Isolation and identification
Isfahan University of Medical Sciences' microbiology lab received five samples of traditional kefir dough from the local sources. Lyophilized Standard strains S. mutans (ATCC 35668) and P. gingivalis (ATCC 33277) were prepared from the Iranian industrial microbial collection.
Examination of morphological characteristics of LAB
LAB strains were identified morphologically using the catalase test, gram staining, temperature growth at 15°C and 45°C and pH levels using the procedures in Bergey's book. The physical properties of each colony, as well as the cell appearance characteristics were examined via gram staining. To perform the catalase test and confirm the lactobacillus genus, colonies identical to Lactobacillus with bacterial features of rod-shape, gram positive and without spores were sampled. Each strain was cultivated several times in MRS medium to ensure the purity of MRS culture bacterial [11].
Fermentation of carbohydrates of LAB
The bacteria were cultivated on MRS in order so that fermentation and acid generation tests could be performed. The grown isolate was inoculated in a- tube containing fermentation liquid medium (1% of the desired sugar and phenol red reagent). The tubes were incubated at 37 ° C under 5% carbon dioxide for 72 hours. Sugar consumption and acid production were attributed to the red color change of the culture media to yellow and the formation of bubbles in the tubes [12].
Molecular identification of LAB
To begin with, Murray and Thomson procedures were used to extract the isolate's DNA, with minor modifications. This procedure involved centrifuging 10 mL of bacterial solution (from a 24-hour culture) for 10 minutes at 13,000 rpm. Sediments were transferred into the micro tube. A milliliter of TBE lubricating buffer was added to them after half an hour. Subsequently, at a temperature of 60°C (on a hot plate), chloroform isoamyl alcohol (1:24) was added and well mixed. The materials were again centrifuged at 13,000 rpm for 5 minutes. The supernatant was transferred to new vials and the same volume of pure isopropanol was added. After completely mixing the contents of each vial, they were placed on ice for 10 minutes. The materials were centrifuged at 13,000 rpm for 10 minutes to precipitate, following which 500 µl of 70% ethanol was added. The samples were centrifuged for 5 minutes at 5,000 rpm, with the supernatant removed gently. The DNA vials were then left to dry for an hour at the room temperature. After the sediment dried, each microtube was filled with 100 liters of sterile deionized distilled water. A 1% agarose gel was used to validate the quality of the extracted DNA through electrophoresis[13]. For checking the specificity of the selected primers in genus and species, they were blasted at NCBI. Afterwards the primers were purchased from Gene Technologies.
Table 1
Optimized primer
Reference
|
Product Size
|
Sequence
|
Target Gene
|
Bacteria
|
[14]
|
245
|
F:CTCAAAACTAAACAAAGTTTC
R:CTTGTACACACCGCCCGTCA
|
|
Lacto genus
|
12))
|
176
|
F:CGAGACAGCAATTCCTGCACTCG
CCTCAGAAACAGTCCGGTTGA:R
|
apbE2
|
Lactobacillus plantarum
|
12))
|
124
|
F:ATTTAACCGCAAGTGGCAGC
AAATTGTGTGAACCGGCGTA:R
|
aes
|
Lactobacillus rhamnosus
|
Probiotic Lactobacilli preparation:
Lactic acid bacteria (LAB) were cultured on MRS broth and incubated at 37° C for 18-24 hours under anaerobic conditions. The bacterial growth was then centrifuged for 15 minutes at 13000 rpm/min. The supernatant was collected and filtered through a Millipore 0.22 m filter after being adjusted to a pH of 7.5 with NaOH[14].
Assay for sensitivity to lactobacillus
Sensitivity of pathogenic bacteria to different strains of lactobacillus was determined via the minimum inhibitory concentration (MIC) assay. The assay was done using the method described by Andrews [16]. According to this method, stock solutions containing 20 mg/ml of 10 different selected Lactobacillus were prepared. For preparation of the test inoculums the 48 h active cultures of pathogenic bacteria were adjusted to 0.5 McFarland standards (107 to 108 cfu/ml of bacteria) by adding several dilution of each probiotic powder in each well and microtiter plate incubated for 48 h at 37°C[15, 16].
The well agar diffusion method for antimicrobial screening:
Using well diffusion technique proposed by Cadirci and Citak, the antibacterial activity of Lactobacillus spp. on and Porphyromonas gingivalis was tested. P. gingivalis was cultured on blood agar enriched with vitamin K1 and hemin (at a concentration equivalent to McFarland 1 standard) and S. mutans suspension (at a concentration comparable to McFarland 0.5 standard) was cultured on blood agar complete with 5% defibrinated blood sheep medium. A number of the wells were drilled in the culture media. The wells were filled with100 µl of SCS. For Porphyromonas gingivalis and Streptococcus mutans, inhibition zones were determined in millimeters after 72 hours of anaerobic incubation at 37°C and 48 hours of aerobic incubation at 37°C (14)[15].
The effect of Lactobacillus species on formation of biofilm:
For biofilm assays Streptococcus mutans was grown in BHI containing 2% sucrose, Porphyromonas gingivalis was grown in BHI containing vitamin K and hemin while Lactobacillus species were grown in deMan Rogosa and Sharpe (MRS) broth without sucrose. All the microorganisms were incubated at 37°C in an anaerobic jar for 48h. To evaluate the effect of Lactobacillus spp. on formation of the biofilm of Streptococcus mutans, the suspensions of each isolate were prepared as stated above. The suspensions were adjusted with their respected broth to 0.5 McFarland turbidity standards and several dilutions. Formation of S. mutans and P. gingivalis biofilm was assayed in the presence or absence of Lactobacillus strains in a 96-well polystyrene culture plate. Lactobacillus strains and pathogenic bacteria were mixed at an equal ratio (1:1). Blank wells contained culture medium instead of probiotic strains. The plates were incubated at 37° C for 48 hrs. Quantitation of biofilms was performed using crystal violet based microtiter plate assay [17].
Gas chromatography-mass spectrometry:
The selected strains were inoculated in MRS broth and incubated at 30°C for 4 days. Subsequently the samples were centrifuged at 4000 rpm for 20 minutes. Equal amounts of ethyl acetate were added to the broth and incubated in a rotary shaker for 1 h. The downer layer of the broth was separated. The samples were analyzed with a Hewlett Packard 6850 Gas chromatograph, 5973 mass selective detector, and 7683B series injector (Agilent Technologies, Palo Alto, CA, USA) with helium as the carrier gas at a flow of 1.0 mL/min. One microliter of each sample was injected with 1 min of split flow delay and resolved on a 30 m × 0.25 mm × 0.25 µm DB5MS column (Agilent Technologies, Palo Alto, CA, USA). Inlet, interface, and ion source temperatures were 300 ◦C. Oven starting and final temperatures were within the rate of 5 ◦C/min for 36 min and then for 2 min at a constant temperature. Metabolite annotation was achieved by mass spectra comparison with analytical standards, in house library and the NIST14 database (National Institute of Standards and Technology, Gaithersburg, MD, USA)To prepare dried probiotic powder the upper layer of the broth was incubated, and allowed to dry [18].
Streptococcus gene expression:
We used reverse transcription real-time PCR to evaluated the mRNA levels of S. mutans genes encoding virulence proteins related to carbohydrate metabolism (gtfB) and biofilm formation (brpA) to examine the anti-biofilm formation mechanism, as described previously. For growth curve analysis, the reagent Pars Tous kit was used to extract total RNA and cDNA. A Nanodrop ND-2000 spectrophotometer utilized to assess RNA concentration (ThermoFisher Scientific). The cDNA was amplified with SYBR Premix Taq and the primer sets are given in Table 2 on an ABI 7500 system (Applied Biosystems, Foster City, CA, USA). For gtfB and brpA, the following real-time PCR conditions were used: 95°C for 10 minutes, followed by 40 cycles of 95°C for 30 seconds, 52°C for gtfB, 55° for brpA, and 60°C for 1 minute. The temperature was reduced at a rate of 0.1°C/s from 95°C to 60°C for melting curve analysis, while the fluorescence signal intensity was continuously measured. After adjusting to the 16SrRNA level, variations in mRNA expression levels were determined using ABI 7500 v.2.2 software (Applied Biosystems). The results are reported as a fold change compared to the control group, and fold changes were taken into account.
Table2
Group-specific primer sets used for quantitative reverse transcription real-time PCR :
Reference
|
Sequence(5ˊ–3)
|
Primers
|
Target gene
|
Function
|
[19]
|
ACGAACTTTGCCGTTATTGTCA
AGCAATGCAGCCAATCTACAA
|
For
Rev
|
gtfB
|
Carbohydrate metabolism-promoting genes
|
[20]
|
CGTGAGGTCATCAGCAAGGTC
CGCTGTACCCCAAAAGTTTAGG
|
For
Rev
|
brpA
|
Regulatory protein-encoding genes
|
[21]
|
ATGTTGGGTTAAGTCCCG
CTAGCGATTCCRRCTTCA
|
For
Rev
|
16SrRNA
|
Housekeeping gene
|