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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 -
Journal of Agricultural and Food... May 2014The antimicrobial effects of red wine and its inherent components on oral microbiota were studied by using a 5-species biofilm model of the supragingival plaque that...
The antimicrobial effects of red wine and its inherent components on oral microbiota were studied by using a 5-species biofilm model of the supragingival plaque that includes Actinomyces oris, Fusobacterium nucleatum, Streptococcus oralis, Streptococcus mutans and Veillonella dispar. Microbiological analysis (CFU counting and confocal laser scanning microscopy) of the biofilms after the application of red wine, dealcoholized red wine, and red wine extract solutions spiked or not with grape seed and inactive dry yeast extracts showed that the solutions spiked with seed extract were effective against F. nucleatum, S. oralis and A. oris. Also, red wine and dealcoholized wine had an antimicrobial effect against F. nucleatum and S. oralis. Additional experiments showed almost complete and early degradation of flavan-3-ol precursors [(+)-catechin and procyanidin B2] when incubating biofilms with the red wine extract. To our knowledge, this is the first study of antimicrobial properties of wine in an oral biofilm model.
Topics: Actinomyces; Anti-Bacterial Agents; Biofilms; Color; Dental Plaque; Fusobacterium nucleatum; Humans; Plant Extracts; Streptococcus; Veillonella; Vitis; Wine
PubMed: 24773294
DOI: 10.1021/jf501768p -
Frontiers in Nutrition 2023Very Low Birth Weight (VLBW) infants, born weighing less than 1,500 grams, are at risk for both gut dysbiosis and later neuropsychological developmental deficits....
INTRODUCTION
Very Low Birth Weight (VLBW) infants, born weighing less than 1,500 grams, are at risk for both gut dysbiosis and later neuropsychological developmental deficits. Behavioral effects, while related to neurodevelopment, are often more subtle and difficult to measure. The extent of later neurobehavioral consequences associated with such microbial dysbiosis has yet to be determined. We explored associations between the infants' gut microbiome and early childhood behavior at 4 years of age and identified the bacterial taxa through a multivariate analysis by linear models.
METHODS
Parents completed the Child Behavior Checklist (CBCL) focused on different DSM diagnostic categories: affective, anxiety, pervasive developmental, attention deficit/hyperactivity, and oppositional defiant. All the CBCL scores were corrected for gender, delivery method, gestational age, infant birth weight, occurrence of sepsis, and days on antibiotics prior statistical analyses. Canonical correlation analysis (CCA) was performed to determine the relationship between early life gut microbiome and the adjusted CBCL scores. The association of bacterial Amplicon sequence Variants (ASVs) to the CBCL scores were tested with multivariate analysis by linear models (MaAsLin).
RESULTS
Nineteen children who were previously born with very low birth weight and studied while hospitalized in the Neonatal Intensive Care Unit (NICU) were included in this study. Statistically significant associations were observed between early life gut bacteria such as , and to later behavior at 4 years. No significant association could be observed with early-life gut microbiome alpha diversity and behavioral measures at 4 years.
DISCUSSION
These preliminary observational data provide insight into the relationships between VLBW gut microbiome dysbiosis and childhood behavior. This study contributes to the literature on gut microbiome analysis by examining various behavioral domains using a standardized tool linked to the Diagnostic and Statistical Manual of Mental Disorders (DSM).
PubMed: 38419643
DOI: 10.3389/fnut.2023.1294549 -
Anaerobe Apr 2014Solobacterium moorei has recently been implicated as a causative agent of halitosis. In vitro experiments to evaluate the role of S. moorei in halitosis have, however,...
Solobacterium moorei has recently been implicated as a causative agent of halitosis. In vitro experiments to evaluate the role of S. moorei in halitosis have, however, been complicated by a paucity of information on the ideal conditions for culturing this organism. This work aimed to optimize a liquid culture medium for S. moorei, and to determine the growth-curve of the organism. Further, the ability of S. moorei to generate volatile sulfur compounds was investigated and compared quantitatively to other oral anaerobes by an optimized head-space gas chromatography method. Serum-supplementation of standard liquid growth media gave greater growth of S. moorei than non-supplemented broths, with the best medium found to be serum-supplemented tryptone soya broth. S. moorei was able to metabolize cysteine directly to hydrogen sulfide, but was unable to produce methanethiol from methionine. S. moorei produced 2-3 times more hydrogen sulfide (normalized for colony forming units) than Porphyromonas gingivalis and Veillonella dispar, but considerably less than Fusobacterium nucleatum. The study has identified reliable growth conditions for culture of S. moorei, which were employed to show that S. moorei has the requisite biochemistry consistent with a potential role in halitosis.
Topics: Chromatography, Gas; Culture Media; Cysteine; Gram-Positive Bacteria; Halitosis; Humans; Hydrogen Sulfide
PubMed: 24487184
DOI: 10.1016/j.anaerobe.2014.01.007 -
PloS One 2013The aim of this study was to investigate the impact of early colonizing species on the structure and the composition of the bacterial community developing in a...
The aim of this study was to investigate the impact of early colonizing species on the structure and the composition of the bacterial community developing in a subgingival 10-species biofilm model system. The model included Streptococcus oralis, Streptococcus anginosus, Actinomycesoris, Fusobacterium nucleatum subsp. nucleatum, Veillonella dispar, Campylobacter rectus, Prevotella intermedia, Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola. Based on literature, we considered Streptococcus oralis, Streptococcus anginosus, and Actinomyces oris as early colonizers and examined their role in the biofilms by either a delayed addition to the consortium, or by not inoculating at all the biofilms with these species. We quantitatively evaluated the resulting biofilms by real-time quantitative PCR and further compared the structures using confocal laser scanning microscopy following fluorescence in situ hybridisation. The absence of the early colonizers did not hinder biofilm formation. The biofilms reached the same total counts and developed to normal thickness. However, quantitative shifts in the abundances of individual species were observed. In the absence of streptococci, the overall biofilm structure appeared looser and more dispersed. Moreover, besides a significant increase of P. intermedia and a decrease of P. gingivalis , P. intermedia appeared to form filamented long chains that resembled streptococci. A. oris, although growing to significantly higher abundance in absence of streptococci, did not have a visible impact on the biofilms. Hence, in the absence of the early colonizers, there is a pronounced effect on P. intermedia and P. gingivalis that may cause distinct shifts in the structure of the biofilm. Streptococci possibly facilitate the establishment of P. gingivalis into subgingival biofilms, while in their absence P. intermedia became more dominant and forms elongated chains.
Topics: Actinomyces; Biofilms; Campylobacter rectus; Colony Count, Microbial; Fusobacterium nucleatum; Gingiva; Humans; In Situ Hybridization, Fluorescence; Microbial Consortia; Microscopy, Confocal; Porphyromonas gingivalis; Prevotella intermedia; Real-Time Polymerase Chain Reaction; Streptococcus; Streptococcus anginosus; Streptococcus oralis; Treponema denticola; Veillonella
PubMed: 24340084
DOI: 10.1371/journal.pone.0083090 -
Scientific Reports Nov 2020Given that sustained remission is the ultimate treatment goal in the management of patients with ulcerative colitis (UC), the decision to stop anti-tumor necrosis factor...
Given that sustained remission is the ultimate treatment goal in the management of patients with ulcerative colitis (UC), the decision to stop anti-tumor necrosis factor (anti-TNF) treatment in UC patients is difficult. The aim of this study was to evaluate mucosal microbiota and gene expression profiles associated with long-term remission after discontinuation of anti-TNF therapy. In nine UC patients who received anti-TNF therapy for 6 months, microbiota isolated from uninflamed mucosae and gene expression in inflamed and uninflamed mucosae were investigated at week 0 and at week 24. At treatment initiation, Fusobacterium sp. and Veillonella dispar were over-represented in the relapse group compared with the non-relapse group. After treatment, Dorea sp. and Lachnospira sp. were over-represented in the non-relapse group. In the relapse group only, a significant shift in gut bacterial community composition was found between week 0 and week 24. Gene expression of ALIX (PDCD6IP) and SLC9A3 was significantly higher in the non-relapse group than in the relapse group. Lastly, we used machine learning methods to identify relevant gene signatures associated with sustained remission. Statistical analyses of microbiota and expression profiles revealed differences between UC patients who did or did not keep remission after the discontinuation of TNF inhibitors.Trial registration: UMIN000020785: Evaluation of adalimumab therapy in mesalazine-resistant or -intolerant ulcerative colitis; an observational study (EARLY study).
Topics: Adalimumab; Adolescent; Adult; Anti-Inflammatory Agents; Colitis, Ulcerative; Female; Gastrointestinal Microbiome; Gene Expression; Humans; Intestinal Mucosa; Male; Middle Aged; Remission Induction; Treatment Outcome; Young Adult
PubMed: 33154436
DOI: 10.1038/s41598-020-76175-2 -
Clinical Oral Implants Research Jul 2016Staphylococcus spp. are postulated to play a role in peri-implantitis. This study aimed to develop a "submucosal" in vitro biofilm model, by integrating two...
OBJECTIVES
Staphylococcus spp. are postulated to play a role in peri-implantitis. This study aimed to develop a "submucosal" in vitro biofilm model, by integrating two staphylococci into its composition.
MATERIALS AND METHODS
The standard "subgingival" biofilm contained Actinomyces oris, Fusobacterium nucleatum, Streptococcus oralis, Veillonella dispar, Campylobacter rectus, Prevotella intermedia, Streptococcus anginosus, Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola, and was further supplemented with Staphyoccous aureus and/or Staphylococcus epidermidis. Biofilms were grown anaerobically on hydroxyapatite or titanium discs and harvested after 64 h for real-time polymerase chain reaction, to determine their composition. Confocal laser scanning microscopy and fluorescence in situ hybridization were used for identifying the two staphylococci within the biofilm.
RESULTS
Both staphylococci established within the biofilms when added separately. However, when added together, only S. aureus grew in high numbers, whereas S. epidermidis was reduced almost to the detection limit. Compared to the standard subgingival biofilm, addition of the two staphylococci had no impact on the qualitative or quantitative composition of the biofilm. When grown individually in the biofilm, S. epidermidis and S. aureus formed small distinctive clusters and it was confirmed that S. epidermidis was not able to grow in presence of S. aureus.
CONCLUSIONS
Staphyoccous aureus and S. epidermidis can be individually integrated into an oral biofilm grown on titanium, hence establishing a "submucosal" biofilm model for peri-implantitis. This model also revealed that S. aureus outcompetes S. epidermidis when grown together in the biofilm, which may explain the more frequent association of the former with peri-implantitis.
Topics: Biofilms; Gingiva; Humans; In Vitro Techniques; Models, Biological; Peri-Implantitis; Staphylococcus aureus; Staphylococcus epidermidis; Titanium
PubMed: 26461083
DOI: 10.1111/clr.12715 -
Clinical Oral Investigations Nov 2019To identify the microbiome in sockets with alveolar osteitis and compare it with a control group using metagenomic techniques.
OBJECTIVE
To identify the microbiome in sockets with alveolar osteitis and compare it with a control group using metagenomic techniques.
MATERIALS AND METHODS
A case-control study was conducted in subjects that had undergone a tooth extraction. Microbiological samples were taken from the sockets of 10 patients with dry socket after tooth extraction (AO group) and 10 patients in whom exodontia resulted in no postoperative complications (control group). Bacterial DNA was isolated, and the 16S rRNA gene was amplified and sequenced. Multiplexed tag-encoded sequencing of DNA from the samples was performed, and the reads were processed by Metagenomic Rapid Annotation.
RESULTS
A total of 151 different species were found: 55 bacteria were only found in the AO group, 51 were specific to the control group, and 45 were common to both groups. The most frequently found genera in both groups were Prevotella. Prevotella nanceiensis, Actinomyces odontolyticus, Treponema maltophilum, Veillonella dispar, Tannerella forsythia, and Leuconostoc mesenteroides were found in several patients with alveolar osteitis, with an abundance greater than 0.5%, and were absent in all the control group samples.
CONCLUSIONS
Patients who develop alveolar osteitis after dental extractions might have a different microbiota from that of patients without postoperative complications. Since this is a preliminary report, further research is needed to assess whether bacteria play an important role in the etiology of dry socket.
CLINICAL RELEVANCE
This study seems to indicate that bacteria may play an important role in the alveolar osteitis etiology. Thus, new prevention and treatment strategies should be considered.
Topics: Bacteria; Case-Control Studies; Dry Socket; Female; Humans; Male; Metagenome; RNA, Ribosomal, 16S; Tooth Extraction
PubMed: 30937543
DOI: 10.1007/s00784-019-02855-7 -
Journal of Medical Microbiology Mar 2018Micro-organisms are important triggers of peri-implant inflammation and analysing their diversity is necessary for peri-implantitis treatment. This study aimed to...
PURPOSE
Micro-organisms are important triggers of peri-implant inflammation and analysing their diversity is necessary for peri-implantitis treatment. This study aimed to analyse and compare the microbiota associated with individuals with peri-implantitis, as well as clinically healthy implant sites.
METHODOLOGY
Subgingival biofilm samples were taken from 10 individuals with peri-implantitis and from at least 1 clinically healthy implant. DNA was extracted and bacterial 16S rRNA genes were amplified using universal primers. After cloning the PCR-products, amplified inserts of positive clones were digested using restriction endonucleases, and the chosen clones were sequenced. The 16S rDNA-sequences were compared to those from the public sequence databases GenBank, EMBL and DDBJ to determine the corresponding taxa.
RESULTS
Differing distributions of taxa belonging to the phyla Firmicutes, Bacteroidetes, Fusobacteria, Actinobacteria, Proteobacteria, Synergistetes, Spirochaetae and TM 7 were detected in both the healthy implant (HI) and the peri-implantitis (PI) groups. A significantly higher relative abundance of phylum Bacteroidetes, as well as of the species Fusobacterium nucleatum, were found in the PI group (P<0.05). The putative periodontal red complex (Porphyromonas gingivalis, Tannerella forsythia) was also detected at significantly higher levels in the PI group (P<0.05), whereas the yellow group, as well as the species Veillonella dispar, tended to be associated with the HI group.
CONCLUSION
A shift in the healthy subgingival microbiota was shown in peri-implantitis-associated biofilm. Anaerobic Gram-negative periopathogens, including P. gingivalis and T. forsythia, seem to play an important role in peri-implantitis development and should be considered in treatment and prevention strategies.
Topics: Aged; Aged, 80 and over; Bacteria; Bacterial Load; Bacterial Physiological Phenomena; Bacteroides; Biofilms; Female; Fusobacterium nucleatum; Genes, rRNA; Gingiva; Humans; Male; Microbiota; Middle Aged; Peri-Implantitis; Porphyromonas gingivalis; Prevotella intermedia; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 29458668
DOI: 10.1099/jmm.0.000682 -
Journal of Dental Research Jan 2001The study of biofilm structure and function mandates the use of model systems for which a host of environmental variables can be rigorously controlled. We describe a...
The study of biofilm structure and function mandates the use of model systems for which a host of environmental variables can be rigorously controlled. We describe a model of supragingival plaque containing Actinomyces naeslundii, Veillonella dispar, Fusobacterium nucleatum, Streptococcus sobrinus, and Streptococcus oralis wherein cells are cultivated anaerobically in a saliva-based medium on hydroxyapatite discs coated with a salivary pellicle, with material and pieces of apparatus common to all microbiology laboratories. After 0.5 hr, 16.5 hrs, 40.5 hrs, and 64.5 hrs, the composition of adherent biofilms was analyzed by culture techniques, live/dead fluorescence staining, and confocal laser scanning microscopy. Repeated independent trials demonstrated the repeatability of biofilm formation after 40.5 hrs and 64.5 hrs. Brief exposures of biofilms to chlorhexidine or Triclosan produced losses in viability similar to those observed in vivo. This biofilm model should prove very useful for pre-clinical testing of prospective anti-plaque agents at clinically relevant concentrations.
Topics: Actinomyces; Analysis of Variance; Anti-Infective Agents, Local; Biofilms; Chlorhexidine; Colony Count, Microbial; Dental Pellicle; Dental Plaque; Durapatite; Fusobacterium nucleatum; Humans; Microbial Sensitivity Tests; Microscopy, Confocal; Models, Biological; Reproducibility of Results; Saliva; Streptococcus oralis; Streptococcus sobrinus; Triclosan; Veillonella
PubMed: 11269730
DOI: 10.1177/00220345010800011201