous high frequency studies. We derive spectral age estimates for the lobes, as well as particle densities of the IGM at various locations. We propose that the morphological differences between the lobes are driven by variations in the ambient medium density as well as the source activity history.

The Measurement of Low Frequency Impedance Using an Impedance Tube

Journal of Low Frequency Noise Vibration and Active Control ◽

10.1177/026309239801700101 ◽

1998 ◽

Vol 17 (1) ◽

pp. 1-10 ◽

Cited By ~ 2

Author(s):

C Peng ◽

D Morrey ◽

P Sanders

Keyword(s):

Theoretical Analysis ◽

Low Frequency ◽

Reliable Prediction ◽

Low Frequencies ◽

Impedance Tube ◽

Half Wavelength ◽

Quarter Wavelength ◽

Significant Step ◽

Accuracy Of Measurement ◽

The Ideal

An accurate and reliable prediction of car interior noise would be a significant step towards improving the design of car body panels and trim for a quieter vehicle. Automobile noise is dominated by low frequencies, from 50 to 300 Hz and therefore a technique is necessary to measure acoustic impedance of the trim materials at low frequencies. This paper presents the use of a two-microphone technique to measure impedance at low frequencies. A purpose built impedance tube has been developed based on theoretical analysis of the influence of microphone location on the estimate of impedance. It has been found that the location of the two microphones is crucial to the accuracy of measurement. Analytical results have shown that the ideal microphone location is with both the microphone spacing and the distance from the tested material to the nearest microphone taking the value of a quarter wavelength. Microphone spacing of a half wavelength should be avoided.

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

Chemical and Biochemical Engineering Quarterly ◽

10.15255/cabeq.2013.1934 ◽

2014 ◽

Vol 28 (2) ◽

pp. 225-231 ◽

Cited By ~ 8

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

rPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree

10.1101/404624 ◽

2018 ◽

Cited By ~ 2

Author(s):

Alexander M. Wailan ◽

Francesc Coll ◽

Eva Heinz ◽

Gerry Tonkin-Hill ◽

Jukka Corander ◽

...

Keyword(s):

Infectious Disease ◽

Phylogenetic Tree ◽

Bacterial Species ◽

Genomic Data ◽

Transmission Dynamics ◽

Whole Genome Sequence ◽

List Type ◽

Bacterial Populations ◽

Link Type ◽

Hospital Outbreak

ABSTRACTThe ability to distinguish between pathogens is a fundamental requirement to understand the epidemiology of infectious diseases. Phylogenetic analysis of genomic data can provide a powerful platform to identify lineages within bacterial populations, and thus inform outbreak investigation and transmission dynamics. However, resolving differences between pathogens associated with low variant (LV) populations carrying low median pairwise single nucleotide variant (SNV) distances, remains a major challenge. Here we present rPinecone, an R package designed to define sub-lineages within closely related LV populations. rPinecone uses a root-to-tip directional approach to define sub-lineages within a phylogenetic tree according to SNV distance from the ancestral node. The utility of this program was demonstrated using genomic data of two LV populations: a hospital outbreak of methicillin-resistant Staphylococcus aureus and endemic Salmonella Typhi from rural Cambodia. rPinecone identified the transmission branches of the hospital outbreak and geographically-confined lineages in Cambodia. Sub-lineages identified by rPinecone in both analyses were phylogenetically robust. It is anticipated that rPinecone can be used to discriminate between lineages of bacteria from LV populations where other methods fail, enabling a deeper understanding of infectious disease epidemiology for public health purposes.DATA SUMMARYSource code for rPinecone is available on GitHub under the open source licence GNU GPL 3; (url: https://github.com/alexwailan/rpinecone).Newick format files for both phylogenetic trees have been deposited in Figshare; (url: https://doi.org/10.6084/m9.figshare.7022558)Geographical analysis of the S. Typhi Dataset using Microreact is available at https://microreact.org/project/r1IqkrN1X.Accession numbers, meta data and sample lineage results of both datasets used in this paper are listed in the supplementary tables.I/We confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. ⊠IMPACT STATEMENTWhole genome sequence data from bacterial pathogens is increasingly used in the epidemiological investigation of infectious disease, both in outbreak and endemic situations. However, distinguishing bacterial species which are both very similar and which are likely to come from a small geographical and temporal range presents a major technical challenge for epidemiologists. rPinecone was designed to address this challenge and utilises phylogenetic data to define lineages within bacterial populations that have limited variation. This approach is therefore of great interest to epidemiologists as it adds a further level of clarity above and beyond that which is offered by existing approaches which have not been designed to consider bacterial isolates containing variation that only transiently exist, but which is epidemiologically informative. rPinecone has the flexibility to be applied to multiple pathogens and has direct application for investigations of clinical outbreaks and endemic disease to understand transmission dynamics or geographical hotspots of disease.

Pseudomonas aeruginosa is capable of natural transformation in biofilms

Microbiology ◽

10.1099/mic.0.000956 ◽

2020 ◽

Vol 166 (10) ◽

pp. 995-1003 ◽

Cited By ~ 1

Author(s):

Laura M. Nolan ◽

Lynne Turnbull ◽

Marilyn Katrib ◽

Sarah R. Osvath ◽

Davide Losa ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Type Species ◽

Natural Transformation ◽

Bacterial Species ◽

Extracellular Dna ◽

Virulence Determinants ◽

Bacterial Populations ◽

Exogenous Dna ◽

Content Type ◽

Link Type

Natural transformation is a mechanism that enables competent bacteria to acquire naked, exogenous DNA from the environment. It is a key process that facilitates the dissemination of antibiotic resistance and virulence determinants throughout bacterial populations. Pseudomonas aeruginosa is an opportunistic Gram-negative pathogen that produces large quantities of extracellular DNA (eDNA) that is required for biofilm formation. P. aeruginosa has a remarkable level of genome plasticity and diversity that suggests a high degree of horizontal gene transfer and recombination but is thought to be incapable of natural transformation. Here we show that P. aeruginosa possesses homologues of all proteins known to be involved in natural transformation in other bacterial species. We found that P. aeruginosa in biofilms is competent for natural transformation of both genomic and plasmid DNA. Furthermore, we demonstrate that type-IV pili (T4P) facilitate but are not absolutely essential for natural transformation in P. aeruginosa .

High Resolution Observations of Low frequency Variables at 932 MHz

Symposium - International Astronomical Union ◽

10.1017/s0074180900134199 ◽

1988 ◽

Vol 129 ◽

pp. 117-118

Author(s):

Lars B. Bååth

Keyword(s):

High Resolution ◽

Low Frequency ◽

Structural Variations ◽

Low Frequencies

Fifteen sources known to be varying at low frequencies have been observed at six epochs during 1983–84 with a global VLBI array. Some of the sources show structural variations similar to the superluminals. Beaming effect may therefore play an important role at low frequencies as well as at higher.

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

Israel Journal of Ecology and Evolution ◽

10.1560/ijee_52_3-4_527 ◽

2006 ◽

Vol 52 (3-4) ◽

pp. 527-542 ◽

Cited By ~ 6

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.