scholarly journals Complete Genome Sequences from Three Genetically Distinct Strains Reveal High Intraspecies Genetic Diversity in the Microsporidian Encephalitozoon cuniculi

2013 ◽  
Vol 12 (4) ◽  
pp. 503-511 ◽  
Author(s):  
Jean-François Pombert ◽  
Jinshan Xu ◽  
David R. Smith ◽  
David Heiman ◽  
Sarah Young ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
De Novo ◽  
Genomic Diversity ◽  
Nucleotide Polymorphisms ◽  
Entire Genome ◽  
Content Type ◽  
Large Numbers ◽  
Intracellular Parasites ◽  
Intergenic Regions ◽  
Identical Gene

ABSTRACTMicrosporidia from the Encephalitozoonidae are obligate intracellular parasites with highly conserved and compacted nuclear genomes: they have few introns, short intergenic regions, and almost identical gene complements and chromosome arrangements. Comparative genomics ofEncephalitozoonand microsporidia in general have focused largely on the genomic diversity between different species, and we know very little about the levels of genetic diversity within species. Polymorphism studies withEncephalitozoonare so far restricted to a small number of genes, and a few genetically distinct strains have been identified; most notably, three genotypes (ECI, ECII, and ECIII) of the model speciesE. cuniculihave been identified based on variable repeats in the rRNA internal transcribed spacer (ITS). To determine ifE. cuniculigenotypes are genetically distinct lineages across the entire genome and at the same time to examine the question of intraspecies genetic diversity in microsporidia in general, we sequencedde novogenomes from each of the three genotypes and analyzed patterns of single nucleotide polymorphisms (SNPs) and insertions/deletions across the genomes. Although the strains have almost identical gene contents, they harbor large numbers of SNPs, including numerous nonsynonymous changes, indicating massive intraspecies variation within the Encephalitozoonidae. Based on this diversity, we conclude that the recognized genotypes are genetically distinct and propose new molecular markers for microsporidian genotyping.

scholarly journals Assessing Genetic Diversity among Brettanomyces Yeasts by DNA Fingerprinting and Whole-Genome Sequencing

2014 ◽  
Vol 80 (14) ◽  
pp. 4398-4413 ◽  
Author(s):  
Sam Crauwels ◽  
Bo Zhu ◽  
Jan Steensels ◽  
Pieter Busschaert ◽  
Gorik De Samblanx ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Fingerprinting ◽  
Wine Industry ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Content Type ◽  
Carbon And Nitrogen ◽  
Spoilage Yeasts ◽  
Off Flavors ◽  
Carbon And Nitrogen Metabolism

ABSTRACTBrettanomycesyeasts, with the speciesBrettanomyces(Dekkera)bruxellensisbeing the most important one, are generally reported to be spoilage yeasts in the beer and wine industry due to the production of phenolic off flavors. However,B. bruxellensisis also known to be a beneficial contributor in certain fermentation processes, such as the production of certain specialty beers. Nevertheless, despite its economic importance,Brettanomycesyeasts remain poorly understood at the genetic and genomic levels. In this study, the genetic relationship between more than 50Brettanomycesstrains from all presently known species and from several sources was studied using a combination of DNA fingerprinting techniques. This revealed an intriguing correlation between theB. bruxellensisfingerprints and the respective isolation source. To further explore this relationship, we sequenced a (beneficial) beer isolate ofB. bruxellensis(VIB X9085; ST05.12/22) and compared its genome sequence with the genome sequences of two wine spoilage strains (AWRI 1499 and CBS 2499). ST05.12/22 was found to be substantially different from both wine strains, especially at the level of single nucleotide polymorphisms (SNPs). In addition, there were major differences in the genome structures between the strains investigated, including the presence of large duplications and deletions. Gene content analysis revealed the presence of 20 genes which were present in both wine strains but absent in the beer strain, including many genes involved in carbon and nitrogen metabolism, and vice versa, no genes that were missing in both AWRI 1499 and CBS 2499 were found in ST05.12/22. Together, this study provides tools to discriminateBrettanomycesstrains and provides a first glimpse at the genetic diversity and genome plasticity ofB. bruxellensis.

scholarly journals Evolution of the U.S. Biological Select AgentRathayibacter toxicus

mBio ◽  
2018 ◽  
Vol 9 (4) ◽  
Author(s):  
Edward W. Davis ◽  
Javier F. Tabima ◽  
Alexandra J. Weisberg ◽  
Lucas Dantas Lopes ◽  
Michele S. Wiseman ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Adaptive Immune System ◽  
The United States ◽  
Genomic Diversity ◽  
Data Set ◽  
Important Species ◽  
Content Type ◽  
Low Genetic Diversity ◽  
History Of ◽  
Short Palindromic Repeat

ABSTRACTRathayibacter toxicusis a species of Gram-positive, corynetoxin-producing bacteria that causes annual ryegrass toxicity, a disease often fatal to grazing animals. A phylogenomic approach was employed to model the evolution ofR. toxicusto explain the low genetic diversity observed among isolates collected during a 30-year period of sampling in three regions of Australia, gain insight into the taxonomy ofRathayibacter, and provide a framework for studying these bacteria. Analyses of a data set of more than 100 sequencedRathayibactergenomes indicated thatRathayibacterforms nine species-level groups.R. toxicusis the most genetically distant, and evidence suggested that this species experienced a dramatic event in its evolution. Its genome is significantly reduced in size but is colinear to those of sister species. Moreover,R. toxicushas low intergroup genomic diversity and almost no intragroup genomic diversity between ecologically separated isolates.R. toxicusis the only species of the genus that encodes a clustered regularly interspaced short palindromic repeat (CRISPR) locus and that is known to host a bacteriophage parasite. The spacers, which represent a chronological history of infections, were characterized for information on past events. We propose a three-stage process that emphasizes the importance of the bacteriophage and CRISPR in the genome reduction and low genetic diversity of theR. toxicusspecies.IMPORTANCERathayibacter toxicusis a toxin-producing species found in Australia and is often fatal to grazing animals. The threat of introduction of the species into the United States led to its inclusion in the Federal Select Agent Program, which makesR. toxicusa highly regulated species. This work provides novel insights into the evolution ofR. toxicus.R. toxicusis the only species in the genus to have acquired a CRISPR adaptive immune system to protect against bacteriophages. Results suggest that coexistence with the bacteriophage NCPPB3778 led to the massive shrinkage of theR. toxicusgenome, species divergence, and the maintenance of low genetic diversity in extant bacterial groups. This work contributes to an understanding of the evolution and ecology of an agriculturally important species of bacteria.

scholarly journals Genomic Epidemiology of a Protracted Hospital Outbreak Caused by a Toxin A-Negative Clostridium difficile Sublineage PCR Ribotype 017 Strain in London, England

2015 ◽  
Vol 53 (10) ◽  
pp. 3141-3147 ◽  
Author(s):  
M. D. Cairns ◽  
M. D. Preston ◽  
T. D. Lawley ◽  
T. G. Clark ◽  
R. A. Stabler ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
De Novo ◽  
University Hospital ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Conjugative Transposon ◽  
Content Type ◽  
Genomic Epidemiology ◽  
Hospital Outbreak ◽  
Nosocomial Diarrhea

Clostridium difficileremains the leading cause of nosocomial diarrhea worldwide, which is largely considered to be due to the production of two potent toxins: TcdA and TcdB. However, PCR ribotype (RT) 017, one of five clonal lineages of human virulentC. difficile, lacks TcdA expression but causes widespread disease. Whole-genome sequencing was applied to 35 isolates from hospitalized patients withC. difficileinfection (CDI) and two environmental ward isolates in London, England. The phylogenetic analysis of single nucleotide polymorphisms (SNPs) revealed a clonal cluster of temporally variable isolates from a single hospital ward at University Hospital Lewisham (UHL) that were distinct from other London hospital isolates.De novoassembled genomes revealed a 49-kbp putative conjugative transposon exclusive to this hospital clonal cluster which would not be revealed by current typing methodologies. This study identified three sublineages ofC. difficileRT017 that are circulating in London. Similar to the notorious RT027 lineage, which has caused global outbreaks of CDI since 2001, the lineage of toxin-defective RT017 strains appears to be continually evolving. By utilization of WGS technologies to identify SNPs and the evolution of clonal strains, the transmission of outbreaks caused by near-identical isolates can be retraced and identified.

scholarly journals Whole-Genome Sequencing and Phenotypic Analysis of Bacillus subtilis Mutants following Evolution under Conditions of Relaxed Selection for Sporulation

2011 ◽  
Vol 77 (19) ◽  
pp. 6867-6877 ◽  
Author(s):  
Christopher T. Brown ◽  
Laura K. Fishwick ◽  
Binna M. Chokshi ◽  
Marissa A. Cuff ◽  
Jay M. Jackson ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Chromosomal Rearrangements ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Relaxed Selection ◽  
Phenotypic Analysis ◽  
Competitive Fitness ◽  
Content Type ◽  
Intergenic Regions ◽  
Selection For

ABSTRACTLittle is known about how genetic variation at the nucleotide level contributes to competitive fitness within species. During a 6,000-generation study ofBacillus subtilisevolved under relaxed selection for sporulation, a new strain, designated WN716, emerged with significantly different colony and cell morphologies; loss of sporulation, competence, acetoin production, and motility; multiple auxotrophies; and increased competitive fitness (H. Maughan and W. L. Nicholson, Appl. Environ. Microbiol.77:4105–4118, 2011). The genome of WN716 was analyzed by OpGen optical mapping, whole-genome 454 pyrosequencing, and the CLC Genomics Workbench. No large chromosomal rearrangements were found; however, 34 single-nucleotide polymorphisms (SNPs) and +1 frameshifts were identified in WN716 that resulted in amino acid changes in coding sequences of annotated genes, and 11 SNPs were located in intergenic regions. Several classes of genes were affected, including biosynthetic pathways, sporulation, competence, and DNA repair. In several cases, attempts were made to link observed phenotypes of WN716 with the discovered mutations, with various degrees of success. For example, a +1 frameshift was identified at codon 13 ofsigW, the product of which (SigW) controls a regulon of genes involved in resistance to bacteriocins and membrane-damaging antibiotics. Consistent with this finding, WN716 exhibited sensitivity to fosfomycin and to a bacteriocin produced byB. subtilissubsp.spizizeniiand exhibited downregulation of SigW-dependent genes on a transcriptional microarray, consistent with WN716 carrying a knockout ofsigW. The results suggest that propagation ofB. subtilisfor less than 2,000 generations in a nutrient-rich environment where sporulation is suppressed led to rapid initiation of genomic erosion.

scholarly journals Biochemical and Localization Analyses of Putative Type III Secretion Translocator Proteins CopB and CopB2 of Chlamydia trachomatis Reveal Significant Distinctions

2011 ◽  
Vol 79 (8) ◽  
pp. 3036-3045 ◽  
Author(s):  
B. Chellas-Géry ◽  
K. Wolf ◽  
J. Tisoncik ◽  
T. Hackstadt ◽  
K. A. Fields
Keyword(s):  
Type Iii Secretion ◽  
De Novo ◽  
Ectopic Expression ◽  
Effector Proteins ◽  
Developmental Cycle ◽  
Inclusion Membrane ◽  
Content Type ◽  
Type Iii ◽  
Intracellular Parasites ◽  
The Many

ABSTRACTChlamydiaspp. are among the many pathogenic Gram-negative bacteria that employ a type III secretion system (T3SS) to overcome host defenses and exploit available resources. Significant progress has been made in elucidating contributions of T3S to the pathogenesis of these medically important, obligate intracellular parasites, yet important questions remain. Chief among these is how secreted effector proteins traverse eukaryotic membranes to gain access to the host cytosol. Due to a complex developmental cycle, it is possible that chlamydiae utilize a different complement of proteins to accomplish translocation at different stages of development. We investigated this possibility by extending the characterization ofC. trachomatisCopB and CopB2. CopB is detected early during infection but is depleted and not detected again until about 20 h postinfection. In contrast, CopB2 was detectible throughout development. CopB is associated with the inclusion membrane. Biochemical and ectopic expression analyses were consistent with peripheral association of CopB2 with inclusion membranes. This interaction correlated with development and required both chlamydialde novoprotein synthesis and T3SS activity. Collectively, our data indicate that it is unlikely that CopB serves as the sole chlamydial translocation pore and that CopB2 is capable of association with the inclusion membrane.

scholarly journals Phylogeographical Analyses and Antibiotic Resistance Genes of Acinetobacter johnsonii Highlight Its Clinical Relevance

mSphere ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Santiago Castillo-Ramírez ◽  
Valeria Mateo-Estrada ◽  
Gerardo Gonzalez-Rocha ◽  
Andrés Opazo-Capurro
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Clinical Importance ◽  
Antibiotic Resistance Genes ◽  
Genomic Diversity ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Content Type ◽  
Acinetobacter Johnsonii ◽  
Well Differentiated

ABSTRACT Acinetobacter johnsonii has been severely understudied and its population structure and the presence of antibiotic resistance genes (ARGs) are very much uncertain. Our phylogeographical analysis shows that intercontinental transmission has occurred frequently and that different lineages are circulating within single countries; notably, clinical and nonclinical strains are not well differentiated from one another. Importantly, in this species recombination is a significant source of single nucleotide polymorphisms. Furthermore, our results show this species could be an important reservoir of ARGs since it has a significant amount of ARGs, and many of them show signals of horizontal gene transfer. Thus, this study clearly points out the clinical importance of A. johnsonii and the urgent need to better appreciate its genomic diversity.

scholarly journals Following the Fate of Bacterial Cells Experiencing Sudden Chromosome Loss

mBio ◽  
2015 ◽  
Vol 6 (3) ◽  
Author(s):  
Maya Elbaz ◽  
Sigal Ben-Yehuda
Keyword(s):  
De Novo ◽  
Vaccination Strategy ◽  
Time Lapse ◽  
Chromosome Loss ◽  
Bacterial Cells ◽  
Chromosomal Dna ◽  
Entire Genome ◽  
Content Type ◽  
Intact Membrane ◽  
Efficient Induction

ABSTRACTChromosomal DNA is a constant source of information, essential for any given cell to respond and adapt to changing conditions. Here, we investigated the fate of exponentially growing bacterial cells experiencing a sudden and rapid loss of their entire chromosome. UtilizingBacillus subtiliscells harboring an inducible copy of the endogenous toxinyqcG, which encodes an endonuclease, we induced the formation of a population of cells that lost their genetic information simultaneously. Surprisingly, these DNA-less cells, termed DLCs, did not lyse immediately and exhibited normal cellular morphology for a period of at least 5 h after DNA loss. This cellular integrity was manifested by their capacity to maintain an intact membrane and membrane potential and cell wall architecture similar to those of wild-type cells. Unlike growing cells that exhibit a dynamic profile of macromolecules, DLCs displayed steady protein and RNA reservoirs. Remarkably, following DLCs by time lapse microscopy revealed that they succeeded in synthesizing proteins, elongating, and dividing, apparently formingde novoZ rings at the midcell position. Taken together, the persistence of key cellular events in DLCs indicates that the information to carry out lengthy processes is harbored within the remaining molecular components.IMPORTANCEPerturbing bacterial growth by the use of antibiotics targeting replication, transcription, or translation has been a subject of study for many years; however, the consequences of a more dramatic event, in which the entire bacterial chromosome is lost, have not been described. Here, we followed the fate of bacterial cells encountering an abrupt loss of their entire genome. Surprisingly, the cells preserved an intact envelope and functioning macromolecules. Furthermore, cells lacking their genome could still elongate and divide hours after the loss of DNA. Our data suggest that the information stored in the transient reservoir of macromolecules is sufficient to carry out complex and lengthy processes even in the absence of the chromosome. Based on our study, the formation of DNA-less bacteria could serve as a novel vaccination strategy, enabling an efficient induction of the immune system without the risk of bacterial propagation within the host.

scholarly journals The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels

2018 ◽  
Vol 2018 ◽  
pp. 1-10 ◽  
Author(s):  
Andrey A. Ayginin ◽  
Ekaterina V. Pimkina ◽  
Alina D. Matsvay ◽  
Anna S. Speranskaya ◽  
Marina V. Safonova ◽  
...  
Keyword(s):  
De Novo ◽  
Virus Detection ◽  
Rapid Identification ◽  
Genomic Diversity ◽  
Entire Genome ◽  
Viral Pathogens ◽  
Detection And Identification ◽  
Low Sensitivity ◽  
Next Generation Sequencing Ngs ◽  
Targeted Enrichment

Advances in the next generation sequencing (NGS) technologies have significantly increased our ability to detect new viral pathogens and systematically determine the spectrum of viruses prevalent in various biological samples. In addition, this approach has also helped in establishing the associations of viromes with many diseases. However, unlike the metagenomic studies using16SrRNA for the detection of bacteria, it is impossible to create universal oligonucleotides to target all known and novel viruses, owing to their genomic diversity and variability. On the other hand, sequencing the entire genome is still expensive and has relatively low sensitivity for such applications. The existing approaches for the design of oligonucleotides for targeted enrichment are usually involved in the development of primers for the PCR-based detection of particular viral species or genera, but not for families or higher taxonomic orders. In this study, we have developed a computational pipeline for designing the oligonucleotides capable of covering a significant number of known viruses within various taxonomic orders, as well as their novel variants. We have subsequently designed a genus-specific oligonucleotide panel for targeted enrichment of viral nucleic acids in biological material and demonstrated the possibility of its application for virus detection in bird samples. We have tested our panel using a number of collected samples and have observed superior efficiency in the detection and identification of viral pathogens. Since a reliable, bioinformatics-based analytical method for the rapid identification of the sequences was crucial, an NGS-based data analysis module was developed in this study, and its functionality in the detection of novel viruses and analysis of virome diversity was demonstrated.

scholarly journals Loss of Bacitracin Resistance Due to a Large Genomic Deletion amongBacillus anthracisStrains

mSystems ◽  
2018 ◽  
Vol 3 (5) ◽  
Author(s):  
Yoshikazu Furuta ◽  
Hayato Harima ◽  
Emiko Ito ◽  
Fumito Maruyama ◽  
Naomi Ohnishi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphisms ◽  
Bacillus Cereus ◽  
Bacillus Anthracis ◽  
Bacterial Species ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genomic Deletion ◽  
Content Type ◽  
Large Genomic Deletion

ABSTRACTBacillus anthracisis a Gram-positive endospore-forming bacterial species that causes anthrax in both humans and animals. In Zambia, anthrax cases are frequently reported in both livestock and wildlife, with occasional transmission to humans, causing serious public health problems in the country. To understand the genetic diversity ofB. anthracisstrains in Zambia, we sequenced and compared the genomic DNA ofB. anthracisstrains isolated across the country. Single nucleotide polymorphisms clustered these strains into three groups. Genome sequence comparisons revealed a large deletion in strains belonging to one of the groups, possibly due to unequal crossing over between a pair of rRNA operons. The deleted genomic region included genes conferring resistance to bacitracin, and the strains with the deletion were confirmed with loss of bacitracin resistance. Similar deletions between rRNA operons were also observed in a fewB. anthracisstrains phylogenetically distant from Zambian strains. The structure of bacitracin resistance genes flanked by rRNA operons was conserved only in members of theBacillus cereusgroup. The diversity and genomic characteristics ofB. anthracisstrains determined in this study would help in the development of genetic markers and treatment of anthrax in Zambia.IMPORTANCEAnthrax is caused byBacillus anthracis, an endospore-forming soil bacterium. The genetic diversity ofB. anthracisis known to be low compared with that ofBacillusspecies. In this study, we performed whole-genome sequencing of Zambian isolates ofB. anthracisto understand the genetic diversity between closely related strains. Comparison of genomic sequences revealed that closely related strains were separated into three groups based on single nucleotide polymorphisms distributed throughout the genome. A large genomic deletion was detected in the region containing a bacitracin resistance gene cluster flanked by rRNA operons, resulting in the loss of bacitracin resistance. The structure of the deleted region, which was also conserved among species of theBacillus cereusgroup, has the potential for both deletion and amplification and thus might be enabling the species to flexibly control the level of bacitracin resistance for adaptive evolution.

scholarly journals Leptospire Genomic Diversity Revealed by Microarray-Based Comparative Genomic Hybridization

2012 ◽  
Vol 78 (9) ◽  
pp. 3045-3050 ◽  
Author(s):  
Broderick Eribo ◽  
Sirima Mingmongkolchai ◽  
Tingfen Yan ◽  
Padunsri Dubbs ◽  
Karen E. Nelson
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Comparative Genomic Hybridization ◽  
Virulence Factors ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Leptospira Interrogans ◽  
Genomic Hybridization ◽  
Content Type ◽  
Reference Genomes

ABSTRACTComparative genomic hybridization was used to compare genetic diversity of five strains ofLeptospira(Leptospira interrogansserovars Bratislava, Canicola, and Hebdomadis andLeptospira kirschneriserovars Cynopteri and Grippotyphosa). The array was designed based on two available sequencedLeptospirareference genomes, those ofL. interrogansserovar Copenhageni andL. interrogansserovar Lai. A comparison of genetic contents showed thatL. interrogansserovar Bratislava was closest to the reference genomes whileL. kirschneriserovar Grippotyphosa had the least similarity to the reference genomes. Cluster analysis indicated thatL. interrogansserovars Bratislava and Hebdomadis clustered together first, followed byL. interrogansserovar Canicola, before the twoL. kirschneristrains. Confirmed/potential virulence factors identified in previous research were also detected in the tested strains.

Sign in / Sign up

Export Citation Format

Share Document