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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 -
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 -
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 -
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 -
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 -
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