-
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 Journal of Systematic and... Aug 2019A novel actinobacterial strain, designated KGMB04489, was isolated from the faeces of a healthy Korean. Cells of the strain were strictly anaerobic, Gram-stain-positive...
A novel actinobacterial strain, designated KGMB04489, was isolated from the faeces of a healthy Korean. Cells of the strain were strictly anaerobic, Gram-stain-positive and short-rod-shaped. On the basis of 16S rRNA gene sequence similarity, strain KGMB04489 belonged to the genus Olsenella and was most closely related to Olsenella scatoligenes SK9K4 (94.3 %), Olsenella uli ATCC 49627 (93.5 %), Olsenella umbonata lac31 (93.4 %) and Olsenella profusa D315A-29 (93.3 %). The major end product was lactic acid. The DNA G+C content was 65.5 mol%. The major cellular fatty acids of strain KGMB04489 were C18 : 1cis9, C18 : 1cis9 DMA and C16 : 0. Strain KGMB04489 contained meso-diaminopimelic acid as the diamino acid in the peptidoglycan. The polar lipids consisted of an unidentified phospholipid, six unidentified glycolipids and an unidentified lipid. Based on phylogenetic, physiological and chemotaxonomic characteristics, strain KGMB04489 is considered to represent a novel species within the genus Olsenella, for which the name Olsenellafaecalis sp. nov. is proposed. The type strain is KGMB04489 (=KCTC 15699=CCUG 72345).
Topics: Actinobacteria; Bacterial Typing Techniques; Base Composition; Cell Wall; DNA, Bacterial; Diaminopimelic Acid; Fatty Acids; Feces; Glycolipids; Humans; Peptidoglycan; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Republic of Korea; Sequence Analysis, DNA
PubMed: 31135332
DOI: 10.1099/ijsem.0.003469 -
International Journal of Systematic and... Apr 2015Strain SK9K4(T), which is a strictly anaerobic, non-motile, non-sporulating, Gram-stain-positive, saccharolytic coccobacillus, was isolated from pig faeces. SK9K4(T)...
Strain SK9K4(T), which is a strictly anaerobic, non-motile, non-sporulating, Gram-stain-positive, saccharolytic coccobacillus, was isolated from pig faeces. SK9K4(T) metabolized indol-3-acetic acid to 3-methylindole (skatole), which is the main contributor to boar taint; it also produced 4-methylphenol (p-cresol) from p-hydroxyphenylacetic acid. Phylogenetic analyses, based on 16S rRNA gene sequences, revealed that the isolate represented a new lineage within the genus Olsenella of the family Atopobiaceae . Strain SK9K4(T) was most closely related to the type strains of the three species of the genus Olsenella with validly published names; Olsenella profusa DSM 13989(T) (93.6%), Olsenella uli DSM 7084(T) (93.5%) and Olsenella umbonata DSM 22620(T) (92.7%). DNA-DNA relatedness values of strain SK9K4(T) with O. profusa , O. uli and O. umbonata were 28.3%, 69.1% and 27.2%, respectively. The genomic DNA G+C content was 62.1 mol% and the major cellular fatty acids (constituting >10% of the total) were C(14 : 0) and C(18 : 1)ω9c. The major end product of glucose fermentation was lactic acid, with minor amounts of acetic acid and formic acid; no H2 was produced. Discrepancies in the fatty acid profiles, the MALDI-TOF mass spectra of cell extracts and the physiological and biochemical characteristics differentiated strain SK9K4(T) from other species of the genus Olsenella and indicate that the isolate represents a novel species within this genus. The name Olsenella scatoligenes sp. nov., is proposed and the type strain is SK9K4(T) ( = JCM 19907(T) = DSM 28304(T)).
Topics: Actinobacteria; Animals; Bacterial Typing Techniques; Base Composition; Cresols; DNA, Bacterial; Fatty Acids; Feces; Fermentation; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Skatole; Sus scrofa
PubMed: 25634945
DOI: 10.1099/ijs.0.000083 -
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 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 -
International Journal of Systematic and... Apr 2018Strain 2CBEGH3, which is an obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-positive coccobacillus, was isolated from a faecal sample of a...
Strain 2CBEGH3, which is an obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-positive coccobacillus, was isolated from a faecal sample of a healthy Japanese man. The 16S rRNA gene sequence analysis showed that strain 2CBEGH3 represented a member of the family Atopobiaceae and formed a monophyletic cluster with Olsenella uli DSM 7084 (93.6 % sequence similarity), Olsenella umbonata strain lac31 (93.0 %), Olsenella profusa JCM 14553 (92.7 %) and Olsenella scatoligenes strain SK9K4 (92.7 %) as closest neighbours and Atopobium species. The hsp60 gene sequence analysis supported the phylogenetic relationships based on the 16S rRNA gene sequences, with sequence similarity values of 82.1-84.7 % to the four species described above. A unique three-base (one amino acid residue) insertion was found in the alignment regions of the hsp60 gene sequence of strain 2CBEGH3. The major end products from d-glucose were d- and l-lactic acids produced at the ratio of 75 : 25, while four species of the genus Olsenella produced d- and l-lactic acids at ratios of 94-98 : 2-6. The isolate formed characteristic crater-like colonies on Eggerth-Gagnon agar plates. The major cellular fatty acids were C18 : 1ω9c, C18 : 1ω9c dimethyl acetal (DMA) and C16 : 0 DMA. The G+C content of the genomic DNA was 68.4 mol%. On the basis of these data, strain 2CBEGH3 represents a novel species in a novel genus of the family Atopobiaceae, for which the name Parolsenella catena gen. nov., sp. nov. is proposed. The type strain of P. catena is 2CBEGH3 (=JCM 31932=DSM 105194).
Topics: Actinobacteria; Adult; Bacteria, Anaerobic; Bacterial Typing Techniques; DNA, Bacterial; Fatty Acids; Feces; Genes, Bacterial; Humans; Japan; Male; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 29458507
DOI: 10.1099/ijsem.0.002645 -
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 -
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 -
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