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Microbiome Nov 2017Colonization by the pathogen Clostridium difficile often occurs in the background of a disrupted microbial community. Identifying specific organisms conferring...
BACKGROUND
Colonization by the pathogen Clostridium difficile often occurs in the background of a disrupted microbial community. Identifying specific organisms conferring resistance to invasion by C. difficile is desirable because diagnostic and therapeutic strategies based on the human microbiota have the potential to provide more precision to the management and treatment of Clostridium difficile infection (CDI) and its recurrence.
METHODS
We conducted a longitudinal study of adult patients diagnosed with their first CDI. We investigated the dynamics of the gut microbiota during antibiotic treatment, and we used microbial or demographic features at the time of diagnosis, or after treatment, to predict CDI recurrence. To check the validity of the predictions, a meta-analysis using a previously published dataset was performed.
RESULTS
We observed that patients' microbiota "before" antibiotic treatment was predictive of disease relapse, but surprisingly, post-antibiotic microbial community is indistinguishable between patients that recur or not. At the individual OTU level, we identified Veillonella dispar as a candidate organism for preventing CDI recurrence; however, we did not detect a corresponding signal in the conducted meta-analysis.
CONCLUSION
Although in our patient population, a candidate organism was identified for negatively predicting CDI recurrence, results suggest the need for larger cohort studies that include patients with diverse demographic characteristics to generalize species that robustly confer colonization resistance against C. difficile and accurately predict disease relapse.
Topics: Aged; Anti-Bacterial Agents; Clostridioides difficile; Clostridium Infections; Feces; Female; Gastrointestinal Microbiome; Humans; Longitudinal Studies; Male; Meta-Analysis as Topic; Middle Aged; RNA, Ribosomal, 16S; Recurrence; Veillonellaceae
PubMed: 29132405
DOI: 10.1186/s40168-017-0368-1 -
Journal of Oral Science Dec 2017Dietary nitrate is reduced to nitrite and nitric oxide by microbial flora, and this activity is beneficial to vascular health. It has been reported that this bacterial...
Dietary nitrate is reduced to nitrite and nitric oxide by microbial flora, and this activity is beneficial to vascular health. It has been reported that this bacterial process is inhibited by chlorhexidine mouthwash, although the effects of other products are largely unknown. This study examined the effects of several treatments on salivary nitrate/nitrite and nitrate-reducing bacteria. Twelve university staff and students performed mouth-washing with water (control), essential oil, 0.35% povidone-iodine, or 0.0025% chlorhexidine and then ate 100 g lettuce (110 mg nitrate content), followed by collection of saliva and tongue bacteria at the baseline, and 1, 5, and 10 h thereafter. The individual treatments were separated by an interval of one week. Salivary nitrate/nitrite was measured by the calorimetric method, and a representative nitrate-reducing bacterial species, Veillonella dispar, was detected and semi-quantified using a polymerase chain reaction (PCR) assay. Significant increases in salivary nitrate/nitrite were observed for all treatments (all P < 0.05). The PCR assay showed that water, essential oil, and povidone-iodine mouthwash had little effect, whereas V. dispar DNA bands were markedly inhibited after washing with chlorhexidine. These results suggest that essential oil and povidone-iodine mouthwash have little effect on oral nitrate-reducing activity. Salivary nitrite production was not reduced by chlorhexidine, but the fainter band of V. dispar DNA suggests that longer daily use might blunt this nitrate-reducing activity.
Topics: Adult; Case-Control Studies; Chlorhexidine; DNA, Bacterial; Electrophoresis, Agar Gel; Female; Humans; Male; Mouthwashes; Nitrates; Nitrites; Oils, Volatile; Oxidation-Reduction; Polymerase Chain Reaction; Povidone-Iodine; Saliva; Veillonella; Young Adult
PubMed: 29093281
DOI: 10.2334/josnusd.16-0593 -
PloS One 2017Poor oral hygiene often leads to chronic diseases such as periodontitis and dental caries resulting in substantial economic costs and diminished quality of life in not...
Poor oral hygiene often leads to chronic diseases such as periodontitis and dental caries resulting in substantial economic costs and diminished quality of life in not only adults but also in children. In this study, the salivary microbiome was characterized in a group of children stratified by the Simplified Oral Hygiene Index (OHI-S). Illumina MiSeq high-throughput sequencing based on the 16S rRNA was utilized to analyze 90 salivary samples (24 Good, 31 Moderate and 35 Poor oral hygiene) from a cohort of Thai children. A total of 38,521 OTUs (Operational Taxonomic Units) with a 97% similarity were characterized in all of the salivary samples. Twenty taxonomic groups (Seventeen genera, two families and one class; Streptococcus, Veillonella, Gemellaceae, Prevotella, Rothia, Porphyromonas, Granulicatella, Actinomyces, TM-7-3, Leptotrichia, Haemophilus, Selenomonas, Neisseria, Megasphaera, Capnocytophaga, Oribacterium, Abiotrophia, Lachnospiraceae, Peptostreptococcus, and Atopobium) were found in all subjects and constituted 94.5-96.5% of the microbiome. Of these twenty genera, the proportion of Streptococcus decreased while Veillonella increased with poor oral hygiene status (P < 0.05). Furthermore, an unassigned species of Veillonella, Veillonella dispar and Veillonella parvula tended to be elevated in the Poor oral hygiene group. This is the first study demonstrating an important association between increase of Veillonella and poor oral hygiene status in children. However, further studies are required to identify the majority of Veillonella at species level in salivary microbiome of the Poor oral hygiene group.
Topics: Adolescent; Child; Female; Humans; Male; Microbiota; Oral Hygiene Index; RNA, Bacterial; RNA, Ribosomal, 16S; Saliva
PubMed: 28934367
DOI: 10.1371/journal.pone.0185274 -
International Journal of Chronic... 2017The study aimed to determine the relationship between throat microbiome and COPD. Sixty-five Chinese males (n=20, smokers without COPD; n=45 smokers with COPD) were...
The study aimed to determine the relationship between throat microbiome and COPD. Sixty-five Chinese males (n=20, smokers without COPD; n=45 smokers with COPD) were included. Nonmetric multidimensional scaling indicated differences of microbiome between COPD and controls, but no difference was observed between COPD patients with differing degrees of lung function or disease severity. Rarefaction analyses suggested that operational taxonomic units (OTUs, species-level) richness decreased in COPD. The dominant taxa between COPD and controls were similar, but the proportions of taxonomic distribution were different. The dominant phyla were and . The dominant genera were and . Two dominant OTUs, otu3 (_) and otu4 (s_unclassified), were identified. Otu3 and its father-level taxa, which were negatively correlated with predicted percent of forced expiratory volume in a second (FEV%pred), were increased in COPD. By contrast, otu4 and its father-level taxa, which were positively correlated with FEV%pred, were decreased in COPD. Otu4 also showed a slight potential as a COPD biomarker. To conclude, the throat microbiome was different between smokers with or without COPD, which is similar to findings from the lower respiratory tract. This study may strengthen our understanding of the relationship between microbiomes of different airway sites and COPD.
Topics: Aged; Bacteria; Case-Control Studies; China; Cross-Sectional Studies; Forced Expiratory Volume; Humans; Lung; Male; Microbiota; Middle Aged; Pharynx; Pulmonary Disease, Chronic Obstructive; Ribotyping; Severity of Illness Index; Smoking
PubMed: 28740374
DOI: 10.2147/COPD.S140243 -
PeerJ 2017The study of ancient microorganisms in mineralized dental plaque or calculi is providing insights into microbial evolution, as well as lifestyles and disease states of...
BACKGROUND
The study of ancient microorganisms in mineralized dental plaque or calculi is providing insights into microbial evolution, as well as lifestyles and disease states of extinct cultures; yet, little is still known about the oral microbial community structure and function of pre-Columbian Caribbean cultures. In the present study, we investigated the dental calculi microbiome and predicted function of one of these cultures, known as the Saladoid. The Saladoids were horticulturalists that emphasized root-crop production. Fruits, as well as small marine and terrestrial animals were also part of the Saladoid diet.
METHODS
Dental calculi samples were recovered from the archaeological site of Sorcé, in the municipal island of Vieques, Puerto Rico, characterized using 16S rRNA gene high-throughput sequencing, and compared to the microbiome of previously characterized coprolites of the same culture, as well modern plaque, saliva and stool microbiomes available from the Human Microbiome Project.
RESULTS
Actinobacteria, Proteobacteria and Firmicutes comprised the majority of the Saladoid dental calculi microbiome. The Saladoid dental calculi microbiome was distinct when compared to those of modern saliva and dental plaque, but showed the presence of common inhabitants of modern oral cavities including sp., and . Cell motility, signal transduction and biosynthesis of other secondary metabolites may be unique features of the Saladoid microbiome.
DISCUSSION
Results suggest that the Saladoid dental calculi microbiome structure and function may possibly reflect a horticulturalist lifestyle and distinct dietary habits. Results also open the opportunity to further elucidate oral disease states in extinct Caribbean cultures and extinct indigenous cultures with similar lifestyles.
PubMed: 28480145
DOI: 10.7717/peerj.3277 -
MSphere 2017The aim of the study was to analyze the bacteriome of acute otitis media with a novel modification of next-generation sequencing techniques. Outpatient children with...
Next-Generation Sequencing Combined with Specific PCR Assays To Determine the Bacterial 16S rRNA Gene Profiles of Middle Ear Fluid Collected from Children with Acute Otitis Media.
The aim of the study was to analyze the bacteriome of acute otitis media with a novel modification of next-generation sequencing techniques. Outpatient children with acute otitis media were enrolled in the study, and middle ear fluids were collected during 90 episodes from 79 subjects aged 5 to 42 months (median age, 19 months). The bacteriome profiles of middle ear fluid samples were determined by a nested-PCR amplification of the 16S rRNA gene (V4 region), followed by mass sequencing. The profiling results were compared to the results of specific PCR assays targeting selected prevalent pathogens. Bacteriome profiling using nested amplification of low-volume samples was aided by a bioinformatic subtraction of signal contaminants from the recombinant polymerase, achieving a sensitivity slightly lower than that of specific PCR detection. was detected in 28 (31%) samples, in 24 (27%), in 18 (20%), spp. in 21 (23%), in 5 (5.6%), in 3 (3.3%), and other bacteria in 14 (16%) using bacteriome profiling. was the dominant pathogen in 14 (16%) samples, in 15 (17%), in 5 (5.6%), in 2, and in 2. Weaker signals of , , and were noted in several samples. Fourteen samples (16%) were not explainable by bacterial pathogens; novel causative agents were not detected. In conclusion, unbiased bacteriome profiling helped in depicting the true mutual quantitative ratios of ear bacteria, but at present, its complicated protocol impedes its routine clinical use. Although , , and have been long established as the most important pathogens in acute otitis media using culture and specific PCR assays, the knowledge of their mutual quantitative relations and possible roles of other bacteria is incomplete. The advent of unbiased bacteriome 16S rRNA gene profiling has allowed the detection of nearly all bacteria present in the sample, and it helps in depicting their mutual quantitative ratios. Due to the difficulties in performing mass sequencing in low-volume samples, only a few bacteriome-profiling studies of otitis media have been published, all limited to cases of chronic otitis media. Here, we present a study on samples obtained from young children with acute otitis media, successfully using a strategy of nested PCR coupled with mass sequencing, and demonstrate that the method can confer quantitative information hardly obtainable by other methods.
PubMed: 28357413
DOI: 10.1128/mSphere.00006-17 -
PloS One 2017Peri-implantitis caused by multispecies biofilms is a major complication in dental implant treatment. The bacterial infection surrounding dental implants can lead to...
Peri-implantitis caused by multispecies biofilms is a major complication in dental implant treatment. The bacterial infection surrounding dental implants can lead to bone loss and, in turn, to implant failure. A promising strategy to prevent these common complications is the development of implant surfaces that inhibit biofilm development. A reproducible and easy-to-use biofilm model as a test system for large scale screening of new implant surfaces with putative antibacterial potency is therefore of major importance. In the present study, we developed a highly reproducible in vitro four-species biofilm model consisting of the highly relevant oral bacterial species Streptococcus oralis, Actinomyces naeslundii, Veillonella dispar and Porphyromonas gingivalis. The application of live/dead staining, quantitative real time PCR (qRT-PCR), scanning electron microscopy (SEM) and urea-NaCl fluorescence in situ hybridization (urea-NaCl-FISH) revealed that the four-species biofilm community is robust in terms of biovolume, live/dead distribution and individual species distribution over time. The biofilm community is dominated by S. oralis, followed by V. dispar, A. naeslundii and P. gingivalis. The percentage distribution in this model closely reflects the situation in early native plaques and is therefore well suited as an in vitro model test system. Furthermore, despite its nearly native composition, the multispecies model does not depend on nutrient additives, such as native human saliva or serum, and is an inexpensive, easy to handle and highly reproducible alternative to the available model systems. The 96-well plate format enables high content screening for optimized implant surfaces impeding biofilm formation or the testing of multiple antimicrobial treatment strategies to fight multispecies biofilm infections, both exemplary proven in the manuscript.
Topics: Bacteria; Biofilms; In Situ Hybridization, Fluorescence; Microscopy, Electron, Scanning; Mouth; Species Specificity
PubMed: 28296966
DOI: 10.1371/journal.pone.0173973 -
MSystems 2017Waterfowl, especially ducks and geese, are primary reservoirs for influenza A viruses (IAVs) that evolve and emerge as important pathogens in domestic animals and...
Waterfowl, especially ducks and geese, are primary reservoirs for influenza A viruses (IAVs) that evolve and emerge as important pathogens in domestic animals and humans. In contrast to humans, where IAVs infect the respiratory tract and cause significant morbidity and mortality, IAVs infect the gastrointestinal tract of waterfowl and cause little or no pathology and are spread by fecal-oral transmission. For this reason, we examined whether IAV infection is associated with differences in the cloacal microbiome of mallards (), an important host of IAVs in North America and Eurasia. We characterized bacterial community composition by sequencing the V4 region of 16S rRNA genes. IAV-positive mallards had lower species diversity, richness, and evenness than IAV-negative mallards. Operational taxonomic unit (OTU) cooccurrence patterns were also distinct depending on infection status. Network analysis showed that IAV-positive mallards had fewer significant cooccurring OTUs and exhibited fewer coassociation patterns among those OTUs than IAV-negative mallards. These results suggest that healthy mallards have a more robust and complex cloacal microbiome. By combining analytical approaches, we identified 41 bacterial OTUs, primarily representatives of spp., , and , contributing to the observed differences. This study found that IAV-infected wild mallards exhibited strong differences in microbiome composition relative to noninfected mallards and identified a concise set of putative biomarker OTUs. Using Random Forest, a supervised machine learning method, we verified that these 41 bacterial OTUs are highly predictive of infection status. Seasonal influenza causes 3 to 5 million severe illnesses and 250,000 to 500,000 human deaths each year. While pandemic influenza viruses emerge only periodically, they can be devastating-for example, the 1918 H1N1 pandemic virus killed more than 20 million people. IAVs infect the respiratory tract and cause significant morbidity and mortality in humans. In contrast, IAVs infect the gastrointestinal tract of waterfowl, producing little pathology. Recent studies indicated that viruses can alter the microbiome at the respiratory and gastrointestinal mucosa, but there are no reports of how the microbiota of the natural host of influenza is affected by infection. Here we find that the mallard microbiome is altered during IAV infection. Our results suggest that detailed examination of humans and animals infected with IAVs may reveal individualized microbiome profiles that correspond to health and disease. Moreover, future studies should explore whether the altered microbiome facilitates maintenance and transmission of IAVs in waterfowl populations.
PubMed: 28293681
DOI: 10.1128/mSystems.00188-16 -
PloS One 2016Methanethiol (methyl mercaptan) is an important contributor to oral malodour and periodontal tissue destruction. Porphyromonas gingivalis, Prevotella intermedia and...
Methanethiol (methyl mercaptan) is an important contributor to oral malodour and periodontal tissue destruction. Porphyromonas gingivalis, Prevotella intermedia and Fusobacterium nucleatum are key oral microbial species that produce methanethiol via methionine gamma lyase (mgl) activity. The aim of this study was to compare an mgl knockout strain of P. gingivalis with its wild type using a 10-species biofilm co-culture model with oral keratinocytes and its effect on biofilm composition and inflammatory cytokine production. A P. gingivalis mgl knockout strain was constructed using insertion mutagenesis from wild type W50 with gas chromatographic head space analysis confirming lack of methanethiol production. 10-species biofilms consisting of Streptococcus mitis, Streptococcus oralis, Streptococcus intermedius, Fusobacterium nucleatum ssp polymorphum, Fusobacterium nucleatum ssp vincentii, Veillonella dispar, Actinomyces naeslundii, Prevotella intermedia and Aggregatibacter actinomycetemcomitans with either the wild type or mutant P. gingivalis were grown on Thermanox cover slips and used to stimulate oral keratinocytes (OKF6-TERT2), under anaerobic conditions for 4 and 24 hours. Biofilms were analysed by quantitative PCR with SYBR Green for changes in microbial ecology. Keratinocyte culture supernatants were analysed using a multiplex bead immunoassay for cytokines. Significant population differences were observed between mutant and wild type biofilms; V. dispar proportions increased (p<0.001), whilst A. naeslundii (p<0.01) and Streptococcus spp. (p<0.05) decreased in mutant biofilms. Keratinocytes produced less IL-8, IL-6 and IL-1α when stimulated with the mutant biofilms compared to wild type. Lack of mgl in P. gingivalis has been shown to affect microbial ecology in vitro, giving rise to a markedly different biofilm composition, with a more pro-inflammatory cytokine response from the keratinocytes observed. A possible role for methanethiol in biofilm formation and cytokine response with subsequent effects on oral malodor and periodontitis is suggested.
Topics: Adhesins, Bacterial; Biofilms; Carbon-Sulfur Lyases; Cell Line; Cysteine Endopeptidases; Cytokines; Gene Knockout Techniques; Gingipain Cysteine Endopeptidases; Humans; Inflammation; Keratinocytes; Mouth; Porphyromonas gingivalis; Sulfur
PubMed: 28033374
DOI: 10.1371/journal.pone.0169157 -
PloS One 2016Live attenuated influenza vaccine (LAIV) has demonstrated varying levels of efficacy against seasonal influenza; however, LAIV may be used as a tool to measure...
Live attenuated influenza vaccine (LAIV) has demonstrated varying levels of efficacy against seasonal influenza; however, LAIV may be used as a tool to measure interactions between the human microbiome and a live, replicating virus. To increase our knowledge of this interaction, we measured changes to the nasal microbiome in subjects who received LAIV to determine if associations between influenza-specific IgA production and the nasal microbiome exist after immunization with a live virus vaccine. The anterior nares of 47 healthy subjects were swabbed pre- (Day 0) and post- (Days 7 and 28) LAIV administration, and nasal washes were conducted on Days 0 and 28. We performed next-generation sequencing on amplified 16s rRNA genes and measured mucosal influenza-specific IgA titers via enzyme-linked immunosorbent assay (ELISA). A significant increase in alpha diversity was identified (Observed, CHAO, and ACE) between Days 7 vs 0 (p-values = 0.017, 0.005, 0.005, respectively) and between Days 28 vs 0 (p-values = 0.054, 0.030, 0.050, respectively). Several significant associations between the presence of different microbial species, including Lactobacillus helveticus, Prevotella melaninogenica, Streptococcus infantis, Veillonella dispar, and Bacteroides ovatus, and influenza-specific H1 and H3 IgA antibody response were demonstrated. These data suggest that LAIV alters the nasal microbiome, allowing several less-abundant OTUs to establish a community niche. Additionally, specific alterations in the nasal microbiome are significantly associated with variations in influenza-specific IgA antibody production and could be clinically relevant.
Topics: Adolescent; Adult; Antibodies, Viral; Bacteria; Female; Hemagglutinin Glycoproteins, Influenza Virus; Humans; Immunoglobulin A; Influenza A virus; Influenza Vaccines; Influenza, Human; Male; Microbiota; Nasal Cavity; Vaccines, Attenuated; Young Adult
PubMed: 27643883
DOI: 10.1371/journal.pone.0162803