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Journal of Endodontics May 2024In this study, we used metatranscriptomics for the first time to investigate microbial composition, functional signatures, and antimicrobial resistance gene expression...
INTRODUCTION
In this study, we used metatranscriptomics for the first time to investigate microbial composition, functional signatures, and antimicrobial resistance gene expression in endodontic infections.
METHODS
Root canal samples were collected from ten teeth, including five primary and five persistent/secondary endodontic infections. RNA from endodontic samples was extracted, and RNA sequencing was performed on a NovaSeq6000 system (Illumina). Taxonomic analysis was performed using the Kraken2 bacterial database. Then, sequences with a taxonomic classification were annotated against the Universal Protein Knowledgebase for functional annotation and the Comprehensive Antibiotic Resistance Database for AR-like gene identification.
RESULTS
Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria represented the dominant phyla, whereas Fusobacteria, Spirochetes, and Synergistetes were among the nondominant phyla. The top ten species were mainly represented by obligate (or quasiobligate) anaerobes, including Gram-negative (eg, Capnocytophaga sp. oral taxon 323, Fusobacterium nucleatum, Prevotella intermedia, Prevotella oris, Tannerella forsythia, and Tannerella sp. oral taxon HOT-286) and Gram-positive species (eg, Olsenella uli and Parvimonas micra). Transcripts encoding moonlighting proteins (eg, glycolytic proteins, translational elongation factors, chaperonin, and heat shock proteins) were highly expressed, potentially affecting bacterial adhesion, biofilm formation, host defense evasion, and inflammation induction. Endodontic bacteria expressed genes conferring resistance to antibiotic classes commonly used in dentistry, with a high prevalence and expression of tetracycline and lincosamide resistance genes. Antibiotic efflux and antibiotic target alteration/protection were the main resistance mechanisms.
CONCLUSIONS
Metatranscriptomics revealed the activity of potential endodontic pathogens, which expressed putative virulence factors and a wide diversity of genes potentially involved in AR.
PubMed: 38719087
DOI: 10.1016/j.joen.2024.03.015 -
International Endodontic Journal Apr 2024Microorganisms colonizing the apical root canal system are conceivably the ones directly involved with the causation and maintenance of apical periodontitis. (Review)
Review
BACKGROUND
Microorganisms colonizing the apical root canal system are conceivably the ones directly involved with the causation and maintenance of apical periodontitis.
OBJECTIVES
This article systematically reviews the reports on the microbiome occurring exclusively at the apical root canal of teeth with primary and posttreatment apical periodontitis.
METHODS
The electronic databases PubMed, Embase, Web of Science, Science Direct, and Proquest were searched up to August 2023. Clinical studies using culture and molecular microbiology methods to identify the microbial taxa present exclusively in the apical root canal segment of infected teeth with apical periodontitis were included. Studies were critically assessed using the Joanna Briggs Institute Critical Prevalence Assessment Checklist.
RESULTS
From 2277 articles initially detected, 52 were selected for full reading and 21 were eventually included in this review. Of these, molecular methods were used in 19 and culture in 2 studies. Ten studies evaluated primary infections, 8 evaluated posttreatment infections, and 3 included both. Cryopulverization of the apical root specimens was conducted in 11 studies. All studies evaluated the prevalence and diversity of bacteria, and only one also reported on fungi. Overall, the most frequent/abundant bacterial taxa found in the apical canal of primary infections were Pseudoramibacter alactolyticus, Olsenella uli, Fusobacterium species, Streptococcus species, Porphyromonas endodontalis, Prevotella species, Actinomyces species, Parvimonas micra, Treponema denticola, Synergistetes species, and an as-yet uncharacterized taxon. In posttreatment infections, the most prevalent/abundant bacterial taxa included species of Streptococcus, Enterococcus, Fusobacterium, Actinomyces, Pseudoramibacter, Pseudomonas, and Propionibacterium. At the phylum level, Firmicutes was the most represented. The average apical bacterial load ranged from 10 to 10 in primary infections and from 10 to 10 in posttreatment infections.
DISCUSSION
Microbial diversity in the apical part of the root canal system was examined encompassing data from both primary and posttreatment infections. Heterogeneity amongst the studies, especially in sample collection and microbial identification methods, is an important limitation that prevented a meta-analysis.
CONCLUSIONS
There is a pronounced bacterial diversity in the infected apical canal, with a high interindividual variability. Different microbiome compositions at the species/genus level are observed according to the infection type.
REGISTRATION
PROSPERO CRD42021275886.
PubMed: 38634795
DOI: 10.1111/iej.14071 -
Frontiers in Microbiology 2023This study aimed to identify the bacterial composition in the pancreatic fluid of severe and critical acute pancreatitis (SAP and CAP) patients.
OBJECTIVES
This study aimed to identify the bacterial composition in the pancreatic fluid of severe and critical acute pancreatitis (SAP and CAP) patients.
METHODS
A total of 78 pancreatic fluid samples were collected from 56 SAP and CAP patients and analyze using aerobic culture and gene next-generation sequencing. The clinical data of the patients were obtained from the electronic medical records.
RESULTS
Among the total 78 samples, gene NGS identified a total of 660 bacterial taxa, belonging to 216 species in 123 genera. The dominant aerobic bacteria included , , and , while the dominant anaerobic bacteria included , , and . As compared to aerobic culturing, 95.96% (95/99) of the aerobic cultured bacteria were detected using the gene NGS.
CONCLUSION
The pancreatic infections in SAP and CAP patients might originate not only from the gut but also from the oral cavity and airways as well as related environments. Dynamic analysis of bacterial profile and abundance showed that some bacteria with low abundance might become the main pathogenic bacteria. There were no significant differences in the bacterial diversity between SAP and CAP.
PubMed: 37389346
DOI: 10.3389/fmicb.2023.1185216 -
Clinical Oral Investigations Mar 2023To compare the root canal microbiome profiles of primary and persistent/secondary infections using high-throughput sequencing with the help of a reliable bioinformatics...
OBJECTIVES
To compare the root canal microbiome profiles of primary and persistent/secondary infections using high-throughput sequencing with the help of a reliable bioinformatics algorithm.
MATERIALS AND METHODS
Root canal samples of 10 teeth in the primary endodontic infection (PEI) group and 10 teeth in the persistent/secondary endodontic infection (SEI) group were included resulting in a total of 20 samples. After DNA extraction from the samples, sequencing was performed on the Illumina MiSeq platform. Pair-end Illumina reads were imported to QIIME 2; amplicon sequence variants (ASVs) generated by DADA2 were mapped to GreenGenes database. Weighted UniFrac distances were calculated and principal coordinates analysis (PCoA) was used to compare beta diversity patterns. The multiple response permutation procedure (MRPP), the analysis of similarities (ANOSIM), and permutational multivariate analysis of variance (adonis) were conducted for testing group differences. Linear discriminant analysis effect size (LEfSe) analysis was utilized to identify differentially abundant taxa between the groups. The linear discriminant analysis (LDA) score threshold was set to 4.0.
RESULTS
Within the Gram-negative facultative anaerobic Gammaproteobacteria class outgroup, two orders (Pasteurellales, Vibrionales) and two families (Pasteurellaceae, Vibrionaceae) were significantly more abundant in the PEI group, whereas Gram-positive bacteria, Actinomycetales order, and Gram-positive anaerobic taxa, one genus (Olsenella) and one species (Olsenella uli), were identified as significantly more abundant in the SEI group.
CONCLUSIONS
A few taxa were differentially abundant within either the PEI or SEI group.
CLINICAL RELEVANCE
Reliable bioinformatic tools are needed to define microbial profiles of endodontic infections. Based on a limited number of samples, no distinct variation was determined between the bacterial diversity of initial and recurrent endodontic infections.
Topics: Humans; Dental Pulp Cavity; Coinfection; Root Canal Therapy; Microbiota; High-Throughput Nucleotide Sequencing; RNA, Ribosomal, 16S
PubMed: 36723715
DOI: 10.1007/s00784-023-04882-x -
Journal of Periodontal & Implant Science Feb 2023The objective of this study was to analyze the microbial profile of individuals with peri-implantitis (PI) compared to those of periodontally healthy (PH) subjects and...
PURPOSE
The objective of this study was to analyze the microbial profile of individuals with peri-implantitis (PI) compared to those of periodontally healthy (PH) subjects and periodontitis (PT) subjects using Illumina sequencing.
METHODS
Buccal, supragingival, and subgingival plaque samples were collected from 109 subjects (PH: 30, PT: 49, and PI: 30). The V3-V4 region of 16S rRNA was sequenced and analyzed to profile the plaque microbiota.
RESULTS
Microbial community diversity in the PI group was higher than in the other groups, and the 3 groups showed significantly separated clusters in the buccal samples. The PI group showed different patterns of relative abundance from those in the PH and PT groups depending on the sampling site at both genus and phylum levels. In all samples, some bacterial species presented considerably higher relative abundances in the PI group than in the PH and PT groups, including , , , , , , , , and . Network analysis identified that several well-known periodontal pathogens and newly recognized bacteria were closely correlated with each other.
CONCLUSIONS
The composition of the microbiota was considerably different in PI subjects compared to PH and PT subjects, and these results could shed light on the mechanisms involved in the development of PI.
PubMed: 36468472
DOI: 10.5051/jpis.2202080104 -
Journal of the American Chemical Society Jun 2022Gut microbial decarboxylation of amino acid-derived arylacetates is a chemically challenging enzymatic transformation which generates small molecules that impact host...
Gut microbial decarboxylation of amino acid-derived arylacetates is a chemically challenging enzymatic transformation which generates small molecules that impact host physiology. The glycyl radical enzyme (GRE) indoleacetate decarboxylase from ( IAD) performs the non-oxidative radical decarboxylation of indole-3-acetate (I3A) to yield skatole, a disease-associated metabolite produced in the guts of swine and ruminants. Despite the importance of IAD, our understanding of its mechanism is limited. Here, we characterize the mechanism of IAD, evaluating previously proposed hypotheses of: (1) a Kolbe-type decarboxylation reaction involving an initial 1-e oxidation of the carboxylate of I3A or (2) a hydrogen atom abstraction from the α-carbon of I3A to generate an initial carbon-centered radical. Site-directed mutagenesis, kinetic isotope effect experiments, analysis of reactions performed in DO, and computational modeling are consistent with a mechanism involving initial hydrogen atom transfer. This finding expands the types of radical mechanisms employed by GRE decarboxylases and non-oxidative decarboxylases, more broadly. Elucidating the mechanism of IAD decarboxylation enhances our understanding of radical enzymes and may inform downstream efforts to modulate this disease-associated metabolism.
Topics: Animals; Carbon; Carboxy-Lyases; Hydrogen; Kinetics; Skatole; Swine
PubMed: 35704859
DOI: 10.1021/jacs.1c13580 -
Annals of Clinical Microbiology and... Mar 2022Olsenella uli is anaerobic or microaerophilic bacteria, commonly found in oral cavity or gastrointestinal tract, which has not been reported to be associated with lower...
BACKGROUND
Olsenella uli is anaerobic or microaerophilic bacteria, commonly found in oral cavity or gastrointestinal tract, which has not been reported to be associated with lower respiratory tract infection. Herein, we report the first case of Olsenella uli infection in the lung.
CASE PRESENTATION
A 70-year-old male farmer with no history of other respiratory tract diseases developed a cough with bloody sputum three times a day without obvious causes or other concomitant symptoms. After a period of treatment with empirical antibiotic, his condition did not improve. The computed tomography (CT) and lung biopsy results indicated bilateral pneumonia, and Olsenella uli was identified by micromorphology, sequence analysis and mass spectrometry analysis recovered from sputum. Ceftazidime, a third generation cephalosporin was used for the treatment, and the patient recovered after 10 days.
CONCLUSIONS
Our report suggests a causative role of gingival bacteria in the pathogenesis of pneumonia, thus early diagnosis and prompt antibiotic therapy may play a role in the treatment of Olsenella uli induced pneumonia.
Topics: Actinobacteria; Aged; Humans; Lung; Male; Pneumonia, Bacterial; RNA, Ribosomal, 16S
PubMed: 35232448
DOI: 10.1186/s12941-022-00499-2 -
International Journal of Systematic and... Dec 2021A novel Gram-stain-positive, strictly anaerobic, elliptical, non-motile and non-flagellated bacterium, designed LZLJ-2, was isolated from the mud in a fermentation...
A novel Gram-stain-positive, strictly anaerobic, elliptical, non-motile and non-flagellated bacterium, designed LZLJ-2, was isolated from the mud in a fermentation cellar used for the production of Chinese Luzhou-flavour Baijiu. Growth occurred at 28-45 °C (optimum, 37 °C), at pH 6.0-7.0 (optimum, pH 6.0) and with concentrations of NaCl up to 2 % (w/v; optimum, 0 %). On the basis of 16S rRNA gene sequence similarity, strain LZLJ-2 belonged to the genus and was most closely related to Marseille-P3256 (similarity 96.9 %), ClaCZ62 (similarity 96.6 %) and Marseille-P2912 (similarity 96.4 %). In addition, strain LZLJ-2 had high similarity to the genus , including DSM 13989 (similarity 94.9 %), DSM 22620 (similarity 94.9 %), ATCC 49627 (similarity 94.22 %), DSM 28304 (similarity 93.9 %) and KCTC 15699 (similarity 93.25 %). Comparative genome analysis showed that orthoANI values between strain LZLJ-2 and Marseille-P3256, ClaCZ62, Marseille-P2912, DSM 13989, DSM 22620, ATCC 49627, DSM 28304 and KCTC 15699 were 78.68, 78.99, 78.29, 73.40, 74.00, 74.30, 75.08 and 77.23 %, and the genome-to-genome distance values were respectively 22.3, 22.5, 22.4, 19.6, 20.5, 19.7, 20.5 and 21.5 %. The genomic DNA G+C content of strain LZLJ-2 was 65.21 mol%. The predominant cellular fatty acids (>10 %) of strain LZLJ-2 were C 9 (33.7 %), C (22.0 %) and C 9 DMA (13.5 %). d-Glucose, sucrose, mannose, maltose, lactose (weak), salicin, glycerol (weak), cellobiose and trehalose (weak) could be used by strain LZLJ-2 as sole carbon sources. Enzyme activity results showed positive reactions with valine arylamidase, leucine arylamidase, crystine arylamidase, acid phosphatase, alkaline phosphatase, esterase (C4) (weakly positive), naphthol-AS-BI-phosphohydrolase, -glucosidase and -glucosidase. The major end products of glucose fermentation were lactic acid and acetic acid. It produced skatole from indole acetic acid, and produced -cresol from modified peptone-yeast extract medium with glucose. Based on the 16S rRNA gene trees as well as the genome core gene tree, it is suggested that are transferred to genus as comb. nov. Based on phenotypic, genotypic and phylogenetic data, strain LZLJ-2 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is LZLJ-2 (=KCTC 25162=JCM 34224).
Topics: Actinobacteria; Alcoholic Beverages; Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Fermentation; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology
PubMed: 34914571
DOI: 10.1099/ijsem.0.005192 -
International Endodontic Journal Jan 2022To determine the microorganism in root canal systems of root filled teeth with periapical disease and their relationship with clinical symptoms using next-generation...
AIM
To determine the microorganism in root canal systems of root filled teeth with periapical disease and their relationship with clinical symptoms using next-generation sequencing.
METHODOLOGY
The roots of 10 extracted teeth were collected from 10 patients who presented with post-treatment apical periodontitis (PTAP; six with symptoms and four without symptoms). Each root was divided horizontally into two parts (apical and coronal segments) and cryo-pulverized. Microbial communities were detected using 16S rDNA hypervariable V3-V4 region. The diversity, principal coordinate analysis and linear discriminant analysis effect size were performed in the symptomatic and asymptomatic groups (apical and coronal parts respectively). A Mann-Whitney test and an analysis of similarities were applied for intergroup analysis, at a significance level of 5%.
RESULTS
A total of 23 phyla, 257 genera and 425 species were detected. Firmicutes was the most abundant phylum in all samples. Three phyla (Fusobacteria, Synergistetes and unidentified_Bacteria) and seven genera (Fusobacterium, Porphyromonas, Phocaeicola, Olsenella, Campylobacter, Tannerella and Fretibacterium) were significantly more abundant in the symptomatic patients (p < .05), whereas asymptomatic patients had more Sphingomonas. The species more significantly abundant in the symptomatic samples were Porphyromonas gingivalis, Phocaeicola abscessus, Campylobacter showae, Tannerella forsythia and Olsenella uli (p < .05).
CONCLUSIONS
A greater microbial diversity was observed in root filled teeth with PTAP compared to earlier reports. Several genera and species in root canal systems might be associated with clinical symptoms of PTAP.
Topics: Dental Pulp Cavity; High-Throughput Nucleotide Sequencing; Humans; Microbiota; Periapical Periodontitis; RNA, Ribosomal, 16S; Root Canal Therapy
PubMed: 34592001
DOI: 10.1111/iej.13640 -
Journal of Endodontics Aug 2020Because active bacteria present a higher abundance of ribosomal RNA (rRNA) than DNA (rRNA gene), the rRNA/DNA ratio of next-generation sequencing (NGS) data was measured...
INTRODUCTION
Because active bacteria present a higher abundance of ribosomal RNA (rRNA) than DNA (rRNA gene), the rRNA/DNA ratio of next-generation sequencing (NGS) data was measured to search for active bacteria in endodontic infections.
METHODS
Paired complementary DNA and DNA samples from 5 root canals of teeth with apical periodontitis were subjected to polymerase chain reaction with bar-coded primers amplifying the 16S rRNA gene hypervariable regions V4-V5. High-throughput sequencing was performed using MiSeq (Illumina, San Deigo, CA), and data were analyzed using Quantitative Insights Into Microbial Ecology and Human Oral Microbiome Database. Statistical analysis was performed for relative abundance of bacteria in the DNA- and rRNA-based NGS data using the Mann-Whitney test, whereas differences in the diversity and richness indexes were assessed using a nonparametric 2-sample t test (P < .05). For bacterial taxa detected in both approaches, the rRNA/DNA ratios were calculated by dividing the average abundance of individual species in the respective analysis.
RESULTS
Although no significant difference was found in the indexes of bacterial richness and diversity, the relative abundance of bacterial members varied in both analyses. Comparing rRNA with DNA data, there was a significant decrease in the relative abundance of Firmicutes (P < .05). The bacterial taxa Bacteroidales [G-2] bacterium HMT 274, Porphyromonas endodontalis, Tannerella forsythia, Alloprevotella tannerae, Prevotella intermedia, Pseudoramibacter alactolyticus, Olsenella sp. HMT 809, Olsenella sp. HMT 939, Olsenella uli, and Fusobacterium nucleatum subsp. animalis were both dominant (DNA ≥ 1%) and active (rRNA/DNA ≥ 1).
CONCLUSIONS
The integrated DNA- and rRNA-based NGS strategy was particularly important to disclose the activity of as-yet-uncultivated or difficult-to-culture bacteria in endodontic infections.
Topics: Actinobacteria; Bacteria; Bacterial Infections; Clostridiales; DNA, Bacterial; High-Throughput Nucleotide Sequencing; Humans; RNA, Ribosomal, 16S
PubMed: 32497654
DOI: 10.1016/j.joen.2020.05.004