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author:("Guo, lizhong")
1.  Intercellular communications in multispecies oral microbial communities 
The oral cavity contains more than 700 microbial species that are engaged in extensive cell–cell interactions. These interactions contribute to the formation of highly structured multispecies communities, allow them to perform physiological functions, and induce synergistic pathogenesis. Co-adhesion between oral microbial species influences their colonization of oral cavity and effectuates, to a large extent, the temporal and spatial formation of highly organized polymicrobial community architecture. Individual species also compete and collaborate with other neighboring species through metabolic interactions, which not only modify the local microenvironment such as pH and the amount of oxygen, making it more suitable for the growth of other species, but also provide a metabolic framework for the participating microorganisms by maximizing their potential to extract energy from limited substrates. Direct physical contact of bacterial species with its neighboring co-habitants within microbial community could initiate signaling cascade and achieve modulation of gene expression in accordance with different species it is in contact with. In addition to communication through cell–cell contact, quorum sensing (QS) mediated by small signaling molecules such as competence-stimulating peptides (CSPs) and autoinducer-2 (AI-2), plays essential roles in bacterial physiology and ecology. This review will summarize the evidence that oral microbes participate in intercellular communications with co-inhabitants through cell contact-dependent physical interactions, metabolic interdependencies, as well as coordinative signaling systems to establish and maintain balanced microbial communities.
doi:10.3389/fmicb.2014.00328
PMCID: PMC4076886  PMID: 25071741
oral microbial community; coadhesion; signaling transduction; metabolic interactions; cell-cell communication
2.  Draft Genome Sequences of Two Clinical Isolates of Streptococcus mutans 
Genome Announcements  2014;2(3):e00441-14.
We report the draft genome sequences of PKUSS-HG01 and PKUSS-LG01, two clinical isolates of Streptococcus mutans from human dental plaque. The genomics information will facilitate the study of the mechanisms of pathogenicity and evolution of S. mutans.
doi:10.1128/genomeA.00441-14
PMCID: PMC4056288  PMID: 24926045
3.  An Effective Hybrid Firefly Algorithm with Harmony Search for Global Numerical Optimization 
The Scientific World Journal  2013;2013:125625.
A hybrid metaheuristic approach by hybridizing harmony search (HS) and firefly algorithm (FA), namely, HS/FA, is proposed to solve function optimization. In HS/FA, the exploration of HS and the exploitation of FA are fully exerted, so HS/FA has a faster convergence speed than HS and FA. Also, top fireflies scheme is introduced to reduce running time, and HS is utilized to mutate between fireflies when updating fireflies. The HS/FA method is verified by various benchmarks. From the experiments, the implementation of HS/FA is better than the standard FA and other eight optimization methods.
doi:10.1155/2013/125625
PMCID: PMC3856164  PMID: 24348137
4.  Salivary Biomarkers for Caries Risk Assessment 
Saliva contains various microbes and host biological components that could be used for caries risk assessment. This review focuses on the research topics that connect dental caries with saliva, including both the microbial and host components within saliva.
PMCID: PMC3825179  PMID: 23505756
5.  Phenotypic characterization of the foldase homologue PrsA in Streptococcus mutans 
Molecular oral microbiology  2012;28(2):10.1111/omi.12014.
SUMMARY
Streptococcus mutans is generally considered to be the principal etiological agent for dental caries. Many of the proteins necessary for its colonization of the oral cavity and pathogenesis are exported to the cell surface or the extracellular matrix, a process that requires the assistance of the export machineries. Bioinformatic analysis revealed that the S. mutans genome contains a prsA gene, whose counterparts in other gram positive bacteria, including Bacillus and Lactococcus encode functions involved in protein post-export. In this study, we constructed a PrsA-deficient derivative of S. mutans and demonstrated that the prsA mutant displayed an altered cell wall/ membrane protein profile as well as cell surface related phenotypes, including auto-aggregation, increased surface hydrophobicity, and abnormal biofilm formation. Further analysis revealed that the disruption of the prsA gene resulted in reduced insoluble glucan production by cell surface localized glucosyltransferases, and mutacin as well as cell surface-display of a heterologous expressed GFP fusion to the cell surface protein SpaP. Our study suggested that PrsA in S. mutans encodes functions similar to the ones identified in Bacillus, and thus is likely involved in protein post-export.
doi:10.1111/omi.12014
PMCID: PMC3819222  PMID: 23241367
foldase protein PrsA; protein secretion; Streptococcus mutans
6.  An in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome 
Microbiome  2013;1:25.
Background
Our knowledge of microbial diversity in the human oral cavity has vastly expanded during the last two decades of research. However, much of what is known about the behavior of oral species to date derives from pure culture approaches and the studies combining several cultivated species, which likely does not fully reflect their function in complex microbial communities. It has been shown in studies with a limited number of cultivated species that early oral biofilm development occurs in a successional manner and that continuous low pH can lead to an enrichment of aciduric species. Observations that in vitro grown plaque biofilm microcosms can maintain similar pH profiles in response to carbohydrate addition as plaque in vivo suggests a complex microbial community can be established in the laboratory. In light of this, our primary goal was to develop a robust in vitro biofilm-model system from a pooled saliva inoculum in order to study the stability, reproducibility, and development of the oral microbiome, and its dynamic response to environmental changes from the community to the molecular level.
Results
Comparative metagenomic analyses confirmed a high similarity of metabolic potential in biofilms to recently available oral metagenomes from healthy subjects as part of the Human Microbiome Project. A time-series metagenomic analysis of the taxonomic community composition in biofilms revealed that the proportions of major species at 3 hours of growth are maintained during 48 hours of biofilm development. By employing deep pyrosequencing of the 16S rRNA gene to investigate this biofilm model with regards to bacterial taxonomic diversity, we show a high reproducibility of the taxonomic carriage and proportions between: 1) individual biofilm samples; 2) biofilm batches grown at different dates; 3) DNA extraction techniques and 4) research laboratories.
Conclusions
Our study demonstrates that we now have the capability to grow stable oral microbial in vitro biofilms containing more than one hundred operational taxonomic units (OTU) which represent 60-80% of the original inoculum OTU richness. Previously uncultivated Human Oral Taxa (HOT) were identified in the biofilms and contributed to approximately one-third of the totally captured 16S rRNA gene diversity. To our knowledge, this represents the highest oral bacterial diversity reported for an in vitro model system so far. This robust model will help investigate currently uncultivated species and the known virulence properties for many oral pathogens not solely restricted to pure culture systems, but within multi-species biofilms.
doi:10.1186/2049-2618-1-25
PMCID: PMC3971625  PMID: 24451062
In vitro model; Biofilm; Oral microbiome; Saliva; Streptococcus; Lactobacillus; Uncultivated bacteria
7.  Investigating Acid Production by Streptococcus mutans with a Surface-Displayed pH-Sensitive Green Fluorescent Protein 
PLoS ONE  2013;8(2):e57182.
Acidogenicity and aciduricity are the main virulence factors of the cavity-causing bacterium Streptococcus mutans. Monitoring at the individual cell level the temporal and spatial distribution of acid produced by this important oral pathogen is central for our understanding of these key virulence factors especially when S. mutans resides in multi-species microbial communities. In this study, we explored the application of pH-sensitive green fluorescent proteins (pHluorins) to investigate these important features. Ecliptic pHluorin was functionally displayed on the cell surface of S. mutans as a fusion protein with SpaP. The resulting strain (O87) was used to monitor temporal and spatial pH changes in the microenvironment of S. mutans cells under both planktonic and biofilm conditions. Using strain O87, we revealed a rapid pH drop in the microenviroment of S. mutans microcolonies prior to the decrease in the macro-environment pH following sucrose fermentation. Meanwhile, a non-uniform pH distribution was observed within S. mutans biofilms, reflecting differences in microbial metabolic activity. Furthermore, strain O87 was successfully used to monitor the S. mutans acid production profiles within dual- and multispecies oral biofilms. Based on these findings, the ecliptic pHluorin allows us to investigate in vivo and in situ acid production and distribution by the cariogenic species S. mutans.
doi:10.1371/journal.pone.0057182
PMCID: PMC3585301  PMID: 23468929
8.  Wavelet Neural Network Using Multiple Wavelet Functions in Target Threat Assessment 
The Scientific World Journal  2013;2013:632437.
Target threat assessment is a key issue in the collaborative attack. To improve the accuracy and usefulness of target threat assessment in the aerial combat, we propose a variant of wavelet neural networks, MWFWNN network, to solve threat assessment. How to select the appropriate wavelet function is difficult when constructing wavelet neural network. This paper proposes a wavelet mother function selection algorithm with minimum mean squared error and then constructs MWFWNN network using the above algorithm. Firstly, it needs to establish wavelet function library; secondly, wavelet neural network is constructed with each wavelet mother function in the library and wavelet function parameters and the network weights are updated according to the relevant modifying formula. The constructed wavelet neural network is detected with training set, and then optimal wavelet function with minimum mean squared error is chosen to build MWFWNN network. Experimental results show that the mean squared error is 1.23 × 10−3, which is better than WNN, BP, and PSO_SVM. Target threat assessment model based on the MWFWNN has a good predictive ability, so it can quickly and accurately complete target threat assessment.
doi:10.1155/2013/632437
PMCID: PMC3590761  PMID: 23509436
9.  A Bat Algorithm with Mutation for UCAV Path Planning 
The Scientific World Journal  2012;2012:418946.
Path planning for uninhabited combat air vehicle (UCAV) is a complicated high dimension optimization problem, which mainly centralizes on optimizing the flight route considering the different kinds of constrains under complicated battle field environments. Original bat algorithm (BA) is used to solve the UCAV path planning problem. Furthermore, a new bat algorithm with mutation (BAM) is proposed to solve the UCAV path planning problem, and a modification is applied to mutate between bats during the process of the new solutions updating. Then, the UCAV can find the safe path by connecting the chosen nodes of the coordinates while avoiding the threat areas and costing minimum fuel. This new approach can accelerate the global convergence speed while preserving the strong robustness of the basic BA. The realization procedure for original BA and this improved metaheuristic approach BAM is also presented. To prove the performance of this proposed metaheuristic method, BAM is compared with BA and other population-based optimization methods, such as ACO, BBO, DE, ES, GA, PBIL, PSO, and SGA. The experiment shows that the proposed approach is more effective and feasible in UCAV path planning than the other models.
doi:10.1100/2012/418946
PMCID: PMC3543789  PMID: 23365518
10.  Community-based interference against integration of Pseudomonas aeruginosa into human salivary microbial biofilm 
Molecular Oral Microbiology  2011;26(6):337-352.
As part of the human gastrointestinal tract, the oral cavity represents a complex biological system and harbors diverse bacterial species. Unlike the gut microbiota which is often considered a health asset, studies of the oral commensal microbial flora have been largely limited to their implication in oral diseases such as dental caries and periodontal diseases; Little emphasis has been given to their potential beneficial roles, especially the protective effects against oral colonization by foreign/pathogenic bacteria. In this study, we used the salivary microbiota derived from healthy human subjects to investigate protective effects against the colonization and integration of Pseudomonas aeruginosa, an opportunistic bacterial pathogen, into developing and pre-formed salivary biofilms. When co-cultivated in saliva medium, P. aeruginosa persisted in the planktonic phase, but failed to integrate into salivary microbial community during biofilm formation. Furthermore, in the saliva medium supplemented with 0.05% (w/v) sucrose, the oral flora inhibited the growth of P. aeruginosa by producing lactic acid. More interestingly, while pre-formed salivary biofilms were able to prevent P. aeruginosa colonization, the same biofilms recovered from mild chlorhexidine gluconate treatment displayed a shift in microbial composition and showed a drastic reduction in protection. Our study indicates that normal oral communities with balanced microbial compositions could be important in effectively preventing the integration of foreign/pathogenic bacterial species, such as P. aeruginosa.
doi:10.1111/j.2041-1014.2011.00622.x
PMCID: PMC3327514  PMID: 22053962
bacterial interference; microbial flora; oral cavity; Pseudomonas aeruginosa; salivary biofilm
11.  A Hybrid Metaheuristic DE/CS Algorithm for UCAV Three-Dimension Path Planning 
The Scientific World Journal  2012;2012:583973.
Three-dimension path planning for uninhabited combat air vehicle (UCAV) is a complicated high-dimension optimization problem, which primarily centralizes on optimizing the flight route considering the different kinds of constrains under complicated battle field environments. A new hybrid metaheuristic differential evolution (DE) and cuckoo search (CS) algorithm is proposed to solve the UCAV three-dimension path planning problem. DE is applied to optimize the process of selecting cuckoos of the improved CS model during the process of cuckoo updating in nest. The cuckoos can act as an agent in searching the optimal UCAV path. And then, the UCAV can find the safe path by connecting the chosen nodes of the coordinates while avoiding the threat areas and costing minimum fuel. This new approach can accelerate the global convergence speed while preserving the strong robustness of the basic CS. The realization procedure for this hybrid metaheuristic approach DE/CS is also presented. In order to make the optimized UCAV path more feasible, the B-Spline curve is adopted for smoothing the path. To prove the performance of this proposed hybrid metaheuristic method, it is compared with basic CS algorithm. The experiment shows that the proposed approach is more effective and feasible in UCAV three-dimension path planning than the basic CS model.
doi:10.1100/2012/583973
PMCID: PMC3485495  PMID: 23193383
12.  The influence of iron availability on human salivary microbial community composition 
Microbial Ecology  2012;64(1):152-161.
It is a well-recognized fact that the composition of human salivary microbial community is greatly affected by its nutritional environment. However, most studies are currently focused on major carbon or nitrogen sources with limited attention to trace elements like essential mineral ions. In this study, we examined the effect of iron availability on the bacterial profiles of an in vitro human salivary microbial community as iron is an essential trace element for the survival and proliferation of virtually all microorganisms. Analysis via a combination of PCR with denaturing gradient gel electrophoresis (DGGE) demonstrated a drastic change in species composition of an in vitro human salivary microbiota when iron was scavenged from the culture medium by addition of the iron chelator 2,2’- bipyridyl (Bipy). This shift in community profile was prevented by the presence of excessive ferrous iron (Fe2+). Most interestingly, under iron deficiency, the in vitro grown salivary microbial community became dominated by several hemolytic bacterial species, including Streptococcus spp., Gemella spp. and Granulicatella spp.all of which have been implicated in infective endocarditis. These data provide evidence that iron availability can modulate host-associated oral microbial communities, resulting in a microbiota with potential clinical impact.
doi:10.1007/s00248-012-0013-2
PMCID: PMC3376180  PMID: 22318873
iron availability; microbial flora; oral cavity
13.  Adherence to Streptococci facilitates Fusobacterium nucleatum integration into an oral microbial community 
Microbial Ecology  2011;63(3):532-542.
The development of multispecies oral microbial communities involves complex intra- and interspecies interactions at various levels. The ability to adhere to the resident bacteria or the biofilm matrix and overcome community resistance are among the key factors that determine whether a bacterium can integrate into a community. In this study, we focus on community integration of Fusobacterium nucleatum, a prevalent Gram-negative oral bacterial species that is considered an important member of the oral community due to its ability to adhere to Gram-positive as well as Gram-negative species. This interaction with a variety of different species is thought to facilitate the establishment of multispecies oral microbial community. However, the majority of experiments thus far has focused on the physical adherence between two species as measured by in vitro co-aggregation assays, while the community-based effects on the integration of F. nucleatum into multispecies microbial community remains to be investigated. In this study, we demonstrated using an established in vitro mice oral microbiota (O-mix) that the viability of F. nucleatum was significantly reduced upon addition to the O-mix due to cell contact-dependent induction of hydrogen peroxide (H2O2) production by oral community. Interestingly, this inhibitory effect was significantly alleviated when F. nucleatum was allowed to adhere to its known interacting partner species (such as Streptococcus sanguinis) prior to addition. Furthermore, this aggregate formation-dependent protection was absent in the F. nucleatum mutant strain ΔFn1526 that is unable to bind to a number of Gram-positive species. More importantly, this protective effect was also observed during integration of F. nucleatum into a human salivary microbial community (S-mix). These results support the idea that by adhering to other oral microbes, such as streptococci, F. nucleatum is able to mask the surface components that are recognized by H2O2 producing oral community members. This evasion strategy prevents detection by antagonistic oral bacteria and allows integration into the developing oral microbial community.
doi:10.1007/s00248-011-9989-2
PMCID: PMC3313671  PMID: 22202886
coaggregation; Fusobacterium nucleatum; microbial flora; oral cavity; community resistance
14.  In vitro communities derived from oral and gut microbial floras inhibit the growth of bacteria of foreign origins 
Microbial ecology  2010;60(3):665-676.
The gastrointestinal (GI) tract is home to trillions of microbes. Within the same GI tract substantial differences in the bacterial species that inhabit the oral cavity and intestinal tract have been noted. While the influence of host environments and nutritional availability in shaping different microbial communities is widely accepted, we hypothesize that the existing microbial flora also plays a role in selecting the bacterial species that are being integrated into the community. In this study, we used cultivable microbial communities isolated from different parts of the GI tract of mice (oral cavity and intestines) as a model system to examine this hypothesis. Microbes from these two areas were harvested and cultured using the same nutritional conditions, which led to two distinct microbial communities, each with about 20 different species as revealed by PCR-DGGE analysis. In vitro community competition assays showed that the two microbial floras exhibited antagonistic interactions towards each other. More interestingly, all the original isolates tested and their closely related species displayed striking community preferences: they persisted when introduced into the bacterial community of the same origin, while their viable count declined more than 3 orders of magnitude after 4 days of coincubation with the microbial flora of foreign origin. These results suggest that an existing microbial community might impose a selective pressure on incoming foreign bacterial species independent of host selection. The observed inter-flora interactions could contribute to the protective effect of established microbial communities against the integration of foreign bacteria to maintain the stability of the existing communities.
doi:10.1007/s00248-010-9711-9
PMCID: PMC2954289  PMID: 20625712
15.  Oral-derived bacterial flora defends its domain by recognizing and killing intruders---- a molecular analysis using Escherichia coli as a model intestinal bacterium 
Microbial ecology  2010;60(3):655-664.
Within the same human gastrointestinal (GI) tract, substantial differences in the bacterial species that inhabit oral cavity and intestinal tract have been noted. Previous research primarily attributed the differences to the influences of host environments and nutritional availabilities (“host habitat” effect). Our recent study indicated that, other than the host habitat effect, an existing microbial community could impose a selective pressure on incoming foreign bacterial species independent of host-mediated selection (“community selection” effect). In this study, we employed in vitro microbial floras representing microorganisms that inhabit the oral cavities and intestinal tract of mice in combination with Escherichia coli as a model intestinal bacterium and demonstrated that E. coli displays a striking community preference. It thrived when introduced into the intestinal microbial community, and survived poorly in the microbial flora of foreign origin (oral community). A more detailed examination of this phenomenon showed that the oral community produced oxygen free radicals in the presence of wild type E. coli while mutants deficient in lipopolysaccharides (LPS) did not trigger significant production of these cell damaging agents. Furthermore, mutants of E. coli defective in the oxidative stress response experienced a more drastic reduction in viability when co-cultivated with the oral flora, while the exogenous addition of the anti-oxidant vitamin C was able to rescue it. We concluded that the oral-derived microbial community senses the E. coli LPS and kills the bacterium with oxygen free radicals. This study reveals a new mechanism of community invasion resistance employed by established microflora to defend their domains.
doi:10.1007/s00248-010-9708-4
PMCID: PMC2954290  PMID: 20625713
16.  In Vitro Communities Derived from Oral and Gut Microbial Floras Inhibit the Growth of Bacteria of Foreign Origins 
Microbial Ecology  2010;60(3):665-676.
The gastrointestinal (GI) tract is home to trillions of microbes. Within the same GI tract, substantial differences in the bacterial species that inhabit the oral cavity and intestinal tract have been noted. While the influence of host environments and nutritional availability in shaping different microbial communities is widely accepted, we hypothesize that the existing microbial flora also plays a role in selecting the bacterial species that are being integrated into the community. In this study, we used cultivable microbial communities isolated from different parts of the GI tract of mice (oral cavity and intestines) as a model system to examine this hypothesis. Microbes from these two areas were harvested and cultured using the same nutritional conditions, which led to two distinct microbial communities, each with about 20 different species as revealed by PCR-based denaturing gradient gel electrophoresis analysis. In vitro community competition assays showed that the two microbial floras exhibited antagonistic interactions toward each other. More interestingly, all the original isolates tested and their closely related species displayed striking community preferences: They persisted when introduced into the bacterial community of the same origin, while their viable count declined more than three orders of magnitude after 4 days of coincubation with the microbial flora of foreign origin. These results suggest that an existing microbial community might impose a selective pressure on incoming foreign bacterial species independent of host selection. The observed inter-flora interactions could contribute to the protective effect of established microbial communities against the integration of foreign bacteria to maintain the stability of the existing communities.
Electronic supplementary material
The online version of this article (doi:10.1007/s00248-010-9711-9) contains supplementary material, which is available to authorized users.
doi:10.1007/s00248-010-9711-9
PMCID: PMC2954289  PMID: 20625712
17.  Oral-Derived Bacterial Flora Defends Its Domain by Recognizing and Killing Intruders—A Molecular Analysis Using Escherichia coli as a Model Intestinal Bacterium 
Microbial Ecology  2010;60(3):655-664.
Within the same human gastrointestinal tract, substantial differences in the bacterial species that inhabit oral cavity and intestinal tract have been noted. Previous research primarily attributed the differences to the influences of host environments and nutritional availabilities (“host habitat” effect). Our recent study indicated that, other than the host habitat effect, an existing microbial community could impose a selective pressure on incoming foreign bacterial species independent of host-mediated selection (“community selection” effect). In this study, we employed in vitro microbial floras representing microorganisms that inhabit the oral cavities and intestinal tract of mice in combination with Escherichia coli as a model intestinal bacterium and demonstrated that E. coli displays a striking community preference. It thrived when introduced into the intestinal microbial community and survived poorly in the microbial flora of foreign origin (oral community). A more detailed examination of this phenomenon showed that the oral community produced oxygen-free radicals in the presence of wild-type E. coli while mutants deficient in lipopolysaccharides (LPS) did not trigger significant production of these cell-damaging agents. Furthermore, mutants of E. coli defective in the oxidative stress response experienced a more drastic reduction in viability when cocultivated with the oral flora, while the exogenous addition of the antioxidant vitamin C was able to rescue it. We concluded that the oral-derived microbial community senses the E. coli LPS and kills the bacterium with oxygen-free radicals. This study reveals a new mechanism of community invasion resistance employed by established microflora to defend their domains.
Electronic supplementary material
The online version of this article (doi:10.1007/s00248-010-9708-4) contains supplementary material, which is available to authorized users.
doi:10.1007/s00248-010-9708-4
PMCID: PMC2954290  PMID: 20625713

Results 1-17 (17)