Peter M. Loomer

Bacterial diversity in the oral cavity of 10 healthy individuals.

The composition of the oral microbiota from 10 individuals with healthy oral tissues was determined using culture-independent techniques. From each individual, 26 specimens, each from different oral sites at a single point in time, were collected and pooled. An 11th pool was constructed using portions of the subgingival specimens from all 10 individuals. The 16S ribosomal RNA gene was amplified using broad-range bacterial primers, and clone libraries from the individual and subgingival pools were constructed. From a total of 11 368 high-quality, nonchimeric, near full-length sequences, 247 species-level phylotypes (using a 99% sequence identity threshold) and 9 bacterial phyla were identified. At least 15 bacterial genera were conserved among all 10 individuals, with significant interindividual differences at the species and strain level. Comparisons of these oral bacterial sequences with near full-length sequences found previously in the large intestines and feces of other healthy individuals suggest that the mouth and intestinal tract harbor distinct sets of bacteria. Co-occurrence analysis showed significant segregation of taxa when community membership was examined at the level of genus, but not at the level of species, suggesting that ecologically significant, competitive interactions are more apparent at a broader taxonomic level than species. This study is one of the more comprehensive, high-resolution analyses of bacterial diversity within the healthy human mouth to date, and highlights the value of tools from macroecology for enhancing our understanding of bacterial ecology in human health.

Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome.

Viruses are the most abundant known infectious agents on the planet and are significant drivers of diversity in a variety of ecosystems. Although there have been numerous studies of viral communities, few have focused on viruses within the indigenous human microbiota. We analyzed 2 267 695 virome reads from viral particles and compared them with 263 516 bacterial 16S rRNA gene sequences from the saliva of five healthy human subjects over a 2- to 3-month period, in order to improve our understanding of the role viruses have in the complex oral ecosystem. Our data reveal viral communities in human saliva dominated by bacteriophages whose constituents are temporally distinct. The preponderance of shared homologs between the salivary viral communities in two unrelated subjects in the same household suggests that environmental factors are determinants of community membership. When comparing salivary viromes to those from human stool and the respiratory tract, each group was distinct, further indicating that habitat is of substantial importance in shaping human viromes. Compared with coexisting bacteria, there was concordance among certain predicted host–virus pairings such as Veillonella and Streptococcus, whereas there was discordance among others such as Actinomyces. We identified 122 728 virulence factor homologs, suggesting that salivary viruses may serve as reservoirs for pathogenic gene function in the oral environment. That the vast majority of human oral viruses are bacteriophages whose putative gene function signifies some have a prominent role in lysogeny, suggests these viruses may have an important role in helping shape the microbial diversity in the human oral cavity.

Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time

Viruses may play an important role in the evolution of human microbial communities. Clustered regularly interspaced short palindromic repeats (CRISPRs) provide bacteria and archaea with adaptive immunity to previously encountered viruses. Little is known about CRISPR composition in members of human microbial communities, the relative rate of CRISPR locus change, or how CRISPR loci differ between the microbiota of different individuals. We collected saliva from four periodontally healthy human subjects over an 11- to 17-mo time period and analyzed CRISPR sequences with corresponding streptococcal repeats in order to improve our understanding of the predominant features of oral streptococcal adaptive immune repertoires. We analyzed a total of 6859 CRISPR bearing reads and 427,917 bacterial 16S rRNA gene sequences. We found a core (ranging from 7% to 22%) of shared CRISPR spacers that remained stable over time within each subject, but nearly a third of CRISPR spacers varied between time points. We document high spacer diversity within each subject, suggesting constant addition of new CRISPR spacers. No greater than 2% of CRISPR spacers were shared between subjects, suggesting that each individual was exposed to different virus populations. We detect changes in CRISPR spacer sequence diversity over time that may be attributable to locus diversification or to changes in streptococcal population structure, yet the composition of the populations within subjects remained relatively stable. The individual-specific and traceable character of CRISPR spacer complements could potentially open the way for expansion of the domain of personalized medicine to the oral microbiome, where lineages may be tracked as a function of health and other factors.

Enhanced osteocalcin expression by osteoblast-like cells (MC3T3-E1) exposed to bioactive coating glass (SiO2-CaO-P2O5-MgO-K2O-Na2O system) ions.

This study tested the hypothesis that bioactive coating glass (SiO(2)-CaO-P(2)O(5)-MgO-K(2)O-Na(2)O system), used for implant coatings, enhanced the induction of collagen type 1 synthesis and in turn enhanced the expression of downstream markers alkaline phosphatase, Runx2 and osteocalcin during osteoblast differentiation. The ions from experimental bioactive glass (6P53-b) and commercial Bioglass(TM) (45S5) were added to osteoblast-like MC3T3-E1 subclone 4 cultures as a supplemented ion extract (glass conditioned medium (GCM)). Ion extracts contained significantly higher concentrations of Si and Ca (Si, 47.9+/-10.4 ppm; Ca, 69.8+/-14.0 for 45S5; Si, 33.4+/-3.8 ppm; Ca, 57.1+/-2.8 ppm for 6P53-b) compared with the control extract (Si<0.1 ppm, Ca 49.0 ppm in alpha-MEM) (ANOVA, p<0.05). Cell proliferation rate was enhanced (1.5x control) within the first 3 days after adding 45S5 and 6P53-b GCM. MC3T3-E1 subclone 4 cultures were then studied for their response to the addition of test media (GCM and control medium along with ascorbic acid (AA; 50 ppm)). Each GCM+AA treatment enhanced collagen type 1 synthesis as observed in both gene expression results (day 1, Col1alpha1, 45S5 GCM+AA: 3x control+AA; 6P53-b GCM+AA: 4x control+AA; day 5, Col1alpha2, 45S5 GCM+AA: 3.15x control+AA; 6P53-b GCM+AA: 2.35x control+AA) and in histological studies (Picrosirius stain) throughout the time course of early differentiation. Continued addition of each GCM and AA treatment led to enhanced expression of alkaline phosphatase (1.4x control+AA after 5 days, 2x control+AA after 10 days), Runx2 (2x control+AA after 7 days) and osteocalcin gene (day 3, 45S5 GCM+AA: 14x control+AA; day 5, 6P53-b GCM+AA: 19x control+AA) and protein expression (40x-70x control+AA after 6 days). These results indicated the enhanced effect of bioactive glass ions on key osteogenic markers important for the bone healing process.

The ionic products of bioactive glass particle dissolution enhance periodontal ligament fibroblast osteocalcin expression and enhance early mineralized tissue development

This study resulted in enhanced collagen type 1 and osteocalcin expression in human periodontal ligament fibroblasts (hPDLF) when exposed to bioactive glass conditioned media that subsequently may promote early mineralized tissue development. Commercial Bioglass™ (45S5) and experimental bioactive coating glass (6P53-b), were used to make a glass conditioned media (GCM) for comparison to control medium. ICP-MS analysis showed increased concentrations of Ca(2+), PO(4) (3-), Si(4+), and Na(+), for 45S5 GCM and Mg(2+), K(+), Ca(2+), PO(4)(3-), Si(4+), and Na(+) for 6P53-b GCM (relative to control medium). Differentiating hPDLF cultures exposed to 45S5 and 6P53-b GCM showed enhanced expression of collagen type 1 (Col1α1, Col1α2), osteocalcin, and alkaline phosphatase gene expression. These GCM also enhanced osteocalcin protein expression. After 16 d of culture, 45S5 and 6P53-b GCM treated cells showed regions of deep red Alizarin staining, indicating increased Ca within their respective extracellular matrices (ECM), while control-treated cells did not exhibit these features. SEM analysis showed more developed ECM in GCM treated cultures, indicated by multiple tissue layering and abundant collagen fiber bundle formation, while control treated cells did not exhibit these features. SEM analysis showed polygonal structures suggestive of CaP in 45S5 GCM treated cultures. These results indicate the osteogenic potential of bioactive coating glass in periodontal bone defect filling applications.

Combinatorial effect of Si4 +, Ca2 +, and Mg2 +released from bioactive glasses on osteoblast osteocalcin expression and biomineralization

Osteocalcin (OCN) expression is an essential osteogenic marker of successful bone regeneration therapies. This study hypothesizes that Si(4+) and Ca(2+) combinatorial released by bioactive glass enhance osteoblast biomineralization through up-regulation of OCN expression; and Mg(2+) release delays such enhancement. Osteoblasts (MC3T3-E1) were treated with ionic products of bioactive glass dissolution (6P53-b experimental bioactive glass and 45S5 commercial Bioglass™). Results showed that gene expressions, including OCN and its up-stream transcription factors (Runx2, ATF4, MSX1, SP7/OSX), growth factors and signaling proteins (BMP2, BMP6, SMAD3), were enhanced in both 45S5 and 6P53-b glass conditioned mediums (GCMs). This up-regulation led to enhanced mineral formation by 45S5 glass conditioned mediums ([GCM], Si(4+)+Ca(2+)) after 20 days, and by 45S5 GCM and 6P53-b GCM (Si(4+)+Ca(2+)+Mg(2+)) after 30 days. In examining the extracellular matrix generated by cells when exposed to each GCM, it was found that 45S5 GCM had slightly elevated levels of mineral content within ECM as compared to 6P53-b GCM after 30 days while control treatments exhibited no mineral content. The formation of well-defined mineralized nodules (distinct PO4(3-) [960 cm(-1)] and CO3(2-) [1072 cm(-1)] peaks from Raman Spectra) was observed for each GCM as the soluble glass content increased. In examining the individual and combined ion effects between Si(4+), Ca(2+), and Mg(2+), it was found Mg(2+) down-regulates OCN expression. Thus, ions released from both 45S5 and 6P53-b bioactive glasses up-regulate OCN expression and biomineralization while 6P53-b GCM Mg(2+) release down-regulated OCN expression and delayed osteoblast biomineralization. These results indicate that Si(4+), Ca(2+), and Mg(2+) combinatorially regulate osteoblast OCN expression and biomineralization.

Si and Ca individually and combinatorially target enhanced MC3T3-E1 subclone 4 early osteogenic marker expression.

This study tests the hypothesis that silicon and calcium ions combinatorially target gene expression during osteoblast differentiation. MC3T3-E1 subclone 4 osteoblast progenitors (transformed mouse calvarial osteoblasts) were exposed to Si(4+) (from Na(2)SiO(3)) and Ca(2+) (from CaCl(2):H(2)O) ion treatments both individually (0.4 mM each + control treatment) and combinatorially (0.4 mM Si(4+) + 0.4 mM Ca(2+) + control treatment) and compared to control treated (α-minimum essential medium, 10% fetal bovine serum, and 1% penicillin-streptomycin) cells. Cell proliferation studies showed no significant increase in cell density between treatments over 5 days of culture. Cellular differentiation studies involved addition of ascorbic acid (50 mg/L) for all treatments. Relative gene expression was determined for collagen type 1 (Col(I)α1/Col(I)α2), core-binding factor a (cbfa1/Runx2), and osteocalcin (OCN), which indicated osteoblast progenitor differentiation into a mineralizing phenotype. Increased Si(4+) or Ca(2+) ion treatments enhanced Col(I)α1, Col(I)α2, Runx2, and OCN expression, while increased Si(4+) + Ca(2+) ion treatments enhanced OCN expression. Moreover, it was found that a Si(4+)/Ca(2+) ratio of unity was optimal for maximal expression of OCN. Collagen fiber bundles were dense, elongated, and thick within extracellular matrices (ECM) exposed to Si(4+) and Si(4+) + Ca(2+) treatments, while collagen fiber bundles were sparse, short, and thin within Ca(2+) and control treated ECM. These results indicated that individual ions enhance multiple osteogenic gene expression, while combined ion treatments enhance individual gene expression. In addition, these results indicated that Si(4+) enhanced osteoblast gene expression and ECM formation at higher levels than Ca(2+). These results support the larger concept that ions (possibly released from bioactive glasses) could control bone formation by targeting osteoblast marker expression.

The impact of microgravity on bone metabolism in vitro and in vivo.

Exposure to microgravity has been associated with several physiological changes in astronauts and cosmonauts, including an osteoporosis-like loss of bone mass. In-flight measures used to counteract this, including intensive daily exercise regimens, have been only partially successful in reducing the bone loss and in the process have consumed valuable work time. If this bone loss is to be minimized or, preferably, prevented, more effective treatment strategies are required. This, however, requires a greater understanding of the mechanisms through which bone metabolism is affected by microgravity. Various research strategies have been used to examine this problem, including in vitro studies using bone cells and in vivo studies on humans and rats. These have been conducted both in flight and on the ground, by strategies that produce weightlessness to mimic the effects of microgravity. Overall, the majority of the studies have found that marked decreases in gravitation loading result in the loss of bone mass. The processes of bone formation and bone resorption become uncoupled, with an initial transitory increase in resorption accompanied by a prolonged decrease in formation. Loss of bone mass is not uniform throughout the skeleton, but varies at different sites depending on the type of bone and on the mechanical load received. It appears that the skeletal response is a physiologic adaptation to the space environment which, after long space flights or repeated shorter ones, could eventually lead to significant reductions in the ability of the skeletal tissues to withstand the forces of gravity and increased susceptibility to fracture.

Osteogenic and osteoclastic cell interaction: development of a co-culture system

Abstract The processes involved in the regulation of bone cell metabolism are complex, including those implicated in bone cell coupling. This study was undertaken to develop a model that would permit real-time interaction between osteoclastic cells and osteoblasts in vitro. Osteogenic bone marrow stromal cells were isolated from 18-day-old embryonic chickens, while osteoclastic cells were isolated from laying White Leghorn hens on calcium-deficient diets. Osteoclastic cells (5×105) were seeded onto mineral thin films and suspended above osteogenic cells (1×104) already plated on the bottoms of tissue culture plate wells. The data showed that after 4 days of incubation there was up to a fivefold (P<0.05) reduction in all measured parameters of osteogenesis (mineralization, alkaline phosphatase activity and type I collagen production) in osteogenic cultures grown in the presence of osteoclastic cells. Similarly, osteoclastic cell-induced mineral resorption was reduced up to threefold (P<0.05). Co-culture effects on cellular responses could be manipulated by known antiresorptive agents (e.g., pamidronate) altering either the source or the age of osteoclastic cells. The results indicate that the co-culture model may be useful in the study of bone cell interactions.

Effectiveness of systemic antimicrobial therapy in combination with scaling and root planing in the treatment of periodontitis: A systematic review

BACKGROUND The use of systemic antibiotics in conjunction with scaling and root planing (SRP) may improve the clinical outcome and even could be essential for a successful treatment of periodontitis. However, the effectiveness and clinical safety of this combination of therapy remain unclear. The authors of this study reviewed the available literature related to this hypothesis, evaluating the effectiveness of the use of systemic antimicrobials in combination with SRP versus SRP alone in the treatment of chronic periodontitis (CP) or aggressive periodontitis (AgP). METHODS The authors used 3 electronic databases and hand searched articles published from April 2001 through October 2013 in selected journals. The authors selected clinical trials with a minimum of 6 months follow-up during which patients with either CP or AgP had been treated with systemic antibiotics plus SRP in comparison with SRP alone or with placebo. The authors analyzed the gain in clinical attachment level (CAL), reduction in probing pocket depth (PPD), reduction in bleeding on probing (BOP), and patient-related variables (that is, adverse effects). RESULTS After the selection process, the authors included 23 clinical trials in this review. Assessment of the quality of the studies revealed the risk of bias as a common finding. Overall, there was a tendency toward improvement of the measured outcomes, CAL, PPD, and BOP in studies for which systemic antibiotics were used as adjunctive therapy with SRP. CONCLUSION Owing to the high level of heterogeneity of the studies included in this review, the authors could not establish definitive conclusions and guidelines regarding the use of adjunctive systemic antibiotics. However, within the limitations of this review, the use of systemic antibiotics with SRP may be beneficial for specific populations. Standardized clinical disease diagnostic criteria and additional randomized controlled clinical trials are necessary to verify the effectiveness of the use of adjunctive systemic antimicrobials with SRP. PRACTICAL IMPLICATIONS Owing to methodological differences and biases among clinical trials evaluating systemic antibiotics adjunctive to SRP, clinicians should base their decisions to prescribe on the results of weighing both benefits and risks for each patient.