Extracellular proteolytic activities expressed by Bacillus pumilus isolated from endodontic and periodontal lesions

Comparative genomic analyses reveal genetic characteristics and pathogenic factors of Bacillus pumilus HM-7

Bacillus pumilus plays an important role in industrial application and biocontrol activities, as well as causing humans and plants disease, leading to economic losses and biosafety concerns. However, until now, the pathogenesis and underlying mechanisms of B. pumilus strains remain unclear. In our previous study, one representative isolate of B. pumilus named HM-7 has been recovered and proved to be the causal agent of fruit rot on muskmelon (Cucumis melo). Herein, we present a complete and annotated genome sequence of HM-7 that contains 4,111 coding genes in a single 3,951,520 bp chromosome with 41.04% GC content. A total of 3,481 genes were functionally annotated with the GO, COG, and KEGG databases. Pan-core genome analysis of HM-7 and 20 representative B. pumilus strains, as well as six closely related Bacillus species, discovered 740 core genes and 15,205 genes in the pan-genome of 21 B. pumilus strains, in which 485 specific-genes were identified in HM-7 genome. The average nucleotide identity (ANI), and whole-genome-based phylogenetic analysis revealed that HM-7 was most closely related to the C4, GR8, MTCC-B6033, TUAT1 and SH-B11 strains, but evolutionarily distinct from other strains in B. pumilus. Collinearity analysis of the six similar B. pumilus strains showed high levels of synteny but also several divergent regions for each strains. In the HM-7 genome, we identified 484 genes in the carbohydrate-active enzymes (CAZyme) class, 650 genes encoding virulence factors, and 1,115 genes associated with pathogen-host interactions. Moreover, three HM-7-specific regions were determined, which contained 424 protein-coding genes. Further investigation of these genes showed that 19 pathogenesis-related genes were mainly associated with flagella formation and secretion of toxic products, which might be involved in the virulence of strain HM-7. Our results provided detailed genomic and taxonomic information for the HM-7 strain, and discovered its potential pathogenic mechanism, which lay a foundation for developing effective prevention and control strategies against this pathogen in the future.

Diverse microbiota in palatal radicular groove analyzed by Illumina sequencing: Four case reports

BACKGROUND

A palatal radicular groove is an unusual developmental deformity of the tooth, which may serve as a channel linking the periodontal and periapical inflammation, and yet no literature could be obtained analyzing microbiota within the palatal radicular grooves.

CASE SUMMARY

Four patients diagnosed with palatal radicular groove and concomitant periodontal-endodontic deformity in permanent maxillary lateral incisors were enrolled in this work. Twelve bacterial samples from 4 patients were collected from different parts of the palatal radicular groove during intentional replantation surgery. Illumina sequencing was performed to analyze the taxonomical composition and microbiome structure inside the palatal grooves, and 1162 operational taxonomic units were obtained. The phyla of Firmicutes and Proteobacteria predominated in most of the samples. An unknown genus from the Bacillaceae family, Lactococcus, and Porphyromonas were the most abundant genera identified. There was no difference in the microbiota richness and diversity in three sections of the groove.

CONCLUSION

The unique ecological niches inside the palatal grooves harbored bacterial communities that shared some component features of both the endodontic and periodontal infections. The existence of palatal groove may play an interaction bridge between the root apex and tooth cervix and thus impair the outcome of traditional therapeutic methods such as root canal treatment and periodontal management.

Treatment of an Endo-Perio Lesion with Ozone Gas in a Patient with Aggressive Periodontitis: A Clinical Case Report and Literature Review

The pulp and periodontium have obvious relationships that have been described in many studies. Pulp infections may affect periodontal tissues and vice versa. Teeth with endo-perio lesions have a worse prognosis than isolated endodontic or periodontal lesions. Elimination of endodontic and periodontal infections is essential for successful treatment, so co-operation between endodontists and periodontists is necessary. In this clinical case, a 44-year-old male presented with primary periodontal disease with secondary endodontic involvement in his lower right canine because of aggressive periodontitis. There was 10 mm of clinical attachment loss and 8 mm periodontal pocket mesial from the tooth and bone radiolucency periapical and lateral from the root. Periodontal therapy was followed by endodontic treatment. Periodontal therapy included root scaling and planing, treatment of the periodontal pocket with ozone gas, systemic antibiotics, oral hygiene instructions, and chlorhexidine rinsing. Endodontic therapy included root canal instrumentation with rotary endodontic files, irrigation, root canal treatment with ozone gas, and obturation with lateral compaction. Radiographs at a 6-month follow-up appointment showed complete healing of the periapical lesion and alveolar bone lateral to the root. Using an interdisciplinary approach to treat endo-perio lesions provides favorable clinical outcomes. Ozone therapy is beneficial for the successful treatment of endo-perio lesions with narrow periodontal pockets in patients with aggressive periodontitis and poor prognosis.

Antibiofilm efficacy of biosynthesized silver nanoparticles against endodontic-periodontal pathogens: An in vitro study

Background:

Endodontic-periodontal pathogens exist as biofilms which are difficult to eliminate. Biosynthesized silver nanoparticles (AgNPs) emerged as newer antimicrobial agents with potential benefits.

Aim:

The aim of this study is to determine the minimum inhibitory concentration (MIC); evaluate the antibiofilm efficacy of fungal-derived AgNPs against Porphyromonas gingivalis, Bacillus pumilus, and Enterococcus faecalis.

Materials and Methods:

MIC of AgNPs against test pathogens was determined using micro broth dilution method. Serial dilutions of AgNPs ranging from 80 to 1 μg/ml concentration were added to wells containing 10 μl of bacterial inoculum in culture media and control group without AgNPs. For biofilm models, 120 dentin blocks were prepared, sterilized, and contaminated for 2 weeks with (n = 40 each). Group 1: B. pumilus, Group 2: E. faecalis, and Group 3: P. gingivalis and each group is divided into four subgroups (n = 10 each) and treated with distilled water, AgNPs, 2% and 0.2% chlorhexidine (CHX). Colonies counted after 24 h of incubation and statistically analyzed using one-way ANOVA and post hoc Tukey tests.

Results:

MIC for B. pumilus was determined as 20 μg/ml and 30 μg/ml for E. faecalis and P. gingivalis. AgNPs were effective as 2% CHX against all biofilms compared to control group. Post hoc Tukey test (P < 0.0001) shows no significant difference between groups.

Conclusion:

Fungal-derived AgNPs are effective against endo-perio pathogens.

Evaluation of antibacterial efficacy of biosynthesized silver nanoparticles derived from fungi against endo-perio pathogens Porphyromonas gingivalis, Bacillus pumilus, and Enterococcus faecalis

Background

Even after rapid progress in contemporary dental practice, we encounter the failures due to endodontic, periodontal, or combined lesions. Complex anatomy of tooth and resistant microbes demands the development of new treatment strategies.

Aim

The aim of this study is to biosynthesize silver nanoparticles (AgNPs) using fungi and determine the antibacterial efficacy against Porphyromonas gingivalis, Bacillus pumilus, and Enterococcus faecalis.

Materials and Methods

Fungi isolated from healthy leaves of Withania somnifera were used to biosynthesize AgNPs. The biosynthesized AgNPs were characterized by different methods, and antibacterial efficacy was evaluated by agar well diffusion method measuring the zone of inhibition. Test microorganisms were divided as Group 1: B. pumilus 27142 (American Type Culture Collection [ATCC]), Group 2: E. faecalis 29212 (ATCC), and Group 3: P. gingivalis 33277 (ATCC). Agents used for antibacterial efficacy were grouped as: AgNPs: A (20 μl), B (40 μl), C (60 μl), D (80 μl), E (100 μl), F (0.2% chlorhexidine [CHX]), G (2% CHX), H (Ampicillin), and I (sterile distilled water).

Results

Characterization studies showed the color change from colorless to reddish brown color; ultraviolet spectrum showed peak at 420 nm, transmission electron microscope revealed the particles spherical in shape and 10-20 nm size. Fourier transform infrared spectroscopy analysis revealed the presence of functional groups. Data collected for antibacterial efficacy were analyzed using one-way ANOVA and post hoc Tukey's multiple shows no significant difference among three groups (P < 0.0001). AgNPs were as effective as CHX and positive control ampicillin. No zones were seen for I (distilled water).

Conclusion

Biosynthesized AgNPs showed efficient antibacterial efficacy. Therefore, it creates a new horizon in the management of endodontic, periodontal, and combined lesions.

Making soy sauce using direct fermentation of defatted soybean meal without the meju (soybean Koji) preparation process

Soy sauce prepared via direct fermentation of defatted soybean meal (DFSM) using halophiles without addition of dried, fermented soybeans or meju was evaluated. DFSM was fermented using single and mixed cultures of Oceanobacillus kimchii and Bacillus pumilus under 18% salinity conditions. Amounts of total organic nitrogen, free amino acids, and organic acids in soy sauce prepared with the mixed culture were slightly higher than sauces prepared with single culture. The ingredient content was higher in soy sauce prepared via direct fermentation of DFSM than soy sauce prepared with meju. Microorganisms detected in DFSM fermentation were not detected in the meju culture, except for the 2 halophiles, based on metagenomic analysis. Direct fermentation of DFSM is better than using meju for preparation of soy sauce.

Differentiation of Bacillus pumilus and Bacillus safensis using MALDI-TOF-MS

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) despite being increasingly used as a method for microbial identification, still present limitations in which concerns the differentiation of closely related species. Bacillus pumillus and Bacillus safensis, are species of biotechnological and pharmaceutical significance, difficult to differentiate by conventional methodologies. In this study, using a well-characterized collection of B. pumillus and B. safensis isolates, we demonstrated the suitability of MALDI-TOF-MS combined with chemometrics to accurately and rapidly identify them. Moreover, characteristic species-specific ion masses were tentatively assigned, using UniProtKB/Swiss-Prot and UniProtKB/TrEMBL databases and primary literature. Delineation of B. pumilus (ions at m/z 5271 and 6122) and B. safensis (ions at m/z 5288, 5568 and 6413) species were supported by a congruent characteristic protein pattern. Moreover, using a chemometric approach, the score plot created by partial least square discriminant analysis (PLSDA) of mass spectra demonstrated the presence of two individualized clusters, each one enclosing isolates belonging to a species-specific spectral group. The generated pool of species-specific proteins comprised mostly ribosomal and SASPs proteins. Therefore, in B. pumilus the specific ion at m/z 5271 was associated with a small acid-soluble spore protein (SASP O) or with 50S protein L35, whereas in B. safensis specific ions at m/z 5288 and 5568 were associated with SASP J and P, respectively, and an ion at m/z 6413 with 50S protein L32. Thus, the resulting unique protein profile combined with chemometric analysis, proved to be valuable tools for B. pumilus and B. safensis discrimination, allowing their reliable, reproducible and rapid identification.

Phylogenetic and clonality analysis of Bacillus pumilus isolates uncovered a highly heterogeneous population of different closely related species and clones

Bacillus pumilus is a Gram-positive bacterium with a wide range of attributed applications, namely as a plant growth promoting rhizobacteria (PGPR), animal, and human probiotic. However, a rare putative role in human diseases has been reported, namely in food poisoning or as anthrax-like cutaneous infectious agent. This species is difficult to distinguish from its closely related species on the basis of phenotypic or biochemical characteristics and 16S rRNA gene sequences. In this study, the phylogenetic analysis of gyrB and rpoB gene sequences of a collection of isolates previously identified as B. pumilus, assigned most of them (93%, 38 of 41 isolates) to B. safensis or to the new recently described B. invictae. Moreover, we extended the previously reported recognized habitats of these species and unveiled a human health or biotechnological relevance (e.g. as implicated in food poisoning or PGPR) for them. Additionally, we demonstrated that both B. safensis and B. invictae species encompass a clonally diverse population, which can justify their great adaptation ability to different niches, with evidence of clonal-host specificity.