Population Structure of Plasmid-Containing Strains of Streptococcus mutans, a Member of the Human Indigenous Biota

ABSTRACT There are suggestions that the phylogeny of Streptococcus mutans, a member of the human indigenous biota that is transmitted mostly mother to child, might parallel the evolutionary history of its human host. The relatedness and phylogeny of plasmid-containing strains of S. mutans were examined based on chromosomal DNA fingerprints (CDF), a hypervariable region (HVR) of a 5.6-kb plasmid, the rRNA gene intergenic spacer region (IGSR), serotypes, and the genotypes of mutacin I and II. Plasmid-containing strains were studied because their genetic diversity was twice as great as that of plasmid-free strains. The CDF of S. mutans from unrelated human hosts were unique, except those from Caucasians, which were essentially identical. The evolutionary history of the IGSR, with or without the serotype and mutacin characters, clearly delineated an Asian clade. Also, a continuous association with mutacin II could be reconstructed through an evolutionary lineage with the IGSR, but not for serotype e. DNA sequences from the HVR of the plasmid produced a well-resolved phylogeny that differed from the chromosomal phylogeny, indicating that the horizontal transfer of the plasmid may have occurred multiple times. The plasmid phylogeny was more congruent with serotype e than with mutacin II evolution, suggesting a possible functional correlation. Thus, the history of this three-tiered relationship between human, bacterium, and plasmid supported both coevolution and independent evolution.

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Identification of Bifidobacterium Animalis Ssp. Lactis from Egyptian Women Breast Milk and Feces of Breast Fed Infant Based On 16S-23S rRNA Gene

Advances in Nutrition & Food Science ◽

10.33140/anfs/01/01/00009 ◽

2016 ◽

Vol 1 (1) ◽

Keyword(s):

Dna Sequences ◽

Patent Protection ◽

Health Benefit ◽

Intergenic Spacer ◽

23S Rrna ◽

Species Discrimination ◽

Rrna Gene ◽

Accession Number ◽

Intergenic Spacer Region ◽

Breast Fed

Bifidobacterium represent one of the major genera of the intestinal tract of human and animals used as probiotics in dairy and nondairy foods for restore the intestinal microflora which confers a health benefit. The identification of Bifidobacterium by phenotypic features is commonly unreliable, time, money, and effort consuming. We sought to improve the Bifidobacterium identification method based on molecular level to identify probiotic bacteria in complex microbial communities. The application of 16S-23S rRNA oligonucleotide primers is the best and most reliable, rapid, and precise species and sub species identification approach. The ribosomal intergenic spacer region (ISR) located between the highly conserved 16S rRNA and 23S rRNA shows a high degree of variation in length and sequence and potential for intra species discrimination and providing the phylogenetic Relationship of the Genus Bifidobacterium spp. Results showed that one of the two primer sets Bflac2-Bflac5 species specific gives positive results differentiating between B. animalis ssp. Lactis isolated from breast fed infants milk of human and that isolated from feces of breast fed infant and detecting reference strain for B. animalis ssp. Lactis DSM10140. DNA sequences of the two strains were submitted to the Genbank NCBI under accession number (KT758845) named as B. animalis ssp. Lactis Egm1 (Egyptian milk) and accession number (KT758846) named as Egf1 Egyptian feces while the second primer give false positive result. Also, we aim to obtain patent protection under Intellectual property rights (IPRs) for B. animalis ssp. Lactis which was isolated from Egyptian resources to be used for a better and healthier food and dairy products.

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New PCR-based assay for the identification of Pectobacterium carotovorum causing potato soft rot

Plant Disease ◽

10.1094/pdis-08-21-1676-re ◽

2021 ◽

Author(s):

M. Belén Suárez ◽

Marta Diego ◽

F. J. Feria ◽

M J Martín-Robles ◽

Sergio Moreno ◽

...

Keyword(s):

Real Time ◽

Dna Sequences ◽

Real Time Pcr ◽

Bacterial Species ◽

Intergenic Spacer ◽

Soft Rot ◽

Pcr Analysis ◽

Rrna Gene ◽

Accurate Identification ◽

Intergenic Spacer Region

Soft rot on potato tuber is a destructive disease caused by pathogenic bacterial species of the genera Pectobacterium and Dickeya. Accurate identification of the causal agent is necessary to ensure adequate disease management, since different species may have distinct levels of aggressiveness and host range. One of the most important potato pathogens is P. carotovorum, a highly heterogeneous species capable of infecting multiple hosts. The complexity of this species, until recently divided into several subspecies, has made it difficult to develop precise diagnostic tests. This study proposes a PCR assay based on the new pair of primers Pcar1F/R to facilitate the identification of potato isolates of P. carotovorum according to the most recent taxonomic description of this species. The new primers were designed on a variable segment of the 16S rRNA gene and the intergenic spacer region (ITS) of available DNA sequences from classical and recently established species in the genus Pectobacterium. The results of the PCR analysis of genomic DNA from 32 Pectobacterium and Dickeya strains confirmed that the Pcar1F/R primers have sufficient nucleotide differences to discriminate between P. carotovorum and other Pectobacterium species associated with damage to potato crops, with the exception of P. versatile, which improves the specificity of the currently available primers. The proposed assay was originally developed as a conventional PCR but was later adapted to the real-time PCR format for application in combination with the existing real-time PCR test for the potato-specific pathogen P. parmentieri. This should be useful for the routine diagnosis of potato soft rot.

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Characterization of Fusarium spp. isolates by PCR-RFLP analysis of the intergenic spacer region of the rRNA gene (rDNA)

International Journal of Food Microbiology ◽

10.1016/j.ijfoodmicro.2005.09.005 ◽

2006 ◽

Vol 106 (3) ◽

pp. 297-306 ◽

Cited By ~ 36

Author(s):

A. Llorens ◽

M.J. Hinojo ◽

R. Mateo ◽

M.T. González-Jaén ◽

F.M. Valle-Algarra ◽

...

Keyword(s):

Intergenic Spacer ◽

Rflp Analysis ◽

Rrna Gene ◽

Fusarium Spp ◽

Intergenic Spacer Region ◽

Pcr Rflp

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A rapid loss of stripes: the evolutionary history of the extinct quagga

Biology Letters ◽

10.1098/rsbl.2005.0323 ◽

2005 ◽

Vol 1 (3) ◽

pp. 291-295 ◽

Cited By ~ 34

Author(s):

Jennifer A Leonard ◽

Nadin Rohland ◽

Scott Glaberman ◽

Robert C Fleischer ◽

Adalgisa Caccone ◽

...

Keyword(s):

South African ◽

Dna Sequences ◽

Evolutionary History ◽

Climate Changes ◽

Rapid Loss ◽

Mt Dna ◽

Pleistocene Climate ◽

Equus Burchelli ◽

History Of ◽

Plains Zebra

Twenty years ago, the field of ancient DNA was launched with the publication of two short mitochondrial (mt) DNA sequences from a single quagga ( Equus quagga ) museum skin, an extinct South African equid ( Higuchi et al . 1984 Nature 312 , 282–284). This was the first extinct species from which genetic information was retrieved. The DNA sequences of the quagga showed that it was more closely related to zebras than to horses. However, quagga evolutionary history is far from clear. We have isolated DNA from eight quaggas and a plains zebra (subspecies or phenotype Equus burchelli burchelli ). We show that the quagga displayed little genetic diversity and very recently diverged from the plains zebra, probably during the penultimate glacial maximum. This emphasizes the importance of Pleistocene climate changes for phylogeographic patterns in African as well as Holarctic fauna.

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The Western Progression of Lyme Disease: Infectious and NonclonalBorrelia burgdorferi Sensu LatoPopulations in Grand Forks County, North Dakota

Applied and Environmental Microbiology ◽

10.1128/aem.02422-14 ◽

2014 ◽

Vol 81 (1) ◽

pp. 48-58 ◽

Cited By ~ 12

Author(s):

Brandee L. Stone ◽

Nathan M. Russart ◽

Robert A. Gaultney ◽

Angela M. Floden ◽

Jefferson A. Vaughan ◽

...

Keyword(s):

Lyme Disease ◽

16S Rrna ◽

16S Rrna Gene ◽

North Dakota ◽

Intergenic Spacer ◽

Rrna Gene ◽

Content Type ◽

Intergenic Spacer Region ◽

Grand Forks ◽

The 16S Rrna Gene

ABSTRACTScant attention has been paid to Lyme disease,Borrelia burgdorferi,Ixodes scapularis, or reservoirs in eastern North Dakota despite the fact that it borders high-risk counties in Minnesota. Recent reports ofB. burgdorferiandI. scapularisin North Dakota, however, prompted a more detailed examination. Spirochetes cultured from the hearts of five rodents trapped in Grand Forks County, ND, were identified asB. burgdorferi sensu latothrough sequence analyses of the 16S rRNA gene, the 16S rRNA gene-ileTintergenic spacer region,flaB,ospA,ospC, andp66. OspC typing revealed the presence of groups A, B, E, F, L, and I. Two rodents were concurrently carrying multiple OspC types. Multilocus sequence typing suggested the eastern North Dakota strains are most closely related to those found in neighboring regions of the upper Midwest and Canada. BALB/c mice were infected withB. burgdorferiisolate M3 (OspC group B) by needle inoculation or tick bite. Tibiotarsal joints and ear pinnae were culture positive, andB. burgdorferiM3 was detected by quantitative PCR (qPCR) in the tibiotarsal joints, hearts, and ear pinnae of infected mice. Uninfected larvalI. scapularisticks were able to acquireB. burgdorferiM3 from infected mice; M3 was maintained inI. scapularisduring the molt from larva to nymph; and further, M3 was transmitted from infectedI. scapularisnymphs to naive mice, as evidenced by cultures and qPCR analyses. These results demonstrate that isolate M3 is capable of disseminated infection by both artificial and natural routes of infection. This study confirms the presence of unique (nonclonal) and infectiousB. burgdorferipopulations in eastern North Dakota.

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Molecular phylogeny of diploid Hordeum species and incongruence between chloroplast and nuclear datasets

Genome ◽

10.1139/g11-063 ◽

2011 ◽

Vol 54 (12) ◽

pp. 986-992 ◽

Cited By ~ 7

Author(s):

Huan Wang ◽

Dongfa Sun ◽

Genlou Sun

Keyword(s):

Evolutionary History ◽

Nuclear Gene ◽

Intergenic Spacer ◽

Molecular Data ◽

Genome Species ◽

Different Types ◽

History Of ◽

Morphological And Molecular Data ◽

Hordeum Species ◽

Eurasian Species

The phylogeny of diploid Hordeum species has been studied using both chloroplast and nuclear gene sequences. However, the studies of different nuclear datasets of Hordeum species often arrived at similar conclusions, whereas the studies of different chloroplast DNA data generally resulted in inconsistent conclusions. Although the monophyly of the genus is well supported by both morphological and molecular data, the intrageneric phylogeny is still a matter of controversy. To better understand the evolutionary history of Hordeum species, two chloroplast gene loci (trnD-trnT intergenic spacer and rps16 gene) and one nuclear marker (thioreoxin-like gene (HTL)) were used to explore the phylogeny of Hordeum species. Two obviously different types of trnD-trnT sequences were observed, with an approximately 210 base pair difference between these two types: one for American species, another for Eurasian species. The trnD-trnT data generally separated the diploid Hordeum species into Eurasian and American clades, with the exception of Hordeum marinum subsp. gussoneanum. The rps16 data also grouped most American species together and suggested that Hordeum flexuosum has a different plastid type from the remaining American species. The nuclear gene HTL data clearly divided Hordeum species into two clades: the Xu + H genome clade and the Xa + I genome clade. Within clades, H genome species were well separated from the Xu species, and the I genome species were well separated from the Xa genome species. The incongruence between chloroplast and nuclear datasets was found and discussed.

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Evolutionary Relationship between Two Firefly Species,Curtos costipennisandC. okinawanus(Coleoptera, Lampyridae), in the Ryukyu Islands of Japan Revealed by the Mitochondrial and Nuclear DNA Sequences

The Scientific World JOURNAL ◽

10.1100/2012/653013 ◽

2012 ◽

Vol 2012 ◽

pp. 1-9 ◽

Cited By ~ 2

Author(s):

Masahiko Muraji ◽

Norio Arakaki ◽

Shigeo Tanizaki

Keyword(s):

Dna Sequences ◽

Evolutionary History ◽

Nuclear Dna ◽

Evolutionary Relationship ◽

Early Pleistocene ◽

Ryukyu Islands ◽

Mtdna Sequences ◽

Northern Half ◽

The Ryukyu Islands ◽

History Of

The phylogenetic relationship, biogeography, and evolutionary history of closely related two firefly species,Curtos costipennisandC. okinawanus, distributed in the Ryukyu Islands of Japan were examined based on nucleotide sequences of mitochondrial (2.2 kb long) and nuclear (1.1-1.2 kb long) DNAs. In these analyses, individuals were divided among three genetically distinct local groups,C. costipennisin the Amami region,C. okinawanusin the Okinawa region, andC. costipennisin the Sakishima region. Their mtDNA sequences suggested that ancestralC. costipennispopulation was first separated between the Central and Southern Ryukyu areas, and the northern half was then subdivided betweenC. costipennisin the Amami andC. okinawanusin the Okinawa. The application of the molecular evolutionary clocks of coleopteran insects indicated that their vicariance occurred 1.0–1.4 million years ago, suggesting the influence of submergence and subdivision of a paleopeninsula extending between the Ryukyu Islands and continental China through Taiwan in the early Pleistocene.

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Karyotype Evolution and Distinct Evolutionary History of the W Chromosomes in Swallows (Aves, Passeriformes)

Cytogenetic and Genome Research ◽

10.1159/000500621 ◽

2019 ◽

Vol 158 (2) ◽

pp. 98-105 ◽

Cited By ~ 3

Author(s):

Suziane A. Barcellos ◽

Rafael Kretschmer ◽

Marcelo S. de Souza ◽

Alice L. Costa ◽

Tiago M. Degrandi ◽

...

Keyword(s):

Dna Sequences ◽

Evolutionary History ◽

Karyotype Evolution ◽

Sex Chromosome ◽

Repetitive Sequences ◽

Z Chromosome ◽

W Chromosome ◽

The Family ◽

Agnor Staining ◽

History Of

As in many other bird groups, data on karyotype organization and distribution of repetitive sequences are also lacking in species belonging to the family Hirundinidae. Thus, in the present study, we analyzed the karyotypes of 3 swallow species (Progne tapera, Progne chalybea, and Pygochelidon cyanoleuca) by Giemsa and AgNOR staining, C-banding, and FISH with 11 microsatellite sequences. The diploid chromosome number was 2n = 76 in all 3 species, and NORs were observed in 2 chromosome pairs each. The microsatellite distribution pattern was similar in both Progne species, whereas P. cyanoleuca presented a distinct organization. These repetitive DNA sequences were found in the centromeric, pericentromeric, and telomeric regions of the macrochromosomes, as well as in 2 interstitial blocks in the W chromosome. Most microchromosomes had mainly telomeric signals. The Z chromosome displayed 1 hybridization signal in P. tapera but none in the other species. In contrast, the W chromosome showed an accumulation of different microsatellite sequences. The swallow W chromosome is larger than that of most Passeriformes. The observed enlargement in chromosome size might be explained by these high amounts of repetitive sequences. In sum, our data highlight the significant role that microsatellite sequences may play in sex chromosome differentiation.

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Differentiation of group VIII Spiroplasma strains with sequences of the 16S–23S rDNA intergenic spacer region

Canadian Journal of Microbiology ◽

10.1139/w04-091 ◽

2004 ◽

Vol 50 (12) ◽

pp. 1061-1067 ◽

Cited By ~ 14

Author(s):

Laura B Regassa ◽

Kimberly M Stewart ◽

April C Murphy ◽

Frank E French ◽

Tao Lin ◽

...

Keyword(s):

Intergenic Spacer ◽

Analytical Models ◽

23S Rrna ◽

Rrna Gene ◽

Group Viii ◽

Similarity Coefficients ◽

Intergenic Spacer Region ◽

Intergenic Sequences ◽

The Stability ◽

The 16S Rrna Gene

Spiroplasma species (Mollicutes: Spiroplasmataceae) are associated with a wide variety of insects, and serology has classified this genus into 34 groups, 3 with subgroups. The 16S rRNA gene has been used for phylogenetic analysis of spiroplasmas, but this approach is uninformative for group VIII because the serologically distinct subgroups generally have similarity coefficients >0.990. Therefore, we investigated the utility of the 16S–23S rRNA spacer region as a means to differentiate closely related subgroups or strains. We generated intergenic sequences and detailed serological profiles for 8 group VIII Spiroplasma strains. Sequence analyses using Maximum Parsimony, Neighbor Joining, and Maximum Likelihood placed the strains into 2 clades. One clade consisted of strains BARC 2649 and GSU5367. The other clade was divided into clusters containing representatives of the 3 designated group VIII subgroups (EA-1, DF-1, and TAAS-1) and 3 previously unclassified strains. The stability of the positions of the strains in various analytical models and the ability to provide robust support for groupings tentatively supported by serology indicates that the 16S–23S intergenic rDNA sequence will prove useful in intragroup analysis of group VIII spiroplasmas.Key words: Mollicutes, Spiroplasma, phylogeny, Tabanidae.

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Seeing is believing: Can biofilm diagnostics guide individualized therapy in endocarditis?

10.5194/biofilms9-116 ◽

2020 ◽

Author(s):

Judith Kikhney ◽

Laura Kursawe ◽

Swb Eichinger ◽

Walter Eichinger ◽

Julia Schmidt ◽

...

Keyword(s):

Antibiotic Therapy ◽

Biofilm Formation ◽

Heart Valves ◽

Single Cells ◽

Intergenic Spacer ◽

Rrna Gene ◽

Bacterial Cells ◽

Intergenic Spacer Region ◽

Causative Microorganism ◽

The Impact

Introduction In Infective Endocarditis (IE), early diagnosis of the causative microorganism is crucial for correct antibiotic therapy, which improves the patients&#8217; outcome. Objectives We studies the impact of biofilm formation in IE samples. Materials & methods We used Fluorescence in situ Hybridization (FISH) combined with 16S rRNA-gene PCR and sequencing to visualize and identify the infectious agents in native as well as prosthetic valves and to study any biofilm formation. The signal intensity of the fluorescence-labelled FISH probes correlates to a high ribosome content of the bacteria indicating metabolic activity at the time point of surgery. We developed a spacer FISH assay for the detection of the 16S-23S intergenic spacer region that is only present in actively transcribing cells to detect the activity of bacterial cells more precisely on a single cell level. Results FISH visualized bacteria in the heart valves ranging from single cells to highly organized biofilms. Interestingly, we found FISH positive bacteria in culture negative samples and samples from patients under antibiotic therapy. Using the spacer FISH, we visualized positive microbial cells in heart valves of patients under adequate therapy. Preliminary data point to a correlation between the biofilm state and treatment inefficiency. Conclusion FISH/PCR not only allows timely identification of the pathogens in IE, but also biofilm-staging and visualization of the effect of antimicrobial therapy at time of surgery. The technique provides crucial information for successful targeted antibiotic therapy, and it might guide therapeutical decisions in relation to biofilm state in the future.

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