scholarly journals Chromosomal barcoding of E. coli populations reveals lineage diversity dynamics at high resolution

2019 ◽  
Author(s):  
Jesse Lerner ◽  
Michael Manhart ◽  
Weronika Jasinska ◽  
Louis Gauthier ◽  
Adrian W.R. Serohijos ◽  
...  
Keyword(s):  
High Resolution ◽  
Evolutionary Dynamics ◽  
Frequency Resolution ◽  
Low Frequencies ◽  
Bacterial Populations ◽  
E Coli ◽  
Asexual Populations ◽  
Diversity Dynamics ◽  
Lineage Diversity ◽  
New Mutations

Evolutionary dynamics in large asexual populations is strongly influenced by multiple competing beneficial lineages, most of which segregate at very low frequencies. However, technical barriers to tracking a large number of these rare lineages have so far prevented a detailed elucidation of evolutionary dynamics in large bacterial populations. Here, we overcome this hurdle by developing a chromosomal barcoding technique that allows simultaneous tracking of ∼450,000 distinct lineages in E. coli. We used this technique to gather insights into the evolutionary dynamics of large (>107 cells) E. coli populations propagated for ∼420 generations in the presence of sub-inhibitory concentrations of common antibiotics. By deep sequencing the barcodes, we reconstructed trajectories of individual lineages at high frequency resolution (< 10−5). Using quantitative tools from ecology, we found that populations lost lineage diversity at distinct rates corresponding to their antibiotic regimen. Additionally, by quantifying the reproducibility of these dynamics across replicate populations, we found that some lineages had similar fates over independent experiments. Combined with an analysis of individual lineage trajectories, these results suggest how standing genetic variation and new mutations may contribute to adaptation to sub-inhibitory antibiotic levels. Altogether, our results demonstrate the power of high-resolution barcoding in studying the dynamics of bacterial evolution.

scholarly journals Chromosomal barcoding of E. coli populations reveals lineage diversity dynamics at high resolution

2020 ◽  
Vol 4 (3) ◽  
pp. 437-452 ◽  
Author(s):  
Weronika Jasinska ◽  
Michael Manhart ◽  
Jesse Lerner ◽  
Louis Gauthier ◽  
Adrian W. R. Serohijos ◽  
...  
Keyword(s):  
High Resolution ◽  
E Coli ◽  
Diversity Dynamics ◽  
Lineage Diversity

scholarly journals Quantitative evolutionary dynamics using high-resolution lineage tracking

Nature ◽  
2015 ◽  
Vol 519 (7542) ◽  
pp. 181-186 ◽  
Author(s):  
Sasha F. Levy ◽  
Jamie R. Blundell ◽  
Sandeep Venkataram ◽  
Dmitri A. Petrov ◽  
Daniel S. Fisher ◽  
...  
Keyword(s):  
High Resolution ◽  
Evolutionary Dynamics ◽  
Lineage Tracking

scholarly journals Decay of Fecal Indicator Bacterial Populations and Bovine-Associated Source-Tracking Markers in Freshly Deposited Cow Pats

2013 ◽  
Vol 80 (1) ◽  
pp. 110-118 ◽  
Author(s):  
Adelumola Oladeinde ◽  
Thomas Bohrmann ◽  
Kelvin Wong ◽  
S. T. Purucker ◽  
Ken Bradshaw ◽  
...  
Keyword(s):  
Decay Rate ◽  
Fecal Indicator Bacteria ◽  
Decay Rates ◽  
Indicator Bacteria ◽  
Source Tracking ◽  
Fecal Indicator ◽  
Bacterial Populations ◽  
Content Type ◽  
E Coli ◽  
Decay Dynamic

ABSTRACTUnderstanding the survival of fecal indicator bacteria (FIB) and microbial source-tracking (MST) markers is critical to developing pathogen fate and transport models. Although pathogen survival in water microcosms and manure-amended soils is well documented, little is known about their survival in intact cow pats deposited on pastures. We conducted a study to determine decay rates of fecal indicator bacteria (Escherichia coliand enterococci) and bovine-associated MST markers (CowM3, Rum-2-bac, and GenBac) in 18 freshly deposited cattle feces from three farms in northern Georgia. Samples were randomly assigned to shaded or unshaded treatment in order to determine the effects of sunlight, moisture, and temperature on decay rates. A general linear model (GLM) framework was used to determine decay rates. Shading significantly decreased the decay rate of theE. colipopulation (P< 0.0001), with a rate of −0.176 day−1for the shaded treatment and −0.297 day−1for the unshaded treatment. Shading had no significant effect on decay rates of enterococci, CowM3, Rum-2-bac, and GenBac (P> 0.05). In addition,E. colipopulations showed a significant growth rate (0.881 day−1) in the unshaded samples during the first 5 days after deposition. UV-B was the most important parameter explaining the decay rate ofE. colipopulations. A comparison of the decay behaviors among all markers indicated that enterococcus concentrations exhibit a better correlation with the MST markers thanE. coliconcentrations. Our results indicate that bovine-associated MST markers can survive in cow pats for at least 1 month after excretion, and although their decay dynamic differs from the decay dynamic ofE. colipopulations, they seem to be reliable markers to use in combination with enterococci to monitor fecal pollution from pasture lands.

scholarly journals High-resolution crystal structures of Escherichia coli FtsZ bound to GDP and GTP

2020 ◽  
Vol 76 (2) ◽  
pp. 94-102 ◽  
Author(s):  
Maria A. Schumacher ◽  
Tomoo Ohashi ◽  
Lauren Corbin ◽  
Harold P. Erickson
Keyword(s):  
Escherichia Coli ◽  
Staphylococcus Aureus ◽  
Cell Division ◽  
High Resolution ◽  
Crystal Structures ◽  
Bacterial Cell ◽  
Model System ◽  
E Coli ◽  
Z Ring ◽  
Main Model

Bacterial cytokinesis is mediated by the Z-ring, which is formed by the prokaryotic tubulin homolog FtsZ. Recent data indicate that the Z-ring is composed of small patches of FtsZ protofilaments that travel around the bacterial cell by treadmilling. Treadmilling involves a switch from a relaxed (R) state, favored for monomers, to a tense (T) conformation, which is favored upon association into filaments. The R conformation has been observed in numerous monomeric FtsZ crystal structures and the T conformation in Staphylococcus aureus FtsZ crystallized as assembled filaments. However, while Escherichia coli has served as a main model system for the study of the Z-ring and the associated divisome, a structure has not yet been reported for E. coli FtsZ. To address this gap, structures were determined of the E. coli FtsZ mutant FtsZ(L178E) with GDP and GTP bound to 1.35 and 1.40 Å resolution, respectively. The E. coli FtsZ(L178E) structures both crystallized as straight filaments with subunits in the R conformation. These high-resolution structures can be employed to facilitate experimental cell-division studies and their interpretation in E. coli.

scholarly journals Quantifying the interplay between rapid bacterial evolution within the mouse intestine and transmission between hosts

2020 ◽  
Author(s):  
Kimberly S. Vasquez ◽  
Lisa Willis ◽  
Nate Cira ◽  
Katharine M. Ng ◽  
Miguel F. Pedro ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Population Genetics ◽  
High Resolution ◽  
Evolutionary Dynamics ◽  
Day Treatment ◽  
Whole Genome ◽  
Germ Free ◽  
Selection Dynamics ◽  
Mouse Intestine ◽  
Ciprofloxacin Resistance

SummaryDue to limitations on high-resolution strain tracking, selection dynamics during gut-microbiota colonization and transmission between hosts remain mostly mysterious. Here, we introduced hundreds of barcoded Escherichia coli strains into germ-free mice and quantified strain-level dynamics and metagenomic changes. Mutants involved in motility and utilization of abundant metabolites were reproducibly selected within days. Even with rapid selection, coprophagy enforced similar barcode distributions across co-housed mice. Whole-genome sequencing of hundreds of isolates quantified evolutionary dynamics and revealed linked alleles. A population-genetics model predicted substantial fitness advantages for certain mutants and that migration accounted for ~10% of the resident microbiota each day. Treatment with ciprofloxacin demonstrated the interplay between selection and transmission. While initial colonization was mostly uniform, in two mice a bottleneck reduced diversity and selected for ciprofloxacin resistance in the absence of drug. These findings highlight the interplay between environmental transmission and rapid, deterministic selection during evolution of the intestinal microbiota.

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 The population and evolutionary dynamics of bacteriophage: Why be temperate revisited

2019 ◽  
Author(s):  
Waqas Chaudhry ◽  
Nicole Vega ◽  
Adithi Govindan ◽  
Rodrigo Garcia ◽  
Esther Lee ◽  
...  
Keyword(s):  
Natural Selection ◽  
Evolutionary Dynamics ◽  
Natural Populations ◽  
Lytic Phage ◽  
Temperate Bacteriophage ◽  
Serial Transfer ◽  
Virulent Phage ◽  
E Coli ◽  
Resistant Refractory

AbstractBacteriophages are deemed either lytic (virulent) or temperate, respectively depending on whether their genomes are transmitted solely horizontally, or both horizontally and vertically. To elucidate the ecological and evolutionary conditions under which natural selection will favor the evolution and maintenance of lytic or temperate modes of phage replication and transmission, we use a comprehensive mathematical model of the dynamics of temperate and virulent phage in populations of bacteria sensitive and resistant to these viruses. For our numerical analysis of the properties of this model, we use parameters estimated with the temperate bacteriophage Lambda, λ, it’s clear and virulent mutants, andE. colisensitive and resistant - refractory to these phages. Using batch and serial transfer population dynamic and reconstruction experiments, we test the hypotheses generated from this theoretical analysis. Based on the results of this jointly theoretical and experimental study, we postulate the conditions under which natural selection will favor the evolution and maintenance of lytic and temperate modes of phage replication and transmission. A compelling and novel prediction thisin silico,in vitro, andin plasticostudy makes is lysogenic bacteria from natural populations will be resistant-refractory to the phage for which they are lysogenic as well as lytic phage sharing the same receptors as these temperate viruses.

scholarly journals An Efficient Adaptive Window Size Selection Method for Improving Spectrogram Visualization

2016 ◽  
Vol 2016 ◽  
pp. 1-13 ◽  
Author(s):  
Shibli Nisar ◽  
Omar Usman Khan ◽  
Muhammad Tariq
Keyword(s):  
Fourier Transform ◽  
Filter Bank ◽  
Window Size ◽  
Fixed Time ◽  
Frequency Resolution ◽  
High Spectral Resolution ◽  
Background Information ◽  
High Temporal Resolution ◽  
Low Frequencies ◽  
Time Frequency

Short Time Fourier Transform (STFT) is an important technique for the time-frequency analysis of a time varying signal. The basic approach behind it involves the application of a Fast Fourier Transform (FFT) to a signal multiplied with an appropriate window function with fixed resolution. The selection of an appropriate window size is difficult when no background information about the input signal is known. In this paper, a novel empirical model is proposed that adaptively adjusts the window size for a narrow band-signal using spectrum sensing technique. For wide-band signals, where a fixed time-frequency resolution is undesirable, the approach adapts the constant Q transform (CQT). Unlike the STFT, the CQT provides a varying time-frequency resolution. This results in a high spectral resolution at low frequencies and high temporal resolution at high frequencies. In this paper, a simple but effective switching framework is provided between both STFT and CQT. The proposed method also allows for the dynamic construction of a filter bank according to user-defined parameters. This helps in reducing redundant entries in the filter bank. Results obtained from the proposed method not only improve the spectrogram visualization but also reduce the computation cost and achieves 87.71% of the appropriate window length selection.

Toward High-Resolution Mechanical Spectroscopy HRMS - Logarithmic Decrement

2012 ◽  
Vol 184 ◽  
pp. 467-472 ◽  
Author(s):  
Leszek B. Magalas ◽  
M. Majewski
Keyword(s):  
High Resolution ◽  
Low Frequency ◽  
Logarithmic Decrement ◽  
Frequency Resolution ◽  
Mechanical Spectroscopy ◽  
Spectral Leakage ◽  
Experimental Noise ◽  
Relative Errors ◽  
The Way

In this work, we present the comparison between different methods used to compute the logarithmic decrement,δ. The parametric OMI method and interpolated DFT (IpDFT) methods are used to compute theδfrom free decaying oscillations embedded in an experimental noise typical for low-frequency mechanical spectrometers. The results are reported forδ= 5×10-4, = 1.12345 Hz and different sampling frequencies, = 1 kHz and 4 kHz. A new YM algorithm yields the smallest dispersion in experimental points of the logarithmic decrement and the smallest relative errors among all investigated IpDFT methods. In general, however, the IpDFT methods suffer from spectral leakage and frequency resolution. Therefore it is demonstrated that the performance of different methods to compute theδcan be listed in the following order: (1) OMI, (2) YM, (3) YMC, and (4) the Yoshida method, Y. For short free decays the order of the best performers is different: (1) OMI and (2) YMC. It is important to emphasize that IpDFT methods (including the Yoshida method, Y) are discouraged for signals that are too short. In conclusion, the best methods to compute the logarithmic decrement are the OMI and the YM. These methods will pave the way toward high-resolution mechanical spectroscopy HRMS.

Predictive Fluorescent Amplified-Fragment Length Polymorphism Analysis of Escherichia coli: High-Resolution Typing Method with Phylogenetic Significance

1999 ◽  
Vol 37 (5) ◽  
pp. 1274-1279 ◽  
Author(s):  
Catherine Arnold ◽  
Lou Metherell ◽  
Geraldine Willshaw ◽  
Anthony Maggs ◽  
John Stanley
Keyword(s):  
Escherichia Coli ◽  
High Resolution ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Polymorphism Analysis ◽  
Enzyme Electrophoresis ◽  
Typing Method ◽  
E Coli

The fluorescent amplified-fragment length polymorphism (FAFLP) assay potentially amplifies a unique set of genome fragments from each bacterial clone. It uses stringently hybridizing primers which carry a fluorescent label. Precise fragment sizing is achieved by the inclusion of an internal size standard in every lane. Therefore, a unique genotype identifier(s) can be found in the form of fragments of precise size or sizes, and these can be generated reproducibly. In order to evaluate the potential of FAFLP as an epidemiological typing method with a valid phylogenetic basis, we applied it to 87 strains ofEscherichia coli. These comprised the EcoR collection, which has previously been classified by multilocus enzyme electrophoresis (MLEE) and which represents the genetic diversity of the species E. coli, plus 15 strains of the clinically important serogroup O157. FAFLP with an unlabelled nonselectiveEcoRI primer (Eco+0) and a labelled selectiveMseI primer (Mse+TA) gave strain-specific profiles. Fragments of identical sizes (in base pairs) were assumed to be identical, and the genetic distances between the strains were calculated. A phylogenetic tree derived from measure of distance correlated closely with the MLEE groupings of the EcoR collection and placed the verocytotoxin-producing O157 strains on an outlier branch. Our data indicate that FAFLP is suitable for epidemiological investigation of E. coli infection, providing well-defined and reproducible identifiers of genotype for each strain. Since FAFLP objectively samples the whole genome, each strain or isolate can be assigned a place within the broad context of the whole species and can also be subjected to a high-resolution comparison with closely related strains to investigate epidemiological clonality.

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