scholarly journals Biochemical fingerprinting of water coliform bacteria, a new method for measuring phenotypic diversity and for comparing different bacterial populations.

1991 ◽  
Vol 57 (11) ◽  
pp. 3171-3177 ◽  
Author(s):  
I Kühn ◽  
G Allestam ◽  
T A Stenström ◽  
R Möllby
Keyword(s):  
Phenotypic Diversity ◽  
New Method ◽  
Coliform Bacteria ◽  
Bacterial Populations ◽  
Biochemical Fingerprinting

Biochemical fingerprinting of coliform bacterial populations – comparisons between polluted river water and factory effluents

1997 ◽  
Vol 35 (11-12) ◽  
pp. 343-350 ◽  
Author(s):  
I. Kühn ◽  
G. Allestam ◽  
M. Engdahl ◽  
T.-A. Stenström
Keyword(s):  
River Water ◽  
Water Samples ◽  
Pollution Sources ◽  
Coliform Bacteria ◽  
Polluted Water ◽  
Bacterial Populations ◽  
Polluted River ◽  
River Water Samples ◽  
Contamination Sources ◽  
Biochemical Fingerprinting

Bacteria from different pollution sources may consist of essentially the same species but with different strains predominating. Therefore, sub-typing of bacterial strains recovered in the polluted water and comparison with those present in possible pollution sources is a valuable tool for identification of the source. Since such studies require investigations of large numbers of isolates, simple laboratory methods combined with automated data evaluation and presentation are necessary. The Phene Plate (PhP) system for biochemical fingerprinting of bacteria is based on measurements of the kinetics of biochemical tests, performed in micro-plates. The system also includes mathematical models to calculate the diversity (Di) of the bacterial flora within samples, as well as the similarities between bacterial populations in different samples as the population similarity coefficient (Sp). We have used the PhP system to type coliform bacteria isolated from a polluted river in Sweden and from the outlets from three paper mills that were suspected contamination sources. From each of 27 river water samples and 8 samples from factory outlets, collected on eight sampling occasions, between 10 and 50 coliforms were typed, yielding altogether 1,027 isolates. The diversity among the bacteria in river water samples was generally high (mean Di = 0.95) compared with factory outlets (mean Di = 0.63) which usually were dominated by isolates belonging to a few PhP types. These PhP types were very rarely recovered from the river water samples which is also reflected in low similarities between bacterial populations in river water and factory outlets (mean Sp = 0.03). Thus the bacteria from factory outlets did not seem to have spread downstream. In contrast, bacterial populations from sampling sites close to each other in the river were more similar to each other (mean Sp 0.13), indicating the presence of several, diffuse contamination sources, possibly from animal or human faecal material.

scholarly journals A mechanism for migrating bacterial populations to non-genetically adapt to new environments

2021 ◽  
Author(s):  
Henry H Mattingly ◽  
Thierry Emonet
Keyword(s):  
Collective Behavior ◽  
Group Composition ◽  
Phenotypic Diversity ◽  
Population Expansion ◽  
Migration Speed ◽  
Diverse Population ◽  
Genetic Inheritance ◽  
Bacterial Populations ◽  
Physical Environments ◽  
Varying Environments

Populations of chemotactic bacteria can rapidly expand into new territory by consuming and chasing an attractant cue in the environment, increasing the population's overall growth in nutrient-rich environments. Although the migrating fronts driving this expansion contain cells of multiple swimming phenotypes, the consequences of non-genetic diversity for population expansion are unknown. Here, through theory and simulations, we predict that expanding populations non-genetically adapt their phenotype composition to migrate effectively through multiple physical environments. Swimming phenotypes in the migrating front are spatially sorted by chemotactic performance, but the mapping from phenotype to performance depends on the environment. Therefore, phenotypes that perform poorly localize to the back of the group, causing them to selectively fall behind. Over cell divisions, the group composition dynamically enriches for high-performers, enhancing migration speed and overall growth. Furthermore, non-genetic inheritance controls a trade-off between large composition shifts and slow responsiveness to new environments, enabling a diverse population to out-perform a non-diverse one in varying environments. These results demonstrate that phenotypic diversity and collective behavior can synergize to produce emergent functionalities. Non-genetic inheritance may generically enable bacterial populations to transiently adapt to new situations without mutations, emphasizing that genotype-to-phenotype mappings are dynamic and context-dependent.

scholarly journals PaReBrick: PArallel REarrangements and BReaks identification toolkit

2021 ◽  
Author(s):  
Alexey Zabelkin ◽  
Yulia Yakovleva ◽  
Olga Bochkareva ◽  
Nikita Alexeev
Keyword(s):  
Antigenic Variation ◽  
Phenotypic Diversity ◽  
Genome Rearrangements ◽  
Supplementary Information ◽  
High Plasticity ◽  
Bacterial Strains ◽  
Bacterial Genomes ◽  
Phyletic Pattern ◽  
Bacterial Populations ◽  
Different Strains

Abstract Motivation High plasticity of bacterial genomes is provided by numerous mechanisms including horizontal gene transfer and recombination via numerous flanking repeats. Genome rearrangements such as inversions, deletions, insertions, and duplications may independently occur in different strains, providing parallel adaptation or phenotypic diversity. Specifically, such rearrangements might be responsible for virulence, antibiotic resistance, and antigenic variation. However, identification of such events requires laborious manual inspection and verification of phyletic pattern consistency. Results Here we define the term “parallel rearrangements” as events that occur independently in phylogenetically distant bacterial strains and present a formalization of the problem of parallel rearrangements calling. We implement an algorithmic solution for the identification of parallel rearrangements in bacterial populations as a tool PaReBrick. The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as input data. It identifies rearrangements, tests them for consistency with a tree, and sorts the events by their parallelism score. The tool provides diagrams of the neighbors for each block of interest, allowing the detection of horizontally transferred blocks or their extra copies and the inversions in which copied blocks are involved.We demonstrated PaReBrick’s efficiency and accuracy and showed its potential to detect genome rearrangements responsible for pathogenicity and adaptation in bacterial genomes. Availability PaReBrick is written in Python and is available on GitHub https://github.com/ctlab/parallelrearrangements Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Genotypic and Phenotypic Diversity among Induced, stx2-Carrying Bacteriophages from Environmental Escherichia coli Strains

2008 ◽  
Vol 75 (2) ◽  
pp. 329-336 ◽  
Author(s):  
Cristina García-Aljaro ◽  
Maite Muniesa ◽  
Juan Jofre ◽  
Anicet R. Blanch
Keyword(s):  
Escherichia Coli ◽  
Shiga Toxin ◽  
Phenotypic Diversity ◽  
Morphological Diversity ◽  
Lytic Cycle ◽  
Animal Origin ◽  
Bacterial Populations ◽  
Shiga Toxin 2 ◽  
Different Strains ◽  
High Level

ABSTRACT Shiga toxin 2 (stx 2) gene-carrying bacteriophages have been shown to convert Escherichia coli strains to Shiga toxin-producing Escherichia coli (STEC). In this study, 79 E. coli strains belonging to 35 serotypes isolated from wastewaters of both human and animal origin were examined for the presence of stx2 -carrying bacteriophages in their genomes. The lytic cycle of the bacteriophages was induced by mitomycin, and the bacteriophage fraction was isolated and used for morphological and genetic characterization. The induced bacteriophages showed morphological diversity, as well as restriction fragment length polymorphism variation, in the different strains belonging to different serotypes. The ability to infect new hosts was highly variable, although most of the induced phages infected Shigella sonnei host strain 866. In summary, in spite of carrying either the same or different stx 2 variants and in spite of the fact that they were isolated from strains belonging to the same or different serotypes, the induced bacteriophages were highly variable. The high level of diversity and the great infectious capacity of these phages could enhance the spread of the stx 2 gene and variants of this gene among different bacterial populations in environments to which humans may be exposed.

scholarly journals Vertical and horizontal composition of fecal pollution indicator bacteria in lotic and lentic ecosystems at Turkish Thrace

2017 ◽  
Vol 118 (4) ◽  
Author(s):  
Pinar Altinoluk-Mimiroglu ◽  
Belgin Camur-Elipek
Keyword(s):  
Water Column ◽  
Heterotrophic Bacteria ◽  
Similarity Index ◽  
Freshwater Ecosystems ◽  
Indicator Bacteria ◽  
Coliform Bacteria ◽  
Freshwater Ecosystem ◽  
Bacterial Populations ◽  
Running Water ◽  
Pollution Indicator

Background and Purpose:Although freshwater ecosystems have natural bacterial populations, their distributions are negatively affected by agricultural activities, domestic and industrial discharges. Bacterial composition at different depths can limit the usage of the water column for drinking, irrigation or other intentions. This study was designed to give similar indications concerning the nature of distribution of indicator bacteria in two different freshwater ecosystem types (lotic and lentic biotopes), and also to identify the factors that might be responsible in shaping them.Materials and Methods:For this aim, stagnant and running water resources located in Meric-Ergene River Basin at Turkish Thrace were sampled at three water depths (surface, middle, bottom) and two sediment depths (shore and bottom) between the dates October 2014 and September 2015 at seasonal intervals. While the heterotrophic bacteria, total and fecal coliform bacteria, and Escherichia coli were recorded by the CFU and MPN techniques, some features (temperature, dissolved oxygen, pH, conductivity, salinity, nutrients, ions, and elements) were also measured by classical chemical, chromatographic or spectrometric methods.Results and Conslusions:According to the data, the bacterial distribution in each ecosystem was found as similar for the bottom and the surface water columns. Results were also supported statistically by Bray-Curtis similarity index and correspondence analyse. The relationships between the bacterial distribution and environmental features were evaluated by Spearman correlation index. Consequently, it was observed that the bacterial distribution can differ in both water column/sediment depths and lotic/lentic ecosystems. And, it was suggested that the middle water column in each ecosystem is the most proper column for human usage.

scholarly journals Programmed Heterogeneity: Epigenetic Mechanisms in Bacteria

2013 ◽  
Vol 288 (20) ◽  
pp. 13929-13935 ◽  
Author(s):  
Josep Casadesús ◽  
David A. Low
Keyword(s):  
Dna Methylation ◽  
Single Cell Analysis ◽  
Phenotypic Diversity ◽  
Feedback Loops ◽  
Harsh Environments ◽  
Epigenetic Mechanisms ◽  
Cell Analysis ◽  
Bacterial Populations ◽  
Methylation Patterns ◽  
Simple Feedback

Contrary to the traditional view that bacterial populations are clonal, single-cell analysis reveals that phenotypic heterogeneity is common in bacteria. Formation of distinct bacterial lineages appears to be frequent during adaptation to harsh environments, including the colonization of animals by bacterial pathogens. Formation of bacterial subpopulations is often controlled by epigenetic mechanisms that generate inheritable phenotypic diversity without altering the DNA sequence. Such mechanisms are diverse, ranging from relatively simple feedback loops to complex self-perpetuating DNA methylation patterns.

BACTERIOLOGICAL CONDITION OF WATER SUPPLIES IN DAIRY PLANTS1

1957 ◽  
Vol 20 (7) ◽  
pp. 196-199 ◽  
Author(s):  
L. G. Harmon
Keyword(s):  
Water Samples ◽  
Total Coliform ◽  
Coliform Bacteria ◽  
Sufficient Information ◽  
Water Supplies ◽  
Bacterial Populations ◽  
Plant Use ◽  
Dairy Plant ◽  
The Individual

Samples of water supplies used in 14 butter and 12 cottage plants were examined for total, coliform, lipolytic, proteolytic and psychrophilic bacterial populations. Most of the water samples were free from coliform bacteria but contained psychrophylic, proteolytic and lipolytic organisms indicating that the coliform test alone does not afford sufficient information about the microbiological condition of water supplies intended for dairy plant use. Water samples taken at or near the source where the water entered the plant usually contained fewer bacteria than samples taken at the churn door or cheese vat, suggesting contamination of the water lines within the individual plants.

scholarly journals Oscillating bacterial expression states generate herd immunity to viral infection

2018 ◽  
Author(s):  
Christopher J. R. Turkington ◽  
Andrey Morozov ◽  
Martha R. J. Clokie ◽  
Christopher D. Bayliss
Keyword(s):  
Phenotypic Diversity ◽  
Receptor Gene ◽  
Herd Immunity ◽  
Infectious Agent ◽  
Phase Variable ◽  
Tetranucleotide Repeat ◽  
Bacterial Populations ◽  
Fixed Area ◽  
Rapid Generation ◽  
Phage Receptor

AbstractHypermutable loci are widespread in bacteria as mechanisms for rapid generation of phenotypic diversity, enabling individual populations to survive fluctuating, often antagonistic, selection pressures. As observed for adaptive immunity, hypermutation may facilitate survival of multiple, spatially-separated bacterial populations. We developed an ‘oscillating prey assay’ to examine bacteriophage (phage) spread through populations ofHaemophilus influenzaewhose phage receptor gene,lic2A, is switched ‘ON’ and ‘OFF’ by mutations in a hypermutable tetranucleotide repeat tract. Phage extinction was frequently observed when the proportion of phage-resistant sub-populations exceeded 34%.In silicomodelling indicated that phage extinction was interdependent on phage loss during transfer between populations and the frequency of resistant populations. In a fixed-area oscillating prey assay, heterogeneity in phage resistance was observed to generate vast differences in phage densities across multiple bacterial populations resulting in protective quarantining of some populations from phage attack. We conclude that phase-variable hypermutable loci produce bacterial ‘herd immunity’ with resistant intermediary-populations acting as a barricade to reduce the viral load faced by phage-sensitive sub-populations. This paradigm of meta-population protection is applicable to evolution of hypermutable loci in multiple bacteria-phage and host-pathogen interactions.ImportanceHerd immunity is a survival strategy wherein populations are protected against invading pathogens by resistant individuals within the population acting as a barrier to spread of the infectious agent. Although, this concept is normally only applied to higher eukaryotes, prokaryotic organisms also face invasion by infectious agents, such as bacterial viruses, bacteriophage (phage). Here we use novel experimental approaches and mathematical modelling, to show that bacteria exhibit a form of herd immunity through stochastically generated resistant variants acting as barricades to phage predation of sensitive cells. With hypermutable loci found in many prokaryotic systems, this phenomenon may be widely applicable to phage-bacteria interactions and could even impact phage-driven evolution in bacteria.

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