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International Endodontic Journal Jul 2024To evaluate the root canal microbiome composition and bacterial functional capability in cases of primary and secondary apical periodontitis utilizing whole-metagenome...
AIM
To evaluate the root canal microbiome composition and bacterial functional capability in cases of primary and secondary apical periodontitis utilizing whole-metagenome shotgun sequencing.
METHODOLOGY
Twenty-two samples from patients with primary root canal infections, and 18 samples obtained from previously treated teeth currently diagnosed with apical periodontitis were analysed with whole-metagenome shotgun sequencing at a depth of 20 M reads. Taxonomic and functional gene annotations were made using MetaPhlAn3 and HUMAnN3 software. The Shannon and Chao1 indices were utilized to measure alpha diversity. Differences in community composition were evaluated utilizing analysis of similarity (ANOSIM) using Bray-Curtis dissimilarities. The Wilcoxon rank sum test was used to compare differences in taxa and functional genes.
RESULTS
Microbial community variations within a community were significantly lower in secondary relative to primary infections (alpha diversity p = .001). Community composition was significantly different in primary versus secondary infection (R = .11, p = .005). The predominant taxa observed among samples (>2.5%) were Pseudopropionibacterium propionicum, Prevotella oris, Eubacterium infirmum, Tannerella forsythia, Atopobium rimae, Peptostreptococcus stomatis, Bacteroidetes bacterium oral taxon 272, Parvimonas micra, Olsenella profusa, Streptococcus anginosus, Lactobacillus rhamnosus, Porphyromonas endodontalis, Pseudoramibacter alactolyticus, Fusobacterium nucleatum, Eubacterium brachy and Solobacterium moorei. The Wilcoxon rank test revealed no significant differences in relative abundances of functional genes in both groups. Genes with greater relative abundances (top 25) were associated with genetic, signalling and cellular processes including the iron and peptide/nickel transport system. Numerous genes encoding toxins were identified: exfoliative toxin, haemolysins, thiol-activated cytolysin, phospholipase C, cAMP factor, sialidase, and hyaluronic glucosaminidase.
CONCLUSIONS
Despite taxonomic differences between primary and secondary apical periodontitis, the functional capability of the microbiomes was similar.
Topics: Humans; Microbiota; Dental Pulp Cavity; Periapical Periodontitis; Metagenome; Adult; Female; Male; Middle Aged; Bacteria
PubMed: 36861850
DOI: 10.1111/iej.13911 -
BMC Oral Health Jan 2023Biofilm-free implant surface is ultimate prerequisite for successful soft and bone tissue integration. Objective of the study was to estimate the effects of argon plasma...
PURPOSE
Biofilm-free implant surface is ultimate prerequisite for successful soft and bone tissue integration. Objective of the study was to estimate the effects of argon plasma healing abutment pre-treatment (PT) on peri-implant soft-tissue phenotype (PiSP), inflammation, plaque accumulation and the microbiome (PiM) between non-treated (NPT) and treated (PT) abutments following 3-months healing period. The hypothesis was that cell-conductive and antimicrobial properties of PT would yield optimal conditions for soft tissue integration.
MATERIAL AND METHODS
Two months following second-phase surgery, microbiological and clinical parameters were assessed around thirty-six healing abutments with two types of microtopography, smooth surface (MACHINED) and ultrathin threaded microsurface (ROUGH). A two level randomization schema was used to achieve equal distribution and abutments were randomly divided into rough and machined groups, and then divided into PT and NPT groups. PiM was assessed using next-generation DNA sequencing.
RESULTS
PiM bacterial composition was highly diverse already two months post-implantation, consisting of key-stone pathogens, early and late colonizers, while the mycobiome was less diverse. PT was associated with lower plaque accumulation and inflammation without significant impact on PiSP, while in NPT clinical parameters were increased and associated with periopathogens. NPT mostly harbored late colonizers, while PT exerted higher abundance of early colonizers suggesting less advanced plaque formation. Interaction analysis in PT demonstrated S. mitis co-occurrence with pro-healthy Rothia dentocariosa and co-exclusion with Parvimonas micra, Porphyromonas endodontalis and Prevotella oris. PiSP parameters were generally similar between the groups, but significant association between PiM and keratinized mucosa width was observed in both groups, with remarkably more expressed diversity in NPT compared to PT. PT resulted in significantly lower BOP and PI around rough and machined abutments, respectively, without specific effect on PiM and PiSP.
CONCLUSIONS
PT contributed to significantly the less advanced biofilm accumulation and inflammation without specific effects on PiSP.
Topics: Humans; Argon; Dental Implantation, Endosseous; Dental Implants; Dental Plaque; Dental Prosthesis Design; Inflammation; Microbiota; Plasma Gases; Titanium
PubMed: 36650477
DOI: 10.1186/s12903-023-02729-1 -
International Journal of Molecular... Sep 2022A common symptom in Alzheimer's disease (AD) is cognitive decline, of which the potential pathogenesis remains unclear. In order to understand the mechanism of gut...
A common symptom in Alzheimer's disease (AD) is cognitive decline, of which the potential pathogenesis remains unclear. In order to understand the mechanism of gut microbiota in AD, it is necessary to clarify the relationship between gut microbiota and metabolites. Behavioral tests, pathological examination, metagenomics, and metabolomics were applied to analyze the difference of gut microbiota and metabolome between APP/PS1 (PAP) mice with cognitive decline and age-matched controls, and their possible correlations. Our results showed that PAP mice and health mice had different structures of the bacterial communities in the gut. The abundances and diversities of the bacterial communities in health mice were higher than in PAP mice by metagenomics analysis. The abundances of , , and were significantly increased in PAP mice, while the abundances of , , and were greatly reduced. Furthermore, PAP mice possessed peculiar metabolic phenotypes in stool, serum, and hippocampus relative to WT mice, as is demonstrated by alterations in neurotransmitters metabolism, lipid metabolism, aromatic amino acids metabolism, energy metabolism, vitamin digestion and absorption, and bile metabolism. Microbiota-host metabolic correlation analysis suggests that abnormal metabolism in stool, serum, and hippocampus of PAP mice may be modulated by the gut microbiota, especially , , and . Therefore, abnormal metabolism activity is associated with gut microbiota in Alzheimer's disease mice. Our results imply that modifying host metabolism through targeting gut microbiota may be a novel and viable strategy for the prevention and treatment of AD in the future.
Topics: Alzheimer Disease; Amino Acids, Aromatic; Animals; Bacteria; Gastrointestinal Microbiome; Metabolome; Mice; Neurotransmitter Agents; Vitamins
PubMed: 36232865
DOI: 10.3390/ijms231911560 -
Frontiers in Cellular and Infection... 2022Spontaneous bacterial peritonitis (SBP) is a severe infection in cirrhotic patients that requires early diagnosis to improve the long-term outcome. Alterations in the...
BACKGROUND
Spontaneous bacterial peritonitis (SBP) is a severe infection in cirrhotic patients that requires early diagnosis to improve the long-term outcome. Alterations in the gut microbiota have been shown to correlate with the development and progression of liver cirrhosis. However, the relationship between SBP and gut microbiota remains unknown.
METHODS
In this study, we applied 16S rRNA pyrosequencing of feces to ascertain possible links between the gut microbiota and SBP. We recruited 30 SBP patients, 30 decompensated cirrhotic patients without SBP (NSBP) and 30 healthy controls. Metagenomic functional prediction of bacterial taxa was achieved using PICRUSt.
RESULTS
The composition of the gut microbiota in the SBP patients differed remarkably from that in the NSBP patients and healthy individuals. The microbial richness was significantly decreased, while the diversity was increased in the SBP patients. Thirty-four bacterial taxa containing 15 species, mainly pathogens such as , and , were dominant in the SBP group, while 42 bacterial taxa containing 16 species, especially beneficial species such as , and , were enriched in the NSBP group. Notably, we found that 18 gene functions of gut microbiota were different between SBP patients and NSBP patients, which were associated with energy metabolism and functional substance metabolism. Five optimal microbial markers were determined using a random forest model, and the combination of , , , and achieved an area under the curve (AUC) value of 0.8383 to distinguish SBP from decompensated cirrhosis.
CONCLUSIONS
We described the obvious dysbiosis of gut microbiota in SBP patients and demonstrated the potential of microbial markers as noninvasive diagnostic tools for SBP at an early stage.
Topics: Bacteria; Dysbiosis; Feces; Gastrointestinal Microbiome; Humans; Limosilactobacillus reuteri; Liver Cirrhosis; Peritonitis; RNA, Ribosomal, 16S
PubMed: 36147601
DOI: 10.3389/fcimb.2022.999418 -
Anaerobe Dec 2022Prevotella are gram negative, obligate anaerobes and includes pigmented and non-pigmented species. They are typically regarded as commensals, especially of the...
Prevotella are gram negative, obligate anaerobes and includes pigmented and non-pigmented species. They are typically regarded as commensals, especially of the gastrointestinal tract and oral cavity, although opportunistic endogenous infections are known to be caused by a small number of strains. We report a case of a 51-year-old man with right-sided chest pain. Chest X-ray showed mild haziness in the right lung and he was diagnosed with right sided pleural effusion. Prevotella oris was isolated after pleural pus culture.
Topics: Male; Humans; Middle Aged; Pleural Effusion; Prevotella
PubMed: 36116686
DOI: 10.1016/j.anaerobe.2022.102644 -
Frontiers in Cellular and Infection... 2022The combination of maxillofacial infections (MI) with descending necrotizing mediastinitis (DNM) is a complex disease characterized by rapid development and high...
The combination of maxillofacial infections (MI) with descending necrotizing mediastinitis (DNM) is a complex disease characterized by rapid development and high mortality. Here, we performed metagenomic next-generation sequencing (mNGS) using samples from 21 patients with MI and eight patients with DNM. In this study, we found that the species richness of the DNM group was higher than that of the MI group, and the species diversity of the DNM group was higher than that of the MI group, with no statistically significant differences between groups (P > 0.05). LefSE analysis revealed that the main species differing between groups were , , , and ( and ). In addition, the PLS-DA analysis revealed that the dominant groups in the DNM group at the species level were , , , , , and . Next, we correlated the clinical characteristics of the patients with the relative abundance of the pathogens identified in the LefSe and PLS-DA analyses. The relative abundance of was positively correlated with C-reactive protein (CRP) and calcitoninogen (PCT) but negatively correlated with the percentage of lymphocytes (Lymph%) (P < 0.05). On the other hand, was positively correlated with the percentage of neutrophils (Neut%) and glycated hemoglobin (GLU) (P < 0.05), and was positively correlated with CRP (P < 0.05).
Topics: Eubacterium; Humans; Mediastinitis; Streptococcus
PubMed: 35755831
DOI: 10.3389/fcimb.2022.873161 -
Anaerobe Aug 2022Prevotella species are Gram-negative anaerobic bacilli mainly involved in oral cavity infections. We report a rare case of bacteremia due to P. oris of probable hepatic...
Prevotella species are Gram-negative anaerobic bacilli mainly involved in oral cavity infections. We report a rare case of bacteremia due to P. oris of probable hepatic origin. A 70-year-old man with a history of diabetes mellitus was admitted for general malaise, fever and dyspnea. The patient was admitted to the ICU due to septic shock. Two sets of blood cultures yielded a pure culture of an anaerobic microorganism identified as P. oris by MALDI-TOF MS. The same microorganism was isolated from a hepatic abscess drainage. Only resistance to penicillin was documented. Treatment with piperacillin-tazobactam and levofloxacin was administered, and the patient was discharged following his recovery.
Topics: Aged; Bacteremia; Humans; Male; Prevotella; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 35598874
DOI: 10.1016/j.anaerobe.2022.102586 -
European Journal of Ophthalmology Nov 2022To study the metagenomics of the microbes isolated from the canaliculus of patients with infective canaliculitis.
PURPOSE
To study the metagenomics of the microbes isolated from the canaliculus of patients with infective canaliculitis.
METHODS
A prospective study was performed on five consecutive canalicular samples obtained for the metagenomic analysis from the patients with infective canaliculitis who underwent non-incisional canalicular curettage at a tertiary care Dacryology service. The canalicular concretions were collected intraoperatively soon after a canalicular curettage and immediately transported on ice to the laboratory. Following DNA extraction and library preparation, a whole shotgun metagenome sequencing was performed on the Illumina™ platform. The downstream processing and bioinformatics of the samples were performed using multiple software packaged in SqueezeMeta™ pipeline or MG-RAST™ pipeline.
RESULTS
The taxonomic hit distribution across the samples showed that bacteria were the most common isolates (mean-80.5%), followed by viruses (mean-0.74%), and archaea (0.01%). The five major phyla identified across the samples of infective canaliculitis were, Fusobacteria, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes. The prevalent organisms include and amongst few others. was noted in all the samples, though it was not the most abundant. The microbial gene mapping and protein prediction demonstrated proteins with known functions to range from 69.91% to 87.09% across the samples. The functional subsystem profiling demonstrated genes associated with carbohydrate, amino acid, and co-enzyme transport and metabolism, cell wall or cell membrane biogenesis, energy production and conversion, transcription, translation, and cellular communications.
CONCLUSION
This is the first whole metagenome sequencing of infective canaliculitis. Infected canaliculi harbor diverse microbial communities, including bacteria, viruses, and archaea. Functional analysis has provided newer insights into the ecosystem dynamics and strategies of microbial communities.
Topics: Amino Acids; Bacteria; Canaliculitis; Carbohydrates; DNA; Ecosystem; Humans; Ice; Prospective Studies
PubMed: 35354326
DOI: 10.1177/11206721221091646 -
The American Journal of Case Reports Nov 2021BACKGROUND Bacterial pericarditis can present a diagnostic challenge due to the difficulty of obtaining tissue for bacterial identification. This report is of a...
BACKGROUND Bacterial pericarditis can present a diagnostic challenge due to the difficulty of obtaining tissue for bacterial identification. This report is of a 34-year-old man who presented with fever and cough. Diagnosis was initially delayed without a tissue sample, but the patient was later found to have polymicrobial bacterial pericarditis. CASE REPORT A 34-year-old man from the Democratic Republic of Congo presented to the emergency room with cough, fever, and night sweats. He was admitted and found to have pericardial thickening and fluid collection with calcifications. A tissue sample was not obtained for diagnosis, and he was discharged on RIPE (rifampin, isoniazid, pyrazinamide, and ethambutol) and steroids for presumed tuberculosis pericarditis. He worsened clinically and was readmitted to the hospital with evolving pericardial effusion with air present, in addition to new pleural effusion and parenchymal consolidation. He subsequently underwent thoracotomy and pericardial biopsy. Tissue cultures and sequence-based bacterial analysis eventually revealed the presence of Prevotella oris and Fusobacterium nucleatum. He improved dramatically with appropriate antibiotic therapy. CONCLUSIONS This report demonstrates the importance of undergoing further diagnostic work-up for bacterial pericarditis, especially in resource-rich settings. Although tuberculosis pericarditis should remain high on the differential, it is imperative not to anchor on that diagnosis. Instead, when feasible and safe, tissue biopsy should be obtained and sent for organism identification. AFB smears and cultures, Xpert MTB/RIF, and sequence-based bacterial analysis have all been used for identification. Delay in diagnosis can lead to progression of disease and unnecessary incorrect therapies.
Topics: Adult; Humans; Male; Pericardial Effusion; Pericarditis; Pericarditis, Tuberculous; Prevotella
PubMed: 34782592
DOI: 10.12659/AJCR.933684 -
American Journal of Otolaryngology 2022The aim of this study was to determine the adequacy and safety of needle aspiration (NA) as an alternative to open surgical drainage for oral-maxillofacial abscesses....
The aim of this study was to determine the adequacy and safety of needle aspiration (NA) as an alternative to open surgical drainage for oral-maxillofacial abscesses. Fifteen consecutive patients who were diagnosed with oral-maxillofacial abscesses via contrast-enhanced CT from January 2020 to December 2020 were included. All patients were on antibiotics and treated with NA under local anaesthesia using a 20 mL syringe. Data collection included patient characteristics, signs and symptoms, physical examinations, laboratory tests, imaging findings, and outcomes. Next-generation sequencing (NGS) was used to identify the infectious microorganisms from the abscess samples. The study included 15 patients with oral-maxillofacial abscesses. None of our 15 patients required surgical incision and drainage, although repeat aspiration was required. However, after the first NA, the pain was reportedly extremely relieved for all patients. The average duration of antibiotic treatment was 9.20 ± 5.15 days (range 4-23 days). The abscess-affected spaces mainly included the masseter space and submandibular space. Odontogenic infection was the most common aetiology in 15 patients (10/15). The average volume of the abscesses on CT was 5866.26 ± 3627.18 mm. The main pathogens identified in this study were Prevotella oris (5/15), Peptostreptococcus stomatis (4/15) and Porphyromonas endodontalis (2/15). According to the results of our study, the data support the use of NA as an effective, minimally invasive treatment modality for oral-maxillofacial abscesses. Surgeons should familiarise themselves with this technique, as it can easily be performed in the clinic using local anaesthesia, culture samples may be obtained, and airway obstruction and pain may be relieved.
Topics: Abscess; Adult; Aged; Anti-Bacterial Agents; Female; Humans; Male; Middle Aged; Mouth Diseases; Paracentesis; Retrospective Studies; Treatment Outcome; Young Adult
PubMed: 34536922
DOI: 10.1016/j.amjoto.2021.103216