Skip to main content
PMC home page
Scientific Reports logoLink to Scientific Reports
. 2016 Sep 21;6:33665. doi: 10.1038/srep33665

Biochemical and genome sequence analyses of Megasphaera sp. strain DISK18 from dental plaque of a healthy individual reveals commensal lifestyle

Nayudu Nallabelli 1,*, Prashant P Patil 1,*, Vijay Kumar Pal 1, Namrata Singh 1, Ashish Jain 2, Prabhu B Patil 1, Vishakha Grover 2,a, Suresh Korpole 1,b
PMCID: PMC5030485  PMID: 27651180

Abstract

Much of the work in periodontal microbiology in recent years has focused on identifying and understanding periodontal pathogens. As the majority of oral microbes have not yet been isolated in pure form, it is essential to understand the phenotypic characteristics of microbes to decipher their role in oral environment. In this study, strain DISK18 was isolated from gingival sulcus and identified as a Megasphaera species. Although metagenomics studies revealed Megasphaera species as a major group within the oral habitat, they have never been isolated in cultivable form to date. Therefore, we have characterized the DISK18 strain to better understand its role in the periodontal ecosystem. Strain Megasphaera sp. DISK18 displayed the ability to adhere and self-aggregate, which are essential requisite features for inhabiting and persisting in oral cavity. It also coaggregated with other pioneer oral colonizers like Streptococcus and Lactobacillus species but not with Veillonella. This behaviour points towards its role in the ecologic succession of a multispecies biofilm as an early colonizer. The absence of virulence determining genes as observed in whole genome sequence analysis coupled with an inability to degrade collagen reveals that Megasphaera sp. strain DISK18 is likely not a pathogenic species and emphasizes its commensal lifestyle.

The ‘‘oral microbiome’’ represent an ecological community of mutualistic, symbiotic, commensal and pathogenic microorganisms which are significant determinants of oral health and disease1. Many dental diseases like caries or periodontitis are the result of dysbiosis of microbial communities in dental plaque2. After initial colonization, commensal bacterial species tend to persist in the mouth for years and co-evolve with host, maintaining the health of the host by preventing access of pathogenic bacteria and stimulating the immune response3,4. In fact, dental caries are a result of disequilibrium in acid and alkali producing bacteria present in dental plaque/environment2. The current paradigm of microbial dysbiosis has highlighted the significance of resident microflora in the maintenance of oral health2,4.

The use of advanced genomics and molecular biology techniques have revolutionized studies examining the structural and functional complexity of oral microflora. In particular, culture-independent molecular methods using 16S rRNA gene sequence analysis have identified numerous bacterial species in oral environment (http://www.homd.org)5. Most of these species belong to six major phyla including Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Spirochaetes, Fusobacteria. Other common strains that have been identified include Euryarchaeota, Chlamydia, Chloroflexi, Synergistetes and Tenericutes. Interestingly, strains also represented the uncharacterized phyla like SR1 and TM71,5,6. Even though oral ecosystem found to harbour such vast microbial diversity, till date only about 280 bacterial species have been isolated by cultivable methods, characterized and formally named1,5. Owing to the stringent growth conditions and technical difficulties, only few microbes have been cultivated from the periodontal environment. Megasphaera is one such genus, strains of which have been frequently identified by culture-independent analysis and reported to play an important role in human oral cavity1,5,7,8,9. Indeed, Megasphaera spp. are reported to be present in greater proportions in above mentioned studies on microbial analysis of periodontal disease conditions by metagenomics approaches, raising the possibility of its role as a disease associated microbe (periopathogen). Nevertheless, recently it is found that the Megasphaera is overrepresented in diseased conditions10. In the present study we have isolated a bacterial strain designated as DISK18 from a subgingival plaque sample of a healthy human oral cavity, which is identified to be a member of the genus Megasphaera and subsequently characterized to understand the nature of strain and adaptation ability to oral/periodontal environment to understand its role in the oral environment.

Results

Identification of bacterial isolates and characterization of strain DISK18

Few colonies were isolated upon plating subgingival sample on different media. Based on 16S rRNA gene sequence blast analysis, the genotypic identification of isolates DIGK4C, DISK18, DISK25 and DISK26 revealed significant identity with species of genera Veillonella, Megasphaera, Streptococcus and Lactobacillus, respectively. Except Megasphaera, members of all other genera have been isolated in cultivable form from oral environment, therefore, Megasphaera sp. strain DISK18 was studied in detail by growing it in an anaerobic chamber with a gas phase of N2/CO2/H2 (80:15:5). Strain DISK18 formed opaque colonies with undulate margin and irregular configuration on reinforced clostridial agar medium. Microscopic examination revealed strain DISK18 as non-spore forming and non-motile cocci that stained Gram-negative. It grew well between 30–42 °C temperature with an optimum and maximum growth of 37 and 45 °C, respectively. Growth observed between pH 6.0–8.0 with optimal being 7.0. It grew up to a concentration of 1.5% (w/v) NaCl, however, optimal NaCl concentration for growth was 0.5%. The strain DISK18 showed negative reaction for casein and gelatine hydrolysis. Weak acid production was observed from sucrose but not with dextrose, arabinose, mannose, mannitol, inositol, inulin, fructose, rhamnose, galactose, lactose, maltose or trehalose. It showed a positive reaction for the assimilation of urea. It was also sensitive to the antibiotics kanamycin, erythromycin, tetracycline, rifampicin, chloramphenicol, penicillin, ampicillin, streptomycin and gentamycin but showed resistance to vancomycin. The fatty acid profile of the strain differed with other species of the genus Megasphaera as it displayed presence of C20:1 ω7c, C18:3 ω6c and C17:1 is oω5c as major fatty acids. Polar lipid analysis of strain DISK18 revealed amino phospholipids as the major lipids and presence of unknown lipids were also observed (Supplementary Figure S1). Further, phylogenetic analysis of 16S rRNA gene sequence of strain DISK18 showed high identity with Megasphaera massiliensis NP3T (99.73%), however, this species was found to be an invalid species of the genus Megasphaera and not included in list of prokaryotic standing nomenclature. The next phylogenetic close relative was M. indica NMBHI10T with an identity of 96.62%. Similarly, the rpoB gene sequence analysis of strain DISK18 also displayed high identity with M. massiliensis DSM 26228T. Consequently, strain DISK18 formed a coherent cluster with closely related species including M. massiliensis NP3T, M. indica NMBHI10T and M. elsdenii LC1T with significant bootstrap value and shared a clade with M. massiliensis NP3T in neighbour–joining phylogenetic tree constructed using 16S rRNA (Fig. 1). Similar pattern observed in phylogenetic tree constructed with available rpoB gene sequences.

Figure 1. Phylogenetic tree based on 16S rRNA gene sequence using neighbour-joining algorithm.

Figure 1

Open in a new tab

Strain DISK18 formed a distinct cluster with members of the genus Megasphaera, and shared a clade with M. massiliensis strain NP3T, which is an invalid species. A consensus tree was made based on 1000 replications and bootstrap values are expressed as percentage. Bar, 0.05 substitutions per site. Clostridium schirmacherense DSM 17394 was used as an outgroup.

Coaggregation of Megasphaera sp. strain DISK18 with other oral isolates

The ability of Megasphaera sp. strain DISK18 to self-aggregate and coaggregate with other oral isolates including Streptococcus sp. strain DISK25 Lactobacillus sp. strain DISK26 and Veillonella sp. strain DIGK4C was investigated. The results displayed similar self-aggregation ability of Megasphaera sp. strain DISK18 compared to Lactobacillus sp. DISK26 or Streptococcus sp. DISK25 (Fig. 2A,B). However, sharp decrease in OD600 observed for Veillonella sp. strain DIGK4C (Fig. 2C) reveals highest self-aggregation ability. The coaggregation pattern of efficient strains pairs were examined by interacting the strain DISK18 with each of the other isolate. We found in results that significant coaggregation occurred between the strains Megasphaera sp. DISK18 and of Lactobacillus sp. DISK26. Similar results were also found with Streptococcus sp. DISK25. In contrast to self-aggregation ability of individual strain, the coaggregation efficiency of Veillonella sp. DIGK4C with Megasphaera sp. strain DISK18 revealed substantial reduction (Fig. 2C).

Figure 2. Coaggregation of Megasphaera sp. strain DISK 18 with other dental plaque isolates.

Figure 2

Open in a new tab

(A) Coaggregation with Lactobacillus sp. strain DISK26. (B) Coaggregation with Streptococcus sp. strain DISK 25. (C) Coaggregation with Veillonella sp. strain DIGK4C. Error bars indicate the standard deviation (SD) values obtained for triplicate experiments.

Effect of sugar, temperature, pH and proteases on self and co aggregation

Among the various sugars used to test their influence on self-aggregation or coaggregation, glucose and xylitol were found to increase the self-aggregation ability of Megasphaera sp. strain DISK18 (Fig. 3A). The coaggregation between pairs of Megasphaera sp. strain DISK18 and different isolates was found to increase in the presence of glucose, fructose, mannitol, xylitol and raffinose (Fig. 3B,C,E). Though similar trends were observed for Megasphaera strain DISK18 and S. mutans MTCC890, they differed with respect to the presence of galactose and raffinose. While galactose increased the coaggregation between the pair, raffinose did not show any effect (Fig. 3D). Increase in temperature up to 42 °C did not show any influence on self-aggregation of strains but minor reduction observed in coaggregation for different pair combinations (Fig. 4A) and no self-aggregation or coaggregation was observed at 80 °C temperature (data not shown). Self-aggregation or coaggregation at different pH values did not show any differences of any oral isolates or their combinations (Fig. 4B). Additionally, isolates treated with proteolytic enzymes trypsin, pronase E or proteinase K also did not show any significant alterations in either self-aggregation or coaggregation (Fig. 4C).

Figure 3. Effect of sugars on self-aggregation and coaggregation of Megasphaera sp. strain DISK18.

Figure 3

Open in a new tab

(A) Self-aggregation of Meghasphaera sp. strain DISK18. (B) Coaggregation with Lactobacillus sp. strain DISK26. (C) Coaggregation with Streptococcus sp. strain DISK25. (D) Coaggregation with S. mutans MTCC 890. (E) Coaggregation with Veillonella sp. strain DIGK4C. The data shown is representing three individual experiments and the error bar represents standard deviations (SD).

Figure 4. Influence of physiological conditions and proteolytic enzymes on coaggregation of Megasphaera sp. strain DISK18 with other oral isolates.

Figure 4

Open in a new tab

(A) Effect of temperature on coaggregation. (B) Coaggregation under different pH conditions. (C) Influence of protease enzymes on coaggregation. Error bars indicate the standard deviation (SD) values obtained for triplicate experiments.

Surface hydrophobicity analysis of the isolates

Since property of hydrophobicity in bacteria is associated with biofilm formation11, we have tested the surface hydrophobicity of all isolates using chloroform, diethyl ether and hexane. While Megasphaera sp. strain DISK18, Lactobacillus sp. DISK26 and Streptococcus sp. DISK25 isolates revealed higher affinity to chloroform compared to Veillonella sp. strain DIGK4C (Supplementary Figure S2). Megasphaera sp. strain DISK18 showed lesser affinity to hexane and diethyl ether.

Biofilm formation ability of Megasphaera sp. strain DISK18

Based on the results obtained for self-aggregation, coaggregation and hydrophobicity analysis, biofilm formation was assayed for the Megasphaera sp. strain DISK18 alone as well as in mixed cultures with other oral isolates to test the multispecies biofilm formation efficiency. Results of the crystal violet microtiter plate biofilm formation assay revealed Megasphaera sp. strain DISK18 could form biofilm with moderate-density as a single culture and formed efficient biofilm in combination with Streptococcus sp. strain DISK25 and MTCC 890 (Fig. 5). Formation of biofilm by Megasphaera sp. strain DISK18 was also confirmed with electron microscopy experiment where the formation of pilus like appendages clearly observed during initial phase of biofilm and with the increase in incubation duration they extended towards each other bacterial cells (Fig. 6A,B). The mature biofilm contained multiple layers of cells attached with each other (Fig. 6C).

Figure 5. Biofilm formation ability of individual oral isolates and in combination with Megasphaera sp. strain DISK18.

Figure 5

Open in a new tab

The biofilm was quantified by crystal violet assay and the values obtained upon subtraction with background control. The data shown is representing three individual experiments and error bar represents standard deviations (SD).

Figure 6. Scanning electron microscopic analysis of biofilm formation by Megasphaera sp. strain DISK18.

Figure 6

Open in a new tab

(A) Initial stage of biofilm observed after incubation of 3 h. (B) Formation of biofilm with pili like appendages after 6 h incubation. (C) Matured biofilm upon incubation of 12 h.

Volatile sulfur compounds (VSC) production by Megasphaera sp. strain DISK18

To analyse the role of Megasphaera sp. strain DISK18 in halitosis, we tested the production of volatile sulfur compounds (VSC). Though colonies were formed within 24 h on differential agar, they stained black only after 72–96 h incubation. Accordingly, delayed VSC production was observed by microscopic assay (Supplementary Figure S3) and the same was confirmed with differential agar method. However, quantification of VSC levels was not performed.

Fluoride resistance of Megasphaera sp. strain DISK18

We have tested the tolerance ability of Megasphaera sp. strain DISK18 towards different fluoride concentrations as fluoride is one of the most common ion available in local environment from various oral hygiene products used in oral cavity.Results showed that it could tolerate up to 1000 μg/ml concentration of fluoride and no growth was observed above this concentration.

Genome features of Megasphaera sp. strain DISK18

To understand the genetic structure of Megasphaera sp. strain DISK18 towards the observed phenotypic characters, we sequenced the whole genome of the isolate DISK18 and reads were de novo assembled by using CLC Genomics Workbench 7.5 (CLC Bio-Qiagen, Aarhus, Denmark) and further annotated by using Rapid Annotations using Subsystems Technology (RAST) server12 as mentioned in methods. The genome size of the Megasphaera sp. DISK18 was 2.4 Mbp with 50.06% of G+C content which assembled into 65 contigs. General genome features and assembly statistics of the strain DISK18 are provided in Table 1. Genome annotation based on RAST analysis predicted there were 2297 genes amongst which 2235 were coding sequences (CDS). The subsystem distribution, representing a collection of functionally related protein families and distribution statistics of CDS in the genome of Megasphaera sp. DISK18 revealed a total of 324 subsystems. Amongst these, amino acid and derivatives subsystem featured with largest number (291) of the assigned CDS. Other major subsystems annotated were carbohydrate (229), protein metabolism (196), cofactors, vitamins, prosthetic groups and pigments (179) and RNA metabolism (125). While only two CDS represented the sulfur metabolism, no CDS involved in motility or chemotaxis were annotated (Fig. 7). There were also eight clustered regularly interspaced short palindromic repeats (CRISPR) observed but no secondary metabolite gene clusters were predicted in the genome of the Megasphaera sp. strain DISK18.

Table 1. Comparison of genome features of Megasphaera sp. strain DISK18 with close relatives.

Attribute Strain DISK18 M. misseliensis strain NP3 M. indica strain DSM25563
Genome Size (bp) 2,486,826 2,661,757 2,615,280
G+C content (%) 50.06 50.20 54.30
Fold Coverage (X) 179 19 74
N50 77144 NA NA
Contig count 65 114 NA
No. of coding sequences 2,235 2,577 2,432
No. of rRNA operons 5 2 8
No. of tRNA operons 56 61 58
CRISPR repeats 8 7 4
NCBI-GeneBank database accession number LUGJ00000000 CAVO00000000 APHY00000000
Open in a new tab

Figure 7. Subsystem category distribution of major protein coding genes of Megasphaera sp. strain DISK18 as annotated by Rapid Annotation System Technology (RAST) server12.

Figure 7

Open in a new tab

Bar chart (at leftmost) shows the subsystem coverage in percentage (green bar corresponds to percentage of proteins included). The pie chart depicting percentage distribution of 20 most abundant subsystem categories in strain DISK18. Representative slices in pie chart indicated with colour in right panel along with count of subsystem feature.

Genome based comparison with other Megasphaera species

The genome sequence of Megasphaera sp. strain DISK18 was compared with other Megasphaera species whose genome sequences are available at NCBI database. For assessment of genome similarity we used Average Nucleotide Identity (ANI) and digital DNA –DNA hybridization (dDDH). The whole genome ANI value between Megasphaera sp. strain DISK18 and close relatives including M. massiliensis DSM 26228T 13, M. indica DSM 25563T 14 and M. elsdnii DSM 205460T 15 displayed 96.5%, 80.5% and 80.3%, respectively. The digital DNA-DNA hybridization (dDDH) of strain DISK18 with above mentioned strains revealed an identity of 71.7%, 24.4% and 24.1%, respectively. The ANI and dDDH values for strain Megasphaera sp. DISK18 with M. cerevisiae DSM 25563T were found to be much lower than above mentioned strains. Further, whole genome comparison of all above mentioned Megasphaera strains was performed using BLAST Ring Image Generator (BRIG) tool16 (Fig. 8) using genome of strain DISK18 as a reference. The comparison revealed a large scale variation in the genomes of different strains with Megasphaera sp. strain DISK18 that were further compared using RAST annotation.

Figure 8. The whole genome based comparison of the Megasphaera sp. strain DISK18 with closely related members of the genus Megasphaera using BLAST Ring Image Generator16.

Figure 8

Open in a new tab

Megasphaera sp. strain DISK18 is used as reference genome. Each ring represents a single genome. From the inside out, the inner ring represents GC content followed by Megasphaera sp. strain DISK18. From third circle to next five rings represent the genomes of M. cerevisae DSM 25583, M. massiliensis NP3, M. elsdenii DSM 20460, M. indica NM10 and M. micronuciformis F0350, respectively.

Gene content analysis of Megasphaera sp. strain DISK18 whole-genome sequence

Detailed analysis of the subsystems features revealed that the strain DISK18 contained numerous genes involved in combating oxidative stress. For example, genes encoding glutathione peroxidase, lactoylglutathione lyase, hydroxyacyl glutathione hydrolase, rubreythrin and superoxidase reductase were present. In addition, rex and PerR systems that are involved in anaerobic metabolism were also found on genome17. Several annotated genes of Megasphaera sp. strain DISK18 genome sequence were involved in the biosynthesis of Vitamin B complex, cofactors and prosthetic groups. Interestingly, Megasphaera sp. strain DISK18 did not contain virulence factors like tpr, prtC (collagenase), rgpA (arg-gingipain), fimA and mgl1 or any other pathogenic genes involved in development of oral diseases as observed for strains of the genus Porphyromonas, particularly, dental pathogen P. gingivalis18. However, strain DISK18 contained antibiotic resistance genes including beta lactam, fluroquinolone and vancomycin resistance genes. Additionally, efflux pump like cmeABC and mexC-mecD efflux pump, Acriflavine resistance (acrA and acrB genes) belonging to RND family and YdhE/NorM efflux pump of MATE family that are known to impart antibiotic, heavy metal and bile salts resistance19 were also observed in genome of Megasphaera sp. strain DISK18. Remarkably, many genes encoding adhesins such as auto transporter adhesions, AidA adhesion and fibronectin/fibrinogen-binding protein that are also involved in biofilm formation20 were found in the annotated genome of strain DISK18. Moreover, type II/IV secretion system RcpA/CpaC associated with Flp pilus assembly and involved in biofilm formation was also present21. Genes regulating the peptidoglycan synthesis and exopolysaccharide production, primarily mannose and rhamnose containing exopolysaccharide glycans were found in the genome sequence annotation. Pathway analysis using KEGG showed the presence of fewer/partial metabolic genes involved in sulfur reduction process indicating the ability of Megasphaera sp. strain DISK18 to contribute in sulfur reduction process. However, these genes included only sulfate adenylyl transferase subunit 1 and subunit 2, adenylyl sulfate reductase beta-subunit and adenylyl sulfate reductase alpha-subunit. Other related genes present were serine acetyltransferase, ferredoxin–sulfite reductase, cysteine synthase, homoserine O-succinyltransferase, O-acetylhomoserine sulfhydrylase. Unusually, Megashpera sp. strain DISK18 contained gene crcB associated with the recently discovered fluoride riboswitch, which contributes towards the fluoride resistance.

Discussion

The microflora of the oral cavity reside in different habitat niches with in the oral cavity according to the local environmental conditions3. While most of the microbes in the mouth are beneficial, selected few are harmful and cause damage to teeth4. The narrow space between the tooth surface and adjacent gingiva (i.e. the subgingival area) is regarded primarily as an anaerobic zone, harbouring subgingival dental plaque, usually containing periodontal pathogenic microorganisms. A recent culture independent study using a species-specific PCR primer set for the detection of Megasphaera suggested that members of M. micronuciformis, which have been isolated from liver abscess and pus samples22, are widely distributed in the oral cavities of the Japanese population9. Other studies based upon culture-independent 16S rRNA gene cloning and sequence analysis of biofilms associated with chronic periodontitis have reported elevated levels of the genus Megasphaera including the oral clones like BB166, MCE3_141 and BS0737,8. These were reported to be essentially involved in periodontitis disease as Megasphaera clone BB166 was frequently observed in chronic periodontitis patients7,8. In spite of these observations, there is no direct evidence demonstrating the role of Megasphaera species in disease. The genus Megasphaera includes 6 validly published species (M. cerevisiae, M. elsdenii, M. indica, M. micronuciformis, M. paucivorans and M. sueciensis) isolated from various sources such as the rumen, spoiled beer and human clinical specimens14,15,22,23,24. Although Megasphaera like phylotypes have been found in abundant quantities during metagenomic analysis of oral samples7,8,9, but there has been no strain isolated in culture or characterized directly from oral environment. Thus, in this study we have performed a series of experiments including the whole genome sequence analysis to decipher the role of an isolated Megasphaera sp. strain DISK18, in dental plaque oral ecology. Though strain DISK18 showed high sequence identity with M. massiliensis DSM 26228, the latter was isolated from different environment (fecal sample of an HIV infected patient) and is not a validly published strain. Therefore, Megasphaera sp. strain DISK18 might be a potential novel species of the genus Megasphaera based on its differences with the closest validly published species M. indica DSM 25563.

The inability to cause a disease by Megasphaera sp. strain DISK18 was established by comparing the whole genome sequence against the genome of a known periopathogen, P. gingivalis. As a result, whole genome sequence of strain DISK18 did not show any homologs to major virulence genes including tpr, prtC (collagenase), rgpA (arg-gingipain), fimA or mgl1 that are associated with pathogenesis in P. gingivalis18,25. The 53 virulence related genes identified during annotation were found to be antibiotic resistance genes involved in drug resistance, nevertheless, Megasphaera sp. strain DISK18 was found to be sensitive to most of the antibiotics except vancomycin. The degradation of dento-epithelial collagen tissue by collagenase activity leads to the formation of a periodontal pocket with low redox levels, thus favouring the growth of anaerobic species and leads to periodontal disease resulting in loss of alveolar bone26. However, the inability of strain DISK18 to hydrolyse gelatin or collagen and the absence of any genes encoding collagenase or gelatinase enzymes clearly suggests that Megasphaera sp. strain DISK18 is not involved in periodontal disease. Interestingly, the close relatives like M. massiliensis and M. elsdenii have demonstrated the ability to hydrolyse gelatin13.

A series of experiments was carried out to check the adaptability of the isolated strain in the oral/periodontal environment. Since adherence to naturally available surfaces in the oral cavity is a prime requisite for any microbe inhabiting oral cavity27, the ability of the strain DISK18 to adhere was investigated through cell surface hydrophobicity experiments along with other oral isolates. It is pertinent to mention that all of the isolates showed significant affinity to nonpolar solvents indicating their hydrophobic nature. In biological systems, hydrophobic interactions are usually considered to be the strongest of all long-range non-covalent interactions and play an important role in the adhesion process11. The bacteria showing hydrophobic surfaces have been demonstrated to be more adherent to polystyrene coated surfaces, than hydrophilic cells in vitro28.

The majority of oral microbial flora forms biofilms of complex communities in dental plaque that leads to successful colonization29. This multispecies biofilm often displays characteristics like adherence and coaggregation with bacterial strains within the biofilm. In fact, this is considered as one of the central mechanisms of plaque formation30,31. Dental plaque is a result of coaggregation, a process where genetically distinct bacteria become attached to one another, thereby developing a complex multispecies biofilm30. Coaggregation between pairs of bacteria was previously shown as a highly specific reaction31 and often observed as a common phenomenon between strains of diverse genera found within dental plaque32,33. In this study Megasphaera sp. strain DISK18 coaggregated well with strains of Streptococcus and Lactobacillus which are considered as early colonizers of the tooth surface during plaque formation. This observation suggests the potential role of isolate DISK18 in forming multispecies biofilm with these colonizing strains in oral cavity. In contrast, despite displaying self-aggregation ability, strains Megasphaera sp. DISK18 and Veillonella sp. DIGK4C did not show coaggregation. This suggests that Megasphaera and Veillonella species may not coexist together, but may play diverse roles in dental plaque ecology via interactions with other oral inhabitants.

Knowledge of coaggregation profiles is helpful in understanding the vital role of coaggregation in bacterial succession and colonization of hard tissue surfaces. To analyse the nature of coaggregation, a variety of experiments were carried out under different temperatures, sugars and treatment with protease. The coaggregation was influenced by different sugars, further it was inhibited by the addition of lactose, galactose and sucrose. The inhibition by sugar might be mediated by lectin and carbohydrate interactions, since inhibition was driven by specific sugars, as a result of the presence of receptor polysaccharides and reciprocal adhesins31. The coaggregation ability of Megasphaera sp. DISK18 with Lactobacillus and Streptococcus isolates may plausibly be related to the utilization of lactic acid, a metabolic end product from these species, as a nutrient. This may contribute to a symbiotic relationship between these two species and Megasphaera sp. strain DISK18 creating a simple food chain or web within the interacting species. Similar interactions have been documented for Veillonella species with Streptococcus34, therefore, there may be a competitive interaction that exists between the two strains that do not co-aggregate. Interestingly, the inability to coaggregate between Megasphaera sp. DISK18 and Veillonella sp. DIGK4C could be attributed to competition for the similar binding sites or same coaggregation partner due to homology on their surface receptors (as both strains belong to the class Veillonellaceae) that resulted in lowering the coaggregation in comparison to self-aggregation31,34.

Megasphaera sp. DISK18 showed moderate biofilm formation ability individually, but strong mixed-species biofilm formation was observed when combined with Streptococcus sp. DISK25 isolate (Fig. 5). It also displayed an ability to form biofilm with other strains of Streptococcus. In line with this, we found that, the genome sequence also contained several genes that are involved in biofilm formation such as fimbriae, autotransporters and AIDA genes. These genes are known for adhesion of Gram negative anaerobic bacteria20. Among these genes, AIDA is an autotransporter glycoprotein, a potential bacterial adhesion found in E. coli35 that mediates bacterial aggregation via intercellular self-recognition. Essentially, it is reported to mediate bacterial attachment to a variety of animal and human cell lines36. A heptosyltransferase known as autotransporter adhesin heptosyltransferase (AAH) involved in modification of the AIDA adhesion or binding to mammalian cells is also found in the genome sequence of Megasphaera sp. strain DISK18. Further, SEM analysis of biofilm revealed the cellular interactions via fibril like threads between the cells (Fig. 6B), which possibly are kind of pilli associated with the cell surface appendages in isolate Megasphaera sp. DISK18.

The microflora of oral cavity experiences constant changes in pH, oxygen tension, and nutrient availability, in response to variations in diet and a variety of physical and nutritional interactions within the biofilm community. The complexity of the periodontal microflora combined with a host of variable environmental parameters make this system particularly challenging for bacteria to adapt and flourish as a commensal or resident flora. Gingival sulcus provides a relatively anaerobic environment, so the bacteria residing in this region are subjected to varying concentrations of oxygen depending upon the composition and age of the biofilm. The MoxR family of AAA+ ATPases, widespread among bacteria and archaea are present in Megasphaera sp. strain DISK18. MoxR proteins have been found to be important modulators of multiple stress response pathways in different organisms. Many stress response proteins like chaperone dnaK gene cluster, heat shock protein 33, Grp E, Hsp 60 GroEL co-chaperone GroES were also identified on genome sequence of Megasphaera sp. strain DISK18. Phosphate starvation protein Pho H and stringent starvation a & b related to carbon starvation were also present. Associated with the gene clusters of particular significance are the genes ATP phosphoribosyltransferase (EC 2.4.2.17) which may have a role in histidine biosynthesis in Megasphaera. Similar mechanisms have been documented in Lactobacillus casei, in response to acid adaptation37. It was suggested that the histidine operon resulted in increased intra-cellular levels of histidine which may be contributing to intracellular buffering capacity as the pKa value of the imidazole groups of histidine and histidine-containing peptides is near 6.038. These stress response genes may help the organism by the induction of many proteins in response to a variety of environmental stress conditions and have significant impact on bacterial physiology and survival.

The fluoride riboswitch, an adaptive strategy of oral microbes to deal with fluoride ion39, which is present in majority of oral hygiene products. Though members of the family Veillonellaceae were unaffected by fluoride presence40, they were never reported to contain fluoride riboswitch. This is the first report that reveals adaptive strategies developed in Megasphaera strain DISK18 compared to its closest phylogenetic relatives. Moreover, in Megasphaera sp. strain DISK18 genome we also observed the gene crcB located upstream of the sodium solute transporter and type IV secretion system. The presence of genes encoding sulfate reductase enzymes involved in sulfur reduction confirmed the production of VSC, though, in low quantities. Similarly, the presence of enzyme carbamate kinase, which mediates the terminal step in ammonia degradation in the strain Megasphaera sp. DISK18 suggests its ability to neutralize the periodontal environment and reduce the damage caused by cariogenic bacteria under acidic conditions. Many oral bacteria like S. mitis, S. pneumoniae, S. gordonii, and S. cristatus express arginine deiminase41,42, which is the first enzyme in the arginine deiminase system that converts arginine to ammonia, ornithine, and carbon dioxide. Similarly, strain DISK18 also produced ammonia with the help of enzyme arginine deaminase.

Clinical relevance of Megasphaera as a commensal organism to the host

Most of the normal resident bacteria of the oral environment benefit the host through the production or utilization of metabolites produced through various metabolic pathways. These range from fermentation end products (mostly short chain fatty acids), vitamins and co-factors to numerous other bio-molecules14. In the present study, we identified many genes responsible for such potentially beneficial effects in the genome of Megasphaera sp. strain DISK18 which could contribute to the production of important metabolites, vitamins and cofactors. Usually health associated bacteria do not survive in very low pH41 which is in line for Megasphaera sp. strain DISK18 as well, which resides in an alkaline pH, so, it is quite plausible that Megasphaera spp. may have a beneficial role to the host health via its lactate utilization and alkali generation activities, and compete with the growth of pathogenic organisms.

Conclusion

Though newly developed tools of metagenomics have allowed us to understand the complexity of the oral microbiome, the traditional tools to isolate and culture individual bacterial community members are essentially required. Cultivation and culturing methods help to extend our understanding of the ecologic and metabolic characteristics or behaviours of newly identified microorganisms and to decipher their role in oral health and disease. Thus, present study reports the characterization of an oral isolate Megasphaera sp. DISK18 along with whole genome sequence emphasizing its potential role as a commensal in the oral cavity. In particular, the range of optimal temperature, pH, oxidative stress, antibiotics and fluoride resistance, metabolic end products coupled with absence of pathogenic nature supported by the whole genome sequence data highlight its commensal life style.

Material and Methods

Collection of sample

The subgingival plaque sample was collected from a 24 year old female with a healthy oral cavity at Dr. H.S. Judge Institute of Dental Sciences and Hospital, Panjab University, Chandigarh. Study subject was selected based on absence of any specific dental pathology or associated conditions like dental caries, missing tooth or any prosthesis in her mouth. The clinical indicators of periodontal status were recorded and no sites of pocket depth or attachment level measurements >3 mm, absence of overt gingival redness and/ or bleeding on probing were observed ascertaining a clinically healthy status of oral cavity. The purpose of investigation was explained and a voluntary informed consent was obtained from the subject. All procedures involving sample collection from human subjects were approved by Institutional review committee (Dr. H.S. Judge Institute of Dental Sciences and Hospital) and were carried out in accordance with the approved guidelines. The subgingival plaque sample was collected with sterile paper points. Paper points were inserted into gingival sulcus at 6 sites minimally in each quadrant and kept undisturbed for at least 20 seconds. The pooled plaque was subsequently transferred to a serum vial containing reduced transport fluid media. Airtight sealed vials were transported to the laboratory for isolation of bacteria.

Bacterial strains

All strains, except S. mutans MTCC 890, used in the present study were isolated from the gingival plaque samples. Serially diluted samples were plated on different media and incubated under anaerobic atmosphere (80% N2, 15%, CO2, 5% H2). Bacterial strains designated as DIGK4C and DISK18 were isolated from reinforced clostridial agar (Difco), DISK25 from brain heart infusion agar (Difco) and DISK26 from MRS agar (Difco) plates upon incubation at 37 °C for 48. The individual colonies were streaked onto respective media of isolation, purified and preserved as −70 °C glycerol stocks for further studies. Strain S. mutans MTCC 890 was obtained from Microbial Culture Collection and Gene bank, CSIR-Institute of Microbial Technology, Chandigarh.

Genotypic identification of isolates

All strains were identified based on 16S rRNA gene sequence analysis as described earlier43. The 16S rRNA gene sequence (~1400 bp) was used for BLAST analysis on EzTaxon database44 and closely related sequences were retrieved for manual editing of sequences.

Phenotypic characterization of strain DISK18

To determine the cell morphology, strain DISK18 was grown on reinforced clostridial agar medium at 30 °C under anaerobic condition. An active culture was assigned for Gram's staining by using Gram-staining kit (Himedia) according to the manufacturer’s instructions. Ability to grow at different temperatures was performed by incubating strain DISK18 at 4, 10, 15, 25, 30, 37, 45 and 50 °C. The growth at different pH range was tested at 30 °C temperature using reinforced clostridial agar as basal medium and adjusting the pH between 4.0–11.0 using different buffered solutions as described earlier45. Reinforced clostridial agar medium was supplemented with different concentrations of NaCl (0.5–2.5% w/v with 0.5% interval) to determine salt tolerance of the strain DISK18. Assimilation of different substrates and biochemical characteristics were performed using AN microplates (BIOLOG) and ANC microplates (Vitek2; BioMerieux) following the manufacturer's instructions. Catalase and oxidase activities were determined as described in previous literature46. Hydrolysis of esculin, indole, Voges- Proskauer and methyl red test, H2S production and nitrate reduction were performed as described by Lanyi47. Hydrolysis of casein, gelatin, starch and tween was determined as described by Smibert and Kraig48. Further, acid production from different sugars was checked as mentioned earlier45. Antibiotic susceptibility of the strain was determined using antibiotic discs supplied by Himedia (India). The total polar lipids were extracted using the protocol described by Minnikin49. To determine the membrane lipid content, polar lipids were extracted and separated by two dimensional TLC and sprayed with molybdatophosphoric acid, molybdenum blue and ninhydrin spray reagents to detect total lipids, phospholipids and aminolipids, respectively. Strain DISK18 is deposited at Microbial Type Culture Collection under the accession number MTCC12521.

Phylogenetic analysis of strain DISK18

For phylogenetic analysis, the 16S rRNA gene sequence of strain DISK18 (1481 bp) was used for BLAST analysis on EzTaxon database. Closely related sequences were retrieved and aligned using ClustalW program50. Phylogenetic trees were constructed using the neighbour-joining (NJ)51 and maximum likelihood (ML)52 methods available in MEGA6 software53. Kimura two-parameter54 model was used to calculate the evolutionary distance of NJ and ML tree. Search option NNI (Nearest-Neighbour-Interchange) with very strong branch swap filter was used for ML phylogenetic analysis. A discrete gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 0.3358). All positions containing gaps, missing data were eliminated and bootstrap analyses were performed using 1000 replications for both NJ and ML analyses. The 16S rRNA gene sequence is available at NCBI with accession no. LN998020.

Measurement of surface hydrophobicity

The surface hydrophobicity of all isolates (DISK18, DISK26, DIGK4C and DISK25) was tested using chloroform, diethyl ether and hexane partition method55. In brief, approximately 109 cells were washed twice with 3 mM NaCl containing 0.5 mM CaCl2 and suspended in the same solution. An equal volume of cell suspension was mixed with chloroform, hexane or diethyl ether (5 ml each) into a round bottom test tube. The tubes were mixed by vortex mixing and the hydrophobicity was expressed as the solvent phase adsorption percentage that was calculated based on the measurement of the OD600 of the cell suspension before and after the assay using formula Hydrophobicity (%) = [1 − (OD600 after vortex mixing/OD600 before vortex mixing)] × 100.

Sulfate reduction and volatile sulfur compounds (VSC) production

The production of volatile sulfur compounds by Megasphaera sp. strain DISK18 was performed by microscopic sulfide assay56. Overnight cultures of Megasphaera sp. strain DISK18 (0.5 ml) was added to an equal volume of PBS containing sodium thiosulfate (50 mg) and ferrous sulfate (20 mg) and incubated overnight at 37 °C. The culture was observed under the microscope for VSC production. Further, VSC production was also confirmed by differential agar method57. Strain DISK18 (50 μl)was mixed with 50 μl of PBS and plated on to a differential agar containing sodium thiosulfate (0.5 g) and ferrous sulfate (0.2 g). Plates were incubated at 37 °C under anaerobic conditions and observed for formation of black colonies as a result of VSC production.

Bacterial coaggregation assay between bacterial isolates

Isolates including DISK18, DISK26, DIGK4C, DISK25 and S. mutans MTCC 890 were grown to late exponential or stationary phase (48–72 h). The cells were harvested by centrifugation of liquid culture at 8000 rpm for 10 min. The pellet obtained was washed twice with coaggregation buffer32 (0.1 mM CaCl2, 0.1 mM MgCl2, 0.15 M NaCl, and 3.1 mM NaN3, dissolved in 1 mM Tris adjusted to pH 8) and suspended in the same buffer. The OD600 of the each bacterial cell suspension was measured and adjusted equally before performing self-aggregation and coaggregation assays. Equal amounts (2 ml) of each bacterial culture was mixed with strain DISK18 by vortex mixing to test their coaggregating efficiency. Pure bacterial culture of each strain was also incubated under identical condition to test the self-aggregation. Aliquots were obtained at different time intervals and the coaggregation index was calculated58. Assays were performed in three independent experiments in triplicates.

Effect of sugar, protease pH and temperature on coaggregation

The influence of various external factors such as heat treatment, pH and addition of different sugars on the self-aggregation of strain DISK18 and coaggregation in pairs with other oral isolates was tested. For heat treatment, cell pellets obtained from stationary phase grown cultures of all isolates were resuspended in coaggregation buffer and exposed to various temperatures to test self-aggregation or coaggregation. The bacterial cell suspensions incubated at identical temperatures were used to test the effect of pH on coaggregation as described above. Similarly, cells were resuspended in different buffers ranging pH from 4.0 to 8.0 in 1.0 pH interval to test the effect of pH and untreated strains were used as control. To evaluate the effects of different sugars on self-aggregation of strain DISK18 and coaggregation with other oral isolates, cell pellet obtained from culture grown to stationary phase were mixed with 50 mM solutions of fructose, galactose, glucose, lactose, mannitol, mannose, rhamnose, sucrose and xylitol. The effect of proteolytic enzymes was tested by incubating the cell pellet of isolates with individual enzymes like pronase E, proteinase K and trypsin in recommended buffers with a final protease concentration of 2.5 mg/ml. Upon incubation for one hour at 37 °C, cells were washed with coaggregation buffer and resuspended in same buffer. Equal amounts of strain DISK18 was mixed with each of the other isolates and coaggregation was measured as OD600 using spectrophotometer.

Biofilm formation ability

To understand the ability of strain DISK18 to form biofilm, experiments were performed on strain DISK18 alone and also in combination with other isolates to estimate the multispecies biofilm formation efficiency. The isolates were grown anaerobically in reinforced clostridial broth or trypticase soy broth overnight. After incubation the cultures were diluted 1:100 and 100 μl of this cell suspension was transferred to a 96 well-microtitre plate and incubated at 37 °C for 24 h under anaerobic conditions. Reinforced clostridial broth and trypticase soy broth were used as control. Subsequently, the medium was discarded and wells were washed twice with 200 μl of PBS to remove planktonic or loosely attached bacteria and air dried for 30 min. The bound cells were stained with 120 μl of 0.1% crystal violet solution and plates were incubated at room temperature for 15 min. Excess dye was removed by washing the wells with double distilled water vigorously and allowed to dry. The quantification of biofilm formation was performed by adding 125 μl of 30% acetic acid to each well as a solubilizing agent for crystal violet and incubated for 15 min. The quantification of biofilm was done by measuring OD at 595 nm using 30% acetic acid as blank. All biofilm assay experiments were performed in triplicate. Biofilm formation was also performed in 12 well plate and selected biofilms were processed for scanning electron microscopy (SEM) study.

Whole genome sequence, assembly and annotation

The genomic DNA was extracted and purified using Sambrook method59 and also using ZR Fungal/Bacterial DNA MiniPrep Kit (Zymo Research, USA) as per manufacturer’s instructions. The DNA was quantified by using Qubit 2.0 Fluorometer (Life Technologies) and used for whole genome sequencing. Illumina sequencing libraries were constructed by using the Nextera XT sample preparation kit (Illumina, Inc., San Diego, CA, USA) with dual indexing adaptors from Illumina as per the manufacturer’s guidelines. Sequencing libraries were sequenced by using 2 × 150 bp paired configuration on the in-house Illumina Miseq (Illumina, Inc., San Diego, CA, USA) platform. Illumina reads were de novo assembled using CLC Genomics Workbench 7.5 (CLC Bio-Qiagen, Aarhus, Denmark). The genome was annotated by using NCBI-Prokaryotic genome annotation pipeline and RAST server (htpp://rast.nmpdr.org)12. Subsystem functional categorization of the predicted ORFs and visualization was done by using SEED viewer60. Average nucleotide identity (ANI) values were determined using the tool Jspecies61 and digital DDH was calculated using web tool GGDC 2.0 (http://ggdc.dsmz.de/distcalc2.php). CRISPR repeats were identified using the CRISPR recognition tool62. BLAST Ring Image Generator (BRIG) software was used to compare the genome sequences and visualization16. The whole genome shotgun project has been deposited at DDDBJ/EMBL/GenBank under accession number LUGJ00000000.

Additional Information

Accession codes: EMBL/DDJB/GenBank accession number for 16S rRNA gene sequence of strain is LN998020 and the genome sequence is LUGJ00000000.

How to cite this article: Nallabelli, N. et al. Biochemical and genome sequence analyses of Megasphaera sp. strain DISK18 from dental plaque of a healthy individual reveals commensal lifestyle. Sci. Rep. 6, 33665; doi: 10.1038/srep33665 (2016).

Supplementary Material

Supplementary Information
srep33665-s1.pdf (107.5KB, pdf)

Acknowledgments

Financial assistance from Council of Scientific and Industrial Research (CSIR) – Human Microbiome (HUM) Network project (BSC-119). CSIR-Institute of Microbial Technology. The Department of Biotechnology, Government of India (No. BT/PR7368/INF/22/177/2012) is also duly acknowledged. We thank Dr. Evan Haney, Hancock Laboratory, Department of Microbiology and Immunology, University of British Columbia, BC, Canada for English language review and useful discussions. We would like to thank electron microscopy facility and Mr. Anil Theophilus for their help in electron microscopy.

Footnotes

Author Contributions V.G. and S.K. conceived and designed the experiments. N.N., V.K.P., N.S., A.J. and V.G. isolated and characterized strain and performed experiments. P.P. and P.B.P. involved in genome sequence and annotation. P.P.P., P.B.P., V.G. and S.K. analysed the genomic data. V.G. and S.K. wrote the manuscript.

References

  1. Dewhirst F. E. et al. The human oral microbiome. J Bacteriol 192, 5002–5017 (2010). [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Feng Z. & Weinberg A. Role of bacteria in health and disease of periodontal tissues. Periodontol 2000 40, 50–76 (2006). [DOI] [PubMed] [Google Scholar]
  3. Avila M. et al. The oral microbiota: living with a permanent guest. DNA and cell biol 28, 405–411 (2009). [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Frank A., Roberts F. A. & Darveau R. P. Beneficial bacteria of the periodontium. Periodontol 2000 30, 40–50 (2002). [DOI] [PubMed] [Google Scholar]
  5. Paster B. J. et al. Bacterial diversity in human subgingival plaque. J Bacteriol 183, 3770–3783 (2001). [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Aas J. A., Paster B. J., Stokes L. N., Olsen I. & Dewhirst F. E. Defining the normal bacterial flora of the oral cavity J Clin Microbiol 43, 5721–5732 (2005). [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Kumar P. S. et al. New bacterial species associated with chronic periodontitis. J Dent Res 82, 338–344 (2003). [DOI] [PubMed] [Google Scholar]
  8. Kumar P. S. et al. Identification of candidate periodontal pathogens and beneficial species by quantitative 16S clonal analysis. J Clin Microbiol 43, 3944–3955 (2005). [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Murayama R. et al. Study of the distribution of Megasphaera micronuciformis in oral cavities of the Japanese by species-specific polymerase chain reaction (PCR) assay. African J Microbiol Res 7, 5546–5549 (2013). [Google Scholar]
  10. Peterson S. et al. The dental plaque microbiome in health and disease. PLoS ONE 8, e58487, 10.1371/journal.pone.0058487 (2013). [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Doyle R. J. Contribution of the hydrophobic effect to microbial infection. Microb Infect 2, 391–400 (2000). [DOI] [PubMed] [Google Scholar]
  12. Aziz R. K. et al. The RAST Server: Rapid Annotations using Subsystems Technology. BMC genomics 9, 75, 10.1186/1471-2164-9-75 (2008). [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Padmanabhan R. et al. Non-contiguous finished genome sequence and description of Megasphaera massiliensis sp. nov. Std Genom Sci 8, 525–538 (2013). [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Shetty S. A., Marathe N. P., Lanjekar V., Ranade D. & Shouche Y. S. Comparative genome analysis of Megasphaera sp. reveals niche specialization and its potential role in the human Gut. PLoS ONE 8, e79353, 10.1371/journal.pone.0079353 (2013). [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Marx H. et al. Genome sequence of the ruminal bacterium Megasphaera elsdenii. J. Bacteriol 193, 5578–5579, 10.1128/JB.05861-11 (2011). [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Alikhan N.-F., Petty N. K., Zakour N. L. B. & Beatson S. A. BLAST Ring Image Generator (BRIG): simple prokaryotic genome comparisons. BMC genomics 12, 402, 10.1186/1471-2164-12-402 (2011). [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Pagels M. et al. Redox sensing by a Rex-family repressor is involved in the regulation of anaerobic gene expression in Staphylococcus aureus. Mol Microbiol 76, 1142–1161, 10.1111/j.1365-2958.2010.07105 (2010). [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Brunner J. et al. The core genome of the anaerobic oral pathogenic bacterium Porphyromonas gingivalis. BMC Microbiol 10, 252, 10.1186/1471-2180-10-252 (2010). [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Broges-Walmsley M. I., McKeegan K. S. & Walmsley A. R. Structure and function of efflux pumps that confer resistance to drugs. Biochem J 376, 313–338 (2003). [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Amano A. Bacterial adhesins to host components in periodontitis. Periodontol 2000 52, 12–37 (2010). [DOI] [PubMed] [Google Scholar]
  21. Chagnot C., Zorgani M. A., Astruc T. & Desvaux M. Proteinaceous determinants of surface colonization in bacteria: bacterial adhesion and biofilm formation from a protein secretion perspective. Front Microbiol 14, 303, 10.3389/fmicb.2013.00303. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Marchandin H., Jumas-Bilak E., Gay B., Teyssier C. & Jean-Pierre H. Phylogenetic analysis of some Sporomusa sub-branch members isolated from human clinical specimens: description of Megasphaera micronuciformis sp. nov. Int J Syst Evol Microbiol 53, 547–553 (2003). [DOI] [PubMed] [Google Scholar]
  23. Juvonen R. & Suihko M.-L. Megasphaera paucivorans sp. nov., Megasphaera sueciensis sp. nov. and Pectinatus haikarae sp. nov., isolated from brewery samples, and emended description of the genus Pectinatus. Int J Syst Evol Microbiol 56, 695–702 (2006). [DOI] [PubMed] [Google Scholar]
  24. Rogosa M. Transfer of Peptostreptococcus elsdenii Gutierrez et al. to a new genus, Megasphaera [M. elsdenii (Gutierrez et al.) comb. nov.]. Int J Syst Evol Microbiol 21, 187–189 (1971). [Google Scholar]
  25. Nelson K. E. et al. Complete genome sequence of the oral pathogenic bacterium Porphyromonas gingivalis strain W83. J Bacteriol 185, 5591–5601 (2003). [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Richard P., Darveaau N., Anner N. T. & Roy C. PAGE. Periodontology 2000 14, 12–32 (1997). [DOI] [PubMed] [Google Scholar]
  27. Socransky S. S. & Haffajee A. D. Periodontal microbial ecology. Periodontol 2000, 38, 135–187 (2005). [DOI] [PubMed] [Google Scholar]
  28. Van Loosdrecht M. et al. The role of bacterial cell wall hydrophobicity in adhesion. Appl Environ Microbiol 53, 1893–1897 (1987). [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Marsh P. D., Moter A. & Devine D. A. Dental plaque biofilms: communities, conflict and control. Periodontol 2000 55, 16–35 (2011). [DOI] [PubMed] [Google Scholar]
  30. Kolenbrander P. E. Intergeneric coaggregation among human oral bacteria and ecology of dental plaque. Annu Rev Microbiol 42, 627–656 (1988). [DOI] [PubMed] [Google Scholar]
  31. Kolenbrander P. E. et al. Bacterial interactions and successions during plaque development. Periodontol 2000 42, 47–79 (2006). [DOI] [PubMed] [Google Scholar]
  32. Gibbons R. & Nygaard M. Interbacterial aggregation of plaque bacteria. Arch Oral Biol 15, 1397–IN1339 (1970). [DOI] [PubMed] [Google Scholar]
  33. Cisar J. et al. Specificity of coaggregation reactions between human oral streptococci and strains of Actinomyces viscosus or Actinomyces naeslundii. Infect Immun 24, 742–752 (1979). [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Kreth J., Merritt J. & Qi F. Bacterial and host interactions of oral streptococci. DNA Cell Biol 28, 397–403 (2009). [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Sherlock O. et al. Novel roles for the AIDA adhesin from diarrheagenic Escherichia coli: cell aggregation and biofilm formation. J Bacteriol 186, 8058–8065 (2004). [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Benz I. & Schmidt M. A. Glycosylation with heptose residues mediated by the aah gene product is essential for adherence of the AIDA‐I adhesin. Mol Microbiol 40, 1403–1413 (2001). [DOI] [PubMed] [Google Scholar]
  37. Broadbent J. R., Larsen R. L., Deibel V. & Steele J. L. Physiological and transcriptional response of Lactobacillus casei ATCC 334 to acid stress. J Bacteriol 192, 2445–2458 (2010). [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Abe H. Role of histidine-related compounds as intracellular proton buffering constituents in vertebrate muscle. Biochemistry (Mosc) 65, 757–765 (2000). [PubMed] [Google Scholar]
  39. Baker J. L. et al. Widespread genetic switches and toxicity resistance proteins for fluoride. Science 335, 233–235, 10.1126/science.1215063 (2012). [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Bowden G. H., Odlum O., Nolette N. & Hamilton I. R. Microbial populations growing in the presence of fluoride at low pH isolated from dental plaque of children living in an area with fluoridated water. Infect Immun 36, 247–254 (1982). [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Gross E. L. et al. Bacterial 16S sequence analysis of severe caries in young permanent teeth. J Clin Microbiol 48, 4121–4128 10.1128/JCM.01232-10 (2010). [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Burne R. A. & Marquis R. E. Alkali production by oral bacteria and protection against dental caries. FEMS Microbiol Lett 193, 1–6 (2000). [DOI] [PubMed] [Google Scholar]
  43. Suresh K., Mayilraj S. & Chakrabarti T. Effluviibacter roseus gen. nov., sp. nov., isolated from muddy water, belonging to the family “Flexibacteraceae.” Int J Syst Evol Microbiol 56, 1703–1707 (2006). [DOI] [PubMed] [Google Scholar]
  44. Chun J. et al. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57, 2259–2261 (2007). [DOI] [PubMed] [Google Scholar]
  45. Chaudhry V. et al. Methylobacterium indicum sp. nov., a facultative methylotrophic bacterium isolated from rice seed. Syst Appl Microbiol 39, 25–32 (2016). [DOI] [PubMed] [Google Scholar]
  46. Cowan S. T. & Steel K. J. Manual for the Identification of Medical Bacteria Eugene D. Weinberg (ed) Cambridge University Press, New York (1965). [Google Scholar]
  47. Lanyi B. Classical and Rapid Identification Methods for Medically Important Bacteria. Methods Microbiol 19, 1–67 (1988). [Google Scholar]
  48. Smibert R. M. & Krieg N. R. Phenotypic characterization. In Methods for General and Molecular Bacteriology, pp 607–654. Edited by Gerhardt P.. Washington, DC: American Society for Microbiology (1994).
  49. Minnikin D. E. et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2, 233–241 (1984). [Google Scholar]
  50. Thompson J. D., Higgins D. G. & Gibson T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673–4680 (1994). [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Saitou N. & Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425 (1987). [DOI] [PubMed] [Google Scholar]
  52. Tateno Y., Takezaki N. & Nei M. Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site. Mol Biol Evol 11, 261–277 (1994). [DOI] [PubMed] [Google Scholar]
  53. Tamura K., Stecher G., Peterson D., Filipski A. & Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30, 2725–2729 (2013). [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111–120 (1980). [DOI] [PubMed] [Google Scholar]
  55. Rosenberg M., Gutnik D. & Rosenberg E. Adherence of bacteria to hydrocarbons: a simple method for measuring cell surface hydrophobicity. FEMS Microbiol Lett 9, 29–33 (1980). [Google Scholar]
  56. Sterer N., Hendler A., Davidi M. P. & Rosenberg M. A novel microscopic assay for oral malodour-related microorganisms. J Breath Res 2, 026003 (2008). [DOI] [PubMed] [Google Scholar]
  57. Hartley M. G., El-Maaytah M. A., McKenzie C. & Greenman J. The tongue microbiota of low odour and malodorous individuals. Microb Ecol Health Dis 9, 215–223 (1996). [Google Scholar]
  58. Malik A. et al. Coaggregation among nonflocculating bacteria isolated from activated sludge. Appl Environ Microbiol 69, 6056–6063 (2003). [DOI] [PMC free article] [PubMed] [Google Scholar]
  59. Sambrook J., Russell D. W. & Russell D. W. Molecular cloning, a laboratory manual (3-volume set) Cold spring harbor laboratory press Cold Spring Harbor, New York (2001). Sterer, N., Hendler, A., Davidi, M. P. & Rosenberg, M. A novel microscopic assay for oral malodour-related microorganisms. J Breath Res 2, 026003 (2008). [DOI] [PubMed] [Google Scholar]
  60. Overbeek R. et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 42, D202–D214, 10.1093/nar/gkt1226. [DOI] [PMC free article] [PubMed] [Google Scholar]
  61. Richter M. & Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 106, 19126–31, 10.1073/pnas.0906412106. [DOI] [PMC free article] [PubMed] [Google Scholar]
  62. Bland C. et al. CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics 8, 209, 10.1186/1471-2105-8-209 (2007). [DOI] [PMC free article] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Supplementary Information
srep33665-s1.pdf (107.5KB, pdf)

Articles from Scientific Reports are provided here courtesy of Nature Publishing Group

RESOURCES