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Gut Mar 2022Long-term complications after COVID-19 are common, but the potential cause for persistent symptoms after viral clearance remains unclear.
BACKGROUND
Long-term complications after COVID-19 are common, but the potential cause for persistent symptoms after viral clearance remains unclear.
OBJECTIVE
To investigate whether gut microbiome composition is linked to post-acute COVID-19 syndrome (PACS), defined as at least one persistent symptom 4 weeks after clearance of the SARS-CoV-2 virus.
METHODS
We conducted a prospective study of 106 patients with a spectrum of COVID-19 severity followed up from admission to 6 months and 68 non-COVID-19 controls. We analysed serial faecal microbiome of 258 samples using shotgun metagenomic sequencing, and correlated the results with persistent symptoms at 6 months.
RESULTS
At 6 months, 76% of patients had PACS and the most common symptoms were fatigue, poor memory and hair loss. Gut microbiota composition at admission was associated with occurrence of PACS. Patients without PACS showed recovered gut microbiome profile at 6 months comparable to that of non-COVID-19 controls. Gut microbiome of patients with PACS were characterised by higher levels of , and lower levels of . Persistent respiratory symptoms were correlated with opportunistic gut pathogens, and neuropsychiatric symptoms and fatigue were correlated with nosocomial gut pathogens, including and (all p<0.05). Butyrate-producing bacteria, including and showed the largest inverse correlations with PACS at 6 months.
CONCLUSION
These findings provided observational evidence of compositional alterations of gut microbiome in patients with long-term complications of COVID-19. Further studies should investigate whether microbiota modulation can facilitate timely recovery from post-acute COVID-19 syndrome.
Topics: COVID-19; Follow-Up Studies; Gastrointestinal Microbiome; Humans; Metagenomics; Prospective Studies; SARS-CoV-2; Severity of Illness Index; Post-Acute COVID-19 Syndrome
PubMed: 35082169
DOI: 10.1136/gutjnl-2021-325989 -
Microorganisms Jan 2023The aim of this study was to investigate and clarify the ambiguous taxonomy of and its closely related species using state-of-the-art high-throughput sequencing...
The aim of this study was to investigate and clarify the ambiguous taxonomy of and its closely related species using state-of-the-art high-throughput sequencing techniques, and, furthermore, to determine whether sub-clusters identified within and in a previous study by multi locus sequence typing (MLST) using concatenation of seven housekeeping genes should either be classified as subspecies or distinct species. The strains in this study were broadly classified under group as genospecies I and genospecies II. Based on MLST data analysis, these were further classified as and . The whole genome sequencing of selected strains of ( = 17) and ( = 19) was carried out using Illumina Genome Analyzer IIxe and Roche 454 allowing paired-end and single-reads sequencing, respectively. The sequences obtained were aligned using CLC Genomic workbench version 5.1 and annotated using RAST (Rapid Annotation using Subsystem Technology) release version 59 accessible online. Additionally, genomes of seven publicly available strains of (k20, MG1, c505, OT175, OT171, OT170, and ) were also included. Comparative genomic analysis (CGA) using Mauve, Progressive Mauve, gene-by-gene, Core, and Pan Genome, and finally Digital DNA-DNA homology (DDH) analysis was carried out. DDH values were obtained using in silico genome-genome comparison. Evolutionary analysis using ClonalFrame was also undertaken. The mutation and recombination events were compared using chi-square test among and isolates (analysis methods are not included in the study). CGA results were consistent with previous traditional classification using MLST. It was found that strains of k20, MG1, c505, and OT175 clustered in group of isolates, while OT171, OT170, and appeared as separate branches. Similar clustering to MLST was observed for other isolates. The mutation and recombination events were significantly higher in than , highlighting the diversity of strains in the oral cavity. These findings suggest that forms six distinct groups, whereas forms three. The correct designation of isolates will help in the identification of clinical isolates found in dental plaque. Easily accessible online genomic sequence data will also accelerate the investigation of the biochemical characterisation and pathogenesis of this important group of micro-organisms.
PubMed: 36838222
DOI: 10.3390/microorganisms11020254 -
Microorganisms Jan 2020The study of bacterial interaction between Streptococcus mutans and Actinomyces naeslundii may disclose important features of biofilm interspecies relationships. The aim...
The study of bacterial interaction between Streptococcus mutans and Actinomyces naeslundii may disclose important features of biofilm interspecies relationships. The aim of this study was to characterize-with an emphasis on biofilm formation and composition and metabolic activity-single- and dual-species biofilms of S. mutans or A. naeslundii, and to use a drip flow reactor (DFR) to evaluate biofilm stress responses to 0.2% chlorhexidine diacetate (CHX). Single- and dual-species biofilms were grown for 24 h. The following factors were evaluated: cell viability, biomass and total proteins in the extracellular matrix, 2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide-"XTT"-reduction and lactic acid production. To evaluate stress response, biofilms were grown in DFR. Biofilms were treated with CHX or 0.9% sodium chloride (NaCl; control). Biofilms were plated for viability assessment. Confocal laser-scanning microscopy (CLSM) was also performed. Data analysis was carried out at 5% significance level. viability and lactic acid production in dual-species biofilms were significantly reduced. showed a higher resistance to CHX in dual-species biofilms. Total protein content, biomass and XTT reduction showed no significant differences between single- and dual-species biofilms. CLSM images showed the formation of large clusters in dual-species biofilms. In conclusion, dual-species biofilms reduced viability and lactic acid production and increased resistance to chlorhexidine.
PubMed: 32023892
DOI: 10.3390/microorganisms8020194 -
BMC Oral Health Jun 2023Streptococcus, Bifidobacteria, Lactobacillus and Actinomyces are acidogenic aciduria that may be associated with root caries (RC). The aim of the study was to analyze...
BACKGROUND
Streptococcus, Bifidobacteria, Lactobacillus and Actinomyces are acidogenic aciduria that may be associated with root caries (RC). The aim of the study was to analyze Streptococcus mutans (S. mutans), Streptococcus sobrinus (S. sobrinus), Bifidobacterium spp., Lactobacillus spp. and Actinomyces naeslundii (A. naeslundii) in the saliva of nursing home elderly, to assess the correlation between bacterial composition and RC for five putative catiogenic organisms.
METHODS
In this study, we collected 43 saliva samples and divided into two groups: the root caries group (RCG, n = 21) and the caries-free group (CFG, n = 22). Bacterial DNA was extracted from the saliva samples. The presence and abundance of the five microorganisms were detected by Quantitative real-time PCR (qPCR). Spearman correlation test was performed to evaluate the relationship between the numbers of root decayed filled surfaces (RDFS) and root caries index (RCI) and salivary levels of the bacteria.
RESULTS
The salivary levels of S. mutans, S. sobrinus, Bifidobacterium spp. and Lactobacillus spp. were significantly higher in RCG than in CFG (p < 0.05). RDFS and RCI (RDFS/RCI) were positively associated with salivary levels of S. mutans, S. sobrinus and Bifidobacterium spp. (r = 0.658/0.635, r = 0.465/0.420 and r = 0.407/0.406, respectively). No significant differences in presence and amounts of A. naeslundii was observed between the two groups (p > 0.05).
CONCLUSION
S. mutans, S. sobrinus and Bifidobacterium spp. in saliva appear to be associated with RC in the elderly. Taken together, the findings indicate that specific salivary bacteria may be involved in the progression of RC.
Topics: Humans; Aged; Root Caries; Streptococcus mutans; Streptococcus sobrinus; Dental Caries; Saliva; Nursing Homes
PubMed: 37270529
DOI: 10.1186/s12903-023-02953-9 -
Journal of Biotechnology May 2017Infections induced by oral biofilms include caries, as well as periodontal, and peri-implant disease, and may influence quality of life, systemic health, and... (Review)
Review
Infections induced by oral biofilms include caries, as well as periodontal, and peri-implant disease, and may influence quality of life, systemic health, and expenditure. As bacterial biofilms are highly resistant and resilient to conventional antibacterial therapy, it has been difficult to combat these infections. An innovative alternative to the biocontrol of oral biofilms could be to use bacteriophages or phages, the viruses of bacteria, which are specific, non-toxic, self-proliferating, and can penetrate into biofilms. Phages for Actinomyces naeslundii, Aggregatibacter actinomycetemcomitans, Enterococcus faecalis, Fusobacterium nucleatum, Lactobacillus spp., Neisseria spp., Streptococcus spp., and Veillonella spp. have been isolated and characterised. Recombinant phage enzymes (lysins) have been shown to lyse A. naeslundii and Streptococcus spp. However, only a tiny fraction of available phages and their lysins have been explored so far. The unique properties of phages and their lysins make them promising but challenging antimicrobials. The genetics and biology of phages have to be further explored in order to determine the most effective way of applying them. Studying the effect of phages and lysins on multispecies biofilms should pave the way for microbiota engineering and microbiota-based therapy.
Topics: Bacterial Infections; Bacteriophages; Biofilms; Humans; Mouth; Mouth Diseases
PubMed: 28108235
DOI: 10.1016/j.jbiotec.2017.01.002 -
FEMS Yeast Research Aug 2015Microbial interactions are necessarily associated with the development of polymicrobial oral biofilms. The objective of this study was to determine the coaggregation of...
Microbial interactions are necessarily associated with the development of polymicrobial oral biofilms. The objective of this study was to determine the coaggregation of eight strains of Candida albicans with Actinomyces naeslundii and Streptococcus mutans. In autoaggregation assays, C. albicans strains were grown in RPMI-1640 and artificial saliva medium (ASM) whereas bacteria were grown in heart infusion broth. C. albicans, A. naeslundii and S. mutans were suspended to give 10(6), 10(7) and 10(8) cells mL(-1) respectively, in coaggregation buffer followed by a 1 h incubation. The absorbance difference at 620 nm (ΔAbs) between 0 h and 1 h was recorded. To study coaggregation, the same protocol was used, except combinations of microorganisms were incubated together. The mean ΔAbs% of autoaggregation of the majority of RPMI-1640-grown C. albicans was higher than in ASM grown. Coaggregation of C. albicans with A. naeslundii and/or S. mutans was variable among C. albicans strains. Scanning electron microscopy images showed that A. naeslundii and S. mutans coaggregated with C. albicans in dual- and triculture. In conclusion, the coaggregation of C. albicans, A. naeslundii and S. mutans is C. albicans strain dependent.
Topics: Actinomyces; Biofilms; Candida albicans; Cell Aggregation; Culture Media; Microscopy, Electron, Scanning; Saliva, Artificial; Streptococcus mutans
PubMed: 26054855
DOI: 10.1093/femsyr/fov038 -
Antibiotics (Basel, Switzerland) Oct 2020Actinomycosis is a chronic bacterial infection characterized by continuous local spread, irrespective of anatomical barriers, and granulomatous suppurative inflammation....
Actinomycosis is a chronic bacterial infection characterized by continuous local spread, irrespective of anatomical barriers, and granulomatous suppurative inflammation. Due to its expansive local growth, it can simulate a malignant tumour. Subsequent hematogenous dissemination to distant organs can mimic metastases and further increase suspicion for malignancy. A case of severe disseminated pelvic actinomycosis associated with intrauterine device is described here. The patient presented with a pelvic mass mimicking a tumour, bilateral ureteral obstruction, ascites, multinodular involvement of the liver, lungs and spleen, inferior vena cava thrombosis and extreme cachexia. Actinomycosis was diagnosed by liver biopsy and confirmed by culture of from extracted intrauterine contraceptive device (IUD). Prolonged treatment with aminopenicillin and surgery resulted in recovery with moderate sequelae.
PubMed: 33137889
DOI: 10.3390/antibiotics9110748 -
Anaerobe Aug 2018Diterpenes are an important class of plant metabolites that can be used in the search for new antibacterial agents. ent-Copalic acid (CA), the major diterpene in...
Diterpenes are an important class of plant metabolites that can be used in the search for new antibacterial agents. ent-Copalic acid (CA), the major diterpene in Copaifera species exudates, displays several pharmacological properties. This study evaluates the CA antibacterial potential against the anaerobic bacteria Peptostreptococcus anaerobius and Actinomyces naeslundii. Antimicrobial assays included time-kill and biofilm inhibition and eradication assays. Time-kill assays conducted for CA concentrations between 6.25 and 12.5 μg/mL evidenced bactericidal activity within 72 h. CA combined with chlorhexidine dihydrochloride (CHD) exhibited bactericidal action against P. anaerobius within 6 h of incubation. As for A. naeslundii, the same combination reduced the number of microorganisms by over 3 log10 at 24 h and exerted a bactericidal effect at 48 h of incubation. CA at 500 and 2000 μg/mL inhibited P. anaerobius and A. naeslundii biofilm formation by at least 50%, respectively. CA at 62.5 and 1.000 μg/mL eradicated 99.9% of pre-formed P. anaerobius and A. naeslundii biofilms, respectively. These results indicated that CA presents in vitro antibacterial activity and is a potential biofilm inhibitory agent. This diterpene may play an important role in the search for novel sources of agents that can act against anaerobic bacteria.
Topics: Actinomyces; Biofilms; Diterpenes; Fabaceae; Microbial Sensitivity Tests; Peptostreptococcus; Plant Extracts
PubMed: 29885640
DOI: 10.1016/j.anaerobe.2018.05.013 -
Journal of Dental Research Mar 2022An intuitive, clinically relevant index of microbial dysbiosis as a summary statistic of subgingival microbiome profiles is needed. Here, we describe a subgingival...
An intuitive, clinically relevant index of microbial dysbiosis as a summary statistic of subgingival microbiome profiles is needed. Here, we describe a subgingival microbial dysbiosis index (SMDI) based on machine learning analysis of published periodontitis/health 16S microbiome data. The raw sequencing data, split into training and test sets, were quality filtered, taxonomically assigned to the species level, and centered log-ratio transformed. The training data set was subject to random forest analysis to identify discriminating species (DS) between periodontitis and health. DS lists, compiled by various "Gini" importance score cutoffs, were used to compute the SMDI for samples in the training and test data sets as the mean centered log-ratio abundance of periodontitis-associated species subtracted by that of health-associated ones. Diagnostic accuracy was assessed with receiver operating characteristic analysis. An SMDI based on 49 DS provided the highest accuracy with areas under the curve of 0.96 and 0.92 in the training and test data sets, respectively, and ranged from -6 (most normobiotic) to 5 (most dysbiotic) with a value around zero discriminating most of the periodontitis and healthy samples. The top periodontitis-associated DS were spp., and , while and were the top health-associated DS. The index was highly reproducible by hypervariable region. Applying the index to additional test data sets in which nitrate had been used to modulate the microbiome demonstrated that nitrate has dysbiosis-lowering properties in vitro and in vivo. Finally, 3 genera (, and ) were identified that could be used for calculation of a simplified SMDI with comparable accuracy. In conclusion, we have developed a nonbiased, reproducible, and easy-to-interpret index that can be used to identify patients/sites at risk of periodontitis, to assess the microbial response to treatment, and, importantly, as a quantitative tool in microbiome modulation studies.
Topics: Dysbiosis; Humans; Microbiota; Periodontitis; RNA, Ribosomal, 16S; Treponema denticola
PubMed: 34428955
DOI: 10.1177/00220345211035775 -
Beneficial Microbes Apr 2017We hypothesised that consumption of beverage rich in both fibre and polyphenols, rather than each bioactive alone, will modulate populations of selected salivary... (Clinical Trial)
Clinical Trial
We hypothesised that consumption of beverage rich in both fibre and polyphenols, rather than each bioactive alone, will modulate populations of selected salivary bacteria, and their adhesion characteristics and that some of these effects may be due to the anti-microbial activity of the beverage bioactives. We investigated the effect of 4 weeks' consumption of beverages, rich in apple fibre, boysenberry polyphenols, or both on salivary bacteria in healthy subjects. In this placebo-controlled crossover study, saliva samples were collected at the beginning and end of each treatment period, and used for qPCR quantitation of Lactobacillus spp., Actinomyces naeslundii and Streptococcus mutans. The counts of salivary A. naeslundii decreased after the consumption of the apple-boysenberry beverage (P<0.05, Student's t-test). We also examined the effect of the subjects' saliva on bacterial adhesion using a mixed species biofilm model. The salivary pellicles prepared before and after each treatment were inoculated with laboratory strains of A. naeslundii, Lactobacillus rhamnosus and S. mutans and tested for biofilm formation. The post appleboysenberry beverage salivary pellicle significantly decreased the adhesion of A. naeslundii at the end of both 3 and 24 h, in the in vitro biofilm. A 1/16 dilution of the apple-boysenberry beverage itself decreased the proliferation of test strains of A. naeslundii and S. mutans by 51 and 55%, respectively (P<0.005), indicating the antimicrobial activity of its bioactives. This study demonstrated that consumption of apple-boysenberry beverage, rather than apple or the boysenberry beverage alone or the placebo, decreased salivary A. naeslundii and their adhesion under laboratory conditions. These changes are factors that influence oral microecology and potentially oral health.
Topics: Actinomyces; Adult; Anti-Bacterial Agents; Bacterial Adhesion; Bacterial Load; Biofilms; Female; Fruit and Vegetable Juices; Humans; Lactobacillus; Male; Malus; Middle Aged; Rubus; Saliva; Streptococcus mutans
PubMed: 28403648
DOI: 10.3920/BM2016.0061