scholarly journals A globally ubiquitous symbiont can drive experimental host evolution

2021 ◽  
Author(s):  
K.A Bates ◽  
J.S. Bolton ◽  
K.C. King
Keyword(s):  
Experimental Host ◽  
Host Evolution

Within Host Evolution of Malaria Parasites Revealed by Single Genome Sequencing

2020 ◽  
Author(s):  
Aliou Dia ◽  
Catherine Jett ◽  
Simon G. Trevino ◽  
Cindy S. Chu ◽  
Kanlaya Sriprawat ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Malaria Parasites ◽  
Single Genome ◽  
Host Evolution

scholarly journals Viral Host Range database, an online tool for recording, analyzing and disseminating virus-host interactions

2021 ◽  
Author(s):  
Quentin Lamy-Besnier ◽  
Bryan Brancotte ◽  
Hervé Ménager ◽  
Laurent Debarbieux
Keyword(s):  
Host Range ◽  
Source Code ◽  
Range Data ◽  
Web Based ◽  
Online Tool ◽  
Experimental Host ◽  
Living World ◽  
Host Interactions ◽  
Experimental Host Range ◽  
Viral Host Range

Abstract Motivation Viruses are ubiquitous in the living world, and their ability to infect more than one host defines their host range. However, information about which virus infects which host, and about which host is infected by which virus, is not readily available. Results We developed a web-based tool called the Viral Host Range database to record, analyze and disseminate experimental host range data for viruses infecting archaea, bacteria and eukaryotes. Availability The ViralHostRangeDB application is available from https://viralhostrangedb.pasteur.cloud. Its source code is freely available from the Gitlab hub of Institut Pasteur (https://gitlab.pasteur.fr/hub/viralhostrangedb).

scholarly journals Reconstruction of Microbial Haplotypes by Integration of Statistical and Physical Linkage in Scaffolding

2021 ◽  
Author(s):  
Chen Cao ◽  
Jingni He ◽  
Lauren Mak ◽  
Deshan Perera ◽  
Devin Kwok ◽  
...  
Keyword(s):  
Single Molecule ◽  
Human Genetics ◽  
Real Data ◽  
Sequencing Technologies ◽  
Bacterial Genomics ◽  
Physical Linkage ◽  
Pooled Sequencing ◽  
Computational Reconstruction ◽  
Host Genetic ◽  
Host Evolution

Abstract DNA sequencing technologies provide unprecedented opportunities to analyze within-host evolution of microorganism populations. Often, within-host populations are analyzed via pooled sequencing of the population, which contains multiple individuals or “haplotypes.” However, current next-generation sequencing instruments, in conjunction with single-molecule barcoded linked-reads, cannot distinguish long haplotypes directly. Computational reconstruction of haplotypes from pooled sequencing has been attempted in virology, bacterial genomics, metagenomics, and human genetics, using algorithms based on either cross-host genetic sharing or within-host genomic reads. Here, we describe PoolHapX, a flexible computational approach that integrates information from both genetic sharing and genomic sequencing. We demonstrated that PoolHapX outperforms state-of-the-art tools tailored to specific organismal systems, and is robust to within-host evolution. Importantly, together with barcoded linked-reads, PoolHapX can infer whole-chromosome-scale haplotypes from 50 pools each containing 12 different haplotypes. By analyzing real data, we uncovered dynamic variations in the evolutionary processes of within-patient HIV populations previously unobserved in single position-based analysis.

scholarly journals Within-host evolution of Helicobacter pylori shaped by niche-specific adaptation, intragastric migrations and selective sweeps

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Florent Ailloud ◽  
Xavier Didelot ◽  
Sabrina Woltemate ◽  
Gudrun Pfaffinger ◽  
Jörg Overmann ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Selective Sweeps ◽  
Specific Adaptation ◽  
Host Evolution

scholarly journals Within-Host Evolution of Pseudomonas aeruginosa Reveals Adaptation toward Iron Acquisition from Hemoglobin

mBio ◽  
2014 ◽  
Vol 5 (3) ◽  
Author(s):  
Rasmus Lykke Marvig ◽  
Søren Damkiær ◽  
S. M. Hossein Khademi ◽  
Trine M. Markussen ◽  
Søren Molin ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Pseudomonas Aeruginosa ◽  
Iron Acquisition ◽  
Chronic Infections ◽  
Content Type ◽  
Mortality And Morbidity ◽  
Airway Infections ◽  
Host Evolution ◽  
Promoter Mutations

ABSTRACTPseudomonas aeruginosaairway infections are a major cause of mortality and morbidity of cystic fibrosis (CF) patients. In order to persist,P. aeruginosadepends on acquiring iron from its host, and multiple different iron acquisition systems may be active during infection. This includes the pyoverdine siderophore and thePseudomonasheme utilization (phu) system. While the regulation and mechanisms of several iron-scavenging systems are well described, it is not clear whether such systems are targets for selection during adaptation ofP. aeruginosato the host environment. Here we investigated the within-host evolution of the transmissibleP. aeruginosaDK2 lineage. We found positive selection for promoter mutations leading to increased expression of thephusystem. By mimicking conditions of the CF airwaysin vitro, we experimentally demonstrate that increased expression ofphuRconfers a growth advantage in the presence of hemoglobin, thus suggesting thatP. aeruginosaevolves toward iron acquisition from hemoglobin. To rule out that this adaptive trait is specific to the DK2 lineage, we inspected the genomes of additionalP. aeruginosalineages isolated from CF airways and found similar adaptive evolution in two distinct lineages (DK1 and PA clone C). Furthermore, in all three lineages,phuRpromoter mutations coincided with the loss of pyoverdine production, suggesting that within-host adaptation toward heme utilization is triggered by the loss of pyoverdine production. Targeting heme utilization might therefore be a promising strategy for the treatment ofP. aeruginosainfections in CF patients.IMPORTANCEMost bacterial pathogens depend on scavenging iron within their hosts, which makes the battle for iron between pathogens and hosts a hallmark of infection. Accordingly, the ability of the opportunistic pathogenPseudomonas aeruginosato cause chronic infections in cystic fibrosis (CF) patients also depends on iron-scavenging systems. While the regulation and mechanisms of several such iron-scavenging systems have been well described, not much is known about how the within-host selection pressures act on the pathogens’ ability to acquire iron. Here, we investigated the within-host evolution ofP. aeruginosa, and we found evidence thatP. aeruginosaduring long-term infections evolves toward iron acquisition from hemoglobin. This adaptive strategy might be due to a selective loss of other iron-scavenging mechanisms and/or an increase in the availability of hemoglobin at the site of infection. This information is relevant to the design of novel CF therapeutics and the development of models of chronic CF infections.

The pig as an experimental host ofTaenia saginata(Ethiopia and Madagascar strains)

1990 ◽  
Vol 84 (1) ◽  
pp. 93-95 ◽  
Author(s):  
P. C. Fan ◽  
W. C. Chung ◽  
C. T. Lo ◽  
C. Y. Lin
Keyword(s):  
Experimental Host

scholarly journals Parallel changes in gut microbiome composition and function in parallel local adaptation and speciation

2019 ◽  
Author(s):  
Diana J. Rennison ◽  
Seth M. Rudman ◽  
Dolph Schluter
Keyword(s):  
Microbial Communities ◽  
Local Adaptation ◽  
Biotic Interactions ◽  
Ecological Speciation ◽  
Microbiome Composition ◽  
Interacting Species ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
And Function ◽  
Host Evolution

AbstractThe processes of local adaptation and ecological speciation are often strongly shaped by biotic interactions such as competition and predation. One of the strongest lines of evidence that biotic interactions drive evolution comes from repeated divergence of lineages in association with repeated changes in the community of interacting species. Yet, relatively little is known about the repeatability of changes in gut microbial communities and their role in adaptation and divergence of host populations in nature. Here we utilize three cases of rapid, parallel adaptation and speciation in freshwater threespine stickleback to test for parallel changes in associated gut microbiomes. We find that features of the gut microbial communities have shifted repeatedly in the same direction in association with parallel divergence and speciation of stickleback hosts. These results suggest that changes to gut microbiomes can occur rapidly and predictably in conjunction with host evolution, and that host-microbe interactions might play an important role in host adaptation and diversification.

Mastomys natalensis as an experimental host for Leishmania mexicana mexicana

1978 ◽  
Vol 72 (2) ◽  
pp. 155-157
Author(s):  
L.H. Pereira ◽  
W. Mayrink ◽  
M. Dias ◽  
M.S.M. Michalick ◽  
C.A. Costa ◽  
...  
Keyword(s):  
Mastomys Natalensis ◽  
Leishmania Mexicana ◽  
Experimental Host

Experimental host range of the potato spindle tuber ‘virus’

1973 ◽  
Vol 50 (4) ◽  
pp. 111-123 ◽  
Author(s):  
R. P. Singh
Keyword(s):  
Host Range ◽  
Experimental Host ◽  
Experimental Host Range

Change of subunit composition of mitochondrial complex II (succinate–ubiquinone reductase/quinol–fumarate reductase) in Ascaris suum during the migration in the experimental host

2008 ◽  
Vol 57 (1) ◽  
pp. 54-61 ◽  
Author(s):  
Fumiko Iwata ◽  
Noriko Shinjyo ◽  
Hisako Amino ◽  
Kimitoshi Sakamoto ◽  
M. Khyrul Islam ◽  
...  
Keyword(s):  
Ascaris Suum ◽  
Fumarate Reductase ◽  
Subunit Composition ◽  
Mitochondrial Complex ◽  
Experimental Host ◽  
Complex Ii
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