-
Journal of Clinical Medicine Feb 2022Different periodontal treatment methods (quadrant-wise debridement, scaling and root planing (Q-SRP), full-mouth scaling (FMS), full-mouth disinfection (FMD), and FMD...
BACKGROUND
Different periodontal treatment methods (quadrant-wise debridement, scaling and root planing (Q-SRP), full-mouth scaling (FMS), full-mouth disinfection (FMD), and FMD with adjuvant erythritol air-polishing (FMDAP)) were applied in periodontitis patients (stage III/IV). The study objective (substudy of ClinicalTrials.gov Identifier: NCT03509233) was to compare the impact of treatments on subgingival colonization.
METHODS
Forty patients were randomized to the treatment groups. Periodontal parameters and subgingival colonization were evaluated at baseline and 3 and 6 months after treatment.
RESULTS
Positive changes in clinical parameters were recorded in every treatment group during the 3-month follow-up period, but did not always continue. In three groups, specific bacteria decreased after 3 months; however, this was associated with a renewed increase after 6 months (FMS: ; FMD: , ; and FMDAP: uncultured sp.).
CONCLUSIONS
The benefit of all clinical treatments measured after 3 months was associated with a decrease in pathogenic bacteria in the FMS, FMD, and FMDAP groups. However, after 6 months, we observed further improvement or some stagnation in clinical outcomes accompanied by deterioration of the microbiological profile. Investigating the subgingival microbiota might help appraise successful periodontal treatment and implement individualized therapy.
PubMed: 35268280
DOI: 10.3390/jcm11051187 -
Oncogene Feb 2023Appendectomy impacts the homeostasis of gut microbiome in patients. We aimed to study the role of appendectomy in colorectal cancer (CRC) risk through causing gut...
Appendectomy impacts the homeostasis of gut microbiome in patients. We aimed to study the role of appendectomy in colorectal cancer (CRC) risk through causing gut microbial dysbiosis. Population-based longitudinal study (cohort 1, n = 129,155) showed a 73.0% increase in CRC risk among appendectomy cases throughout 20 years follow-up (Adjusted sub-distribution hazard ratio (SHR) 1.73, 95% CI 1.49-2.01, P < 0.001). Shotgun metagenomic sequencing was performed on fecal samples from cohort 2 (n = 314). Gut microbial dysbiosis in appendectomy subjects was observed with significant enrichment of 7 CRC-promoting bacteria (Bacteroides vulgatus, Bacteroides fragilis, Veillonella dispar, Prevotella ruminicola, Prevotella fucsa, Prevotella dentalis, Prevotella denticola) and depletion of 5 beneficial commensals (Blautia sp YL58, Enterococcus hirae, Lachnospiraceae bacterium Choco86, Collinsella aerofaciens, Blautia sp SC05B48). Microbial network analysis showed increased correlation strengths among enriched bacteria and their enriched oncogenic pathways in appendectomy subjects compared to controls. Of which, B. fragilis was the centrality in the network of the enriched bacteria. We further confirmed that appendectomy promoted colorectal tumorigenesis in mice by causing gut microbial dysbiosis and impaired intestinal barrier function. Collectively, this study revealed appendectomy-induced microbial dysbiosis characterized by enriched CRC-promoting bacteria and depleted beneficial commensals, signifying that the gut microbiome may play a crucial role in CRC development induced by appendectomy.
Topics: Animals; Mice; Gastrointestinal Microbiome; Dysbiosis; Appendectomy; Longitudinal Studies; Colorectal Neoplasms
PubMed: 36539569
DOI: 10.1038/s41388-022-02569-3 -
International Journal of Molecular... Jan 2024The activation of inflammasomes is thought to induce the inflammatory process around dental implants. No information is available on the correlation between microbiota...
The activation of inflammasomes is thought to induce the inflammatory process around dental implants. No information is available on the correlation between microbiota and inflammasomes in clinical samples from patients suffering peri-implantitis. For this cross-sectional study, 30 biofilm samples were obtained from 19 patients undergoing surgical treatment for peri-implantitis because of the presence of bleeding on probing, probing depth higher than 6 mm, and radiographic bone loss higher than 3 mm. Then, soft tissue samples from around the implant were also collected. The relative abundance of bacteria and alpha-diversity indexes were calculated after analyzing the 16S rRNA gene using next-generation sequencing. The soft-tissue samples were processed for evaluation of the inflammasomes NLRP3 and AIM2 as well as caspase-1 and IL-1β. The relative abundance (mean (SD)) of specific species indicated that the most abundant species were (10.95 (14.17)%), (10.93 (13.18)%), (5.89 (7.23)%), (3.88 (4.94)%), (2.91 (3.19)%), and (2.84 (4.15)%). Several correlations were found between the species and the immunohistochemical detection of the inflammasomes NLRP3 and AIM2 as well as caspase-1 and IL-1β, both in the epithelium and the lamina propria. A network analysis found an important cluster of variables formed by NLRP3 in the lamina propria and AIM2, caspase-1, and IL-1β in the lamina propria and the epithelium with , , , or . Thus, it could be concluded that inflammasomes NLRP3 and AIM2 and their downstream effectors caspase-1 and interleukin-1β can be significantly associated with specific bacteria.
Topics: Humans; Inflammasomes; NLR Family, Pyrin Domain-Containing 3 Protein; Peri-Implantitis; Cross-Sectional Studies; RNA, Ribosomal, 16S; Microbiota; Caspase 1
PubMed: 38256037
DOI: 10.3390/ijms25020961 -
Frontiers in Microbiology 2016The bacterial phylum , characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly,...
The bacterial phylum , characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of as new phylum from and of as new class from . is nested within the older genus and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, is proposed to be included in . is confirmed as being heterogeneous and dissected, yielding six distinct genera. is a later heterotypic synonym of . Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.
PubMed: 28066339
DOI: 10.3389/fmicb.2016.02003 -
Frontiers in Cellular and Infection... 2021Familial hypercholesterolemia (FH) is an inherited rare disease leading to markedly elevated low-density lipoprotein cholesterol (LDL-C) levels and increased risk for...
Familial hypercholesterolemia (FH) is an inherited rare disease leading to markedly elevated low-density lipoprotein cholesterol (LDL-C) levels and increased risk for cardiovascular event. Gut microbiota has been implicated as a pivotal contributing factor in hyperlipidemia, however, its role in FH remains elusive. We performed whole-exome and metagenomics sequencing on a family with 22 members in which myocardial infarctions occurred at a young age with unclear etiology. We confirmed the missense mutation of c.1723C>T accounted for the abnormal cholesterol metabolism in the family through co-segregation analysis. In addition, was found elevated and strongly associated with LDL-C level in FH family members with mutation of c.1723C>T compared to unaffected members with hyperlipidemia. Overall, our work suggests that whole-exome sequencing can facilitate identification of disease-causing variants and enable preventive treatment of FH. Our metagenomics analysis provides early insights into potential contributions of host-microbe interactions in genetic and common hypercholesterolemia.
Topics: Genomics; Heterozygote; Humans; Hyperlipoproteinemia Type II; Metagenomics; Mutation; Phenotype; Prevotella; Receptors, LDL
PubMed: 33747976
DOI: 10.3389/fcimb.2021.605954 -
The Journal of Antimicrobial... Aug 2019Routine sequencing of MRSA could bring about significant improvements to outbreak detection and investigation. Sequencing is commonly performed using DNA extracted from...
BACKGROUND
Routine sequencing of MRSA could bring about significant improvements to outbreak detection and investigation. Sequencing is commonly performed using DNA extracted from a pure culture, but overcoming the delay associated with this step could reduce the time to infection control interventions.
OBJECTIVES
To develop and evaluate rapid sequencing of MRSA using primary clinical cultures.
METHODS
Patients with samples submitted to the clinical laboratory at the Cambridge University Hospitals NHS Foundation Trust from which MRSA was isolated were identified, the routine laboratory culture plates obtained and DNA extraction and sequencing performed.
RESULTS
An evaluation of routine MRSA cultures from 30 patients demonstrated that direct sequencing from bacterial colonies picked from four different culture media was feasible. The 30 clinical MRSA isolates were sequenced on the day of plate retrieval over five runs and passed quality control metrics for sequencing depth and coverage. The maximum contamination detected using Kraken was 1.09% fragments, which were identified as Prevotella dentalis. The most common contaminants were other staphylococcal species (25 isolate sequences) and Burkholderia dolosa (11 isolate sequences). Core genome pairwise SNP analysis to identify clusters based on isolates that were ≤50 SNPs different was used to triage cases for further investigation. This identified three clusters, but more detailed genomic and epidemiological evaluation excluded an acute outbreak.
CONCLUSIONS
Rapid sequencing of MRSA from clinical culture plates is feasible and reduces the delay associated with purity culture prior to DNA extraction.
Topics: Colony Count, Microbial; DNA, Bacterial; Genome, Bacterial; Genomics; Humans; Methicillin-Resistant Staphylococcus aureus; Sequence Analysis, DNA; Staphylococcal Infections
PubMed: 31039248
DOI: 10.1093/jac/dkz170 -
The Journal of Biological Chemistry Sep 2013A gene cluster involved in N-glycan metabolism was identified in the genome of Bacteroides thetaiotaomicron VPI-5482. This gene cluster encodes a major facilitator...
A gene cluster involved in N-glycan metabolism was identified in the genome of Bacteroides thetaiotaomicron VPI-5482. This gene cluster encodes a major facilitator superfamily transporter, a starch utilization system-like transporter consisting of a TonB-dependent oligosaccharide transporter and an outer membrane lipoprotein, four glycoside hydrolases (α-mannosidase, β-N-acetylhexosaminidase, exo-α-sialidase, and endo-β-N-acetylglucosaminidase), and a phosphorylase (BT1033) with unknown function. It was demonstrated that BT1033 catalyzed the reversible phosphorolysis of β-1,4-D-mannosyl-N-acetyl-D-glucosamine in a typical sequential Bi Bi mechanism. These results indicate that BT1033 plays a crucial role as a key enzyme in the N-glycan catabolism where β-1,4-D-mannosyl-N-acetyl-D-glucosamine is liberated from N-glycans by sequential glycoside hydrolase-catalyzed reactions, transported into the cell, and intracellularly converted into α-D-mannose 1-phosphate and N-acetyl-D-glucosamine. In addition, intestinal anaerobic bacteria such as Bacteroides fragilis, Bacteroides helcogenes, Bacteroides salanitronis, Bacteroides vulgatus, Prevotella denticola, Prevotella dentalis, Prevotella melaninogenica, Parabacteroides distasonis, and Alistipes finegoldii were also suggested to possess the similar metabolic pathway for N-glycans. A notable feature of the new metabolic pathway for N-glycans is the more efficient use of ATP-stored energy, in comparison with the conventional pathway where β-mannosidase and ATP-dependent hexokinase participate, because it is possible to directly phosphorylate the D-mannose residue of β-1,4-D-mannosyl-N-acetyl-D-glucosamine to enter glycolysis. This is the first report of a metabolic pathway for N-glycans that includes a phosphorylase. We propose 4-O-β-D-mannopyranosyl-N-acetyl-D-glucosamine:phosphate α-D-mannosyltransferase as the systematic name and β-1,4-D-mannosyl-N-acetyl-D-glucosamine phosphorylase as the short name for BT1033.
Topics: Acetylglucosamine; Adenosine Triphosphate; Bacterial Proteins; Bacteroides; Biological Transport, Active; Glucans; Multigene Family; Phosphorylases
PubMed: 23943617
DOI: 10.1074/jbc.M113.469080 -
Animals : An Open Access Journal From... Nov 2018To identify differences in rumen function as a result of feeding monensin to beef cattle, rumen fluid metagenomics and metabolomics analyses were used to evaluate the...
To identify differences in rumen function as a result of feeding monensin to beef cattle, rumen fluid metagenomics and metabolomics analyses were used to evaluate the functional attributes and metabolites of rumen microbiota in beef steers fed no or 200 mg/d of monensin. Eight rumen-fistulated steers were used in the study for a period of 53 days. Rumen fluid samples were collected on the last day of the experiment. Monensin increased the relative abundance of sp. ND2010, , , , , and , but reduced the relative abundance of sp. KNHs210, , , , sp. LMG29324, and . Monensin increased the relative abundance of functional genes involved in amino acid metabolism and lipid metabolism. A total of 245 metabolites were identified. Thirty-one metabolites were found to be differentially expressed. Pathway analysis of the differentially expressed metabolites revealed upregulated metabolic pathways associated with metabolism of linoleic acid and some amino acids. These findings confirm that monensin affects rumen fermentation of forage-fed beef cattle by modulating the rumen microbiome, and by reducing amino acid degradation and biohydrogenation of linoleic acid in the rumen.
PubMed: 30453603
DOI: 10.3390/ani8110211