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.

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 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.

scholarly journals Coupled Phase-Variable Expression and Epitope Masking of Selective Surface Lipoproteins Increase Surface Phenotypic Diversity in Mycoplasma hominis

2001 ◽  
Vol 69 (8) ◽  
pp. 5177-5181 ◽  
Author(s):  
Qijing Zhang ◽  
Kim S. Wise
Keyword(s):  
Membrane Protein ◽  
High Frequency ◽  
Phenotypic Diversity ◽  
Phase Variation ◽  
Mycoplasma Hominis ◽  
Phase Variable ◽  
Variable Expression ◽  
Adaptive Capabilities ◽  
Frequency Phase

ABSTRACT A new mechanism expanding mycoplasmal surface diversity is described. Exposure of surface epitopes on a constitutively expressed membrane protein (P56) of Mycoplasma hominis was subject to high-frequency phase variation due to phase-variable expression of the P120 antigen and its selective masking of P56 epitopes. Phase-variable masking may confer previously unrealized adaptive capabilities on mycoplasmas.

scholarly journals Is Obesity an Oral Bacterial Disease?

2009 ◽  
Vol 88 (6) ◽  
pp. 519-523 ◽  
Author(s):  
J.M. Goodson ◽  
D. Groppo ◽  
S. Halem ◽  
E. Carpino
Keyword(s):  
Classification Tree ◽  
Bacterial Species ◽  
Infectious Agent ◽  
Oral Bacteria ◽  
Future Research ◽  
Bacterial Disease ◽  
Median Percentage ◽  
Bacterial Populations ◽  
Overweight Women ◽  
Percentage Difference

The world-wide explosion of overweight people has been called an epidemic. The inflammatory nature of obesity is widely recognized. Could it really be an epidemic involving an infectious agent? In this climate of concern over the increasing prevalence of overweight conditions in our society, we focus on the possible role of oral bacteria as a potential direct contributor to obesity. To investigate this possibility, we measured salivary bacterial populations of overweight women. Saliva was collected from 313 women with a body mass index between 27 and 32, and bacterial populations were measured by DNA probe analysis. Levels in this group were compared with data from a population of 232 healthy individuals from periodontal disease studies. The median percentage difference of 7 of the 40 bacterial species measured was greater than 2% in the saliva of overweight women. Classification tree analysis of salivary microbiological composition revealed that 98.4% of the overweight women could be identified by the presence of a single bacterial species ( Selenomonas noxia) at levels greater than 1.05% of the total salivary bacteria. Analysis of these data suggests that the composition of salivary bacteria changes in overweight women. It seems likely that these bacterial species could serve as biological indicators of a developing overweight condition. Of even greater interest, and the subject of future research, is the possibility that oral bacteria may participate in the pathology that leads to obesity.

scholarly journals Scrutinizing the SARS-CoV-2 protein information for the designing an effective vaccine encompassing both the T-cell and B-cell epitopes

2020 ◽  
Author(s):  
Neha Jain ◽  
Uma Shankar ◽  
Prativa Majee ◽  
Amit Kumar
Keyword(s):  
Infectious Virus ◽  
Vaccine Candidate ◽  
Infectious Agent ◽  
Effective Vaccine ◽  
High Efficacy ◽  
Epitope Vaccine ◽  
Vaccine Product ◽  
High Propensity ◽  
Community Transmission ◽  
Rapid Generation

ABSTRACTNovel SARS coronavirus (SARS-CoV-2) has caused a pandemic condition world-wide and has been declared as public health emergency of International concern by WHO in a very short span of time. The community transmission of this highly infectious virus has severely affected various parts of China, Italy, Spain and USA among others. The prophylactic solution against SARS-CoV-2 infection is challenging due to the high mutation rate of its RNA genome. Herein, we exploited a next generation vaccinology approach to construct a multi-epitope vaccine candidate against SARS-CoV-2 with high antigenicity, safety and efficacy to combat this deadly infectious agent. The whole proteome was scrutinized for the screening of highly conserved, antigenic, non-allergen and non-toxic epitopes having high population coverage that can elicit both humoral and cellular mediated immune response against COVID-19 infection. These epitopes along with four different adjuvants were utilized to construct a multi-epitope vaccine candidate that can generate strong immunological memory response having high efficacy in humans. Various physiochemical analyses revealed the formation of a stable vaccine product having a high propensity to form a protective solution against the detrimental SARS-CoV-2 strain with high efficacy. The vaccine candidate interacted with immunological receptor TLR3 with high affinity depicting the generation of innate immunity. Further, the codon optimization and in silico expression show the plausibility of the high expression and easy purification of the vaccine product. Thus, this present study provides an initial platform of the rapid generation of an efficacious protective vaccine for combating COVID-19.

scholarly journals Author response: CRISPR-based herd immunity can limit phage epidemics in bacterial populations

2018 ◽  
Author(s):  
Pavel Payne ◽  
Lukas Geyrhofer ◽  
Nicholas H Barton ◽  
Jonathan P Bollback
Keyword(s):  
Herd Immunity ◽  
Author Response ◽  
Bacterial Populations
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