scholarly journals The oral microbiome of patients with axial spondyloarthritis compared to healthy individuals

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2095 ◽  
Author(s):  
Jordan E. Bisanz ◽  
Praema Suppiah ◽  
W. Murray Thomson ◽  
Trudy Milne ◽  
Nigel Yeoh ◽  
...  
Keyword(s):  
16S Rrna ◽  
Oral Cavity ◽  
16S Rrna Gene ◽  
Disease Activity ◽  
Axial Spondyloarthritis ◽  
Activity Index ◽  
Oral Microbiome ◽  
Healthy Population ◽  
Rrna Gene ◽  
Pocket Depth

Background.A loss of mucosal tolerance to the resident microbiome has been postulated in the aetiopathogenesis of spondyloarthritis, thus the purpose of these studies was to investigate microbial communities that colonise the oral cavity of patients with axial spondyloarthritis (AxSpA) and to compare these with microbial profiles of a matched healthy population.Methods.Thirty-nine participants, 17 patients with AxSpA and 22 age and gender-matched disease-free controls were recruited to the study. For patients with AxSpA, disease activity was assessed using the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI). All participants underwent a detailed dental examination to assess oral health, including the presence of periodontal disease assessed using probing pocket depth (PPD). Plaque samples were obtained and their bacterial populations were profiled using Ion Torrent sequencing of the V6 region of the 16S rRNA gene.Results.Patients with AxSpA had active disease (BASDAI 4.1 ± 2.1 [mean ± SD]), and a significantly greater prevalence of periodontitis (PPD ≥ 4 mm at ≥4 sites) than controls. Bacterial communities did not differ between the two groups with multiple metrics ofαandβdiversity considered. Analysis of operational taxonomic units (OTUs) and higher levels of taxonomic assignment did not provide strong evidence of any single taxa associated with AxSpA in the subgingival plaque.Discussion.Although 16S rRNA gene sequencing did not identify specific bacterial profiles associated with AxSpA, there remains the potential for the microbiota to exert functional and metabolic influences in the oral cavity which could be involved in the pathogenesis of AxSpA.

scholarly journals Microbiome of Odontogenic Abscesses

2021 ◽  
Vol 9 (6) ◽  
pp. 1307
Author(s):  
Sebastian Böttger ◽  
Silke Zechel-Gran ◽  
Daniel Schmermund ◽  
Philipp Streckbein ◽  
Jan-Falco Wilbrand ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Oral Microbiome ◽  
Minor Role ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Bacterial Strains ◽  
16S Rrna Gene Analysis ◽  
Odontogenic Infections ◽  
Odontogenic Abscess

Severe odontogenic abscesses are regularly caused by bacteria of the physiological oral microbiome. However, the culture of these bacteria is often prone to errors and sometimes does not result in any bacterial growth. Furthermore, various authors found completely different bacterial spectra in odontogenic abscesses. Experimental 16S rRNA gene next-generation sequencing analysis was used to identify the microbiome of the saliva and the pus in patients with a severe odontogenic infection. The microbiome of the saliva and the pus was determined for 50 patients with a severe odontogenic abscess. Perimandibular and submandibular abscesses were the most commonly observed diseases at 15 (30%) patients each. Polymicrobial infections were observed in 48 (96%) cases, while the picture of a mono-infection only occurred twice (4%). On average, 31.44 (±12.09) bacterial genera were detected in the pus and 41.32 (±9.00) in the saliva. In most cases, a predominantly anaerobic bacterial spectrum was found in the pus, while saliva showed a similar oral microbiome to healthy individuals. In the majority of cases, odontogenic infections are polymicrobial. Our results indicate that these are mainly caused by anaerobic bacterial strains and that aerobic and facultative anaerobe bacteria seem to play a more minor role than previously described by other authors. The 16S rRNA gene analysis detects significantly more bacteria than conventional methods and molecular methods should therefore become a part of routine diagnostics in medical microbiology.

scholarly journals Clinical Relevance of the Microbiome in Odontogenic Abscesses

Biology ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 916
Author(s):  
Sebastian Böttger ◽  
Silke Zechel-Gran ◽  
Daniel Schmermund ◽  
Philipp Streckbein ◽  
Jan-Falco Wilbrand ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Oral Microbiome ◽  
Molecular Methods ◽  
Gene Analysis ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Cultural Methods ◽  
Odontogenic Abscess ◽  
Polymicrobial Infections

Odontogenic abscesses are usually caused by bacteria of the oral microbiome. However, the diagnostic culture of these bacteria is often prone to errors and sometimes fails completely due to the fastidiousness of the relevant bacterial species. The question arises whether additional pathogen diagnostics using molecular methods provide additional benefits for diagnostics and therapy. Experimental 16S rRNA gene analysis with next-generation sequencing (NGS) and bioinformatics was used to identify the microbiome of the pus in patients with severe odontogenic infections and was compared to the result of standard diagnostic culture. The pus microbiome was determined in 48 hospitalized patients with a severe odontogenic abscess in addition to standard cultural pathogen detection. Cultural detection was possible in 41 (85.42%) of 48 patients, while a pus-microbiome could be determined in all cases. The microbiomes showed polymicrobial infections in 46 (95.83%) cases, while the picture of a mono-infection occurred only twice (4.17%). In most cases, a predominantly anaerobic spectrum with an abundance of bacteria was found in the pus-microbiome, while culture detected mainly Streptococcus, Staphylococcus, and Prevotella spp. The determination of the microbiome of odontogenic abscesses clearly shows a higher number of bacteria and a significantly higher proportion of anaerobes than classical cultural methods. The 16S rRNA gene analysis detects considerably more bacteria than conventional cultural methods, even in culture-negative samples. Molecular methods should be implemented as standards in medical microbiology diagnostics, particularly for the detection of polymicrobial infections with a predominance of anaerobic bacteria.

scholarly journals Prevotella dentasini sp. nov., a black-pigmented species isolated from the oral cavity of donkeys

2010 ◽  
Vol 60 (7) ◽  
pp. 1637-1639 ◽  
Author(s):  
Kazuko Takada ◽  
Kazuhiko Hayashi ◽  
Yutaka Sato ◽  
Masatomo Hirasawa
Keyword(s):  
16S Rrna ◽  
Oral Cavity ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
Rrna Gene Sequencing

Four strains (NUM 1903T, NUM 1904, NUM 1912 and NUM 1925) that were obligately anaerobic, pigmented, Gram-negative-staining rods were isolated from the oral cavity of donkeys. These strains were analysed using the Rapid ID 32A, API 20A and API ZYM systems, by DNA–DNA hybridization with other related species and by 16S rRNA gene sequencing. 16S rRNA gene sequence analysis showed that each of the new isolates was a member of the genus Prevotella and related to Prevotella multiformis PPPA21T, showing about 93 % sequence similarity. Based on phylogenetic and phenotypic evidence, it is proposed that the four strains are representatives of a novel species, for which the name Prevotella dentasini sp. nov. is proposed. The type strain is NUM 1903T (=JCM 15908T=DSM 22229T).

Prevotella aurantiaca sp. nov., isolated from the human oral cavity

2010 ◽  
Vol 60 (3) ◽  
pp. 500-503 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Natsuko Suzuki ◽  
Masaaki Okamoto
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Oral Cavity ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

Two anaerobic, pigmented, non-spore-forming, Gram-stain-negative, rod-shaped strains isolated from the human oral cavity, OMA31T and OMA130, were characterized by determining their phenotypic and biochemical features, cellular fatty acid profiles and phylogenetic positions based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that the new isolates belonged to a single species of the genus Prevotella. The two isolates showed 100 % 16S rRNA gene sequence similarity with each other and were most closely related to Prevotella intermedia ATCC 25611T with 96.4 % 16S rRNA gene sequence similarity; the next most closely related strains to the isolates were Prevotella pallens AHN 10371T (96.1 %) and Prevotella falsenii JCM 15124T (95.3 %). Phenotypic and biochemical characteristics of the isolates were the same as those of P. intermedia JCM 12248T, P. falsenii JCM 15124T and Prevotella nigrescens JCM 12250T. The isolates could be differentiated from P. pallens JCM 11140T by mannose fermentation and α-fucosidase activity. Conventional biochemical tests were unable to differentiate the new isolates from P. intermedia, P. falsenii and P. nigrescens. However, hsp60 gene sequence analysis suggested that strain OMA31T was not a representative of P. intermedia, P. pallens, P. falsenii or P. nigrescens. Based on these data, a novel species of the genus Prevotella, Prevotella aurantiaca sp. nov., is proposed, with OMA31T (=JCM 15754T=CCUG 57723T) as the type strain.

scholarly journals Scardovia wiggsiae sp. nov., isolated from the human oral cavity and clinical material, and emended descriptions of the genus Scardovia and Scardovia inopinata

2011 ◽  
Vol 61 (1) ◽  
pp. 25-29 ◽  
Author(s):  
Julia Downes ◽  
Maria Mantzourani ◽  
David Beighton ◽  
Samuel Hooper ◽  
Melanie J. Wilson ◽  
...  
Keyword(s):  
16S Rrna ◽  
Oral Cavity ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Lipid Analysis ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Human Oral Cavity

Six strains of anaerobic, pleomorphic Gram-positive bacilli, isolated from the human oral cavity and an infected arm wound, were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group. 16S rRNA gene sequence analysis revealed that the isolates were most closely related to Scardovia inopinata CCUG 35729T (94.8–94.9 % 16S rRNA gene sequence similarity). The isolates were saccharolytic and produced acetic and lactic acids as end products of fermentation. The major fatty acids were C16 : 0 (49.8 %) and C18 : 1 ω9c (35.8 %). Polar lipid analysis revealed a variety of glycolipids, diphosphatidylglycerol, an unidentified phospholipid and an unidentified phosphoglycolipid. No respiratory quinones were detected. The peptidoglycan was of the type A4α l-Lys–Thr–Glu, with l-lysine partially replaced by l-ornithine. The DNA G+C content of one of the strains, C1A_55T , was 55 mol%. A novel species, Scardovia wiggsiae sp. nov., is proposed to accommodate the six isolates, with the type strain C1A_55T (=DSM 22547T=CCUG 58090T).

scholarly journals New insights into human nostril microbiome from the expanded Human Oral Microbiome Database (eHOMD): a resource for the microbiome of the human aerodigestive tract

2018 ◽  
Author(s):  
Isabel F. Escapa ◽  
Tsute Chen ◽  
Yanmei Huang ◽  
Prasad Gajare ◽  
Floyd E. Dewhirst ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Clinical Relevance ◽  
Species Level ◽  
Aerodigestive Tract ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Minimum Entropy ◽  
Nasal Passages ◽  
Vital Resource

ABSTRACTThe expanded Human Oral Microbiome Database (eHOMD) is a comprehensive microbiome database for sites along the human aerodigestive tract that revealed new insights into the nostril microbiome. The eHOMD provides well-curated 16S rRNA gene reference sequences linked to available genomes and enables assignment of species-level taxonomy to most NextGeneration sequences derived from diverse aerodigestive tract sites, including the nasal passages, sinuses, throat, esophagus and mouth. Using Minimum Entropy Decomposition coupled with the RDP Classifier and our eHOMD V1-V3 training set, we reanalyzed 16S rRNA V1-V3 sequences from the nostrils of 210 Human Microbiome Project participants at the species level revealing four key insights. First, we discovered that Lawsonella clevelandensis, a recently named bacterium, and Neisseriaceae [G-1] HMT-174, a previously unrecognized bacterium, are common in adult nostrils. Second, just 19 species accounted for 90% of the total sequences from all participants. Third, one of these 19 belonged to a currently uncultivated genus. Fourth, for 94% of the participants, two to ten species constituted 90% of their sequences, indicating nostril microbiome may be represented by limited consortia. These insights highlight the strengths of the nostril microbiome as a model system for studying interspecies interactions and microbiome function. Also, in this cohort, three common nasal species (Dolosigranulum pigrum and two Corynebacterium species) showed positive differential abundance when the pathobiont Staphylococcus aureus was absent, generating hypotheses regarding colonization resistance. By facilitating species-level taxonomic assignment to microbes from the human aerodigestive tract, the eHOMD is a vital resource enhancing clinical relevance of microbiome studies.IMPORTANCEThe eHOMD (ehomd.org) is a valuable resource for researchers, from basic to clinical, who study the microbiomes, and the individual microbes, in health and disease of body sites in the human aerodigestive tract, which includes the nasal passages, sinuses, throat, esophagus and mouth, and the lower respiratory tract. The eHOMD is an actively curated, web-based, open-access resource. eHOMD provides the following: (1) species-level taxonomy based on grouping 16S rRNA gene sequences at 98.5% identity, (2) a systematic naming scheme for unnamed and/or uncultivated microbial taxa, (3) reference genomes to facilitate metagenomic, metatranscriptomic and proteomic studies and (4) convenient cross-links to other databases (e.g., PubMed and Entrez). By facilitating the assignment of species names to sequences, the eHOMD is a vital resource for enhancing the clinical relevance of 16S rRNA gene-based microbiome studies, as well as metagenomic studies.

scholarly journals The Subgingival Microbiome Relationship to Periodontal Disease in Older Women

2019 ◽  
Vol 98 (9) ◽  
pp. 975-984 ◽  
Author(s):  
R.J. Genco ◽  
M.J. LaMonte ◽  
D.I. McSkimming ◽  
M.J. Buck ◽  
L. Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
Periodontal Disease ◽  
Older Women ◽  
Bacterial Species ◽  
Disease Status ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Minimum Entropy ◽  
Pocket Depth ◽  
Severe Periodontal Disease

Understanding of the oral microbiome in relation to periodontal disease in older adults is limited. The composition and diversity of the subgingival microflora and their oligotypes in health and levels of periodontal disease were investigated in this study on older postmenopausal women. The 16S rRNA gene was sequenced using the Illumina MiSeq platform in 1,206 women aged 53 to 81 y. Presence and severity of periodontal disease were defined by Centers for Disease Control and Prevention/American Academy of Periodontology criteria. Composition of the microbiome was determined by 16S rRNA amplicon sequencing and the abundance of taxa described by the centered log2-ratio (CLR) transformed operational taxonomic unit (OTU) values. Differences according to periodontal disease status were determined by analysis of variance with Bonferroni correction. Bacteria oligotypes associated with periodontal disease and health were determined by minimum entropy decomposition and their functions estimated in silico using PICRUSt. Prevalence of none/mild, moderate, and severe periodontal disease was 25.1%, 58.3%, and 16.6%, respectively. Alpha diversity of the microbiome differed significantly across the 3 periodontal disease categories. β-Diversity differed between no/mild and severe periodontal disease, although considerable overlap was noted. Of the 267 bacterial species identified at ≥0.02% abundance, 56 (20.9%) differed significantly in abundance according to periodontal disease status. Significant linear correlations for pocket depth and clinical attachment level with bacterial amounts were observed for several taxa. Of the taxa differing in abundance according to periodontal disease status, 53% had multiple oligotypes appearing to differ between none/mild and severe periodontal disease. Among older women, taxonomic differences in subgingival microbiome composition and diversity were observed in relation to clinical periodontal disease measures. Potential differences in bacterial subspecies (oligotypes) and their function were also identified in periodontal disease compared with health.

Metagenomic analysis of the canine oral cavity as revealed by high-throughput pyrosequencing of the 16S rRNA gene

2013 ◽  
Vol 162 (2-4) ◽  
pp. 891-898 ◽  
Author(s):  
Amy Sturgeon ◽  
Jason W. Stull ◽  
Marcio C. Costa ◽  
J. Scott Weese
Keyword(s):  
16S Rrna ◽  
Oral Cavity ◽  
16S Rrna Gene ◽  
High Throughput ◽  
Metagenomic Analysis ◽  
Rrna Gene ◽  
The 16S Rrna Gene

Streptococcus troglodytae sp. nov., from the chimpanzee oral cavity

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 418-422 ◽  
Author(s):  
Masaaki Okamoto ◽  
Susumu Imai ◽  
Mayu Miyanohara ◽  
Wataru Saito ◽  
Yasuko Momoi ◽  
...  
Keyword(s):  
16S Rrna ◽  
Oral Cavity ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Link Type

Six strains, TKU 25, TKU 28, TKU 30, TKU 31T, TKU 33 and TKU 34, were isolated from the oral cavity of a chimpanzee (Pan troglodytes). Colonies of strains grown on Mitis–Salivarius agar were similar in morphology to that of Streptococcus mutans . The novel strains were Gram-stain-positive, facultatively anaerobic cocci that lacked catalase activity. Analysis of the partial 16S rRNA gene sequences of these isolates showed that the most closely related strain was the type strain of S. mutans (96.4 %). The next closely related strains to the isolates were the type strains of Streptococcus devriesei (94.5 %) and Streptococcus downei (93.9 %). These isolates could be distinguished from S. mutans by inulin fermentation and alkaline phosphatase activity (API ZYM system). The peptidoglycan type of the novel isolates was Glu–Lys–Ala3. Strains were not susceptible to bacitracin. On the basis of phenotypic characterization, partial 16S rRNA gene and two housekeeping gene (groEL and sodA) sequence data, we propose a novel taxon, Streptococcus troglodytae sp. nov.; the type strain is TKU 31T ( = JCM 18038T = DSM 25324T).

scholarly journals Molecular profiling of microbiota in human oral cavity, stomach and intestine

2018 ◽  
Author(s):  
Qianqian Liu ◽  
Feizhou Zhu ◽  
Liyu Chen ◽  
Meihua Xu ◽  
Jianwei Chen ◽  
...  
Keyword(s):  
16S Rrna ◽  
Oral Cavity ◽  
16S Rrna Gene ◽  
Gastric Juice ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Rrna Gene ◽  
Human Oral Cavity ◽  
Stool Microbiota ◽  
The 16S Rrna Gene

The microbiota in the human gut is not only a complicated microecological system but also plays important roles in both health and disease. In order to understand the roles of these gut bacteria, we determined the distribution of microbiota in different regions of the gut by sequencing the 16S rRNA gene V4 region of the bacteria in the saliva, gastric juice, and stool of healthy individuals. The 16S rRNA gene V3-V5 region sequences of saliva and stool microbiota were obtained from Human Microbiome Project (HMP) and the V4 sequence was obtained from the V3-V5 sequences by a program designed by Perl language. We found that the microbiota of the gastric juice is more similar to those in the saliva rather than that in the stool. The frequency of some taxa was significantly different among the three groups with the Streptococcus, Veillonella, Oribacterium, Selenomonas, Actinomyces, and Granulicatella most abundant in the saliva; the Prevotella, Neisseria, Actinobacillus, Treponema, and Helicobacter most abundant in the gastric juice; and the Bacteroides, Parabacteroides, Faecalibacterium, Sutterella, Ruminococcus, Oscillospira and Phascolarctobacterium most abundant in the stool. In addition, results from PICRUSt analyses suggest that the functions of microbiota in the gastric juice are more similar as those in the saliva than in the stool. Moreover, we also found that the membrane transport of the microbiota in the saliva is higher than that in the stool and gastric juice. To our knowledge, this is the first comprehensive comparison of microbiota in the human oral cavity, stomach, and intestine.

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