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MSystems Nov 2019Globally, dental caries is the most prevalent chronic oral disease and affects roughly half of all children. The aim of this report was to use metagenomic analyses to...
Globally, dental caries is the most prevalent chronic oral disease and affects roughly half of all children. The aim of this report was to use metagenomic analyses to investigate the relationship between the oral microbiome and caries in preschool children. A total of 25 preschoolers, aged 3 to 5 years old with severe early childhood caries (ECC), and 19 age-matched, caries-free children as controls were recruited. Saliva samples were collected from the participants and were subjected to metagenomic analyses, whereby the oral microbial communities were investigated. The metagenomic analyses revealed substantial microbiota differences between the two groups, indicating apparent shifts of the oral microbiome present in the ECC group. At the species level, the ECC-enriched microbes included , , and Interestingly, and exhibited apparent differences at the strain level but not the species level between the ECC and control groups. Functional examination showed that the ECC group displayed extensive alterations in metabolic genes/pathways/modules, including enriched functions in sugar metabolism. Finally, an SVM (support vector machine) classifier comprising seven species was developed and generated a moderately good performance in predicting caries onset (area under the receiver operating characteristic curve [AUC] = 78.33%). Together, these findings indicate that caries is associated with considerable changes in the oral microbiome, some of which can potentially be exploited as therapeutic targets or diagnostic markers. (This study has been registered at ClinicalTrials.gov under registration no. NCT02341352.) Dental caries is a highly prevalent oral disease that can lead to severe dental damage and may greatly compromise the quality of life of the affected individuals. Previous studies, including those based on 16S rRNA gene, have revealed that the oral microbiota plays a prominent role in development of the disease. But the approach of those studies was limited in analyzing several key microbiome traits, including species- or strain-level composition and functional profile. Here, we performed metagenomic analyses for a cohort of preschool children with or without caries. Our results showed that caries was associated with extensive microbiota differences at various taxonomic and functional levels. Some caries-associated species had not been previously reported, some of which may have significant clinical implications. A microbiome gene catalogue from children with caries was constructed for the first time. The results demonstrated that caries is associated with alterations of the oral microbiome, including changes in microbial composition and metabolic functional profile.
PubMed: 31690590
DOI: 10.1128/mSystems.00450-19 -
Nature Communications Aug 2019Phosphonates are rare and unusually bioactive natural products. However, most bacterial phosphonate biosynthetic capacity is dedicated to tailoring cell surfaces with...
Phosphonates are rare and unusually bioactive natural products. However, most bacterial phosphonate biosynthetic capacity is dedicated to tailoring cell surfaces with molecules like 2-aminoethylphosphonate (AEP). Although phosphoenolpyruvate mutase (Ppm)-catalyzed installation of C-P bonds is known, subsequent phosphonyl tailoring (Pnt) pathway steps remain enigmatic. Here we identify nucleotidyltransferases in over two-thirds of phosphonate biosynthetic gene clusters, including direct fusions to ~60% of Ppm enzymes. We characterize two putative phosphonyl tailoring cytidylyltransferases (PntCs) that prefer AEP over phosphocholine (P-Cho) - a similar substrate used by the related enzyme LicC, which is a virulence factor in Streptococcus pneumoniae. PntC structural analyses reveal steric discrimination against phosphocholine. These findings highlight nucleotidyl activation as a predominant chemical logic in phosphonate biosynthesis and set the stage for probing diverse phosphonyl tailoring pathways.
Topics: Actinobacteria; Aminoethylphosphonic Acid; Bacteria; Bacterial Proteins; Biosynthetic Pathways; Cell Wall; Crystallization; Crystallography, X-Ray; Escherichia coli; N-Acylneuraminate Cytidylyltransferase; Nucleotidyltransferases; Organophosphonates; Phospholipids; Phosphorylcholine; Phosphotransferases (Phosphomutases); Polysaccharides; Substrate Specificity
PubMed: 31420548
DOI: 10.1038/s41467-019-11627-6 -
International Journal of Systematic and... Aug 2019A novel actinobacterial strain, designated KGMB04489, was isolated from the faeces of a healthy Korean. Cells of the strain were strictly anaerobic, Gram-stain-positive...
A novel actinobacterial strain, designated KGMB04489, was isolated from the faeces of a healthy Korean. Cells of the strain were strictly anaerobic, Gram-stain-positive and short-rod-shaped. On the basis of 16S rRNA gene sequence similarity, strain KGMB04489 belonged to the genus Olsenella and was most closely related to Olsenella scatoligenes SK9K4 (94.3 %), Olsenella uli ATCC 49627 (93.5 %), Olsenella umbonata lac31 (93.4 %) and Olsenella profusa D315A-29 (93.3 %). The major end product was lactic acid. The DNA G+C content was 65.5 mol%. The major cellular fatty acids of strain KGMB04489 were C18 : 1cis9, C18 : 1cis9 DMA and C16 : 0. Strain KGMB04489 contained meso-diaminopimelic acid as the diamino acid in the peptidoglycan. The polar lipids consisted of an unidentified phospholipid, six unidentified glycolipids and an unidentified lipid. Based on phylogenetic, physiological and chemotaxonomic characteristics, strain KGMB04489 is considered to represent a novel species within the genus Olsenella, for which the name Olsenellafaecalis sp. nov. is proposed. The type strain is KGMB04489 (=KCTC 15699=CCUG 72345).
Topics: Actinobacteria; Bacterial Typing Techniques; Base Composition; Cell Wall; DNA, Bacterial; Diaminopimelic Acid; Fatty Acids; Feces; Glycolipids; Humans; Peptidoglycan; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Republic of Korea; Sequence Analysis, DNA
PubMed: 31135332
DOI: 10.1099/ijsem.0.003469 -
PloS One 2018Recent developments in High-Throughput DNA sequencing (HTS) technologies and ancient DNA (aDNA) research have opened access to the characterization of the microbial...
Recent developments in High-Throughput DNA sequencing (HTS) technologies and ancient DNA (aDNA) research have opened access to the characterization of the microbial communities within past populations. Most studies have, however, relied on the analysis of dental calculus as one particular material type particularly prone to the molecular preservation of ancient microbial biofilms and potential of entire teeth for microbial characterization, both of healthy communities and pathogens in ancient individuals, remains overlooked. In this study, we used shotgun sequencing to characterize the bacterial composition from historical subjects showing macroscopic evidence of oral pathologies. We first carried out a macroscopic analysis aimed at identifying carious or periodontal diseases in subjects belonging to a French rural population of the 18th century AD. We next examined radiographically six subjects showing specific, characteristic dental pathologies and applied HTS shotgun sequencing to characterize the microbial communities present in and on the dental material. The presence of Streptococcus mutans and also Rothia dentocariosa, Actinomyces viscosus, Porphyromonas gingivalis, Tannerella forsythia, Pseudoramibacter alactolyticus, Olsenella uli and Parvimonas micra was confirmed through the presence of typical signatures of post-mortem DNA damage at an average depth-of-coverage ranging from 0.5 to 7X, with a minimum of 35% (from 35 to 93%) of the positions in the genome covered at least once. Each sampled tooth showed a specific bacterial signature associated with carious or periodontal pathologies. This work demonstrates that from a healthy independent tooth, without visible macroscopic pathology, we can identify a signature of specific pathogens and deduce the oral health status of an individual.
Topics: DNA, Ancient; DNA, Bacterial; Dental Caries; Female; France; Health Status; History, 18th Century; Humans; Male; Metagenomics; Microbiota; Oral Health; Paleodontology; Periodontitis; Rural Population
PubMed: 29768437
DOI: 10.1371/journal.pone.0196482 -
International Journal of Systematic and... Apr 2018Strain 2CBEGH3, which is an obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-positive coccobacillus, was isolated from a faecal sample of a...
Strain 2CBEGH3, which is an obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-positive coccobacillus, was isolated from a faecal sample of a healthy Japanese man. The 16S rRNA gene sequence analysis showed that strain 2CBEGH3 represented a member of the family Atopobiaceae and formed a monophyletic cluster with Olsenella uli DSM 7084 (93.6 % sequence similarity), Olsenella umbonata strain lac31 (93.0 %), Olsenella profusa JCM 14553 (92.7 %) and Olsenella scatoligenes strain SK9K4 (92.7 %) as closest neighbours and Atopobium species. The hsp60 gene sequence analysis supported the phylogenetic relationships based on the 16S rRNA gene sequences, with sequence similarity values of 82.1-84.7 % to the four species described above. A unique three-base (one amino acid residue) insertion was found in the alignment regions of the hsp60 gene sequence of strain 2CBEGH3. The major end products from d-glucose were d- and l-lactic acids produced at the ratio of 75 : 25, while four species of the genus Olsenella produced d- and l-lactic acids at ratios of 94-98 : 2-6. The isolate formed characteristic crater-like colonies on Eggerth-Gagnon agar plates. The major cellular fatty acids were C18 : 1ω9c, C18 : 1ω9c dimethyl acetal (DMA) and C16 : 0 DMA. The G+C content of the genomic DNA was 68.4 mol%. On the basis of these data, strain 2CBEGH3 represents a novel species in a novel genus of the family Atopobiaceae, for which the name Parolsenella catena gen. nov., sp. nov. is proposed. The type strain of P. catena is 2CBEGH3 (=JCM 31932=DSM 105194).
Topics: Actinobacteria; Adult; Bacteria, Anaerobic; Bacterial Typing Techniques; DNA, Bacterial; Fatty Acids; Feces; Genes, Bacterial; Humans; Japan; Male; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 29458507
DOI: 10.1099/ijsem.0.002645 -
Journal of Oral Microbiology 2018It is unknown whether bacteria play a role in the collagen matrix degradation that occurs during caries progression. Our aim was to characterize the expression level of...
It is unknown whether bacteria play a role in the collagen matrix degradation that occurs during caries progression. Our aim was to characterize the expression level of genes involved in bacterial collagenolytic proteases in root biofilms with and without caries. we collected samples from active cavitated root caries lesions (RC, n = 30) and from sound root surfaces (SRS, n = 10). Total microbial RNA was isolated and cDNA sequenced on the Illumina Hi-Seq2500. Reads were mapped to 162 oral bacterial reference genomes. Genes encoding putative bacterial collagenolytic proteases were identified. Normalization and differential expression analysis was performed on all metatranscriptomes (FDR<10-3). Genes encoding collagenases were identified in 113 bacterial species the majority were peptidase U32. In RC, Streptococcus mutans and Veillonella parvula expressed the most collagenases. Organisms that overexpressed collagenolytic protease genes in RC (Log2FoldChange>8) but none in SRS were Pseudoramibacter alactolyticus [HMPREF0721_RS02020; HMPREF0721_RS04640], Scardovia inopinata [SCIP_RS02440] and Olsenella uli DSM7084 [OLSU_RS02990]. Our findings suggest that the U32 proteases may be related to carious dentine. The contribution of a small number of species to dentine degradation should be further investigated. These proteases may have potential in future biotechnological and medical applications, serving as targets for the development of therapeutic agents.
PubMed: 34394852
DOI: 10.1080/20002297.2018.1424475 -
PloS One 2018Acute apical abscess is caused by bacteria that leave the infected dental root canal to invade the periodontal tissues. Most species occurring in abscesses are also... (Comparative Study)
Comparative Study
INTRODUCTION
Acute apical abscess is caused by bacteria that leave the infected dental root canal to invade the periodontal tissues. Most species occurring in abscesses are also found in asymptomatic infections; therefore, the possibility exists that not only the presence of certain species but also their specific counts influence the appearance of symptoms. This molecular study compared the frequency and levels of several candidate endodontic pathogens in teeth with acute apical abscesses and asymptomatic apical periodontitis.
METHODS
Samples were taken from the root canals of teeth with asymptomatic apical periodontitis (n = 73) and by aspiration of purulent exudate from acute abscesses (n = 55). DNA was extracted from samples and bacterial identifications were performed by a closed-ended semi-quantitative reverse-capture checkerboard approach targeting 40 bacterial species/phylotypes.
RESULTS
Bacterial DNA was detected in all cases. In abscesses, the most prevalent taxa were Fusobacterium nucleatum (60%), Porphyromonas endodontalis (53%), Parvimonas micra (51%), and Streptococcus species (45%). The most frequently detected taxa in asymptomatic teeth were P. endodontalis (63%), Dialister invisus (58%), Olsenella uli (56%), and F. nucleatum (51%). None of the targeted taxa were significantly associated with abscesses when only mere presence was evaluated (p>0.05). However, semi-quantitative data demonstrated that P. endodontalis, Prevotella baroniae, Treponema denticola and Streptococcus species were significantly more frequent at levels >105 in abscesses than in asymptomatic cases (p<0.05).
CONCLUSION
None of the target species/phylotypes were associated with abscesses in terms of frequency. However, some taxa were significantly found in higher levels in abscesses. Presence of a potentially virulent pathogen in high counts may increase the collective pathogenicity of the bacterial community and give rise to symptoms.
Topics: Abscess; Adolescent; Adult; Aged; Bacteria; Female; Humans; Male; Middle Aged; Periapical Periodontitis; Tooth Apex; Young Adult
PubMed: 29293651
DOI: 10.1371/journal.pone.0190469 -
Anaerobe Apr 2017Strain KHD7, a Gram-stain-positive rod-shaped, non-sporulating, strictly anaerobic bacterium, was isolated from the vaginal swab of a woman with bacterial vaginosis. We...
Strain KHD7, a Gram-stain-positive rod-shaped, non-sporulating, strictly anaerobic bacterium, was isolated from the vaginal swab of a woman with bacterial vaginosis. We studied its phenotypic characteristics and sequenced its complete genome. The major fatty acids were C16:0 (44%), C18:2n6 (22%), and C18:1n9 (14%). The 1,806,744 bp long genome exhibited 49.24% G+C content; 1549 protein-coding and 51 RNA genes. Strain KHD7 exhibited a 93.5% 16S rRNA similarity with Olsenella uli, the phylogenetically closest species in the family Coriobacteriaceae. Therefore, strain KHD7 is sufficiently distinct to represent a new genus, for which we propose the name Olegusella massiliensis gen. nov., sp. nov. The type strain is KHD7.
Topics: Actinobacteria; Adult; Anaerobiosis; Bacterial Typing Techniques; Base Composition; Cluster Analysis; Cytosol; DNA, Bacterial; DNA, Ribosomal; Fatty Acids; Female; Genome, Bacterial; Humans; Microscopy; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Vagina; Vaginosis, Bacterial
PubMed: 28223255
DOI: 10.1016/j.anaerobe.2017.02.012 -
The Journal of Contemporary Dental... Jan 2017Apical periodontitis usually results from bacterial accumulation and contamination occurring in the root-canal system, and extending beyond the apical foramen to involve...
INTRODUCTION
Apical periodontitis usually results from bacterial accumulation and contamination occurring in the root-canal system, and extending beyond the apical foramen to involve the periapical tissues. Literature has a paucity of the studies that stress on the division and analysis of the pulp canal segments. The reason for this disparity might be the technique used for collecting the samples from the pulp canals. Hence, we carried out the present study to evaluate the microbial flora in the apical part of the roots with necrotic pulp canals.
MATERIALS AND METHODS
The present study included the assessment of 40 freshly extracted teeth that had necrotized pulpal tissue along with the presence of periapical periodontal lesions. Removal of the soft tissue lesions attached to the root portion of the teeth along with apical periodontal lesions was done with the help of scalpel blade, after rinsing them with a sterile solution of saline. Thorough cleaning of the root surfaces was done with hydrogen peroxide followed by rapid disinfection with the help of sodium hypochlorite at varying concentrations. Sectioning of the root portion of all the specimens with the help of a disk was done perpendicular to the long axis of the teeth at a distance of roughly 5 to 6 mm from the teeth's apicalmost point. Cryotubes were used for transferring the specimens of apical portions containing 1 mL of buffer and were subjected to immediate frozen processing at a temperature of -20°C. A 10 K-type file was used for the initial collection of the samples followed by subsequent incubation of the files and paper pints in the incubation cabinet. Subsequent deoxyribonucleic acid (DNA) extraction from the samples was done following the procedure described by Siqueira et al. Paster et al's modification of the reverse-capture checkerboard assay was used in the present study. Semiquantitative data were used for overcoming the difficulties arising due to obtaining the counts of the polymerase chain reaction (PCR)-based analysis of specimens.
RESULTS
A positive result for the 16S ribosomal ribonucleic acid (rRNA) gene primer was observed only in two examined specimens of all the samples of the apical portion of the root canals in the present study. Negative result was shown by all the control group specimens, which were sterile samples. Presence of bacteria was confirmed by PCR in 38 out of 40 examined specimens. Amount of bacterial taxa, out of these 24 samples, ranged up to 6. Pseudoramibacter alactolyticus, Porphyromonas endodontalis, Dialister oral species, Bacteroidetes species, Streptococcus species, Olsenella uli, Synergistes species, Fusobacterium nucleatum, Parvimonas micra, Treponema denticola, and Filifactor alocis were the specific species detected. Bacteroidetes species was the only species that were detected at levels at or above 10. Heavy bacterial infections were noticed in more than 45% of the cases at the periradicular part of the root canals.
CONCLUSION
Microbial flora of the apical segment of the root with necrotized pulp tissue comprises a vast variety of pathogenic bacteria.
CLINICAL SIGNIFICANCE
For better prognosis of the treatment of such cases, adequate knowledge of the microbial flora of the root, especially the apical portion is necessary.
Topics: Bacteroidetes; Fusobacterium nucleatum; Humans; Periapical Periodontitis; Polymerase Chain Reaction; Porphyromonas endodontalis; RNA, Ribosomal, 16S; Streptococcus; Tooth Apex; Tooth Root; Treponema denticola
PubMed: 28050984
DOI: 10.5005/jp-journals-10024-1986 -
Journal of the Formosan Medical... Jun 2017Bacteria in the tooth root canal may cause apical periodontitis. This study examined the bacterial species present in the apical root canal of teeth with apical...
BACKGROUND/PURPOSE
Bacteria in the tooth root canal may cause apical periodontitis. This study examined the bacterial species present in the apical root canal of teeth with apical periodontitis. Antibiotic sensitivity tests were performed to evaluate whether these identified bacterial species were susceptible to specific kinds of antibiotics.
METHODS
Selective media plating and biochemical tests were used first to detect the bacterial species in samples taken from the apical portion of root canals of 62 teeth with apical periodontitis. The isolated bacterial species were further confirmed by matrix-assisted laser desorption ionization-time of flight mass spectrometry.
RESULTS
We found concomitant presence of two (32 teeth) or three species (18 teeth) of bacteria in 50 (80.6%) out of 62 tested teeth. However, only 34 bacterial species were identified. Of a total of 118 bacterial isolates (83 anaerobes and 35 aerobes), Prophyromonas endodontalis was detected in 10; Bacteroides, Dialister invisus or Fusobacterium nucleatum in 9; Treponema denticola or Enterococcus faecalis in 8; Peptostreptococcus or Olsenella uli in 6; and Veillonella in 5 teeth. The other 25 bacterial species were detected in fewer than five teeth. Approximately 80-95% of bacterial isolates of anaerobes were sensitive to ampicillin/sulbactam (Unasyn), amoxicillin/clavulanate (Augmentin), cefoxitin, and clindamycin. For E. faecalis, 85-90% of bacterial isolates were sensitive to gentamicin and linezolid.
CONCLUSION
Root canal infections are usually caused by a mixture of two or three species of bacteria. Specific kinds of antibiotic can be selected to control these bacterial infections after antibiotic sensitivity testing.
Topics: Anti-Bacterial Agents; Dental Pulp Cavity; Humans; Periapical Periodontitis
PubMed: 27745799
DOI: 10.1016/j.jfma.2016.08.010