Oral microbial communities: biofilms, interactions, and genetic systems

Genetic characterization of the oral Actinomyces

Actinomyces are difficult to identify using serological and biochemical methods but genotyping is an efficient and reliable means of bacterial characterization and can be used to determine clonal identity. The purpose here was to genotype 13 American type culture collection (ATCC) reference strains representing six different oral Actinomyces spp. by using chromosomal DNA fingerprinting (CDF), arbitrarily primed-polymerase chain reaction (AP-PCR) and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). In CDF analysis, BamHI, BstEII and SmaI yielded digestion patterns revealing characteristic differences among the known Actinomyces spp., with SmaI demonstrating optimal resolution. Amplicons generated by AP-PCR with primer OPB-07 displayed banding patterns that permitted discrimination of all Actinomyces strains tested. PCR-RFLP with MnlI digests generated fragment patterns that also characterized the reference strains. Collectively, genotypic profiles generated by CDF, AP-PCR and PCR-RFLP permitted differentiation of all 13 ATCC Actinomyces strains. SmaI CDF analysis of 18 clinical isolates of catalase-positive A. naeslundii genospecies 2 revealed extensive genetic diversity among these strains. These molecular approaches may be useful in determining genetic diversity within oral Actinomyces populations and fidelity of Actinomyces transmission between mother and child.

Actinobacillus actinomycetemcomitans proportion of subgingival bacterial flora in relation to its clonal type

We investigated whether certain Actinobacillus actinomycetemcomitans clones occur in elevated proportions in subgingival flora, and if the proportions relate to other bacteria in the samples. A total of 121 A. actinomycetemcomitans strains from 121 patients with periodontitis were serotyped and 60 strains were also genotyped. The 121 strains were divided into three groups and the 60 strains into two groups according proportion of A. actinomycetemcomitans. The samples from the 60 patients with genotyped strains were cultured for five other species. Among the 121 strains, serotype b occurred significantly more frequently in the high- (n = 14, proportions > 5%, mean = 18.09, SD = 20.07%) than low- (n = 49, proportions < or = 0.1%), mean = 0.04, SD = 0.03%) or intermediate-proportion groups (n = 58, proportions > 0.5%, mean = 1.31, SD = 1.24%). Genotype 3 occurred significantly more frequently in samples with low A. actinomycetemcomitans proportions (n = 28, < or = 0.1%, mean = 0.04, SD = 0.03%) than in those with high proportions (n = 32, > 0.1%, mean = 5.70, SD = 14.60%). No differences were seen in the detection frequencies or proportions of the five bacterial species between the samples with low or high A. actinomycetemcomitans proportions. The results indicate that certain clonotypes of A. actinomycetemcomitans may preferentially occur as low proportions, suggesting their controlled growth. Conversely, some serotype b clones may have a competitive advantage in subgingival flora.

Salivary microbiota levels in relation to periodontal status, experience of caries and miswak use in Sudanese adults

OBJECTIVES

The purpose of the present investigation was to assess the salivary levels of 25 oral bacteria in relation to periodontal status and experience of caries, and to compare the levels of these bacteria between habitual miswak and toothbrush users in adult Sudanese subjects.

MATERIAL AND METHODS

The study subjects consisted of 56 individuals with age range 19-53 years (mean 35.2 years) and included 30 miswak and 26 toothbrush users. The periodontal status and presence of dental caries were assessed clinically. Whole saliva was collected from all subjects, and the levels of 25 selected bacterial species in saliva were assessed by the checkerboard DNA-DNA hybridization method using whole genomic DNA probes.

RESULTS

A high percentage of the subjects had detectable levels (> or = 105 bacterial cells) of several bacterial species in saliva. Between 12% and 16% of the subjects showed high (> or = 106 cells) salivary levels of the periodontitis-associated bacteria A. actinomycetemcomitans, P. melaninogenica, P. intermedia, C. rectus and E. corrodens, whereas only two (3.6%) and four (7.1%) subjects had high levels of P. gingivalis and F. nucleatum, respectively. There were no significant differences in the levels of all or most bacterial species by age group, gender or periodontal status. Presence of > or = 105 L. acidophilus bacterial cells in saliva was associated with high caries scores (p = 0.02). There were significantly higher levels of A. actinomycetemcomitans, P. melaninogenica, C. rectus, P. micros, V. parvula, S. mutans, S. anginosus, A. israelii, C. sputigena, and C. gingivalis, and significantly lower levels of P. intermedia, F. nucleatum, S. sputigena, E. corrodens, L. acidophilus, S. sanguis, S. salivarius, S. oralis, and S. mitis in the miswak than in the toothbrush group.

CONCLUSIONS

: The findings suggest that miswak may have a selective inhibitory effect on the level of certain bacteria in saliva, particularly several oral streptococci species. This is the first report that the checkerboard DNA-DNA hybridization method can be useful for assessing the levels of a wide range of bacterial taxa in saliva.

Biofilm formation by nontypeable Haemophilus influenzae: strain variability, outer membrane antigen expression and role of pili

BACKGROUND

Nontypeable Haemophilus influenzae is an important cause of otitis media in children and lower respiratory tract infection in adults with chronic obstructive pulmonary disease (COPD). Several lines of evidence suggest that the bacterium grows as a biofilm in the human respiratory tract.

RESULTS

Fifteen clinical isolates from middle ear fluid of children with otitis media and 15 isolates from sputum of adults with COPD were studied in an in vitro assay of biofilm formation. Striking variability among isolates was observed in their ability to form biofilms. Analysis of cell envelopes revealed minimal differences in banding patterns in polyacrylamide gels, alteration of expression of an epitope on lipooligosaccharide, and preservation of expression of selected epitopes on outer membrane proteins P2, P5 and P6 in biofilms compared to planktonically grown cells. A pilus-deficient variant showed a marked impairment in biofilm formation compared to its isogenic parent.

CONCLUSIONS

Nontypeable H. influenzae forms biofilms in vitro. Clinical isolates show substantial variability in their ability to grow as biofilms. Three major outer membrane proteins (P2, P5 and P6) are expressed during growth as a biofilm. Expression of lipooligosaccharide is altered during growth as a biofilm compared to planktonic growth. Pili are important in biofilm formation. As the role of biofilms in human infection becomes better defined, characterization of biofilms may be important in understanding the pathogenesis of infection and immune response to nontypeable H. influenzae in children with otitis media and adults with COPD.

Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586

We present a complete DNA sequence and metabolic analysis of the dominant oral bacterium Fusobacterium nucleatum. Although not considered a major dental pathogen on its own, this anaerobe facilitates the aggregation and establishment of several other species including the dental pathogens Porphyromonas gingivalis and Bacteroides forsythus. The F. nucleatum strain ATCC 25586 genome was assembled from shotgun sequences and analyzed using the ERGO bioinformatics suite (http://www.integratedgenomics.com). The genome contains 2.17 Mb encoding 2,067 open reading frames, organized on a single circular chromosome with 27% GC content. Despite its taxonomic position among the gram-negative bacteria, several features of its core metabolism are similar to that of gram-positive Clostridium spp., Enterococcus spp., and Lactococcus spp. The genome analysis has revealed several key aspects of the pathways of organic acid, amino acid, carbohydrate, and lipid metabolism. Nine very-high-molecular-weight outer membrane proteins are predicted from the sequence, none of which has been reported in the literature. More than 137 transporters for the uptake of a variety of substrates such as peptides, sugars, metal ions, and cofactors have been identified. Biosynthetic pathways exist for only three amino acids: glutamate, aspartate, and asparagine. The remaining amino acids are imported as such or as di- or oligopeptides that are subsequently degraded in the cytoplasm. A principal source of energy appears to be the fermentation of glutamate to butyrate. Additionally, desulfuration of cysteine and methionine yields ammonia, H(2)S, methyl mercaptan, and butyrate, which are capable of arresting fibroblast growth, thus preventing wound healing and aiding penetration of the gingival epithelium. The metabolic capabilities of F. nucleatum revealed by its genome are therefore consistent with its specialized niche in the mouth.

Unseen forces: the influence of bacteria on animal development

The diversity of developmental programs present in animal phyla first evolved within the world's oceans, an aquatic environment teeming with an abundance of microbial life. All stages in the life histories of these early animals became adapted to microorganisms bathing their tissues, and countless examples of animal-bacterial associations have arisen as a result. Thus far, it has been difficult for biologists to design ways of determining the extent to which these associations have influenced the biology of animals, including their developmental patterns. The following review focuses on an emerging field, the goal of which is to understand the influence of bacteria on animal developmental programs. This integrative area of research is undergoing a revolution that has resulted from advances in technology and the development of suitable animal-bacterial systems for the study of these complex associations. In this contribution, the current status of the field is reviewed and the emerging research horizons are examined.

Numerical dominance and phylotype diversity of marine Rhodobacter species during early colonization of submerged surfaces in coastal marine waters as determined by 16S ribosomal DNA sequence analysis and fluorescence in situ hybridization

Early stages of surface colonization in coastal marine waters appear to be dominated by the marine Rhodobacter group of the alpha subdivision of the division Proteobacteria (alpha-Proteobacteria). However, the quantitative contribution of this group to primary surface colonization has not been determined. In this study, glass microscope slides were incubated in a salt marsh tidal creek for 3 or 6 days. Colonizing bacteria on the slides were examined by fluorescence in situ hybridization by employing DNA probes targeting 16S or 23S rRNA to identify specific phylogenetic groups. Confocal laser scanning microscopy was then used to quantify and track the dynamics of bacterial primary colonists during the early stages of surface colonization and growth. More than 60% of the surface-colonizing bacteria detectable by fluorescence staining (Yo-Pro-1) could also be detected with the Bacteria domain probe EUB338. Archaea were not detected on the surfaces and did not appear to participate in surface colonization. Of the three subdivisions of the Proteobacteria examined, the alpha-Proteobacteria were the most abundant surface-colonizing organisms. More than 28% of the total bacterial cells and more than 40% of the cells detected by EUB338 on the surfaces were affiliated with the marine Rhodobacter group. Bacterial abundance increased significantly on the surfaces during short-term incubation, mainly due to the growth of the marine Rhodobacter group organisms. These results demonstrated the quantitative importance of the marine Rhodobacter group in colonization of surfaces in salt marsh waters and confirmed that at least during the early stages of colonization, this group dominated the surface-colonizing bacterial assemblage.

The buccale puzzle: The symbiotic nature of endogenous infections of the oral cavity

The indigenous, 'normal', microflora causes the majority of localized infectious diseases of the oral cavity (eg, dental caries, alveolar abscesses, periodontal diseases and candidiasis). The same microflora also protects the host from exogenous pathogens by stimulating a vigorous immune response and provides colonization resistance. How can a microflora that supports health also cause endogenous oral disease? This paradoxical host-symbiont relationship will be discussed within the dynamic of symbiosis.Symbiosis means 'life together' - it is capable of continuous change as determined by selective pressures of the oral milieu. Mutualistic symbiosis, where both the host and the indigenous microflora benefit from the association, may shift to a parasitic symbiosis, where the host is damaged and the indigenous microflora benefit. Importantly, these are reversible relationships. This microbial dynamism, called amphibiosis, is the essential adaptive process that determines the causation of endogenous oral disease by a parasitic microflora or the maintenance of oral health by a mutualistic microflora.Complex microbial consortiums, existing as a biofilm, usually provide the interfaces that initiate and perpetuate the infectious assault on host tissue. The ecology of the various oral microhabitats is critical for the development of the appropriate selecting milieux for pathogens. The microbiota associated with dental caries progression is primarily influenced by the prevailing pH, whereas periodontal diseases and pulpal infection appear to be more dependent on redox potential. Candidiasis results from host factors that favour yeast overgrowth or bacterial suppression caused by antibiotics. Oral health or disease is an adventitious event that results from microbial adaptation to prevailing conditions; prevention of endogenous oral disease can occur only when we realize that ecology is the heart of these host-symbiont relationships.

Identification of independent Streptococcus gordonii SspA and SspB functions in coaggregation with Actinomyces naeslundii

The initial stages of dental plaque formation involve the adherence of early colonizing organisms such as Streptococcus gordonii and Actinomyces naeslundii to the saliva-coated tooth surface and to each other. The S. gordonii surface proteins SspA and SspB are known to play a role in adherence to salivary proteins and mediate coaggregation with other bacteria. Coaggregation is the adhesin receptor-mediated interaction between genetically distinct cell types and appears to be ubiquitous among oral isolates. To define the function of SspA and SspB separately on the surface of their natural host, we constructed and analyzed the coaggregation properties of an isogenic sspB mutant of S. gordonii DL1, an sspAB double mutant, and a previously described sspA mutant. A. naeslundii strains have been previously classified into six coaggregation groups based on the nature of their coaggregations with S. gordonii DL1 and other oral streptococci. Coaggregation assays with the sspA and sspB mutants showed that SspA and SspB are the streptococcal proteins primarily responsible for defining these coaggregation groups and, thus, are highly significant in the establishment of early dental plaque. SspA exhibited two coaggregation-specific functions. It participated in lactose-inhibitable and -noninhibitable interactions, while SspB mediated only lactose-noninhibitable coaggregations. Accordingly, the sspAB double mutant lacked these functions and allowed us to detect a third coaggregation interaction with one of these organisms. These proteins may play an important role in development of S. gordonii-A. naeslundii communities in early dental plaque. Understanding these adhesin proteins will aid investigations of complex microbial communities that characterize periodontal diseases.

Cell density modulates acid adaptation in Streptococcus mutans: implications for survival in biofilms

Streptococcus mutans normally colonizes dental biofilms and is regularly exposed to continual cycles of acidic pH during ingestion of fermentable dietary carbohydrates. The ability of S. mutans to survive at low pH is an important virulence factor in the pathogenesis of dental caries. Despite a few studies of the acid adaptation mechanism of this organism, little work has focused on the acid tolerance of S. mutans growing in high-cell-density biofilms. It is unknown whether biofilm growth mode or high cell density affects acid adaptation by S. mutans. This study was initiated to examine the acid tolerance response (ATR) of S. mutans biofilm cells and to determine the effect of cell density on the induction of acid adaptation. S. mutans BM71 cells were first grown in broth cultures to examine acid adaptation associated with growth phase, cell density, carbon starvation, and induction by culture filtrates. The cells were also grown in a chemostat-based biofilm fermentor for biofilm formation. Adaptation of biofilm cells to low pH was established in the chemostat by the acid generated from excess glucose metabolism, followed by a pH 3.5 acid shock for 3 h. Both biofilm and planktonic cells were removed to assay percentages of survival. The results showed that S. mutans BM71 exhibited a log-phase ATR induced by low pH and a stationary-phase acid resistance induced by carbon starvation. Cell density was found to modulate acid adaptation in S. mutans log-phase cells, since pre-adapted cells at a higher cell density or from a dense biofilm displayed significantly higher resistance to the killing pH than the cells at a lower cell density. The log-phase ATR could also be induced by a neutralized culture filtrate collected from a low-pH culture, suggesting that the culture filtrate contained an extracellular induction component(s) involved in acid adaptation in S. mutans. Heat or proteinase treatment abolished the induction by the culture filtrate. The results also showed that mutants defective in the comC, -D, or -E genes, which encode a quorum sensing system essential for cell density-dependent induction of genetic competence, had a diminished log-phase ATR. Addition of synthetic competence stimulating peptide (CSP) to the comC mutant restored the ATR. This study demonstrated that cell density and biofilm growth mode modulated acid adaptation in S. mutans, suggesting that optimal development of acid adaptation in this organism involves both low pH induction and cell-cell communication.

Cloning of the Streptococcus mutans gene encoding glucan binding protein B and analysis of genetic diversity and protein production in clinical isolates

Streptococcus mutans, the primary etiological agent of dental caries, produces several activities that promote its accumulation within the dental biofilm. These include glucosyltransferases, their glucan products, and proteins that bind glucan. At least three glucan binding proteins have been identified, and GbpB, the protein characterized in this study, appears to be novel. The gbpB gene was cloned and the predicted protein sequence contained several unusual features and shared extensive homology with a putative peptidoglycan hydrolase from group B streptococcus. Examination of gbpB genes from clinical isolates of S. mutans revealed that DNA polymorphisms, and hence amino acid changes, were limited to the central region of the gene, suggesting functional conservation within the amino and carboxy termini of the protein. The GbpB produced by clinical isolates and laboratory strains showed various distributions between cells and culture medium, and amounts of protein produced by individual strains correlated positively with their ability to grow as biofilms in an in vitro assay.

Commensal host-bacterial relationships in the gut

One potential outcome of the adaptive coevolution of humans and bacteria is the development of commensal relationships, where neither partner is harmed, or symbiotic relationships, where unique metabolic traits or other benefits are provided. Our gastrointestinal tract is colonized by a vast community of symbionts and commensals that have important effects on immune function, nutrient processing, and a broad range of other host activities. The current genomic revolution offers an unprecedented opportunity to identify the molecular foundations of these relationships so that we can understand how they contribute to our normal physiology and how they can be exploited to develop new therapeutic strategies.

The evolution of social behavior in microorganisms

Recent studies of microorganisms have revealed diverse complex social behaviors, including cooperation in foraging, building, reproducing, dispersing and communicating. These microorganisms should provide novel, tractable systems for the analysis of social evolution. The application of evolutionary and ecological theory to understanding their behavior will aid in developing better means to control the many pathogenic bacteria that use social interactions to affect humans.

Bacterial biofilms and human disease

The term biofilm is used to denote a polymer-encased community of microbes which accumulates at a surface. Biofilms are responsible for a number of diseases of man and, because of the intrinsic resistance of these structures to antibiotics and host defence systems, such diseases are very difficult to treat effectively. The application of new microscopic and molecular techniques to biofilms has revolutionised our understanding of their structure, composition, organisation and activities. This review will describe the role that biofilms play in human disease and will outline our new millennial view of these complex and fascinating bacterial communities.

Expression of green fluorescent protein in Streptococcus gordonii DL1 and its use as a species-specific marker in coadhesion with Streptococcus oralis 34 in saliva-conditioned biofilms in vitro

Streptococcus gordonii is one of the predominant streptococci in the biofilm ecology of the oral cavity. It interacts with other bacteria through receptor-adhesin complexes formed between cognate molecules on the surfaces of the partner cells. To study the spatial organization of S. gordonii DL1 in oral biofilms, we used green fluorescent protein (GFP) as a species-specific marker to identify S. gordonii in a two-species in vitro oral biofilm flowcell system. To drive expression of gfp, we isolated and characterized an endogenous S. gordonii promoter, PhppA, which is situated upstream of the chromosomal hppA gene encoding an oligopeptide-binding lipoprotein. A chromosomal chloramphenicol acetyltransferase (cat) gene fusion with PhppA was constructed and used to demonstrate that PhppA was highly active throughout the growth of bacteria in batch culture. A promoterless 0.8-kb gfp ('gfp) cassette was PCR amplified from pBJ169 and subcloned to replace the cat cassette downstream of the S. gordonii-derived PhppA in pMH109-HPP, generating pMA1. Subsequently, the PhppA-'gfp cassette was PCR amplified from pMA1 and subcloned into pDL277 and pVA838 to generate the Escherichia coli-S. gordonii shuttle vectors pMA2 and pMA3, respectively. Each vector was transformed into S. gordonii DL1 aerobically to ensure GFP expression. Flow cytometric analyses of aerobically grown transformant cultures were performed over a 24-h period, and results showed that GFP could be successfully expressed in S. gordonii DL1 from PhppA and that S. gordonii DL1 transformed with the PhppA-'gfp fusion plasmid stably maintained the fluorescent phenotype. Fluorescent S. gordonii DL1 transformants were used to elucidate the spatial arrangement of S. gordonii DL1 alone in biofilms or with the coadhesion partner Streptococcus oralis 34 in two-species biofilms in a saliva-conditioned in vitro flowcell system. These results show for the first time that GFP expression in oral streptococci can be used as a species-specific marker in model oral biofilms.