Comparative genome analysis of Prevotella intermedia strain isolated from infected root canal reveals features related to pathogenicity and adaptation

Efficacy of avocado seed extract in preventing, inhibiting, and eliminating Prevotella intermedia biofilms: An in vitro study

Background and Aim

Prevotella intermedia is a significant contributor to periodontitis, capable of forming biofilms that resist antibiotics and complicate treatment. Avocado seeds (Persea americana Mill.) are rich in bioactive compounds, including flavonoids, tannins, saponins, and alkaloids, which exhibit potential antibiofilm activity. This study aims to evaluate the efficacy of avocado seed ethanol extract in preventing biofilm attachment, inhibiting biofilm formation, and eradicating established biofilms of P. intermedia in vitro.

Materials and Methods

A post-test-only control group design was employed using P. intermedia (ATCC 25611). Ten groups were included: Bacterial and negative controls, a positive control (chlorhexidine), and experimental groups with ethanol extract concentrations (3.25%-9.25%). Biofilm activity was assessed using 96-well microtiter plates, crystal violet staining, and optical density measurements at 595 nm to determine the minimum biofilm prevention (MBPC), inhibition (MBIC), and eradication concentrations (MBEC). Statistical analysis was conducted using one-way ANOVA and Bonferroni post hoc tests.

Results

Biofilm assays showed a dose-dependent increase in antibiofilm efficacy. The highest attachment prevention (82.67%), biofilm formation inhibition (84.26%), and biofilm eradication (86.04%) were observed at 9.25%. Significant differences (p < 0.05) were found between the extract and negative control groups, with no significant differences (p > 0.05) between the 8.25%-9.25% extracts and chlorhexidine. The MBPC50, MBIC50, and MBEC50 were identified at a concentration of 6.25%, achieving >50% efficacy in biofilm prevention, inhibition, and eradication.

Conclusion

Avocado seed ethanol extract demonstrated significant antibiofilm properties against P. intermedia, comparable to chlorhexidine at higher concentrations. The bioactive compounds - flavonoids, tannins, saponins, and alkaloids - likely contributed to these effects through mechanisms such as quorum sensing inhibition, disruption of bacterial adhesion, and destabilization of biofilm structures. These findings highlight avocado seed extract as a promising natural alternative for managing periodontitis-related biofilm infections.

Enhancement of Activated Carbon on Anaerobic Fermentation of Heavy-Metal-Contaminated Plants: Insights into Microbial Responses

Anaerobic fermentation is a potentially cost-effective approach to disposing of metal-contaminated biowaste collected during phytoremediation. However, the compound heavy metals contained in the biowaste may limit the efficiency of anaerobic fermentation. In this study, anaerobic fermentation with alfalfa harvested from an iron tailing as the feedstock was set up and further enhanced by granular activated carbon (AC). The results showed that adding AC improved the cumulative biogas yields of alfalfa contaminated with metals (AM) by 2.26 times. At the biogas peak stage, plenty of microbes were observed on the surface of the AC, and the functional groups of AC contributed to better electron transfer, lower heavy metal toxicity and higher CH4 contents. AC increased the richness and decreased the diversity of bacteria while reducing both the richness and diversity of archaea. The AC addition resulted in higher relative abundance of Prevotella_7, Bacteroides and Ruminiclostridium_1, which enhanced the hydrolysis of substrate and produced more precursors for methanogenesis. Meanwhile, the relative abundances of Methanosarcina and Methanobacterium were remarkably increased together with the metabolism of cofactors and vitamins, indicating the enhancement of both the acetoclastic and hydrotrophic methanogenesis. The present study provided new insights into the microbial responses of the anaerobic fermentation in heavy-metal-contaminated plants and proved the possibility of enhancing the biogas production by AC.

Case report: isolated prevotella intermedia causing intracranial infection detected using metagenomic next generation sequencing

BACKGROUND

Isolated Prevotella intermedia, a rare gram-negative, rod-shaped, anaerobic bacterium, is rarely detected in clinical practice. It has been associated with infections of the oral cavity and female genital tract, but has never been detected in cerebrospinal fluid (CSF) of patients in China. Accurate detection of causative pathogens is still an arduous task owing to the difficult conditions of anaerobic bacterial culture. Isolated Prevotella intermedia can be detected by metagenomic next generation sequencing (mNGS) of the CSF. Correct diagnosis and antibiotic treatment can help patients avoid life-threatening events.

CASE PRESENTATION

Herein, we describe the case of a 64-year-old Chinese woman who presented with typical features of meningoencephalitis. Routine CSF culture failed to identify the causative pathogen. Isolated Prevotella intermedia was detected by mNGS, and the patient was treated with antibacterial agents including ceftriaxone, vancomycin, moxifloxacin, meropenem, metronidazole, and linezolid. The patient underwent surgical treatment for abscess of left frontal parietal lobe, which was observed on magnetic resonance imaging (MRI) and was suspected to be caused by Prevotella intermedia. It was further confirmed that it was a secondary infection from the oral cavity, and the possible etiology might have been dental surgery. Treatment was rendered to the patient based on metagenomic test result, and her condition improved after two months.

CONCLUSIONS

This case highlights the role of mNGS in accurate diagnosis of patients with central nervous system infection. In particular, mNGS can be used to identify rare pathogens and confirm the diagnosis in patients with unknown etiology.

Western and non-western gut microbiomes reveal new roles of Prevotella in carbohydrate metabolism and mouth-gut axis

The abundance and diversity of host-associated Prevotella species have a profound impact on human health. To investigate the composition, diversity, and functional roles of Prevotella in the human gut, a population-wide analysis was carried out on 586 healthy samples from western and non-western populations including the largest Indian cohort comprising of 200 samples, and 189 Inflammatory Bowel Disease samples from western populations. A higher abundance and diversity of Prevotella copri species enriched in complex plant polysaccharides metabolizing enzymes, particularly pullulanase containing polysaccharide-utilization-loci (PUL), were found in Indian and non-western populations. A higher diversity of oral inflammations-associated Prevotella species and an enrichment of virulence factors and antibiotic resistance genes in the gut microbiome of western populations speculates an existence of a mouth-gut axis. The study revealed the landscape of Prevotella composition in the human gut microbiome and its impact on health in western and non-western populations.

The role of nanohydroxyapatite on the morphological, physical, and biological properties of chitosan nanofibers

OBJECTIVES

This study aimed to evaluate the effects of nanohydroxyapatite (nHAp) particles on the morphological, chemical, physical, and biological properties of chitosan electrospun nanofibers.

MATERIALS AND METHODS

nHAp particles with a 1.67 Ca/P ratio were synthesized via the aqueous precipitation method, incorporated into chitosan polymer solution (0.5 wt%), and electrospun into nHAp-loaded fibers (ChHa fibers). Neat chitosan fibers (nHAp-free, Ch fibers) were used as the control. The electrospun fiber mats were characterized using morphological, topographical, chemical, thermal, and a range of biological (antibacterial, antibiofilm, cell viability, and alkaline phosphatase [ALP] activity) analyses. Data were analyzed using ANOVA and Tukey's test (α = 0.05).

RESULTS

ChHa fibers demonstrated a bead-like morphology, with thinner (331 ± 110 nm) and smoother (Ra = 2.9 ± 0.3 μm) distribution as compared to the control fibers. Despite showing similar cell viability and ALP activity to Ch fibers, the ChHa fibers demonstrated greater antibacterial potential against most tested bacteria (except for P. intermedia), and higher antibiofilm activity against P. gingivalis biofilm.

CONCLUSIONS

The incorporation of nHAp particles did not jeopardize the overall morphology, topography, physical, and biological characteristics of the chitosan nanofibers.

CLINICAL RELEVANCE

The combination of nHAp particles with chitosan can be used to engineer bioactive, electrospun composite nanofibers with potential applications in regenerative dentistry.

Toll like Receptor signalling by Prevotella histicola activates alternative NF-κB signalling in Cystic Fibrosis bronchial epithelial cells compared to P. aeruginosa

Cystic Fibrosis (CF), caused by mutations affecting the CFTR gene, is characterised by viscid secretions in multiple organ systems. CF airways contain thick mucus, creating a gradient of hypoxia, which promotes the establishment of polymicrobial infection. Such inflammation predisposes to further infection, a self-perpetuating cycle in mediated by NF-κB. Anaerobic Gram-negative Prevotella spp. are found in sputum from healthy volunteers and CF patients and in CF lungs correlate with reduced levels of inflammation. Prevotella histicola (P. histicola) can suppress murine lung inflammation, however, no studies have examined the role of P. histicola in modulating infection and inflammation in the CF airways. We investigated innate immune signalling and NF-kB activation in CF epithelial cells CFBE41o- in response to clinical stains of P. histicola and Pseudomonas aeruginosa (P. aeruginosa). Toll-Like Receptor (TLR) expressing HEK-293 cells and siRNA assays for TLRs and IKKα were used to confirm signalling pathways. We show that P. histicola infection activated the alternative NF-kB signalling pathway in CF bronchial epithelial cells inducing HIF-1α protein. TLR5 signalling was responsible for the induction of the alternative NF-kB pathway through phosphorylation of IKKα. The induction of transcription factor HIF-1α was inversely associated with the induction of the alternative NF-kB pathway and knockdown of IKKα partially restored canonical NF-kB activation in response to P. histicola. This study demonstrates that different bacterial species in the respiratory microbiome can contribute differently to inflammation, either by activating inflammatory cascades (P. aeruginosa) or by muting the inflammatory response by modulating similar or related pathways (P. histicola). Further work is required to assess the complex interactions of the lung microbiome in response to mixed bacterial infections and their effects in people with CF.

Inflammatory Biomarkers, Microbiome, Depression, and Executive Dysfunction in Alcohol Users

Alcohol-related disorders (ARD) are highly prevalent among Latin American-Caribbean countries. Mental disorders are common comorbidities in individuals with ARD. However, the etiology of the association between ARD and mental disorders remains unclear. We examined the association of inflammatory cytokines, microbiome, and other biomakers with measures of depression, social anxiety, and executive functions. We observed a significant increase in cytokine and chemokine expression levels in saliva and plasma in the alcohol group (AG) samples. Also, the salivary bacterial composition in the AG revealed an abundance of Prevotella. Depression symptomatology was markedly higher in the AG, but social anxiety levels were negligible. AG also exhibited executive dysfunctions, which negatively correlated with increased plasma levels of pro-inflammatory cytokines and increased salivary concentrations of Prevotella bacteria. Our study suggests that chronic alcohol use correlates with executive dysfunction, immune system dysregulation, and dysbiosis of the salivary microbiota. Additional studies are needed to understand the role of the microbiome and inflammation in alcohol use and mental comorbidities.

Noma (cancrum oris): An unresolved global challenge

Noma (canrum oris) is a mutilating necrotizing disease of uncertain etiology, but it is accepted that it is caused primarily by a polybacterial infection with secondary ischemia. The consequent necrotizing fasciitis, myonecrosis, and osteonecrosis results in destruction of facial structures with severe functional impairment and disfigurement. It most frequently affects children, particularly in sub‐Saharan Africa, who are malnourished or debilitated by systemic conditions including but not limited to malaria, measles, and tuberculosis; and less frequently debilitated HIV‐seropositive subjects. In the vast majority of cases, in susceptible subjects, noma is preceded by necrotizing stomatitis. However, it has been reported, albeit rarely, that noma can arise without any preceding oral lesions being observed. Noma is not recurrent and is not transmissible.

Infection with Prevotella nigrescens induces TLR2 signalling and low levels of p65 mediated inflammation in Cystic Fibrosis bronchial epithelial cells

Prevotella spp. are frequently identified in Cystic Fibrosis sputum. This study examined whether infection with Prevotella nigrescens, a frequently identified member of this species, contributes to inflammation in CF bronchial epithelial cells through activation of TLR- and NF-κB signalling pathways. CFBE41o- cells were infected with either P.nigrescens or Pseudomonas aeruginosa and incubated under anaerobic conditions for 4h. P.nigrescens activated TLR2 signalling but not TLR4 signalling while P.aeruginosa activated TLR4 signalling with a lesser effect on TLR2. P.aeruginosa induced significant IκBα phosphorylation 10min post infection with a return to control levels by 30min post infection. A significant induction in nuclear p65 DNA binding was observed at 2h post infection. In contrast, infection with P.nigrescens induced phosphorylation of IκBα 120min post infection, with significant induction in nuclear p65 DNA binding at 4h post infection only. Cytokine gene and protein responses were lower for P.nigrescens compared to P.aeruginosa. This study demonstrates the ability of a clinical P.nigrescens isolate to provoke a delayed NF-κB(p65) driven response through induction in TLR2 signalling and activation of sustained levels of IKKα.

Process Analysis of Anaerobic Fermentation Exposure to Metal Mixtures

Anaerobic fermentation is a cost-effective biowaste disposal approach. During fermentation, microorganisms require a trace amount of metals for optimal growth and performance. This study investigated the effects of metal mixtures on biogas properties, process stability, substrate degradation, enzyme activity, and microbial communities during anaerobic fermentation. The addition of iron (Fe), nickel (Ni), and zinc (Zn) into a copper (Cu)-stressed fermentation system resulted in higher cumulative biogas yields, ammonia nitrogen (NH₄⁺-N) concentrations and coenzyme F₄₂₀ activities. Ni and Zn addition enhanced process stability and acetate utilization. The addition of these metals also improved and brought forward the peak daily biogas yields as well as increased CH₄ content to 88.94 and 86.58%, respectively. Adding Zn into the Cu-stressed system improved the abundance of Defluviitoga, Fibrobacter and Methanothermobacter, the degradation of cellulose, and the transformation of CO₂ to CH₄. The bacterial and archaeal communities were responsible for the degradation of lignocelluloses and CH₄ production during the fermentation process. This study supports the reutilization of heavy metal-contaminated biowaste and provides references for further research on heavy metals impacted anaerobic fermentation.

Dietary multi-enzyme complex improves In Vitro nutrient digestibility and hind gut microbial fermentation of pigs

This study was conducted in two stages to investigate the potential of multi-enzyme supplementation on the nutrient digestibility, growth performance, and gut microbial composition of pigs. In stage 1, effects of multi-enzyme complex (xylanase, α-amylase, β-glucanase, and protease) supplementation on the ileal and total tract dry matter (DM) digestibility of feed-stuffs were investigated with in vitro two-stage and three-stage enzyme incubation methods. A wide range of feed ingredients, namely, corn meal, wheat meal, soybean meal, fish meal, Oriental herbal extract, Italian rye-grass (IRG) and peanut hull were used as substrates. Supplementation of the multi-enzyme complex increased (P < 0.05) the digestibility of the Oriental herbal extract and corn meal. In stage 2, in vivo animal studies were performed to further investigate the effects of the dietary multi-enzyme complex on the nutrient utilization, growth performance, and fecal microbial composition of pigs. A total of 36 weaned pigs were fed corn- and soybean meal-based diets without (control) and with the multi-enzyme complex (treatment) for 6 weeks. Fecal samples were collected from 12 pigs to analyze the microbial communities by using DNA sequencing and bioinformatics tools. Multi-enzyme supplementation had no effect on apparent digestibility of nutrients and growth performance of pigs compared to control. Taxonomic analysis of the fecal samples indicated that the bacteria in both control and treatment samples predominantly belonged to Firmicutes and Bacteroidetes. In addition, the proportion of the phylum Firmicutes was slightly higher in the treatment group. At the genus level, the abundance of Treponema and Barnesiella increased in the treatment group; whereas the numbers ofthe genera including Prevotella, Butyricicoccus, Ruminococcus and Succinivibrio decreased in the treatment group. These results suggest that multi-enzyme supplementation with basal diets have the potential to improve nutrient digestibility and modify microbial communities in the hind-gut of pigs.

Correlation between crestal alveolar bone loss with intracanal bacteria and apical lesion area in necrotic teeth

OBJECTIVE

This study aimed to analyze the correlation between crestal alveolar bone loss with the presence of some bacterial species in root canals and the apical lesion area of necrotic teeth.

DESIGN

Data from 20 patients with diagnosis of pulp necrosis and acute apical abscesses, without active periodontal diseases, were evaluated. Patients with history of antibiotic usage three months prior to the study, with exposed pulp cavity, and with probing depth >3 mm were not included. The root size, the distance between the bone crest to the tooth apex in the mesial and distal surfaces, and the apical lesion area were measured from standard periapical radiographies by a calibrated examiner. Root canal samples were collected using sterilized paper points. In multirooted teeth, the largest root canal was sampled. Culture, microbial isolation and identification by phenotypic methods were performed. Spearman correlation and exact Fischer test were calculated between higher/lower existing bone crests, according to the median and the presence of specific bacteria.

RESULTS

No statistically significant differences were found between occurrence of pathogenic bacteria, such as Porphyromonas gingivalis, Porphyromonas endodontalis, and Prevotella intermedia, and groups with higher/lower degree of bone loss (p > 0.05). A negative significant correlation was found between Parvimonas micra and periodontal bone loss (p = 0.02). Additionally, no statistically significant association was found between crestal bone loss and the apical lesion area.

CONCLUSIONS

It was concluded that, in patients without active periodontitis, the presence of pathogenic bacteria in the root canal was not correlated with periodontal bone loss.

What is the influence of tonsillectomy on the level of periodontal pathogens on the tongue dorsum and in periodontal pockets

BACKGROUND

For periodontal treatment, the full mouth disinfection approach suggests disinfection of oral soft tissues, such as tongue and tonsils concomitant to scaling and root planning since patients might benefit from treatment of these oral niches either. Periodontopathogenes in tonsillar tissue support this hypothesis. This prospective controlled clinical study investigated the change in the oral flora of patients who underwent tonsillectomy. Pockets were tested for eleven bacterial species before and six weeks after the surgical intervention.

METHODS

Fifty generally healthy adults were included in this study. The test group consisted of 25 patients with tonsillectomy. The control group included 25 patients with otorhinolarynologic surgery without involvement of the oral cavity. Clinical parameters such as probing pocket depth, bleeding-on-probing index and plaque index were registered the evening before surgery. Also bacterial samples from the gingival sulcus and dorsum linguae were taken, and an additional sample from the removed tonsils in the test group. Six weeks after the intervention microbial samples of pockets and tongue were taken again. Data were tested for significant differences using Wilcoxon rank and Whitney-u-test.

RESULTS

No relevant intra- or intergroup differences were found for the change of the eleven investigated species.

CONCLUSION

Based on the results of the present study, tonsillectomy does not seem to have an immediate relevant effect on the bacterial flora of tongue or periodontium. This study design was approved by the ethical committee of Zurich (KEK-ZH-Nr.2013-0419).

TRIAL REGISTRATION

The trial was retrospectively registered in the German Clinical Trials Register ( DRK00014077 ) on February 20, 2018.

Population-Genomic Insights into Variation in Prevotella intermedia and Prevotella nigrescens Isolates and Its Association with Periodontal Disease

High-throughput sequencing has helped to reveal the close relationship between Prevotella and periodontal disease, but the roles of subspecies diversity and genomic variation within this genus in periodontal diseases still need to be investigated. We performed a comparative genome analysis of 48 Prevotella intermedia and Prevotella nigrescens isolates that from the same cohort of subjects to identify the main drivers of their pathogenicity and adaptation to different environments. The comparisons were done between two species and between disease and health based on pooled sequences. The results showed that both P. intermedia and P. nigrescens have highly dynamic genomes and can take up various exogenous factors through horizontal gene transfer. The major differences between disease-derived and health-derived samples of P. intermedia and P. nigrescens were factors related to genome modification and recombination, indicating that the Prevotella isolates from disease sites may be more capable of genomic reconstruction. We also identified genetic elements specific to each sample, and found that disease groups had more unique virulence factors related to capsule and lipopolysaccharide synthesis, secretion systems, proteinases, and toxins, suggesting that strains from disease sites may have more specific virulence, particularly for P. intermedia. The differentially represented pathways between samples from disease and health were related to energy metabolism, carbohydrate and lipid metabolism, and amino acid metabolism, consistent with data from the whole subgingival microbiome in periodontal disease and health. Disease-derived samples had gained or lost several metabolic genes compared to healthy-derived samples, which could be linked with the difference in virulence performance between diseased and healthy sample groups. Our findings suggest that P. intermedia and P. nigrescens may serve as “crucial substances” in subgingival plaque, which may reflect changes in microbial and environmental dynamics in subgingival microbial ecosystems. This provides insight into the potential of P. intermedia and P. nigrescens as new predictive biomarkers and targets for effective interventions in periodontal disease.

Influence of lung CT changes in chronic obstructive pulmonary disease (COPD) on the human lung microbiome

BACKGROUND

Changes in microbial community composition in the lung of patients suffering from moderate to severe COPD have been well documented. However, knowledge about specific microbiome structures in the human lung associated with CT defined abnormalities is limited.

METHODS

Bacterial community composition derived from brush samples from lungs of 16 patients suffering from different CT defined subtypes of COPD and 9 healthy subjects was analyzed using a cultivation independent barcoding approach applying 454-pyrosequencing of 16S rRNA gene fragment amplicons.

RESULTS

We could show that bacterial community composition in patients with changes in CT (either airway or emphysema type changes, designated as severe subtypes) was different from community composition in lungs of patients without visible changes in CT as well as from healthy subjects (designated as mild COPD subtype and control group) (PC1, Padj = 0.002). Higher abundance of Prevotella in samples from patients with mild COPD subtype and from controls and of Streptococcus in the severe subtype cases mainly contributed to the separation of bacterial communities of subjects. No significant effects of treatment with inhaled glucocorticoids on bacterial community composition were detected within COPD cases with and without abnormalities in CT in PCoA. Co-occurrence analysis suggests the presence of networks of co-occurring bacteria. Four communities of positively correlated bacteria were revealed. The microbial communities can clearly be distinguished by their associations with the CT defined disease phenotype.

CONCLUSION

Our findings indicate that CT detectable structural changes in the lung of COPD patients, which we termed severe subtypes, are associated with alterations in bacterial communities, which may induce further changes in the interaction between microbes and host cells. This might result in a changed interplay with the host immune system.

Influence of glycemic control on the levels of subgingival periodontal pathogens in patients with generalized chronic periodontitis and type 2 diabetes

Objective

This study evaluated the influence of glycemic control on the levels and frequency of subgingival periodontal pathogens in patients with type 2 diabetes mellitus (DM) and generalized chronic periodontitis (ChP).

Material and Methods

Fifty-six patients with generalized ChP and type 2 DM were assigned according to the levels of glycated hemoglobin (HbA1c) into one of the following groups: HbA1c<8% (n=28) or HbA1c≥8% (n=28). Three subgingival biofilm samples from sites with probing depth (PD)<5 mm and three samples from sites with PD≥5 mm were analyzed by quantitative Polymerase Chain Reaction (PCR) for the presence and levels of Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Eubacterium nodatum, Parvimona micra, Fusobacterium nucleatum ssp. and Prevotella intermedia.

Results

The mean counts of F. nucleatum ssp. were statistically significantly higher in the sites with PD≥5 mm of the HbA1c≥8% group (p<0.05). Frequencies of detection of T. forsythia, E. nodatum, P. micra and F. nucleatum ssp. were all higher in the sites with PD≥5 mm of the patients with HbA1c≥8%, compared with those of patients with HbA1c<8% (p<0.05). Frequency of detection of P. intermedia was higher in the sites with PD<5 mm of the patients with HbA1c≥8% than those of the patients with HbA1c<8% (p<0.05).

Conclusions

Poor glycemic control, as indicated by HbA1c≥8%, is associated with increased levels and frequencies of periodontal pathogens in the subgingival biofilm of subjects with type 2 DM and ChP.

Ability of Lactobacillus kefiri LKF01 (DSM32079) to colonize the intestinal environment and modify the gut microbiota composition of healthy individuals

BACKGROUND

Probiotics have been observed to positively influence the host's health, but to date few data about the ability of probiotics to modify the gut microbiota composition exist.

AIMS

To evaluate the ability of Lactobacillus kefiri LKF01 DSM32079 (LKEF) to colonize the intestinal environment of healthy subjects and modify the gut microbiota composition.

METHODS

Twenty Italian healthy volunteers were randomized in pre-prandial and post-prandial groups. Changes in the gut microbiota composition were detected by using a Next Generation Sequencing technology (Ion Torrent Personal Genome Machine).

RESULTS

L. kefiri was recovered in the feces of all volunteers after one month of probiotic administration, while it was detected only in three subjects belonging to the pre-prandial group and in two subjects belonging to the post-prandial group one month after the end of probiotic consumption. After one month of probiotic oral intake we observed a reduction of Bilophila, Butyricicomonas, Flavonifractor, Oscillibacter and Prevotella. Interestingly, after the end of probiotic administration Bacteroides, Barnesiella, Butyricicomonas, Clostridium, Haemophilus, Oscillibacter, Salmonella, Streptococcus, Subdoligranolum, and Veillonella were significantly reduced if compared to baseline samples.

CONCLUSION

L. kefiri LKF01 showed a strong ability to modulate the gut microbiota composition, leading to a significant reduction of several bacterial genera directly involved in the onset of pro-inflammatory response and gastrointestinal diseases.

Comparative pan genome analysis of oral Prevotella species implicated in periodontitis

Prevotella is part of the oral bacterial community implicated in periodontitis. Pan genome analyses of eight oral Prevotella species, P. dentalis, P. enoeca, P. fusca, P. melaninogenica, P. denticola, P. intermedia 17, P. intermedia 17-2 and P. sp. oral taxon 299 are presented in this study. Analysis of the Prevotella pan genome revealed features such as secretion systems, resistance to oxidative stress and clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems that enable the bacteria to adapt to the oral environment. We identified the presence of type VI secretion system (T6SS) in P. fusca and P. intermedia strains. For some VgrG and Hcp proteins which were not part of the core T6SS loci, we used gene neighborhood analysis and identified putative effector proteins and putative polyimmunity loci in P. fusca and polymorphic toxin systems in P. intermedia strains. Earlier studies have identified the presence of Por secretion system (PorSS) in P. gingivalis, P. melaninogenica and P. intermedia. We noted the presence of their homologs in six other oral Prevotella studied here. We suggest that in Prevotella, PorSS is used to secrete cysteine proteases such as interpain and C-terminal domain containing proteins with a "Por_secre_tail" domain. We identified subtype I-B CRISPR-Cas system in P. enoeca. Putative CRISPR-Cas system subtypes for 37 oral Prevotella and 30 non-oral Prevotella species were also predicted. Further, we performed a BLASTp search of the Prevotella proteins which are also conserved in the red-complex pathogens, against the human proteome to identify potential broad-spectrum drug targets. In summary, the use of a pan genome approach enabled identification of secretion systems and defense mechanisms in Prevotella that confer adaptation to the oral cavity.

An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data

Background

The Human Microbiome has been variously associated with the immune-regulatory mechanisms involved in the prevention or development of many non-infectious human diseases such as autoimmunity, allergy and cancer. Integrative approaches which aim at associating the composition of the human microbiome with other available information, such as clinical covariates and environmental predictors, are paramount to develop a more complete understanding of the role of microbiome in disease development.

Results

In this manuscript, we propose a Bayesian Dirichlet-Multinomial regression model which uses spike-and-slab priors for the selection of significant associations between a set of available covariates and taxa from a microbiome abundance table. The approach allows straightforward incorporation of the covariates through a log-linear regression parametrization of the parameters of the Dirichlet-Multinomial likelihood. Inference is conducted through a Markov Chain Monte Carlo algorithm, and selection of the significant covariates is based upon the assessment of posterior probabilities of inclusions and the thresholding of the Bayesian false discovery rate. We design a simulation study to evaluate the performance of the proposed method, and then apply our model on a publicly available dataset obtained from the Human Microbiome Project which associates taxa abundances with KEGG orthology pathways. The method is implemented in specifically developed R code, which has been made publicly available.

Conclusions

Our method compares favorably in simulations to several recently proposed approaches for similarly structured data, in terms of increased accuracy and reduced false positive as well as false negative rates. In the application to the data from the Human Microbiome Project, a close evaluation of the biological significance of our findings confirms existing associations in the literature.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-017-1516-0) contains supplementary material, which is available to authorized users.

GAKG-RGEKG an Epitope That Provokes Immune Cross-Reactivity between Prevotella sp. and Human Collagen: Evidence of Molecular Mimicry in Chronic Periodontitis

Periodontal disease afflicts 20% of world population. This process usually occurs in the form of being lethargic and chronic, and consequently this disease is known as chronic process. All chronic diseases constantly cause activation of the immune system, and therefore the presentation of microbial peptides which are presented to lymphocytes by professional antigen presenting cells can present microbial peptides very similar to important structures of human economy causing autoimmune diseases, process known as molecular mimicry. Thus, the aim of this study was to verify the presence of molecular mimicry phenomenon between periodontopathogens and human proteins. Blasting microbes of Socransky periodontal complexes against human collagen were performed and then the proteins with similarities were modelled and were screened in the MHI binding virtual methods. The epitopes selected were produced and plasma of chronic periodontal volunteers was obtained and a dot immunobinding assay was performed. Hypothetical protein of Prevotella sp. and human collagen epitopes with high similarities were positive for dot immunobinding assay. With this result it can be suggested that the mimicry phenomena can occur on periodontal disease.

Novel bioactive tetracycline-containing electrospun polymer fibers as a potential antibacterial dental implant coating

The purpose of this investigation was to determine the ability of tetracycline-containing fibers to inhibit biofilm formation of peri-implantitis-associated pathogens [i.e., Porphyromonas gingivalis (Pg), Fusobacterium nucleatum (Fn), Prevotella intermedia (Pi), and Aggregatibacter actinomycetemcomitans (Aa)]. Tetracycline hydrochloride (TCH) was added to a poly(DL-lactide) [PLA], poly(ε-caprolactone) [PCL], and gelatin [GEL] polymer blend solution at distinct concentrations to obtain the following fibers: PLA:PCL/GEL (TCH-free, control), PLA:PCL/GEL + 5 % TCH, PLA:PCL/GEL + 10 % TCH, and PLA:PCL/GEL + 25 % TCH. The inhibitory effect of TCH-containing fibers on biofilm formation was assessed by colony-forming units (CFU/mL). Qualitative analysis of biofilm inhibition was done via scanning electron microscopy (SEM). Statistical significance was reported at p < 0.05. Complete inhibition of biofilm formation on the fibers was observed in groups containing TCH at 10 and 25 wt%. Fibers containing TCH at 5 wt% demonstrated complete inhibition of Aa biofilm. Even though a marked reduction in CFU/mL was observed with an increase in TCH concentration, Pi proved to be the most resilient microorganism. SEM images revealed the absence of or a notable decrease in bacterial biofilm on the TCH-containing nanofibers. Collectively, our data suggest that tetracycline-containing fibers hold great potential as an antibacterial dental implant coating.

The Identification of Novel Diagnostic Marker Genes for the Detection of Beer Spoiling Pediococcus damnosus Strains Using the BlAst Diagnostic Gene findEr

As the number of bacterial genomes increases dramatically, the demand for easy to use tools with transparent functionality and comprehensible output for applied comparative genomics grows as well. We present BlAst Diagnostic Gene findEr (BADGE), a tool for the rapid prediction of diagnostic marker genes (DMGs) for the differentiation of bacterial groups (e.g. pathogenic / nonpathogenic). DMG identification settings can be modified easily and installing and running BADGE does not require specific bioinformatics skills. During the BADGE run the user is informed step by step about the DMG finding process, thus making it easy to evaluate the impact of chosen settings and options. On the basis of an example with relevance for beer brewing, being one of the oldest biotechnological processes known, we show a straightforward procedure, from phenotyping, genome sequencing, assembly and annotation, up to a discriminant marker gene PCR assay, making comparative genomics a means to an end. The value and the functionality of BADGE were thoroughly examined, resulting in the successful identification and validation of an outstanding novel DMG (fabZ) for the discrimination of harmless and harmful contaminations of Pediococcus damnosus, which can be applied for spoilage risk determination in breweries. Concomitantly, we present and compare five complete P. damnosus genomes sequenced in this study, finding that the ability to produce the unwanted, spoilage associated off-flavor diacetyl is a plasmid encoded trait in this important beer spoiling species.

In Vitro Effects of Polyphosphate against Prevotella intermedia in Planktonic Phase and Biofilm

Polyphosphate (polyP) has gained a wide interest in the food industry due to its potential as a decontaminating agent. In this study, we examined the effect of sodium tripolyphosphate (polyP3; Na5P3O10) against planktonic and biofilm cells of Prevotella intermedia, a major oral pathogen. The MIC of polyP3 against P. intermedia ATCC 49046 determined by agar dilution method was 0.075%, while 0.05% polyP3 was bactericidal against P. intermedia in time-kill analysis performed using liquid medium. A crystal violet binding assay for the assessment of biofilm formation by P. intermedia showed that sub-MICs of polyP3 significantly decreased biofilm formation. Under the scanning electron microscope, decreased numbers of P. intermedia cells forming the biofilms were observed when the bacterial cells were incubated with 0.025% or higher concentrations of polyP3. Assessment of biofilm viability with LIVE/DEAD staining and viable cell count methods showed that 0.05% or higher concentrations of polyP3 significantly decreased the viability of the preformed biofilms in a concentration-dependent manner. The zone sizes of alpha-hemolysis formed on horse blood agar produced by P. intermedia were decreased in the presence of polyP3. The expression of the genes encoding hemolysins and the genes of the hemin uptake (hmu) locus was downregulated by polyP3. Collectively, our results show that polyP is an effective antimicrobial agent against P. intermedia in biofilms as well as planktonic phase, interfering with the process of hemin acquisition by the bacterium.

The complete genome sequencing of Prevotella intermedia strain OMA14 and a subsequent fine-scale, intra-species genomic comparison reveal an unusual amplification of conjugative and mobile transposons and identify a novel Prevotella-lineage-specific repeat

Prevotella intermedia is a pathogenic bacterium involved in periodontal diseases. Here, we present the complete genome sequence of a clinical strain, OMA14, of this bacterium along with the results of comparative genome analysis with strain 17 of the same species whose genome has also been sequenced, but not fully analysed yet. The genomes of both strains consist of two circular chromosomes: the larger chromosomes are similar in size and exhibit a high overall linearity of gene organizations, whereas the smaller chromosomes show a significant size variation and have undergone remarkable genome rearrangements. Unique features of the Pre. intermedia genomes are the presence of a remarkable number of essential genes on the second chromosomes and the abundance of conjugative and mobilizable transposons (CTns and MTns). The CTns/MTns are particularly abundant in the second chromosomes, involved in its extensive genome rearrangement, and have introduced a number of strain-specific genes into each strain. We also found a novel 188-bp repeat sequence that has been highly amplified in Pre. intermedia and are specifically distributed among the Pre. intermedia-related species. These findings expand our understanding of the genetic features of Pre. intermedia and the roles of CTns and MTns in the evolution of bacteria.