-
Journal of Oral Microbiology 2017species are non-motile facultative anaerobic/anaerobic bacteria that are found mostly in the oral cavity and some other parts of the human body, in animals, and even in... (Review)
Review
species are non-motile facultative anaerobic/anaerobic bacteria that are found mostly in the oral cavity and some other parts of the human body, in animals, and even in ocean sediments. Valid species include , , , , , , and . Some species require serum or blood for growth. All species ferment carbohydrates and produce lactic acid that may be involved with tooth decay. Acting as opportunistic pathogens, they are involved in a variety of diseases, and have been isolated from immunocompromised but also immunocompetent individuals. Mucositis, oral lesions, wounds, and abscesses may predispose to septicemia. Because identification of species by phenotypic features occasionally lead to misidentification, genetic techniques such as 16S rRNA gene sequencing is recommended. Early diagnosis and treatment of leptotrichia infections is important for positive outcomes. Over the last years, species have been associated with several changes in taxonomy and new associations with clinical diseases. Such changes are reported in this updated review.
PubMed: 29081911
DOI: 10.1080/20002297.2017.1368848 -
Nature Microbiology Dec 2022CRISPR-Cas13 proteins are RNA-guided RNA nucleases that defend against incoming RNA and DNA phages by binding to complementary target phage transcripts followed by...
CRISPR-Cas13 proteins are RNA-guided RNA nucleases that defend against incoming RNA and DNA phages by binding to complementary target phage transcripts followed by general, non-specific RNA degradation. Here we analysed the defensive capabilities of LbuCas13a from Leptotrichia buccalis and found it to have robust antiviral activity unaffected by target phage gene essentiality, gene expression timing or target sequence location. Furthermore, we find LbuCas13a antiviral activity to be broadly effective against a wide range of phages by challenging LbuCas13a against nine E. coli phages from diverse phylogenetic groups. Leveraging the versatility and potency enabled by LbuCas13a targeting, we applied LbuCas13a towards broad-spectrum phage editing. Using a two-step phage-editing and enrichment method, we achieved seven markerless genome edits in three diverse phages with 100% efficiency, including edits as large as multi-gene deletions and as small as replacing a single codon. Cas13a can be applied as a generalizable tool for editing the most abundant and diverse biological entities on Earth.
Topics: Gene Editing; Bacteriophages; CRISPR-Cas Systems; Escherichia coli; Phylogeny; RNA; Antiviral Agents
PubMed: 36316451
DOI: 10.1038/s41564-022-01258-x -
Journal of Clinical Microbiology Feb 2023species are anaerobic, Gram-negative bacilli increasingly recognized as pathogens capable of causing invasive infections such as bloodstream infection (BSI),... (Review)
Review
species are anaerobic, Gram-negative bacilli increasingly recognized as pathogens capable of causing invasive infections such as bloodstream infection (BSI), particularly among immunocompromised patients. However, there is a paucity of data regarding epidemiology, antimicrobial susceptibility, optimal treatment, and clinical outcomes among patients with bacteremia. Patient risk factors, treatment approaches, and outcomes of a retrospective cohort of adult patients with BSI at a tertiary medical center (Mayo Clinic Rochester [MCR]) were evaluated. Concurrently, species, temporal trends, and antimicrobial susceptibility testing (AST) results of isolates submitted to a reference laboratory (Mayo Clinic Laboratories) over the past 10 years were examined. We identified 224 blood culture isolates of species, with 26 isolates from patients treated at MCR. The most frequent species included L. trevisanii (49%), L. buccalis (24%), and L. wadei (16%). species demonstrated >90% susceptibility to penicillin, metronidazole, ertapenem, and piperacillin-tazobactam. However, 96% (74/77) of isolates were resistant to moxifloxacin. For patients treated at MCR, the mean patient age was 55 years (standard deviation [SD], 17), with 9 females (35%), and all were neutropenic at the time of BSI. The primary sources of infection were gastrointestinal (58%), intravascular catheter (35%), and odontogenic (15%). Patients were treated with metronidazole (42%), piperacillin-tazobactam (27%), or carbapenems (19%). The mean duration of treatment was 11 days (SD, 4.5), with a 60-day all-cause mortality of 19% and no microbiologic relapse. species are rare but important causes of BSI in neutropenic patients. Due to evolving antimicrobial susceptibility profiles, a review of AST results is necessary when selecting optimal antimicrobial therapy.
Topics: Adult; Female; Humans; Middle Aged; Metronidazole; Leptotrichia; Retrospective Studies; Bacteremia; Anti-Infective Agents; Piperacillin, Tazobactam Drug Combination; Gram-Negative Bacteria; Sepsis; Anti-Bacterial Agents; Microbial Sensitivity Tests
PubMed: 36715514
DOI: 10.1128/jcm.01733-22 -
Dentistry Journal Aug 2022To characterize the microflora profile of supragingival biofilm in patients with and without full-crown prostheses. Plaque samples of full-crown prostheses and teeth...
To characterize the microflora profile of supragingival biofilm in patients with and without full-crown prostheses. Plaque samples of full-crown prostheses and teeth in patients with porcelain-fused-to-metal crowns, all-ceramic crowns, and no prostheses were collected (three patients per group), using 16S rRNA high-throughput sequencing technology to conduct DNA sequencing on the samples and using Qiime, R, and PICRUSt2 software to perform bioinformatics analyses and functional analyses on sequencing data. In total, 110,209 valid sequences were obtained in the experiment, corresponding to 11 phyla and 120 genera. The predominant species shared by the three groups were phyla , , , , and and genera , , , , , , , , and . The species-difference analysis showed that genus significantly increased after the patient wore the dental prosthesis. Compared with the no-prosthesis samples, the functional analysis showed that cell motility increased in the samples from full-crown prostheses, while replication and repair, and translation decreased. This study reveals the changes in the oral microbial community of patients with full-crown prostheses, which could provide insights regarding the safety of materials for long-term use in the oral cavity.
PubMed: 36005250
DOI: 10.3390/dj10080152 -
Frontiers in Microbiology 2021Human papillomavirus (HPV) is a known etiological factor of oropharyngeal head and neck cancer (HNC). HPV positivity and periodontal disease have been associated with...
OBJECTIVES
Human papillomavirus (HPV) is a known etiological factor of oropharyngeal head and neck cancer (HNC). HPV positivity and periodontal disease have been associated with higher HNC risk, suggesting a role for oral bacterial species. Our objective was to determine oral microbiome profiles in HNC patients (HPV-positive and HPV-negative) and in healthy controls (HC).
METHODS
Saliva samples and swabs of buccal mucosa, supragingival plaque, and tongue were collected from HNC patients ( = 23 patients, = 92 samples) before cancer therapy. Next-generation sequencing (16S-rRNA gene V3-V4 region) was used to determine bacterial taxa relative abundance (RA). β-Diversities of HNC HPV+ ( = 16 patients, = 64 samples) and HNC HPV- ( = 7 patients, = 28 samples) groups were compared using PERMANOVA (pMonte Carlo < 0.05). LEfSe discriminant analysis was performed to identify differentiating taxa (Log LDA > 2.0). RA differences were analyzed by Mann-Whitney -test (α = 0.05). CombiROC program was used to determine multi-marker bacterial signatures. The Microbial Interaction Network Database (MIND) and LitSuggest online tools were used for complementary analyses.
RESULTS
HNC vs. HC and HNC HPV+ vs. HNC HPV- β-diversities differed significantly (pMonte Carlo < 0.05). was the most abundant genus for HNC and HC groups, while and were the most abundant species in HNC and HC patients, respectively, regardless of antibiotics treatment. LEfSe analysis identified 43 and 44 distinctive species for HNC HPV+ and HNC HPV- groups, respectively. In HNC HPV+ group, 26 periodontal disease-associated species identified by LefSe had a higher average RA compared to HNC HPV- group. The significant species included , , , , and spp. (Mann-Whitney -test, < 0.05). Of 43 LEfSe-identified species in HPV+ group, 31 had a higher RA compared to HPV- group (Mann-Whitney -test, < 0.05). MIND analysis confirmed interactions between and spp., representing a multi-marker signature per CombiROC analysis [area under the curve (AUC) > 0.9]. LitSuggest correctly classified 15 articles relevant to oral microbiome and HPV status.
CONCLUSION
Oral microbiome profiles of HNC HPV+ and HNC HPV- patients differed significantly regarding periodontal-associated species. Our results suggest that oral bacterial species (e.g., spp.), possessing unique niches and invasive properties, coexist with HPV within HPV-induced oral lesions in HNC patients. Further investigation into host-microbe interactions in HPV-positive HNC patients may shed light into cancer development.
PubMed: 35116012
DOI: 10.3389/fmicb.2021.794546 -
Microorganisms Jan 2023The oral microbiome is an emerging field that has been a topic of discussion since the development of next generation sequencing and the implementation of the human... (Review)
Review
The oral microbiome is an emerging field that has been a topic of discussion since the development of next generation sequencing and the implementation of the human microbiome project. This article reviews the current literature surrounding the oral microbiome, briefly highlighting most recent methods of microbiome characterization including cutting edge omics, databases for the microbiome, and areas with current gaps in knowledge. This article also describes reports on microorganisms contained in the oral microbiome which include viruses, archaea, fungi, and bacteria, and provides an in-depth analysis of their significant roles in tissue homeostasis. Finally, we detail key bacteria involved in oral disease, including oral cancer, and the current research surrounding their role in stimulation of inflammatory cytokines, the role of gingival crevicular fluid in periodontal disease, the creation of a network of interactions between microorganisms, the influence of the planktonic microbiome and cospecies biofilms, and the implications of antibiotic resistance. This paper provides a comprehensive literature analysis while also identifying gaps in knowledge to enable future studies to be conducted.
PubMed: 36838283
DOI: 10.3390/microorganisms11020318 -
Frontiers in Microbiology 2019Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas13a, previously known as CRISPR-C2c2, is the most recently identified RNA-guided RNA-targeting...
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas13a, previously known as CRISPR-C2c2, is the most recently identified RNA-guided RNA-targeting CRISPR-Cas system that has the unique characteristics of both targeted and collateral single-stranded RNA (ssRNA) cleavage activities. This system was first identified in . Here, the complete whole genome sequences of 11 strains were determined and compared with 18 publicly available genomes in regard to the composition, occurrence and diversity of the CRISPR-Cas13a, and other CRISPR-Cas systems. Various types of CRISPR-Cas systems were found to be unevenly distributed among the genomes, including types I-B (10/29, 34.4%), II-C (1/29, 2.6%), III-A (6/29, 15.4%), III-D (6/29, 15.4%), III-like (3/29, 7.7%), and VI-A (11/29, 37.9%), while 8 strains (20.5%) had no CRISPR-Cas system at all. The Cas13a effectors were found to be highly divergent with amino acid sequence similarities ranging from 61% to 90% to that of , but their collateral ssRNA cleavage activities leading to impediment of bacterial growth were conserved. CRISPR-Cas spacers represent a sequential achievement of former intruder encounters, and the retained spacers reflect the evolutionary phylogeny or relatedness of strains. Analysis of spacer contents and numbers among species showed considerable diversity with only 4.4% of spacers (40/889) were shared by two strains. The organization and distribution of CRISPR-Cas systems (type I-VI) encoded by all registered species revealed that effector or spacer sequences of the CRISPR-Cas systems were very divergent, and the prevalence of types I, III, and VI was almost equal. There was only one strain carrying type II, while none carried type IV or V. These results provide new insights into the characteristics and divergences of CRISPR-Cas systems among species.
PubMed: 31921024
DOI: 10.3389/fmicb.2019.02838 -
Journal of Dental Research Jul 2023Dental caries lesions are a clinical manifestation of disease, preceded by microbial dysbiosis, which is poorly characterized and thought to be associated with...
Dental caries lesions are a clinical manifestation of disease, preceded by microbial dysbiosis, which is poorly characterized and thought to be associated with saccharolytic taxa. Here, we assessed the associations between the oral microbiome of children and various caries risk factors such as demographics and behavioral and clinical data across early childhood and characterized over time the salivary and dental plaque microbiome of children before clinical diagnosis of caries lesions. Children ( = 266) were examined clinically at ~1, 2.5, 4, and 6.5 y of age. The microbiome samples were collected at 1, 2.5, and 4 y. Caries groups consisted of children who remained caries free (International Caries Detection and Assessment System [ICDAS] = 0) at all time points (CFAT) ( = 50); children diagnosed with caries (ICDAS ≥ 1) at 6.5 y (C6.5), 4 y (C4), or 2.5 y of age (C2.5); and children with early caries or advanced caries lesions at specific time points. Microbial community analyses were performed on zero-radius operational taxonomic units (zOTUs) obtained from V4 of 16S ribosomal RNA gene amplicon sequences. The oral microbiome of the children was affected by various factors, including antibiotic use, demographics, and dietary habits of the children and their caregivers. At all time points, various risk factors explained more of the variation in the dental plaque microbiome than in saliva. At 1 y, composition of saliva of the C4 group differed from that of the CFAT group, while at 2.5 y, this difference was observed only in plaque. At 4 y, multiple salivary and plaque zOTUs of genera and were significantly higher in samples of the C6.5 group than those of the CFAT group. In conclusion, up to 3 y prior to clinical caries detection, the oral microbial communities were already in a state of dysbiosis that was dominated by proteolytic taxa. Plaque discriminated dysbiotic oral ecosystems from healthy ones better than saliva.
Topics: Child; Humans; Child, Preschool; Dental Caries; Dental Plaque; Dysbiosis; Saliva; Microbiota; RNA, Ribosomal, 16S
PubMed: 37042041
DOI: 10.1177/00220345231160756 -
World Journal of Gastroenterology Dec 2020Microbiota profiles differ between patients with pancreatic cancer and healthy people, and understanding these differences may help in early detection of pancreatic...
BACKGROUND
Microbiota profiles differ between patients with pancreatic cancer and healthy people, and understanding these differences may help in early detection of pancreatic cancer. Saliva sampling is an easy and cost-effective way to determine microbiota profiles compared to fecal and tissue sample collection.
AIM
To investigate the saliva microbiome distribution in patients with pancreatic adenocarcinoma (PDAC) and the role of oral microbiota profiles in detection and risk prediction of pancreatic cancer.
METHODS
We conducted a prospective study of patients with pancreatic cancer ( = 41) and healthy individuals ( = 69). Bacterial taxa were identified by 16S ribosomal ribonucleic acid gene sequencing, and a linear discriminant analysis effect size algorithm was used to identify differences in taxa. Operational taxonomic unit values of all selected taxa were converted into a normalized Z-score, and logistic regressions were used to calculate risk prediction of pancreatic cancer.
RESULTS
Compared with the healthy control group, carriage of and (z-score) was associated with a higher risk of PDAC [odds ratio (OR) = 5.344, 95% confidence interval (CI): 1.282-22.282, = 0.021 and OR = 6.886, 95%CI: 1.423-33.337, = 0.016, respectively]. and (z-score) were considered a protective microbe that decreased the risk of PDAC (OR = 0.187, 95%CI: 0.055-0.631, = 0.007 and OR = 0.309, 95%CI: 0.100-0.952, = 0.041, respectively). Among the patients with PDAC, patients reporting bloating have a higher abundance of ( = 0.039), ( = 0.024), and ( = 0.041); while patients reporting jaundice had a higher amount of ( = 0.008); patients reporting dark brown urine had a higher amount of ( = 0.035). Patients reporting diarrhea had a lower amount of and ( = 0.024 and = 0.034), and patients reporting vomiting had decreased ( = 0.036).
CONCLUSION
Saliva microbiome was able to distinguish patients with pancreatic cancer and healthy individuals. may be specific for patients living in Sichuan Province, southwest China. Symptomatic patients had different bacteria profiles than asymptomatic patients. Combined symptom and microbiome evaluation may help in the early detection of pancreatic cancer.
Topics: Adenocarcinoma; China; Humans; Microbiota; Pancreatic Neoplasms; Prospective Studies; RNA, Ribosomal, 16S; Saliva
PubMed: 33505144
DOI: 10.3748/wjg.v26.i48.7679 -
World Journal of Oncology Jun 2023Reports have shown increased positive correlations with the salivary microbiota and pancreatic carcinogenesis. A European study showed that high levels of were... (Review)
Review
Reports have shown increased positive correlations with the salivary microbiota and pancreatic carcinogenesis. A European study showed that high levels of were correlated with periodontium damage and were associated with a risk of pancreatic cancer (two-fold). A recent study, using oral mouthwash samples (n = 361 with pancreatic adenocarcinoma), determined that the presence of and along with and were a risk factor for pancreatic cancer. The link between pancreatic cancer and periodontitis has been documented. Interestingly, periodontitis presents with inflammation and microbial dysbiosis, both of which have been characterized in pancreatic cancer. This review highlights multiple roles in which oral anaerobic bacteria can spread to the pancreas and contribute to pancreatic cancer.
PubMed: 37350809
DOI: 10.14740/wjon1596