Use of quantitative PCR and culture methods to characterize ecological flux in bacterial biofilms

Salivary levels of five microorganisms of root caries in nursing home elderly: a preliminary investigation

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.

Polymicrobial synergy stimulates Porphyromonas gingivalis survival and gingipain expression in a multi-species subgingival community

Background

Dysbiosis in subgingival microbial communities, resulting from increased inflammatory transudate from the gingival tissues, is an important factor in initiation and development of periodontitis. Dysbiotic communities are characterized by increased numbers of bacteria that exploit the serum-like transudate for nutrients, giving rise to a proteolytic community phenotype. Here we investigate the contribution of interactions between members of a sub-gingival community to survival and development of virulence in a serum environment—modelling that in the subgingival pocket.

Methods

Growth and proteolytic activity of three Porphyromonas gingivalis strains in nutrient broth or a serum environment were assessed using A₆₀₀ and a fluorescent protease substrate, respectively. Adherence of P. gingivalis strains to serum-coated surfaces was studied with confocal microscopy and 2D-gel electrophoresis of bacterial supernatants used to investigate extracellular proteins. A model multi-species sub-gingival community containing Fusobacterium nucleatum, Streptococcus constellatus, Parvimonas micra with wild type or isogenic mutants of P. gingivalis was then created and growth and proteolytic activity in serum assessed as above. Community composition over time was monitored using culture techniques and qPCR.

Results

The P. gingivalis strains showed different growth rates in nutrient broth related to the level of proteolytic activity (largely gingipains) in the cultures. Despite being able to adhere to serum-coated surfaces, none of the strains was able to grow alone in a serum environment. Together in the subgingival consortium however, all the included species were able to grow in the serum environment and the community adopted a proteolytic phenotype. Inclusion of P. gingivalis strains lacking gingipains in the consortium revealed that community growth was facilitated by Rgp gingipain from P. gingivalis.

Conclusions

In the multi-species consortium, growth was facilitated by the wild-type and Rgp-expressing strains of P. gingivalis, suggesting that Rgp is involved in delivery of nutrients to the whole community through degradation of complex protein substrates in serum. Whereas they are constitutively expressed by P. gingivalis in nutrient broth, gingipain expression in the model periodontal pocket environment (serum) appeared to be orchestrated through signaling to P. gingivalis from other members of the community, a phenomenon which then promoted growth of the whole community.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12903-021-01971-9.

MiR-21 Is Remotely Governed by the Commensal Bacteria and Impairs Anti-TB Immunity by Down-Regulating IFN-γ

Tuberculosis (TB), which is a frequent and important infectious disease caused by Mycobacterium tuberculosis, has resulted in an extremely high burden of morbidity and mortality. The importance of intestinal dysbacteriosis in regulating host immunity has been implicated in TB, and accumulating evidence suggests that microRNAs (miRNAs) might act as a key mediator in maintaining intestinal homeostasis through signaling networks. However, the involvement of miRNA in gut microbiota, TB and the host immune system remains unknown. Here we showed that intestinal dysbacteriosis increases the susceptibility to TB and remotely increased the expression of miR-21 in lung. Systemic antagonism of miR-21 enhanced IFN-γ production and further conferred immune protection against TB. Molecular experiments further indicated that miR-21a-3p could specifically target IFN-γ mRNA. These findings revealed regulatory pathways implicating intestinal dysbacteriosis induced-susceptibility to TB: intestinal dysbiosis→lung miRNA→targeting IFN-γ→impaired anti-TB immunity. This study also suggested that deregulated miRNAs by commensal bacteria could become promising targets as TB therapeutics.

Association between hypertension, oral microbiome and salivary nitric oxide: A case-control study

BACKGROUND

Nitric oxide (NO) produced in the oral cavity is a powerful resource for the human body, especially when NO-syntethase production is not adequate. The role of oral microbiome in determining blood pressure levels has been linked to the active role of some bacterial species involved in the nitro-reducing process. In the present study we investigated the correlation between selected oral microbiome characteristics, nitric oxide (NO) concentration in saliva and their association with hypertension.

METHODS

A case-control study including 48 (25 normotensive and 23 hypertensive subjects), subjects between 50 and 70 years old, was carried out at the dental clinic of an Italian teaching hospital. Characteristics of participants have been evaluated by means of a physical examination, and by an assisted interview. A real-time polymerase chain reaction in samples of saliva and plaque was used to detect Aggregatibacter actinomycetemcomitans, Prevotella intermedia, Tannerella forsythia, Porphyromonas gingivalis, Treponema denticola, Streptococcus mutans, Streptococcus sanguinis, Veillonella dispar and Neisseria subflava as well as total bacterial count. Nitric oxide in saliva was evaluated by the ELISA method.

RESULTS

Normotensive subjects, compared with hypertensive subjects, had significantly higher concentration of NO (165.77 ± 61.7 vs 57.49 ± 19.61 μmol/l; p = 0.023), and higher bacterial concentration of the supragingival plaque (4.73E+07 ± 4.33+07 vs 4.02E+07 ± 4.00+07; p = 0.024). Bacterial species, usually associated to good oral health status, such as Neisseria subflava, were significantly more present in normotensive subjects than in hypertensive ones (9090.88 ± 5481.49 vs 4791.35 ± 4349.37; p < 0.001). considering the concentration of bacteria as a biomarker of the development of hypertension.

CONCLUSIONS

The results support the association between hypertension, oral microbiome and salivary nitric oxide, in fact do the results allow us to establish any biomarkers (microbial or biochemical, NO) that allow early therapeutic intervention.

Opportunities for caries prevention using an ion-releasing coating material: a randomised clinical study

Ion-releasing materials (containing fluoride and boron, for example) have shown caries-preventive effects in vitro. The purpose of the present study was to investigate the impact of multi-ion-releasing coating material on pH stabilisation, plaque accumulation and the bacterial composition of dental plaque during a time period of 90 days. The null hypothesis tested here was that the evaluated material would not show any differences in pH stabilisation, plaque accumulation or bacterial composition compared with control material.

The study was carried out as a double-blind, split-mouth, randomised, controlled clinical trial in 28 volunteers. Over the evaluation period (days 4, 30, 60 and 90), pH measurements, plaque index and plaque sampling for bacterial analyses were conducted in a calibrated, standardized manner. The study received ethical permission and was carried out in accordance with the Helsinki Declaration.

A significant difference was observed, with less plaque accumulation over time in the subjects in whom the ion-releasing material was applied in comparison to the non-active group. No significant difference was evident in terms of either pH stabilisation or plaque levels of mutans streptococci.

The null hypothesis relating to plaque accumulation was rejected, with a lower plaque index shown for the test group up to 60–90 days. No adverse effects during the observation period were observed. Since the studied cohort was healthy from a caries perspective, more clinical studies are needed to further evaluate the caries-prevention potential of the ion-releasing material in other patient groups.

Rapid Multiplex Real-Time PCR Method for the Detection and Quantification of Selected Cariogenic and Periodontal Bacteria

Dental caries and periodontal diseases are associated with a shift from symbiotic microbiota to dysbiosis. The aim of our study was to develop a rapid, sensitive, and economical method for the identification and quantification of selected cariogenic and periodontal oral bacteria. Original protocols were designed for three real-time multiplex PCR assays to detect and quantify the ratio of 10 bacterial species associated with dental caries (“cariogenic” complex) or periodontal diseases (red complex, orange complex, and Aggregatibacter actinomycetemcomitans). A total number of 60 samples from 30 children aged 2–6 years with severe early childhood caries and gingivitis were tested. In multiplex assays, the quantification of total bacterial (TB) content for cariogenic bacteria and red complex to eliminate differences in quantities caused by specimen collection was included. The mean counts for the TB load and that of ten evaluated specimens corresponded to previously published results. We found a significant difference between the microbial compositions obtained from the area of control and the affected teeth (p < 0.05). Based on this comprehensive microbiological examination, the risk of dental caries or periodontal inflammation may be determined. The test could also be used as a tool for behavioral intervention and thus prevention of the above-mentioned diseases.

Testing Anti-Biofilm Polymeric Surfaces: Where to Start?

Present day awareness of biofilm colonization on polymeric surfaces has prompted the scientific community to develop an ever-increasing number of new materials with anti-biofilm features. However, compared to the large amount of work put into discovering potent biofilm inhibitors, only a small number of papers deal with their validation, a critical step in the translation of research into practical applications. This is due to the lack of standardized testing methods and/or of well-controlled in vivo studies that show biofilm prevention on polymeric surfaces; furthermore, there has been little correlation with the reduced incidence of material deterioration. Here an overview of the most common methods for studying biofilms and for testing the anti-biofilm properties of new surfaces is provided.

Altered fecal bacterial composition correlates with disease activity in inflammatory bowel disease and the extent of IL8 induction

PURPOSE OF THE STUDY

In this study we investigated the presence and relative abundance of important genera of the gut microbiota in IBD patients and their role in induction of IL8 in a cell culture model.

PATIENTS AND METHODS

Stool samples of IBD patients and healthy controls were collected and relative diversity of thirteen bacterial families was measured using quantitative real-time PCR assay. Moreover, filtrate of the stool samples was used for treatment of HT-29 cell line to analyze involvement of diversity of the fecal bacterial communities in the extent of IL8 induction.

RESULTS

Bacteroides, Faecalibacterium prausnitzii, Prevotella spp., and Methanobrevibacterium were significantly less abundant in IBD patients (UC, N = 22; CD, N = 7) compared with control group (N = 29). Increase in relative amounts of Haemophilus, Streptococcus spp., and H. pylori were detected in IBD patients, which was not statistically significant. Relative decrease in amount of Bacteroides spp., Faecalibacterium prausnitzii, and Prevotella spp. were found in UC patients with disease activity score greater than 4; however, higher levels of Streptococcus and Haemophilus were detected in the patients who were at flares. A relationship between the reduction of Haemophilus spp. and higher BMI was shown in IBD patients. Expression of IL8 was significantly higher in the treated cells by the fecal inoculates of IBD patients. Increase in relative amounts of Enterobacteriacea showed a correlation with the higher level of IL8 induction in both groups.

CONCLUSIONS

These results showed that changes in the fecal microbiota composition could affect disease activity, BMI, and IL8 induction.

Effects of statins on multispecies oral biofilm identify simvastatin as a drug candidate targeting Porphyromonas gingivalis

BACKGROUND

Statins effectively reduce risk of cardiovascular-related morbidity and mortality in patients with hyperlipidemia, hypertension, or type 2 diabetes. In addition to lowering cholesterol levels, several studies have attributed statins with immunomodulatory and bactericidal properties. Therefore, the aim of this study was to investigate statins' antimicrobial activity against periodontal homeostasis bacteria.

METHODS

Statin effect on bacterial growth was tested using planktonic monocultures and multibacterial biofilms. The latter consisted of five microbial species (Porphyromonas gingivalis, Fusobacterium nucleatum, Actinomyces naeslundii, Tannerella forsythia, and Streptococcus gordonii) associated with dysbiosis of the oral microbiota underlying establishment and perpetuation of periodontitis.

RESULTS

All four tested statins efficiently inhibited P. gingivalis growth and significantly decreased the cumulative bacterial load in developing and established biofilms. Simvastatin was most efficient and decreased P. gingivalis counts more than 1,300-fold relative to the control.

CONCLUSIONS

These findings suggest that similar effects on bacterial composition of the dental plaque may occur in vivo in patients on statins, thus, leading to a shift of the oral microbiome from a dysbiotic to a more homeostatic one. Simvastatin, being highly effective against P. gingivalis while not affecting commensal microbiota, possesses many properties qualifying it as a potential adjunctive treatment for chronic periodontitis. Further studies are needed to evaluate whether similar effects on bacterial composition of the dental plaque may occur in vivo in patients on statins, thus, leading to a shift of the oral microflora from dysbiotic to a more homeostatic one.

Characterisation of gut, lung, and upper airways microbiota in patients with non-small cell lung carcinoma: Study protocol for case-control observational trial

BACKGROUND

Several studies have confirmed the important role of the gut microbiota in the regulation of immune functions and its correlation with different diseases, including cancer. While brain-gut and liver-gut axes have already been demonstrated, the existence of a lung-gut axis has been suggested more recently, with the idea that changes in the gut microbiota could affect the lung microbiota, and vice versa. Likewise, the close connection between gut microbiota and cancer of proximal sites (intestines, kidneys, liver, etc.) is already well established. However, little is known whether there is a similar relation when looking at world's number one cause of death from cancer-lung cancer.

OBJECTIVE

Firstly, this study aims to characterise the gut, lung, and upper airways (UAs) microbiota in patients with non-small cell lung cancer (NSCLC) treated with surgery or neoadjuvant chemotherapy plus surgery. Secondly, it aims to evaluate a chemotherapy effect on site-specific microbiota and its influence on immune profile. To our knowledge, this is the 1st study that will analyse multi-site microbiota in NSCLC patients along with site-specific immune response.

METHODS

The study is a case-controlled observational trial. Forty NSCLC patients will be divided into 2 groups depending on their anamnesis: Pchir, patients eligible for surgery, or Pct-chir, patients eligible for neoadjuvant chemotherapy plus surgery. Composition of the UAs (saliva), gut (faeces), and lung microbiota (from broncho-alveolar lavage fluid (BALF) and 3 lung pieces: "healthy" tissue distal to tumour, peritumoural tissue and tumour itself) will be analysed in both groups. Immune properties will be evaluated on the local (evaluation of the tumour immune cell infiltrate, tumour classification and properties, immune cell phenotyping in BALF; human neutrophil protein (HNP) 1-3, β-defensin 2, and calprotectin in faeces) and systemic level (blood cytokine and immune cell profile). Short-chain fatty acids (SCFAs) (major products of bacterial fermentation with an effect on immune system) will be dosed in faecal samples. Other factors such as nutrition and smoking status will be recorded for each patient. We hypothesise that smoking status and tumour type/grade will be major factors influencing both microbiota and immune/inflammatory profile of all sampling sites. Furthermore, due to non-selectivity, the same effect is expected from chemotherapy.

Insights into the human oral microbiome

Human oral cavity harbors the second most abundant microbiota after the gastrointestinal tract. The expanded Human Oral Microbiome Database (eHOMD) that was last updated on November 22, 2017, contains the information of approximately 772 prokaryotic species, where 70% is cultivable, and 30% belong to the uncultivable class of microorganisms along with whole genome sequences of 482 taxa. Out of 70% culturable species, 57% have already been assigned to their names. The 16S rDNA profiling of the healthy oral cavity categorized the inhabitant bacteria into six broad phyla, viz. Firmicutes, Actinobacteria, Proteobacteria, Fusobacteria, Bacteroidetes and Spirochaetes constituting 96% of total oral bacteria. These hidden oral micro-inhabitants exhibit a direct influence on human health, from host's metabolism to immune responses. Altered oral microflora has been observed in several diseases such as diabetes, bacteremia, endocarditis, cancer, autoimmune disease and preterm births. Therefore, it becomes crucial to understand the oral microbial diversity and how it fluctuates under diseased/perturbed conditions. Advances in metagenomics and next-generation sequencing techniques generate rapid sequences and provide extensive information of inhabitant microorganisms of a niche. Thus, the retrieved information can be utilized for developing microbiome-based biomarkers for their use in early diagnosis of oral and associated diseases. Besides, several apex companies have shown keen interest in oral microbiome for its diagnostic and therapeutic potential indicating a vast market opportunity. This review gives an insight of various associated aspects of the human oral microbiome.

Variation of Bacterial Communities with Water Quality in an Urban Tropical Catchment

A major challenge for assessment of water quality in tropical environments is the natural occurrence and potential growth of Fecal Indicator Bacteria (FIB). To gain a better understanding of the relationship between measured levels of FIB and the distribution of sewage-associated bacteria, including potential pathogens, in the tropics this study compared the abundance of FIB (Total coliforms and E. coli) and the Bacteroidales (HF183 marker) with bacterial community structure determined by next-generation amplicon sequencing. Water was sampled twice over 6 months from 18 sites within a tropical urban catchment and reservoir, followed by extraction of DNA from microorganisms, and sequencing targeting the V3-V4 region of the 16S rRNA gene. Multivariate statistical analyses indicated that bacterial community composition (BCC) varied between reservoir and catchment, within catchment land-uses, and with E. coli concentration. Beta-regression indicated that the proportion of sequences from sewage-associated taxa (SAT) or pathogen-like sequences (PLS) were predicted most significantly by measured levels of E. coli(log MPN/100 mL) (χ² > 8.7; p < 0.003). In addition, SAT were significantly predicted by log HF183 levels (χ²=13.1; p = 0.0003) while PLS were not. Our study suggests that measurements of E. coli concentration could be useful in predicting samples enriched in sewage-associated and pathogen-like bacteria in tropical environments despite the potential for nonconservative behavior.

Bacteremia after Endodontic Procedures in Patients with Heart Disease: Culture and Molecular Analyses

INTRODUCTION

Infective endocarditis (IE) is still associated with high mortality, and antibiotic prophylaxis strategies are under intense debate. We evaluated the incidence of bacteremia after root canal preparation in teeth with necrotic pulps and apical periodontitis.

METHODS

Blood samples were taken before and 5 and 30 minutes after endodontic treatment in teeth with apical periodontitis from individuals at high (n = 21) or no risk (n = 11) for IE. The former received prophylactic antibiotic therapy. Bacteriologic samples were taken from root canals before chemomechanical preparation to confirm pulp infection. Samples were subjected to aerobic and anaerobic culture and quantitative real-time polymerase chain reaction (qPCR), the latter to determine the total bacterial and streptococcal levels.

RESULTS

Culture revealed no bacteremia in all individuals. Analysis by qPCR showed that bacterial DNA occurred in all root canal samples. qPCR showed a similar incidence of bacteremia between patients who received or did not receive prophylactic antibiotic therapy (P > .05). In blood samples taken 5 minutes after endodontic procedures, bacteria were detected in 2 of 11 (18%) individuals not taking antibiotics and in 4 of 21 (19%) patients under prophylaxis. After 30 minutes, the incidence of bacteremia decreased to 2 of 21 (10%) in patients taking antibiotics and was undetectable in patients at no risk of IE. The incidence of bacteremia by streptococci was identical as that for total bacteria.

CONCLUSIONS

No detectable bacteremia was evident by culture after treatment of infected root canals. Molecular analysis revealed bacterial DNA and streptococci in blood from some patients without a significant difference between individuals receiving or not receiving antibiotic prophylaxis.

Microbial profiling of dental plaque from mechanically ventilated patients

Micro-organisms isolated from the oral cavity may translocate to the lower airways during mechanical ventilation (MV) leading to ventilator-associated pneumonia (VAP). Changes within the dental plaque microbiome during MV have been documented previously, primarily using culture-based techniques. The aim of this study was to use community profiling by high throughput sequencing to comprehensively analyse suggested microbial changes within dental plaque during MV. Bacterial 16S rDNA gene sequences were obtained from 38 samples of dental plaque sampled from 13 mechanically ventilated patients and sequenced using the Illumina platform. Sequences were processed using Mothur, applying a 97 % gene similarity cut-off for bacterial species level identifications. A significant ‘microbial shift’ occurred in the microbial community of dental plaque during MV for nine out of 13 patients. Following extubation, or removal of the endotracheal tube that facilitates ventilation, sampling revealed a decrease in the relative abundance of potential respiratory pathogens and a compositional change towards a more predominantly (in terms of abundance) oral microbiota including Prevotella spp., and streptococci. The results highlight the need to better understand microbial shifts in the oral microbiome in the development of strategies to reduce VAP, and may have implications for the development of other forms of pneumonia such as community-acquired infection.

Lactobacillus fermentum CECT 5716 Reduces Staphylococcus Load in the Breastmilk of Lactating Mothers Suffering Breast Pain: A Randomized Controlled Trial

INTRODUCTION

Recent results indicate that human mastitis and painful breastfeeding may be characterized by a mammary bacterial dysbiosis, a process in which the population of potential pathogens increases at the expense of the normal mammary microbiota. The objective of the present study is the evaluation of three different doses of Lactobacillus fermentum CECT5716 to reduce the load of Staphylococcus in the breastmilk of women suffering from painful breastfeeding.

MATERIALS AND METHODS

A randomized double-blinded controlled study with four study groups was performed. Three groups received the probiotic strain for 3 weeks at doses of 3×10(9) colony-forming units (CFU)/day, 6×10(9) CFU/day, or 9×10(9) CFU/day. The fourth group received a placebo of maltodextrin. The main outcome of the study was Staphylococcus counts in breastmilk. The secondary outcomes were Streptococcus, Lactobacillus, and total bacteria counts in breastmilk, immunoglobulin A and interleukin 8 concentrations in breastmilk, and breast pain scores.

RESULTS

At the end of the study, a significant decrease in the Staphylococcus load was observed in the probiotic groups compared with the baseline loads (p=0.045), whereas the control group maintained similar levels over time. A significant difference in the pain score was observed among the groups receiving the three probiotic doses compared with the control group (p=0.035, p=0.000, and p=0.028, respectively). A dose-response effect could not be observed because the three doses tested induced similar effects, and no significant differences were detected.

CONCLUSIONS

We conclude that L. fermentum CECT5716 is an efficient treatment for breast pain during lactation associated with a high level of Staphylococcus in breastmilk.

Specific amplification of bacterial DNA by optimized so-called universal bacterial primers in samples rich of plant DNA

Universal primers targeting the bacterial 16S-rRNA-gene allow quantification of the total bacterial load in variable sample types by qPCR. However, many universal primer pairs also amplify DNA of plants or even of archaea and other eukaryotic cells. By using these primers, the total bacterial load might be misevaluated, whenever samples contain high amounts of non-target DNA. Thus, this study aimed to provide primer pairs which are suitable for quantification and identification of bacterial DNA in samples such as feed, spices and sample material from digesters. For 42 primers, mismatches to the sequence of chloroplasts and mitochondria of plants were evaluated. Six primer pairs were further analyzed with regard to the question whether they anneal to DNA of archaea, animal tissue and fungi. Subsequently they were tested with sample matrix such as plants, feed, feces, soil and environmental samples. To this purpose, the target DNA in the samples was quantified by qPCR. The PCR products of plant and feed samples were further processed for the Single Strand Conformation Polymorphism method followed by sequence analysis. The sequencing results revealed that primer pair 335F/769R amplified only bacterial DNA in samples such as plants and animal feed, in which the DNA of plants prevailed.

Short-chain Fatty Acids in Infected Root Canals of Teeth with Apical Periodontitis before and after Treatment

INTRODUCTION

Short-chain fatty acids (SCFAs) are bacterial metabolic end products that may function as virulence factors. This study evaluated the occurrence of SCFAs in infected root canals before and after treatment.

METHODS

Samples were taken from root canals of teeth with apical periodontitis before (S1) and after (S2) chemomechanical preparation with either NaOCl or chlorhexidine as the irrigant and then after interappointment medication with calcium hydroxide (S3). High-performance liquid chromatography was used for detection of SCFAs. Selected bacterial taxa that are recognized producers of the target SCFAs were identified by real-time polymerase chain reaction.

RESULTS

Butyric acid was the most common fatty acid in S1, followed by propionic acid. Both molecules were also found in S2 and S3 from both NaOCl and chlorhexidine groups. Lactic acid was not present in detectable levels in S1, but it occurred in 1 postinstrumentation sample and in 9 samples taken after calcium hydroxide medication. Of the target taxa, Fusobacterium nucleatum was the most prevalent in S1 (76%), followed by members of the Actinobacteria phylum (71%), Streptococcus species (59%), and Parvimonas micra (53%). Gram-positive taxa, especially streptococci, were the most prevalent bacteria in S2 and S3. SCFA detection was matched with the respective potential producer species in most cases.

CONCLUSIONS

This first report of SCFAs in infected root canals suggests that these molecules may play a role in the pathogenesis of apical periodontitis. Significance of persistence of SCFAs after treatment and its effects on the long-term outcome await elucidation.

Chair-side quantitative oral-microflora screening for assessing familial correlation of periodontal status and caries prevalence

Aim: Our goal was to investigate the relationship between clinical status and the presence of carious or periodontal pathogens among parent-child familial pairs. Clinical practices of risk assessment with consideration of familial pathogen interaction might reduce the need for therapy, improve patient outcomes, and ultimately reduce oral disease burden. Materials and Methods: In this study, we enrolled 30 parent-child pairs, with the children exhibiting complete deciduous dentition or mixed dentition with only permanent first molars. Clinical statuses were evaluated using caries and periodontal disease indicators, including the sum of decay and the number of missing or filled teeth (DMFT) for adults, decay, extraction caused by dental disease, and filled teeth (deft), for children, probing depth, and plaque control record (PCR). Supra- and sub-gingival bacteria were determined based on semi-quantitative measurements of microbial infection by using data from the Dentocult^® SM test (caries-related organisms) and the PerioCheck^® test (periodontal disease-related organisms). Results: No statistically significant relationship was detected between the prevalence of periodontal pathogens and that of cariogenic pathogens in the oral cavity. However, the clinical status of caries (DMFT) was negatively correlated with the clinical status of periodontal disease (pocket depth) in parents who were infected with dominant periodontal pathogens (r = −0.59, p<0.01). Parents’ DMFT scores were positively correlated with children’s deft and PCR scores. PCR and deft scores of children appeared to decrease significantly with the parent’s pocket depth. Conclusion: The study showed that the quantity of caries pathogens were not significant related to periodontal pathogens, but the caries clinical outcome is negative related with periodontal clinical outcome between familial pairs.

Loss of NHE3 alters gut microbiota composition and influences Bacteroides thetaiotaomicron growth

Changes in the intestinal microbiota have been linked to diabetes, obesity, inflammatory bowel disease, and Clostridium difficile (C. difficile)-associated disease. Despite this, it remains unclear how the intestinal environment, set by ion transport, affects luminal and mucosa-associated bacterial composition. Na(+)/H(+)-exchanger isoform 3 (NHE3), a target of C. difficile toxin B, plays an integral role in intestinal Na(+) absorption. Thus the NHE3-deficient mouse model was chosen to examine the effect of pH and ion composition on bacterial growth. We hypothesized that ion transport-induced change in the intestinal environment would lead to alteration of the microbiota. Region-specific changes in ion composition and pH correlated with region-specific alteration of luminal and mucosal-associated bacteria with general decreases in Firmicutes and increases in Bacteroidetes members. Bacteroides thetaiotaomicron (B. thetaiotaomicron) increased in NHE3(-/-) terminal ileum and was examined in vitro to determine whether altered Na(+) was sufficient to affect growth. Increased in vitro growth of B. thetaiotaomicron occurred in 43 mM Na(+) correlating with the NHE3(-/-) mouse terminal ileum [Na(+)]. NHE3(-/-) terminal ileum displayed increased fut2 mRNA and fucosylation correlating with B. thetaiotaomicron growth. Inoculation of B. thetaiotaomicron in wild-type and NHE3(-/-) terminal ileum organoids displayed increased fut2 and fucosylation, indicating that B. thetaiotaomicron alone is sufficient for the increased fucosylation seen in vivo. These data demonstrate that loss of NHE3 alters the intestinal environment, leading to region-specific changes in bacteria, and shed light on the growth requirements of some gut microbiota members, which is vital for creating better treatments of complex diseases with an altered gut microbiota.

Gut microbiota affects sensitivity to acute DSS-induced colitis independently of host genotype

Caspase-deficient mice and wild-type (WT) mice show significant differences in their gut microbiota composition. These differences coincide with the observation that caspase-3-deficient mice carrying a natural caspase-11 mutation (Casp3/11(-/-)) are less sensitive to acute dextran sodium sulfate-induced colitis than WT mice. For these reasons, we investigated the role of the microbiota in the development of colitis by cohousing WT and Casp3/11(-/-) mice. Microbial community fingerprinting by denaturing gradient gel electrophoresis analysis revealed that the similarities in gut microbial composition of WT and Casp3/11(-/-) mice increased after cohousing. In the acute dextran sodium sulfate-induced colitis model, Casp3/11(-/-) mice that were cohoused with WT mice showed increased weight loss and disease activity scores and increased neutrophil infiltration and inflammatory cytokine levels in their colon tissue compared with Casp3/11(-/-) mice that were not cohoused with WT mice. Also, we demonstrate that only the microbiota of the Casp3/11(-/-) mice cohoused with WT mice showed an important increase in Prevotella species. In conclusion, our cohousing experiments revealed that the colitogenic activity of the WT microbiota is transferable to Casp3/11(-/-) mice and that Prevotella species are likely to be involved. By contrast, the relative protection of Casp3/11(-/-) mice against dextran sodium sulfate damage is not transferred to WT mice after cohousing. These results underscore the need for in-depth studies of the bilateral interaction of host genes and microbiota to gain insight into the mechanisms of disease pathogenesis. Our findings also have important implications for the experimental design of disease studies in genetically modified mice and conclusions drawn from them.

As-yet-uncultivated oral bacteria: breadth and association with oral and extra-oral diseases

It has been shown that 40–60% of the bacteria found in different healthy and diseased oral sites still remain to be grown in vitro, phenotypically characterized, and formally named as species. The possibility exists that these as-yet-uncultivated bacteria play important ecological roles in oral bacterial communities and may participate in the pathogenesis of several oral infectious diseases. There is also a potential for these as-yet-uncultivated oral bacteria to take part in extra-oral infections. For a comprehensive characterization of physiological and pathogenic properties as well as antimicrobial susceptibility of individual bacterial species, strains need to be grown in pure culture. Advances in culturing techniques have allowed the cultivation of several oral bacterial taxa only previously known by a 16S rRNA gene sequence signature, and novel species have been proposed. There is a growing need for developing improved methods to cultivate and characterize the as-yet-uncultivated portion of the oral microbiome so as to unravel its role in health and disease.

Bacteriological effects of a Lactobacillus reuteri probiotic on in vitro oral biofilms

OBJECTIVE

Despite the targeted and incidental exposure of the oral cavity to probiotic bacteria, relatively little information is available concerning their bacteriological effects or ecological fate in this environment. We have investigated the effects of an oral probiotic bacterium, Lactobacillus reuteri on salivary biofilm microcosms.

DESIGN

Nascent in vitro plaques in hydroxyapatite disc model and mature continuous culture plaques within constant depth film fermenters (CDFFs) were exposed to probiotic strains of L. reuteri. Microbial composition was assessed using differential viable counting and CDFF plaques were additionally characterised using qPCR and PCR-DGGE.

RESULTS

Probiotic dosing of nascent plaques was associated with significant increases in lactobacilli and Gram-negative anaerobes in both biofilm and planktonic phases, and with elevated counts of streptococci in the planktonic phase that were not accompanied by decreases in pH. In mature CDFF plaques, differential culture indicated that whilst significant increases in lactobacillus counts occurred during dosing, numbers of other bacterial groups and pH did not significantly change. Monitoring the probiotic strain in CDFFs using selective culture and qPCR indicated that the exogenous bacterium reached and maintained c. 5 log(10)CFU/mm(2) during dosing and 20 days after cessation. The apparent lack of marked bacterial inhibition by L. reuteri in both model systems was supported by the absence of antagonism in binary antagonism assays.

CONCLUSION

The largest compositional changes occurred in nascent plaques where the addition of lactobacilli caused significant increases in streptococci and Gram-negative anaerobes, the latter possibly via lactate syntrophy. Exogenous L. reuteri persisted in mature plaque microcosms after dosing ceased.

NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis

Inflammasomes are multiprotein complexes that function as sensors of endogenous or exogenous damage-associated molecular patterns. Here, we show that deficiency of NLRP6 in mouse colonic epithelial cells results in reduced IL-18 levels and altered fecal microbiota characterized by expanded representation of the bacterial phyla Bacteroidetes (Prevotellaceae) and TM7. NLRP6 inflammasome-deficient mice were characterized by spontaneous intestinal hyperplasia, inflammatory cell recruitment, and exacerbation of chemical colitis induced by exposure to dextran sodium sulfate (DSS). Cross-fostering and cohousing experiments revealed that the colitogenic activity of this microbiota is transferable to neonatal or adult wild-type mice, leading to exacerbation of DSS colitis via induction of the cytokine, CCL5. Antibiotic treatment and electron microscopy studies further supported the role of Prevotellaceae as a key representative of this microbiota-associated phenotype. Altogether, perturbations in this inflammasome pathway, including NLRP6, ASC, caspase-1, and IL-18, may constitute a predisposing or initiating event in some cases of human IBD.

Development of a novel multi-triplex qPCR method for the assessment of bacterial community structure in oral populations

Gingivitis and dental caries are two of the most predominant diseases in humans. Both conditions are easily treated with the removal of the plaque biofilm by brushing or the use of oral hygiene products. In both cases, pathogenic taxa found within the plaque biofilm are the causal agents of the disease. Actinomyces naeslundii, Fusobacterium nucleatum and Prevotalla intermedia have all been implicated in the development of gingivitis, while Streptococcus mutans is the main organism associated with dental caries. Many studies have so far focused on the use of culture methods to detect and enumerate the pathogenic taxa within plaque samples. However, these methods are both labour intensive and biased towards culturable taxa. In the present study, a novel high-throughput multi-triplex quantitative PCR method was developed with the aim to investigate the community dynamics associated with oral communities. Three triplex assays were designed targeting taxa associated with gingivitis and dental caries as well as oral health. Saliva samples collected from healthy individuals were used in order to validate the newly developed method.

Assessment of sample handling practices on microbial activity in sputum samples from patients with cystic fibrosis

AIM

The aim of this study was to quantitatively and qualitatively assess the effect of sample storage on the metabolically active microbial community found in sputum samples from patients with cystic fibrosis (CF).

METHODS

Sputum samples were collected and split in two equal aliquots one of which was immersed in RNAlater and refrigerated immediately, the second stored at room temperature for 24 h and RNAlater was subsequently added. mRNA was extracted, and RT-PCR-DGGE and qPCR analysis of the bacterial and fungal communities was carried out.

RESULTS

Significant differences in the bacterial communities between the two protocols were observed but there were no significant difference seen in the fungal community analyses. Analysis by qPCR demonstrated that room temperature storage gave statistically significant increases in eubacteria and Pseudomonas spp. and a statistically significant decrease in those of Haemophilus influenzae.

CONCLUSIONS

The analysis of metabolically active microbial communities from CF sputum using molecular techniques indicated that samples should be stored at 4 degrees C upon addition of RNAlater to obtain an accurate depiction of the CF lung microbiota. Also, storing respiratory samples at room temperature may cause an over representation of Pseudomonas aeruginosa and mask the presence of other clinically significant organisms.

Actinomyces in chronic granulomatous disease: an emerging and unanticipated pathogen

BACKGROUND

Chronic granulomatous disease (CGD) is a rare inherited disease of the phagocyte NADPH oxidase system that causes defective production of toxic oxygen metabolites, impaired bacterial and fungal killing, and recurrent life-threatening infections, mostly by catalase-producing organisms. We report for the first time, to our knowledge, chronic infections with Actinomyces species in 10 patients with CGD. Actinomycosis is a chronic granulomatous condition that commonly manifests as cervicofacial, pulmonary, or abdominal disease, caused by slowly progressive infection with oral and gastrointestinal commensal Actinomyces species. Treatment of actinomycosis is usually simple in immunocompetent individuals, requiring long-term, high-dose intravenous penicillin, but is more complicated in those with CGD because of delayed diagnosis and an increased risk of chronic invasive or debilitating disease.

METHODS

Actinomyces was identified by culture, staining, 16S ribosomal DNA polymerase chain reaction, and/or a complement fixation test in 10 patients with CGD.

RESULTS

All 10 patients presented with a history of fever and elevated inflammatory signs without evident focus. Diagnosis was delayed and clinical course severe and protracted despite high-dose intravenous antibiotic therapy and/or surgery. These results suggest an unrecognized and unanticipated susceptibility to weakly pathogenic Actinomyces species in patients with CGD because these are catalase-negative organisms previously thought to be nonpathogenic in CGD.

CONCLUSIONS

Actinomycosis should be vigorously sought and promptly treated in patients with CGD presenting with uncommon and prolonged clinical signs of infection. Actinomycosis is a catalase-negative infection important to consider in CGD.

MLPA diagnostics of complex microbial communities: relative quantification of bacterial species in oral biofilms

A multitude of molecular methods are currently used for identification and characterization of oral biofilms or for community profiling. However, multiplex PCR techniques that are able to routinely identify several species in a single assay are not available. Multiplex Ligation-dependent Probe Amplification (MLPA) identifies up to 45 unique fragments in a single tube PCR. Here we report a novel use of MLPA in the relative quantification of targeted microorganisms in a community of oral microbiota. We designed 9 species specific probes for: Actinomyces gerencseriae, Actinomyces naeslundii, Actinomyces odontolyticus, Candida albicans, Lactobacillus acidophilus, Rothia dentocariosa, Streptococcus mutans, Streptococcus sanguinis and Veillonella parvula; and genus specific probes for selected oral Streptococci and Lactobacilli based on their 16S rDNA sequences. MLPA analysis of DNA pooled from the strains showed the expected specific MLPA products. Relative quantification of a serial dilution of equimolar DNA showed that as little as 10 pg templates can be detected with clearly discernible signals. Moreover, a 2 to 7% divergence in relative signal ratio of amplified probes observed from normalized peak area values suggests MLPA can be a cheaper alternative to using qPCR for quantification. We observed 2 to 6 fold fluctuations in signal intensities of MLPA products in DNAs isolated from multispecies biofilms grown in various media for various culture times. Furthermore, MLPA analyses of DNA isolated from saliva obtained from different donors gave a varying number and intensity of signals. This clearly shows the usefulness of MLPA in a quantitative description of microbial shifts.