scholarly journals Molecular characterization of oral bacteria isolated from human saliva

2021 ◽  
Vol 12 (2) ◽  
pp. 1564-1571
Author(s):  
Sharee Leong ◽  
Shamala Marimuthu
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Trees ◽  
Human Saliva ◽  
Oral Bacteria ◽  
16S Ribosomal Rna ◽  
Oral Disease ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Staphylococcus Intermedius ◽  
Two Samples

Periodontitis is an inflammation of gums and bones that supporting the teeth which caused by Staphylococcus intermedius. The saliva from a patient of periodontitis or suspect to periodontitis will have higher levels of Staphylococcus intermedius. Hence, human saliva is clinically informative in diagnosing oral disease and the oral health of an individual. In this study, oral bacteria in human saliva were identified using 16S ribosomal RNA. 16S ribosomal RNA (rRNA) genes from the isolated colonies were amplified through the colony Polymerase Chain Reaction (PCR) method. 16S rRNA genes were used to determine species identity by sequencing and generating the phylogenetic tree. The results showed that Streptococcus sp. and Staphylococcus sp. were the most prevalent oral bacteria found from all the saliva samples, while Lactobacillus sp. was found from two samples. From the constructed phylogenetic trees, bacteria strains B1 and B2 clustered with the Staphylococcus sp. database. Bacteria strains B9 and B10 were categorized as Streptococcus sp. as the confidential level between Streptococcus sp. database is 100% in Neighbour-Joining tree. Sample B15 and B16 clustered with Lactobacillus  sp. database. Oral bacteria species typically associated with periodontitis was detected in all saliva samples. Therefore, it is important to fully understand the nature of the oral bacteria before further research on drug design and administration of oral treatment is executed.

scholarly journals Evaluation of 16S, map1 and pCS20 probes for detection of Cowdria and Ehrlichia species

1999 ◽  
Vol 122 (2) ◽  
pp. 323-328 ◽  
Author(s):  
M. T. E. P. ALLSOPP ◽  
C. M. HATTINGH ◽  
S. W. VOGEL ◽  
B. A. ALLSOPP
Keyword(s):  
16S Rrna ◽  
Ribosomal Rna ◽  
Pcr Amplification ◽  
16S Ribosomal Rna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Amblyomma Hebraeum ◽  
Ribosomal Rna Gene ◽  
Group Iii ◽  
16S Ribosomal Rna Gene

A panel of 16S ribosomal RNA gene probes has been developed for the study of the epidemiology of heartwater; five of these detect different cowdria genotypes, one detects five distinct genotypes; one detects any Group III Ehrlichia species other than Cowdria and one detects any Group II Ehrlichia species. These probes have been used on PCR-amplified rickettsial 16S rRNA genes from over 200 Amblyomma hebraeum ticks. Control ticks were laboratory-reared and either uninfected or fed on sheep experimentally infected with different cowdria isolates, field ticks were collected from animals in heartwater-endemic areas. All tick-derived DNA samples were also examined by PCR amplification and probing for two other cowdria genes (map1 and pCS20) which have previously been used for heartwater epidemiology. This paper describes the first direct comparison of all currently available DNA probes for heartwater-associated organisms.

Heterogeneity between 16S ribosomal RNA gene copies borne by one Desulfitobacterium strain is caused by different 100-200 bp insertions in the 5´ region

2007 ◽  
Vol 53 (1) ◽  
pp. 116-128 ◽  
Author(s):  
Richard Villemur ◽  
Philippe Constant ◽  
Annie Gauthier ◽  
Martine Shareck ◽  
Réjean Beaudet
Keyword(s):  
In Situ Hybridization ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Ribosomal Rna ◽  
16S Ribosomal Rna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Gene Copies

Strains of Desulfitobacterium hafniense, such as strains PCP-1, DP7, TCE1, and TCP-A, have unusual long 16S ribosomal RNA (rRNA) genes due to an insertion of approximately 100 bp in the 5' region. In this report, we analyzed the 16S rRNA genes of different Desulfitobacterium strains to determine if such an insertion is a common feature of desulfitobacteria. We amplified this region by polymerase chain reaction (PCR) from eight Desulfitobacterium strains (D. hafniense strains PCP-1, DP7, TCP-A, TCE1, and DCB-2; D. dehalogenans; D. chlororespirans; and Desulfitobacterium sp. PCE1) and resolved each PCR product by denaturing gradient gel electrophoresis (DGGE). All strains had from two to seven DGGE- migrating bands, suggesting heterogeneity in their 16S rRNA gene copies. For each strain, the 5' region of the 16S rRNA genes was amplified and a clone library was derived. Clones corresponding to most PCR–DGGE migration bands were isolated. Sequencing of representative clones revealed that the heterogeneity was generated by insertions of 100–200 bp. An insertion was found in at least one copy of the 16S rRNA gene in all examined strains. In total, we found eight different types of insertions (INS1–INS8) that varied from 123 to 193 nt in length. Two-dimensional structural analyses of transcribed sequences predicted that all insertions would form an energetically stable loop. Reverse transcriptase – PCR experiments revealed that most of the observed insertions in the Desulfitobacterium strains were excised from the mature 16S rRNA transcripts. Insertions were not commonly found in bacterial 16S rRNA genes, and having a different insertion in several 16S rRNA gene copies borne by a single bacterial species was rarely observed. The function of these insertions is not known, but their occurrence can have an important impact in deriving 16S rRNA oligonucleotidic fluorescence in situ hybridization probes, as these insertions can be excised from 16S rRNA transcripts.Key words: Desulfitobacterium, 16S ribosomal RNA genes, heterogeneity, gene insertions, fluorescence in situ hybridization.

scholarly journals Comparison of oral microbiome profiles in 18-month-old infants and their parents

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ryutaro Jo ◽  
Kazuma Yama ◽  
Yuto Aita ◽  
Kota Tsutsumi ◽  
Chikako Ishihara ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Dental Caries ◽  
Oral Bacteria ◽  
Oral Microbiome ◽  
Commensal Bacteria ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Deciduous Dentition ◽  
The Difference ◽  
Generation Sequencing

AbstractThe onset and progress of dental caries and periodontal disease is associated with the oral microbiome. Therefore, it is important to understand the factors that influence oral microbiome formation. One of the factors that influence oral microbiome formation is the transmission of oral bacteria from parents. However, it remains unclear when the transmission begins, and the difference in contributions of father and mother. Here, we focused on the oral microbiome of 18-month-old infants, at which age deciduous dentition is formed and the oral microbiome is likely to become stable, with that of their parents. We collected saliva from forty 18-month-old infants and their parents and compared the diversity and composition of the microbiome using next-generation sequencing of 16S rRNA genes. The results showed that microbial diversity in infants was significantly lower than that in parents and composition of microbiome were significantly different between infants and parents. Meanwhile, the microbiome of the infants was more similar to that of their mothers than unrelated adults. The bacteria highly shared between infants and parents included not only commensal bacteria but also disease related bacteria. These results suggested that the oral microbiome of the parents influences that of their children aged < 18 months.

Evidence for Iron- and Sulfur-Oxidizing Bacteria and Archaea in a Currently Active Lignite Mining Area of Lusatia (Eastern Germany)

2009 ◽  
Vol 71-73 ◽  
pp. 97-100 ◽  
Author(s):  
H.M. Siebert ◽  
Thore Rohwerder ◽  
Wolfgang Sand ◽  
M. Strzodka ◽  
K.P. Stahmann
Keyword(s):  
16S Rrna ◽  
Mining Area ◽  
16S Rrna Genes ◽  
Open Pit ◽  
Rrna Genes ◽  
Published Data ◽  
Lignite Mining ◽  
Two Samples ◽  
Pure Cultures ◽  
Sulfur Oxidizing

The largest lignite mining area in Europe is located 150 km southeast of Berlin. Acidic lakes exist in this area, known to be caused by marcasite oxidation. Thirty-two samples from the open-pit brown coal-mine Jaenschwalde were analyzed for microorganisms. Cell numbers determined after separation from sand particles revealed concentrations of 102 to 107 microorganisms per g sample. In samples exposed to the air within an hour, up to 4x107 cells were counted. Measurement of metabolic activity by microcalorimetry showed for such samples up to 50 µW per g sand, whereas in heap samples (with low moisture) low or even no activity was measurable. DNA extraction was successful for 28 samples. In 26 samples microbial 16S rRNA genes were amplified by PCR. Acidithiobacillus ferrooxidans and At. thiooxidans specific amplificates were detected by nested PCR in 23 and 10 cases, respectively. A specific signal indicating Leptospirillum ferrooxidans was obtained with nine samples. Random samples were sequenced and showed 96 to 99 % identity with published data of all three species. Surprisingly, in four samples archaeal 16S rRNA genes were amplified by PCR. Sequencing of two samples showed 99 % identity with unidentified or uncultured archaea found in NCBI-databases. Molecular biology results for At. ferrooxidans as well as for At. thiooxidans were supported by successful isolations of pure cultures in 23 cases. Cultivation of the archaea failed so far. These data indicate that iron- and sulfur-oxidizing microorganisms occur at these sites in large numbers. If in addition the evidence for archaea can become verified, a screening for hot spots as the sites of their occurrence would become interesting.

scholarly journals Metagenomic screening for lipolytic genes reveals an ecology-clustered distribution pattern

2021 ◽  
Author(s):  
Mingji Lu ◽  
Dominik Schneider ◽  
Rolf Daniel
Keyword(s):  
Markov Models ◽  
Sequence Similarity ◽  
Ecological Factors ◽  
16S Rrna Genes ◽  
Microbial Consortia ◽  
Rrna Genes ◽  
Lipolytic Enzymes ◽  
Two Samples ◽  
Metagenome Sequencing ◽  
Microbial Groups

AbstractLipolytic enzymes are one of the most important enzyme types for application in various industrial processes. Despite the continuously increasing demand, only a small portion of the so far encountered lipolytic enzymes exhibit adequate stability and activities for biotechnological applications. To explore novel and/or extremophilic lipolytic enzymes, microbial consortia in two composts at thermophilic stage were analyzed using function-driven and sequence-based metagenomic approaches. Analysis of community composition by amplicon-based 16S rRNA genes and transcripts, and direct metagenome sequencing revealed that the communities of the compost samples were dominated by members of the phyla Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes and Chloroflexi. Function-driven screening of the metagenomic libraries constructed from the two samples yielded 115 unique genes encoding lipolytic enzymes. The family assignment of these enzymes was conducted by analyzing the phylogenetic relationship and generation of a protein sequence similarity network according to an integral classification system. The sequence-based screening was performed by using a newly developed database, containing a set of profile Hidden Markov models, highly sensitive and specific for detection of lipolytic enzymes. By comparing the lipolytic enzymes identified through both approaches, we demonstrated that the activity-directed complements sequence-based detection, and vice versa. The sequence-based comparative analysis of lipolytic genes regarding diversity, function and taxonomic origin derived from 175 metagenomes indicated significant differences between habitats. Analysis of the prevalent and distinct microbial groups providing the lipolytic genes revealed characteristic patterns and groups driven by ecological factors. The here presented data suggests that the diversity and distribution of lipolytic genes in metagenomes of various habitats are largely constrained by ecological factors.

Organelle origins and ribosomal RNA

1988 ◽  
Vol 66 (5) ◽  
pp. 325-348 ◽  
Author(s):  
Michael W. Gray
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Trees ◽  
Purple Bacteria ◽  
Plant Mitochondria ◽  
Rrna Genes ◽  
Rna Sequences ◽  
Sequence Organization ◽  
General Acceptance ◽  
Mitochondrial Rrna ◽  
History Of

As the detailed molecular biology of organelle genomes has unfolded, there has been a general acceptance of the view that plastids and mitochondria are of endosymbiotic, eubacterial origin. Plastid genes are strikingly similar to their eubacterial (particularly cyanobacterial) counterparts in sequence, organization, and mode of expression, and such features strongly support the hypothesis that the plastid and its genome were derived in evolution from a blue-green alga-like endosymbiont. Mitochondria, on the other hand, are problematic: mitochondrial genes are organized and expressed in remarkably diverse ways in the different major groups of eukaryotes, and in no case are these features particularly characteristic of either bacterial or nuclear genomes. There is, however, clear evidence derived from gene sequence supporting the eubacterial ancestry of mitochondria, and some of the most compelling data have come from analyses of mitochondrial ribosomal RNA (rRNA). Plant mitochondrial rRNA genes diverge in sequence at a particularly slow rate, and these genes have proven to be especially supportive of the endosymbiont hypothesis, pointing to an origin of mitochondria from within the α subdivision of the purple bacteria. Ribosomal RNA sequences provide a basis for the construction of global phylogenetic trees that probe the evolutionary history of organelles, and that address the question of whether mitochondria and plastids are monophyletic or polyphyletic in origin. Such studies raise the possibility that the rRNA genes of plant mitochondria originated separately from the mitochondrial rRNA genes of other eukaryotes.

scholarly journals Comparative Sequence Analysis of Mycobacterium leprae and the New Leprosy-Causing Mycobacterium lepromatosis

2009 ◽  
Vol 191 (19) ◽  
pp. 6067-6074 ◽  
Author(s):  
Xiang Y. Han ◽  
Kurt C. Sizer ◽  
Erika J. Thompson ◽  
Juma Kabanja ◽  
Jun Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
Phylogenetic Trees ◽  
Mycobacterium Leprae ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Neutral Evolution ◽  
Rrna Gene ◽  
Protein Encoding ◽  
Mycobacterium Lepromatosis ◽  
Encoding Genes

ABSTRACT Mycobacterium lepromatosis is a newly discovered leprosy-causing organism. Preliminary phylogenetic analysis of its 16S rRNA gene and a few other gene segments revealed significant divergence from Mycobacterium leprae, a well-known cause of leprosy, that justifies the status of M. lepromatosis as a new species. In this study we analyzed the sequences of 20 genes and pseudogenes (22,814 nucleotides). Overall, the level of matching of these sequences with M. leprae sequences was 90.9%, which substantiated the species-level difference; the levels of matching for the 16S rRNA genes and 14 protein-encoding genes were 98.0% and 93.1%, respectively, but the level of matching for five pseudogenes was only 79.1%. Five conserved protein-encoding genes were selected to construct phylogenetic trees and to calculate the numbers of synonymous substitutions (dS values) and nonsynonymous substitutions (dN values) in the two species. Robust phylogenetic trees constructed using concatenated alignment of these genes placed M. lepromatosis and M. leprae in a tight cluster with long terminal branches, implying that the divergence occurred long ago. The dS and dN values were also much higher than those for other closest pairs of mycobacteria. The dS values were 14 to 28% of the dS values for M. leprae and Mycobacterium tuberculosis, a more divergent pair of species. These results thus indicate that M. lepromatosis and M. leprae diverged ∼10 million years ago. The M. lepromatosis pseudogenes analyzed that were also pseudogenes in M. leprae showed nearly neutral evolution, and their relative ages were similar to those of M. leprae pseudogenes, suggesting that they were pseudogenes before divergence. Taken together, the results described above indicate that M. lepromatosis and M. leprae diverged from a common ancestor after the massive gene inactivation event described previously for M. leprae.

scholarly journals Species and number of bacterium may alternate IL-1β levels in the odontogenic cyst fluid

2018 ◽  
Vol 43 (6) ◽  
pp. 679-685
Author(s):  
Suzan Cinar ◽  
Fahriye Keskin ◽  
Sevgi Ciftci ◽  
Sirmahan Cakarer ◽  
Firat Selvi ◽  
...  
Keyword(s):  
Oral Bacteria ◽  
Cyst Fluid ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Species Number ◽  
Odontogenic Cysts ◽  
Campylobacter Rectus ◽  
Significant Difference ◽  
Cytokine Levels ◽  
Cyst Fluids

AbstractObjectivesThe role of oral bacteria in the etiopathogenesis of odontogenic cysts (OC) is controversial. Immune response is regulated by the cytokines secreted during infection. This study aims to describe the association in between bacteria and levels of cytokines in OC.MethodsInfected OC fluid samples were obtained from 25 odontogenic keratocysts and 14 radicular cysts (RC). Bacteria detection was performed by polymerase chain reaction on bacterial 16S rRNA genes. Cytokine levels in OC fluids were determined using “luminex” method.ResultsPorphyromonas gingivaliswas the most common bacteria in all samples (41.03%). Bacteria species number was higher in RCs. The significant difference was detected in terms of interleukine (IL)-1β levels to the number of bacteria contained in cyst fluids (p<0.05). IL1-β level of cyst fluid group containing three or more species of bacteria increased compared with cyst fluid group containing two types of bacteria (p<0.05). IL-1β level was high in cyst fluids withCampylobacter rectusandTreponema denticolaor with three or more bacteria species. IL-1β level was higher in the cyst fluids withEnterococcus faecalisnegative thanE. faecalispositives.ConclusionsOur results suggest that species and the number of bacterium may differ IL-1β levels in the OC fluid.

scholarly journals ‘Candidatus Phytoplasma stylosanthis’, a novel taxon with a diverse host range in Australia, characterised using multilocus sequence analysis of 16S rRNA, secA, tuf, and rp genes

2020 ◽  
Author(s):  
Bianca Rodrigues Jardim ◽  
Wycliff M. Kinoti ◽  
Lucy T. T. Tran-Nguyen ◽  
Cherie Gambley ◽  
Brendan Rodoni ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
In Silico ◽  
Phylogenetic Trees ◽  
Gene Tree ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Pattern Similarity ◽  
The 16S Rrna Gene

In Australia, Stylosanthes little leaf (StLL) phytoplasma has been detected in Stylosanthes scabra Vogel, Arachis pintoi Krapov, Saccharum officinarum L., Carica papaya L., Medicago sativa L., and Solanum tuberosum L. The 16S rRNA gene sequence of StLL phytoplasma strains from S. scabra, C. papaya, S. officinarum and S. tuberosum were compared and share 99.93–100 % nucleotide sequence identity. Phylogenetic comparisons between the 16S rRNA genes of StLL phytoplasma and other ‘Candidatus Phytoplasma’ species indicate that StLL represents a distinct phytoplasma lineage. It shares its most recent known ancestry with ‘Ca. Phytoplasma luffae’ (16SrVIII-A), with which it has 97.17–97.25 % nucleotide identity. In silico RFLP analysis of the 16S rRNA amplicon using iPhyClassifier indicate that StLL phytoplasmas have a unique pattern (similarity coefficient below 0.85) that is most similar to that of ‘Ca. Phytoplasma luffae’. The unique in silico RFLP patterns were confirmed in vitro. Nucleotide sequences of genes that are more variable than the 16S rRNA gene, namely tuf (tu-elongation factor), secA (partial translocation gene), and the partial ribosomal protein (rp) gene operon (rps19-rpl22-rps3), produced phylogenetic trees with similar branching patterns to the 16S rRNA gene tree. Sequence comparisons between the StLL 16S rRNA spacer region confirmed previous reports of rrn interoperon sequence heterogeneity for StLL, where the spacer region of rrnB encodes a complete tRNA-Isoleucine gene and the rrnA spacer region does not. Together these results suggest that the Australian phytoplasma, StLL, is unique according to the International Organization for Mycoplasmology (IRPCM) recommendations. The novel taxon ‘Ca. Phytoplasma stylosanthis’ is proposed, with the most recent strain from a potato crop in Victoria, Australia, serving as the reference strain (deposited in the Victorian Plant Pathology Herbarium as VPRI 43683).

scholarly journals Improved Multiplex PCR Using Conserved and Species-Specific 16S rRNA Gene Primers for Simultaneous Detection ofActinobacillus actinomycetemcomitans, Bacteroides forsythus, and Porphyromonas gingivalis

1999 ◽  
Vol 37 (11) ◽  
pp. 3504-3508 ◽  
Author(s):  
Simon Dangtuan Tran ◽  
Joel D. Rudney
Keyword(s):  
16S Rrna ◽  
Multiplex Pcr ◽  
Porphyromonas Gingivalis ◽  
Healthy Subjects ◽  
Simultaneous Detection ◽  
Oral Bacteria ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Subgingival Plaque ◽  
Periodontal Pathogens

Among putative periodontal pathogens, Actinobacillus actinomycetemcomitans, Bacteroides forsythus, andPorphyromonas gingivalis are most convincingly implicated as etiological agents in periodontitis. Therefore, techniques for detection of those three species would be of value. We previously published a description of a multiplex PCR that detects A. actinomycetemcomitans and P. gingivalis. The present paper presents an improvement on that technique, which now allows more sensitive detection of all three periodontal pathogens. Sensitivity was determined by testing serial dilutions of A. actinomycetemcomitans, B. forsythus, and P. gingivalis cells. Primer specificity was tested against (i) all gene sequences from the GenBank-EMBL database, (ii) six A. actinomycetemcomitans, one B. forsythus, and fourP. gingivalis strains, (iii) eight different species of oral bacteria, and (iv) supra- and subgingival plaque samples from 20 healthy subjects and subgingival plaque samples from 10 patients with periodontitis. The multiplex PCR had a detection limit of 10 A. actinomycetemcomitans, 10 P. gingivalis, and 100B. forsythus cells. Specificity was confirmed by the fact that (i) none of our forward primers were homologous to the 16S rRNA genes of other oral species, (ii) amplicons of predicted size were detected for all A. actinomycetemcomitans, B. forsythus, and P. gingivalis strains tested, and (iii) no amplicons were detected for the eight other bacterial species.A. actinomycetemcomitans, B. forsythus, andP. gingivalis were detected in 6 of 20, 1 of 20, and 11 of 20 of supragingival plaque samples, respectively, and 4 of 20, 7 of 20, and 13 of 20 of subgingival plaque samples, respectively, from periodontally healthy subjects. Among patients with periodontitis, the organisms were detected in 7 of 10, 10 of 10, and 7 of 10 samples, respectively. The simultaneous detection of three periodontal pathogens is an advantage of this technique over conventional PCR assays.

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