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Journal of Oral Microbiology 2024Tongue coating microbiota has aroused particular interest in profiling oral and digestive system cancers. However, little is known on the relationship between tongue...
BACKGROUND
Tongue coating microbiota has aroused particular interest in profiling oral and digestive system cancers. However, little is known on the relationship between tongue coating microbiome and colorectal cancer (CRC).
METHODS
Metagenomic shotgun sequencing was performed on tongue coating samples collected from 30 patients with CRC, 30 patients with colorectal polyps (CP), and 30 healthy controls (HC). We further validated the potential of the tongue coating microbiota to predict the CRC by a random forest model.
RESULTS
We found a greater species diversity in CRC samples, and the nucleoside and nucleotide biosynthesis pathway was more apparent in the CRC group. Importantly, various species across participants jointly shaped three distinguishable fur types.The tongue coating microbiome profiling data gave an area under the receiver operating characteristic curve (AUC) of 0.915 in discriminating CRC patients from control participants; species such as , and aided differentiation of CRC patients from healthy participants.
CONCLUSION
These results elucidate the use of tongue coating microbiome in CRC patients firstly, and the fur-types observed contribute to a better understanding of the microbial community in human. Furthermore, the tongue coating microbiota-based biomarkers provide a valuable reference for CRC prediction and diagnosis.
PubMed: 38686186
DOI: 10.1080/20002297.2024.2344278 -
Journal of Clinical Periodontology Jan 2024Periodontitis is caused by dysbiosis of oral microbes and is associated with increased cognitive decline in Alzheimer's disease (AD), and recently, a potential...
AIM
Periodontitis is caused by dysbiosis of oral microbes and is associated with increased cognitive decline in Alzheimer's disease (AD), and recently, a potential functional link was proposed between oral microbes and AD. We compared the oral microbiomes of patients with or without AD to evaluate the association between oral microbes and AD in periodontitis.
MATERIALS AND METHODS
Periodontitis patients with AD (n = 15) and cognitively unimpaired periodontitis patients (CU) (n = 14) were recruited for this study. Each patient underwent an oral examination and neuropsychological evaluation. Buccal, supragingival and subgingival plaque samples were collected, and microbiomes were analysed by next-generation sequencing. Alpha diversity, beta diversity, linear discriminant analysis effect size, analysis of variance-like differential expression analysis and network analysis were used to compare group oral microbiomes.
RESULTS
All 29 participants had moderate to severe periodontitis. Group buccal and supragingival samples were indistinguishable, but subgingival samples demonstrated significant alpha and beta diversity differences. Differential analysis showed subgingival samples of the AD group had higher prevalence of Atopobium rimae, Dialister pneumosintes, Olsenella sp. HMT 807, Saccharibacteria (TM7) sp. HMT 348 and several species of Prevotella than the CU group. Furthermore, subgingival microbiome network analysis revealed a distinct, closely connected network in the AD group comprised of various Prevotella spp. and several anaerobic bacteria.
CONCLUSIONS
A unique microbial composition was discovered in the subgingival region in the AD group. Specifically, potential periodontal pathogens were found to be more prevalent in the subgingival plaque samples of the AD group. These bacteria may possess a potential to worsen periodontitis and other systemic diseases. We recommend that AD patients receive regular, careful dental check-ups to ensure proper oral hygiene management.
Topics: Humans; Alzheimer Disease; Periodontitis; Bacteria; Dental Plaque; Microbiota; RNA, Ribosomal, 16S
PubMed: 37853506
DOI: 10.1111/jcpe.13880 -
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 -
International Endodontic Journal Sep 2021To characterize the bacterial community present in the extraradicular biofilm and periradicular lesions associated with persistent apical periodontitis.
AIM
To characterize the bacterial community present in the extraradicular biofilm and periradicular lesions associated with persistent apical periodontitis.
METHODOLOGY
Eighteen adult patients who presented with persistent periradicular lesions after root canal treatment and scheduled for endodontic surgery were selected. During surgery, extraradicular samples of biofilms and periradicular lesions were collected. Ten pairs of periradicular lesions and extraradicular biofilm samples were randomly selected for ribosomal 16S rRNA cloning and sequencing. A Wilcoxon's rank-sum test was used to compare total bacterial counts and the levels of individual genera and species between the two groups (P < 0.05).
RESULTS
Overall, seventy-three phylotypes belonging to six different phyla were identified from 1000 sequenced clones. Mogibacterium timidum, Streptococcus intermedius and Enterococcus faecalis predominated in both extraradicular biofilm and periapical lesions. Propionibacterium propionicus, Abiotrophia adiacens, Peptostreptococcus prevotii, Campylobacter gracilis and Pseudomonas aeruginosa were found in significantly higher levels in the extraradicular biofilm than periapical lesions, whilst Parvimonas micra and Atopobium rimae were more abundant in periapical lesions (P < 0.05).
CONCLUSIONS
The microbial profile of extraradicular biofilms differed from periapical lesions, indicating the presence of diverse bacterial populations in these regions. Several genera and species were significantly associated with the formation of extraradicular biofilms.
Topics: Actinobacteria; Adult; Biofilms; Campylobacter; Carnobacteriaceae; Clostridiales; Dental Pulp Cavity; Firmicutes; Humans; Periapical Periodontitis; RNA, Ribosomal, 16S
PubMed: 33711170
DOI: 10.1111/iej.13512 -
Arthritis & Rheumatology (Hoboken, N.J.) Feb 2021Changes in gut microbiota have been linked to systemic lupus erythematosus (SLE), but knowledge is limited. Our study aimed to provide an in-depth understanding of the...
OBJECTIVE
Changes in gut microbiota have been linked to systemic lupus erythematosus (SLE), but knowledge is limited. Our study aimed to provide an in-depth understanding of the contribution of gut microbiota to the immunopathogenesis of SLE.
METHODS
Fecal metagenomes from 117 patients with untreated SLE and 52 SLE patients posttreatment were aligned with 115 matched healthy controls and analyzed by whole-genome profiling. For comparison, we assessed the fecal metagenome of MRL/lpr mice. The oral microbiota origin of the gut species that existed in SLE patients was documented by single-nucleotide polymorphism-based strain-level analyses. Functional validation assays were performed to demonstrate the molecular mimicry of newly found microbial peptides.
RESULTS
Gut microbiota from individuals with SLE displayed significant differences in microbial composition and function compared to healthy controls. Certain species, including the Clostridium species ATCC BAA-442 as well as Atopobium rimae, Shuttleworthia satelles, Actinomyces massiliensis, Bacteroides fragilis, and Clostridium leptum, were enriched in SLE gut microbiota and reduced after treatment. Enhanced lipopolysaccharide biosynthesis aligned with reduced branched chain amino acid biosynthesis was observed in the gut of SLE patients. The findings in mice were consistent with our findings in human subjects. Interestingly, some species with an oral microbiota origin were enriched in the gut of SLE patients. Functional validation assays demonstrated the proinflammatory capacities of some microbial peptides derived from SLE-enriched species.
CONCLUSION
This study provides detailed information on the microbiota of untreated patients with SLE, including their functional signatures, similarities with murine counterparts, oral origin, and the definition of autoantigen-mimicking peptides. Our data demonstrate that microbiome-altering approaches may offer valuable adjuvant therapies in SLE.
Topics: Actinobacteria; Actinomyces; Adult; Amino Acids, Branched-Chain; Animals; Antirheumatic Agents; Autoantibodies; Autoantigens; Bacteroides fragilis; Case-Control Studies; Clostridiales; Clostridium; Disease Models, Animal; Female; Gastrointestinal Microbiome; Humans; Lipopolysaccharides; Lupus Erythematosus, Systemic; Male; Metagenomics; Mice; Mice, Inbred MRL lpr; Molecular Mimicry; Mouth; Polymorphism, Single Nucleotide; Young Adult
PubMed: 33124780
DOI: 10.1002/art.41511 -
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 -
Frontiers in Microbiology 2019Periodontal abscess is an oral infective disease caused by various kinds of bacteria. We aimed to characterize the microbiota composition of periodontal abscesses by...
Periodontal abscess is an oral infective disease caused by various kinds of bacteria. We aimed to characterize the microbiota composition of periodontal abscesses by metagenomic methods and compare it to that of the corresponding pocket and healthy gingival crevice to investigate the specific bacteria associated with this disease. Samples from abscess pus (AB), periodontal pocket coronally above the abscess (PO), and the gingival crevice of the periodontal healthy tooth were obtained from 20 periodontal abscess patients. Furthermore, healthy gingival crevice samples were obtained from 25 healthy individuals. Bacterial DNA was extracted and 16S rRNA gene fragments were sequenced to characterize the microbiota and determine taxonomic classification. The beta-diversity analysis results showed that the AB and PO groups had similar compositions. , , and other spp. were the predominant bacteria of human periodontal abscesses. The abundances of and were significantly higher in periodontal abscesses than in the periodontal pocket, suggesting their association with periodontal abscess formation. In conclusion, we characterized the microbiota in periodontal abscess and identified some species that are positively associated with this disease. This provides a better understanding of the components of periodontal abscesses, which will help facilitate the development of antibiotic therapy strategies.
PubMed: 31417518
DOI: 10.3389/fmicb.2019.01723 -
Anaerobe Dec 2018Atopobium rimae and Parvimonas micra are both Gram-positive anaerobes involved infrequently in human infections. We report a polymicrobial anaerobic bacteremia caused by...
Atopobium rimae and Parvimonas micra are both Gram-positive anaerobes involved infrequently in human infections. We report a polymicrobial anaerobic bacteremia caused by these microorganisms. A 43-year-old woman receiving coadjuvant chemotherapy due to a retroperitoneal leiomiosarcoma presented with nausea, vomiting, abdominal pain and fever (38 °C). The two blood cultures resulted in isolation of A. rimae and P. micra, being identified at species level by matrix assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF MS) technology with high log scores. The microorganisms were susceptible to penicilllin, amoxicillin-clavulanate, piperacillin-tazobactam, clindamycin, metronidazole, imipenem, and moxifloxacin. Treatment with levofloxacin was started and subsequently it was changed to piperacillin/tazobactam plus metronidazole and completed for 10 days, but the patient died days later due to her underlying disease.
Topics: Actinobacteria; Adult; Anti-Bacterial Agents; Bacteremia; Female; Firmicutes; Humans; Microbial Sensitivity Tests; Neoplasms; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 29425733
DOI: 10.1016/j.anaerobe.2018.02.002 -
Frontiers in Microbiology 2016Alternative treatment methods for pathogens and microbial biofilms are required due to the widespread rise in antibiotic resistance. Antimicrobial photodynamic therapy...
Photoinactivation Using Visible Light Plus Water-Filtered Infrared-A (vis+wIRA) and Chlorine e6 (Ce6) Eradicates Planktonic Periodontal Pathogens and Subgingival Biofilms.
Alternative treatment methods for pathogens and microbial biofilms are required due to the widespread rise in antibiotic resistance. Antimicrobial photodynamic therapy (aPDT) has recently gained attention as a novel method to eradicate pathogens. The aim of this study was to evaluate the antimicrobial effects of a novel aPDT method using visible light (vis) and water infiltrated infrared A (wIRA) in combination with chlorine e6 (Ce6) against different periodontal pathogens in planktonic form and within subgingival oral biofilms. Eight different periodontal pathogens were exposed to aPDT using vis+wIRA and 100 μg/ml Ce6 in planktonic culture. Additionally, pooled subgingival dental biofilm was also treated by aPDT and the number of viable cells determined as colony forming units (CFU). Live/dead staining was used in combination with confocal laser scanning microscopy to visualize and quantify antimicrobial effects within the biofilm samples. Untreated negative controls as well as 0.2% chlorhexidine-treated positive controls were used. All eight tested periodontal pathogens including , , , , , , , and and the aPDT-treated subgingival biofilm were eliminated over the ranges of 3.43-8.34 and 3.91-4.28 log CFU in the log scale, respectively. Thus, aPDT showed bactericidal effects on the representative pathogens as well as on the subgingival biofilm. The live/dead staining also revealed a significant reduction (33.45%) of active cells within the aPDT-treated subgingival biofilm. Taking the favorable tissue healing effects of vis+wIRA into consideration, the significant antimicrobial effects revealed in this study highlight the potential of aPDT using this light source in combination with Ce6 as an adjunctive method to treat periodontitis as well as periimplantitis. The present results encourage also the evaluation of this method for the treatment of caries and apical periodontitis.
PubMed: 27965635
DOI: 10.3389/fmicb.2016.01900 -
Transplant Infectious Disease : An... Aug 2016
Topics: Actinobacteria; Anti-Infective Agents; Bacteremia; Blood Culture; Drug Therapy, Combination; Glomerulonephritis; Heart Transplantation; Humans; Immunosuppression Therapy; Immunosuppressive Agents; Male; Middle Aged; Myocardial Reperfusion Injury; Renal Dialysis
PubMed: 27145541
DOI: 10.1111/tid.12544