CN112522362A - Preservation solution for preserving bacterial DNA in fecal sample at normal temperature - Google Patents
Preservation solution for preserving bacterial DNA in fecal sample at normal temperature Download PDFInfo
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- 230000002550 fecal effect Effects 0.000 title claims abstract description 38
- 239000003761 preservation solution Substances 0.000 title claims abstract description 30
- 108020000946 Bacterial DNA Proteins 0.000 title claims abstract description 11
- LFQSCWFLJHTTHZ-UHFFFAOYSA-N Ethanol Chemical compound CCO LFQSCWFLJHTTHZ-UHFFFAOYSA-N 0.000 claims abstract description 27
- FAPWRFPIFSIZLT-UHFFFAOYSA-M Sodium chloride Chemical compound [Na+].[Cl-] FAPWRFPIFSIZLT-UHFFFAOYSA-M 0.000 claims abstract description 22
- 239000000022 bacteriostatic agent Substances 0.000 claims abstract description 15
- XLYOFNOQVPJJNP-UHFFFAOYSA-N water Chemical compound O XLYOFNOQVPJJNP-UHFFFAOYSA-N 0.000 claims abstract description 14
- 239000008367 deionised water Substances 0.000 claims abstract description 13
- 229910021641 deionized water Inorganic materials 0.000 claims abstract description 13
- LXAHHHIGZXPRKQ-UHFFFAOYSA-N 5-fluoro-2-methylpyridine Chemical compound CC1=CC=C(F)C=N1 LXAHHHIGZXPRKQ-UHFFFAOYSA-N 0.000 claims abstract description 12
- 239000011780 sodium chloride Substances 0.000 claims abstract description 11
- 210000003608 fece Anatomy 0.000 claims description 7
- 230000001954 sterilising effect Effects 0.000 claims description 5
- 238000007865 diluting Methods 0.000 claims description 2
- 108020004414 DNA Proteins 0.000 abstract description 17
- 239000000243 solution Substances 0.000 abstract description 16
- 238000004321 preservation Methods 0.000 abstract description 15
- 244000005700 microbiome Species 0.000 abstract description 10
- 238000012163 sequencing technique Methods 0.000 abstract description 8
- 230000000694 effects Effects 0.000 abstract description 5
- 238000000034 method Methods 0.000 abstract description 5
- 239000000203 mixture Substances 0.000 abstract description 4
- 230000008901 benefit Effects 0.000 abstract description 3
- 238000007405 data analysis Methods 0.000 abstract description 3
- 230000000968 intestinal effect Effects 0.000 abstract description 3
- 231100000956 nontoxicity Toxicity 0.000 abstract description 2
- 241000894006 Bacteria Species 0.000 description 12
- 238000011282 treatment Methods 0.000 description 10
- HEMHJVSKTPXQMS-UHFFFAOYSA-M Sodium hydroxide Chemical compound [OH-].[Na+] HEMHJVSKTPXQMS-UHFFFAOYSA-M 0.000 description 6
- 238000000605 extraction Methods 0.000 description 6
- 230000000813 microbial effect Effects 0.000 description 6
- 235000019441 ethanol Nutrition 0.000 description 5
- 238000002360 preparation method Methods 0.000 description 5
- 239000003755 preservative agent Substances 0.000 description 5
- 230000002335 preservative effect Effects 0.000 description 5
- 238000010586 diagram Methods 0.000 description 4
- 239000012530 fluid Substances 0.000 description 4
- 230000006872 improvement Effects 0.000 description 4
- 239000007788 liquid Substances 0.000 description 4
- 238000004458 analytical method Methods 0.000 description 3
- 230000009286 beneficial effect Effects 0.000 description 3
- 108090000623 proteins and genes Proteins 0.000 description 3
- 108020004465 16S ribosomal RNA Proteins 0.000 description 2
- FFBHFFJDDLITSX-UHFFFAOYSA-N benzyl N-[2-hydroxy-4-(3-oxomorpholin-4-yl)phenyl]carbamate Chemical compound OC1=C(NC(=O)OCC2=CC=CC=C2)C=CC(=C1)N1CCOCC1=O FFBHFFJDDLITSX-UHFFFAOYSA-N 0.000 description 2
- 238000003766 bioinformatics method Methods 0.000 description 2
- 238000001514 detection method Methods 0.000 description 2
- KWGKDLIKAYFUFQ-UHFFFAOYSA-M lithium chloride Chemical compound [Li+].[Cl-] KWGKDLIKAYFUFQ-UHFFFAOYSA-M 0.000 description 2
- 238000012986 modification Methods 0.000 description 2
- 230000004048 modification Effects 0.000 description 2
- 238000005070 sampling Methods 0.000 description 2
- 238000004659 sterilization and disinfection Methods 0.000 description 2
- 231100000331 toxic Toxicity 0.000 description 2
- 230000002588 toxic effect Effects 0.000 description 2
- QKNYBSVHEMOAJP-UHFFFAOYSA-N 2-amino-2-(hydroxymethyl)propane-1,3-diol;hydron;chloride Chemical compound Cl.OCC(N)(CO)CO QKNYBSVHEMOAJP-UHFFFAOYSA-N 0.000 description 1
- 238000007400 DNA extraction Methods 0.000 description 1
- KCXVZYZYPLLWCC-UHFFFAOYSA-N EDTA Chemical compound OC(=O)CN(CC(O)=O)CCN(CC(O)=O)CC(O)=O KCXVZYZYPLLWCC-UHFFFAOYSA-N 0.000 description 1
- 101710163270 Nuclease Proteins 0.000 description 1
- 241000425347 Phyla <beetle> Species 0.000 description 1
- 239000007853 buffer solution Substances 0.000 description 1
- 230000015556 catabolic process Effects 0.000 description 1
- 238000010276 construction Methods 0.000 description 1
- 238000005138 cryopreservation Methods 0.000 description 1
- 238000006731 degradation reaction Methods 0.000 description 1
- 238000005516 engineering process Methods 0.000 description 1
- 238000001914 filtration Methods 0.000 description 1
- 239000012634 fragment Substances 0.000 description 1
- ZJYYHGLJYGJLLN-UHFFFAOYSA-N guanidinium thiocyanate Chemical compound SC#N.NC(N)=N ZJYYHGLJYGJLLN-UHFFFAOYSA-N 0.000 description 1
- 230000036541 health Effects 0.000 description 1
- 239000012528 membrane Substances 0.000 description 1
- 238000005374 membrane filtration Methods 0.000 description 1
- 238000002156 mixing Methods 0.000 description 1
- 231100000252 nontoxic Toxicity 0.000 description 1
- 230000003000 nontoxic effect Effects 0.000 description 1
- 230000008520 organization Effects 0.000 description 1
- 239000000047 product Substances 0.000 description 1
- 230000035755 proliferation Effects 0.000 description 1
- 239000002994 raw material Substances 0.000 description 1
- 238000005057 refrigeration Methods 0.000 description 1
- 210000003296 saliva Anatomy 0.000 description 1
- 239000008223 sterile water Substances 0.000 description 1
- 239000006228 supernatant Substances 0.000 description 1
- 238000005303 weighing Methods 0.000 description 1
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/02—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving viable microorganisms
- C12Q1/24—Methods of sampling, or inoculating or spreading a sample; Methods of physically isolating an intact microorganisms
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Abstract
The invention provides a preservation solution for preserving bacterial DNA in a fecal sample at normal temperature, which comprises sodium chloride, absolute ethyl alcohol, a biological bacteriostatic agent, EDTA disodium and deionized water; the ratio of each component in the preservation solution is as follows: 0.5-2mol/L of sodium chloride; 20-60% (v/v) of absolute ethyl alcohol; 0.01-0.2% (v/v) of biological bacteriostatic agent; the EDTA disodium is 10-100 mmol/L; the balance of deionized water; wherein the pH of the preservation solution is 7-8, and the biological bacteriostatic agent is Proclin 300. The method can ensure that the DNA of the microorganisms in the fecal sample is not degraded in the normal temperature environment, and the quantity, the composition and the abundance of the microorganisms in the fecal sample are kept stable through good preservation performance, thereby ensuring the accuracy of data analysis after intestinal flora sequencing; the invention realizes normal temperature storage and transportation of the fecal sample, is suitable for long-distance transportation, and has the advantages of good storage effect, simple operation, good applicability and no toxicity compared with the existing storage solution in the market.
Description
Technical Field
The invention relates to the technical field of DNA preserving fluid, in particular to preserving fluid for preserving bacterial DNA in a fecal sample at normal temperature.
Background
The low-temperature cryopreservation is the most common method for preserving microorganisms in the fecal samples, but the low-temperature preservation usually requires large-scale refrigeration equipment, has poor universality and is complex to operate, so that the development of DNA preserving solution suitable for microorganism preservation is necessary.
At present, DNA preservation solution in the market usually contains toxic components such as guanidinium isothiocyanate and the like, or the components are single, so that microorganisms in a sample are easy to pollute, the composition and the quantity of the microorganisms are changed, and biological information of the sample cannot be truly reflected. .
Disclosure of Invention
In order to solve the problems, the invention discloses a preservation solution for preserving bacterial DNA in a fecal sample at normal temperature, which solves the problem of preserving microbial DNA in the fecal sample at normal temperature, is suitable for long-distance transportation, has better preservation effect, simpler operation method and no toxic molecules compared with the prior like products, and has the benefit of ensuring the accuracy of data analysis after intestinal flora sequencing.
The specific scheme is as follows:
the collected excrement sample is placed in the excrement storage solution during sampling, and is uniformly mixed and stored at normal temperature, so that the composition and the quantity of microorganisms are not obviously changed.
A preservation solution for preserving bacterial DNA in a fecal sample at normal temperature is characterized by comprising sodium chloride, ethanol, a biological bacteriostatic agent, EDTA disodium and deionized water.
As a further improvement of the invention, the ratio of each component in the preservation solution is as follows:
the mass ratio of the sodium chloride is 1 mol/L; the volume ratio of the absolute ethyl alcohol is 30% (v/v); the volume ratio of the biological bacteriostatic agent is 0.1% (v/v); the mass ratio of the EDTA disodium is 20 mmol/L; the balance of deionized water; wherein the pH range of the preservation solution is between 7 and 8, and the biological bacteriostatic agent is Proclin 300.
As a further improvement of the invention, the preparation method of the preserving fluid comprises the following steps: dissolving sodium chloride and EDTA disodium in deionized water, diluting to constant volume with deionized water, adjusting pH, sterilizing, and adding anhydrous alcohol and biological bacteriostatic agent to obtain feces preservation solution.
The invention has the beneficial effects that: the method can ensure that the DNA of microorganisms in the fecal sample is not degraded in the normal temperature environment, stabilize the composition and the quantity of the microorganisms in the fecal sample through good preservation performance, and ensure the accuracy of data analysis after intestinal flora sequencing; the invention realizes normal temperature storage and transportation of the fecal sample, is suitable for long-distance transportation, and has the advantages of good storage effect, simple operation, good applicability and no toxicity compared with the existing storage solution in the market.
Drawings
FIG. 1 is a diagram showing the ratio of the phylum of bacteria in fecal samples 1 in different storage modes in the example.
FIG. 2 is a diagram showing the ratio of the phylum of bacteria in fecal samples 2 in different storage modes in the example.
FIG. 3 is a diagram showing the ratio of the phylum of bacteria in fecal samples 3 in different storage modes in the example.
Detailed Description
The present invention will be further illustrated with reference to the accompanying drawings and specific embodiments, which are to be understood as merely illustrative of the invention and not as limiting the scope of the invention.
The invention relates to a preservation solution for preserving bacterial DNA in a fecal sample at normal temperature, which comprises sodium chloride, absolute ethyl alcohol, a biological bacteriostatic agent, EDTA disodium and deionized water.
In this example, the ratio of each component in the preservation solution is as follows:
1mol/L of sodium chloride; absolute ethanol 30% (v/v); 0.1% (v/v) of biological bacteriostatic agent; 20mmol/L of EDTA disodium; the balance being deionized water.
Wherein the pH range of the preservation solution is between 7 and 8, and the biological bacteriostatic agent is Proclin 300.
In this example, the preparation method of the preservation solution was:
(1) taking the raw materials in the proportion;
(2) preparing EDTA disodium weighed in the step (1) into a preparation solution and storing; wherein the pH is 6-8.5 Tris-HCl buffer solution.
(3) Selecting EDTA solution with corresponding volume according to the total volume for preserving the pre-prepared feces and according to the content requirement of each component in the system, adding corresponding amount of sodium chloride, adding sterile water to the total volume for preserving the pre-prepared feces which does not contain absolute ethyl alcohol, and sterilizing by adopting a microporous filter membrane filtration mode to obtain the feces preservation solution preparation liquid. The sterilization condition is that the sterilization is carried out by adopting a mode of filtering with a microporous filter membrane.
(4) Adding corresponding amount of absolute ethyl alcohol and biological bacteriostatic agent into the sterilized excrement storage solution preparation solution, and then adjusting the pH value to obtain the excrement storage solution
According to the scheme, the pH value of the system in the step (4) can be adjusted to be in a range of 7-8 by adding HCl or NaOH when needed, wherein the addition amount of HCl or NaOH is small, and the influence on the concentration of each component in the system is negligible. The preservation temperature is 15-25 deg.C, and the preservation condition is dark preservation.
The using method of the excrement storage liquid comprises the following steps: mixing 0.2-0.5g feces with 2-4ml feces preservation solution, and preserving at room temperature.
The excrement storage solution provided by the invention can protect the integrity of microbial genome DNA and prevent microbial pollution, and the DNA extracted from the storage solution is suitable for downstream multiple gene detection, such as PCR, chip analysis, second-generation sequencing and the like.
Compared with the prior art, the invention has the following beneficial effects because the technology is adopted:
the excrement storage solution disclosed by the invention is used for storing excrement samples, is low in cost and convenient to prepare, can effectively inhibit the activity of nuclease, prevents microbial pollution, ensures that DNA fragments are not degraded, is suitable for being used in a normal-temperature environment, and can ensure the stability of transportation of the samples among various places. The excrement storage liquid is nontoxic and is more beneficial to the health and safety of users.
Examples
Fecal samples were collected from 3 volunteers. The samples of each volunteer were divided into 4 portions, which were subjected to 4 different treatments, 3 samples for each treatment:
(1) and (4) preserving for 0 day: weighing 0.2g of a fecal sample, and extracting DNA by using a fecal genome extraction kit for later use;
(2) the saliva sample preservation solution of the present invention produced in example was preserved for 7 days: 0.2g of a fecal sample is weighed and stored in a collection tube containing the preservation solution of the invention at normal temperature (15-25 ℃) for 7 days at 37 ℃. And after 7 days, extracting the sample by using the fecal genome extraction kit for later use.
(3) Storage in 95% ethanol for 7 days: 0.2g of a fecal sample was weighed and stored in a collection tube containing 95% ethanol at ambient temperature (15-25 ℃) for 7 days at 37 ℃. And after 7 days, extracting the sample by using the fecal genome extraction kit for later use.
(4) The control preservation solution was stored for 7 days: 0.2g of a fecal sample was weighed and stored in a collection tube containing the sharp next preservation solution at room temperature (15 ℃ to 25 ℃) for 7 days at 37 ℃. And after 7 days, extracting the sample by using the fecal genome extraction kit for later use.
The components of the control preservative fluid are as follows: 2.0mol/L of lithium chloride, 30 percent of absolute ethyl alcohol (v/v) and 50mmol/L of EDTA disodium; the balance being deionized water.
Extracting the DNA of the fecal sample according to the operation instruction of the QIAamp fecal genome extraction kit, wherein the sample needs to be centrifuged at high speed before extraction, the supernatant is discarded, and the fecal sample is collected:
2ul of fecal DNA was taken and assayed for concentration (in ng/ul) using Qubit4.0, see Table 1. The DNA concentration of the invention stored for one week is closer to the concentration result of 0 day, while the concentration result of 95% ethanol stored for one week is inferior to that of 0 day, which may cause the degradation of the microbial DNA, and the concentration result of contrast storage liquid stored for one week is obviously superior to that of 0 day, which may be caused by the proliferation of the microbial flora which is not fixed in the initial sampling state.
TABLE 1 DNA concentration (in ng/ul) of fecal samples 1-3 treated with 3 kinds of qubits
Sample number | Sample 1 | Sample 2 | Sample 3 |
Process 1 | 37.7 | 46.5 | 38.4 |
Treatment 2 | 39.2 | 43.5 | 40.6 |
Treatment 3 | 26.9 | 30.1 | 20.8 |
Treatment 4 | 68.3 | 74 | 52.3 |
And (3) carrying out 16s rRNA gene V4 region library construction sequencing on the DNA sample after the sample is extracted, carrying out bioinformatics analysis after sequencing data are obtained, calculating a Shannon index, and comparing from the diversity angle. As shown in Table 2, the shannon diversity of the contrast preservative solution stored for one week is closer to the result of 0-day preservation, the shannon diversity of the contrast preservative solution stored for one week is inferior to the shannon diversity stored for 0-day, the shannon index of the contrast preservative solution stored for one week is obviously superior to the shannon index stored for 0-day, and the shannon index result is consistent with the concentration result.
TABLE 2 detection results of shannon diversity index
Sample number | Sample 1 | Sample 2 | Sample 3 |
Process 1 | 4.60 | 4.82 | 4.52 |
Treatment 2 | 4.65 | 4.76 | 4.55 |
Treatment 3 | 3.89 | 4.10 | 3.87 |
Treatment 4 | 5.61 | 5.86 | 5.47 |
Dissimilarity analysis of phylogenetic horizontal flora organization
And (3) carrying out 16s rRNA gene V4 region library-building sequencing on the extracted DNA samples, carrying out bioinformatics analysis after obtaining sequencing data, calculating which phyla the bacteria in each sample belong to, and comparing. The relative abundance of bacteria based on phylum level is shown in fig. 1, 2 and 3 are schematic diagrams of the proportion of the phylum level of bacteria in three fecal samples under 4 preservation modes, each column represents a treatment mode, and the preservation modes can be seen in the legend. A larger proportion of certain bacteria is present in the column. The results show that the constitutional ratio of the phylum level of the bacteria stored for 7 days in the self-made formula is closer to the result stored for 0 day, while the constitutional ratio of the phylum level of the bacteria stored for 7 days in the 95% ethanol and the constitutional ratio of the phylum level of the bacteria stored for 7 days in the contrast preservative solution are obviously different from the constitutional ratio of the phylum level of the bacteria stored for 0 day.
Based on the DNA extraction concentration, the bacteria abundance analysis and the similarity and dissimilarity result formed by phylum level flora, the formula of the preservation solution disclosed by the invention is obtained, the preservation effect of the formula on the fecal microorganisms is closer to that of the treatment of preservation for 0 day, and the preservation solution is obviously superior to the preservation scheme of a comparison formula.
The technical means disclosed in the invention scheme are not limited to the technical means disclosed in the above embodiments, but also include the technical scheme formed by any combination of the above technical features. It should be noted that those skilled in the art can make various improvements and modifications without departing from the principle of the present invention, and such improvements and modifications are also considered to be within the scope of the present invention.
Claims (4)
1. A preservation solution for preserving bacterial DNA in a fecal sample at normal temperature is characterized by comprising sodium chloride, absolute ethyl alcohol, a biological bacteriostatic agent, EDTA disodium and deionized water.
2. The preservation solution for preserving bacterial DNA in a fecal sample at normal temperature according to claim 1, wherein the ratio of each component in the preservation solution is as follows:
0.5-2mol/L of sodium chloride; 20-60% (v/v) of absolute ethyl alcohol; 0.01-0.2% (v/v) of biological bacteriostatic agent; the EDTA disodium is 10-100 mmol/L; the balance of deionized water; wherein the pH of the preservation solution is 8 + -0.2.
3. The preservation solution for preserving bacterial DNA in a fecal sample at normal temperature according to claim 2, wherein the biological bacteriostatic agent is Proclin 300.
4. The preservation solution for preserving bacterial DNA in a fecal sample at normal temperature according to claim 3 is prepared by the following steps: dissolving sodium chloride and EDTA disodium in deionized water, diluting to constant volume with deionized water, adjusting pH, sterilizing, and adding anhydrous alcohol and biological bacteriostatic agent to obtain feces preservation solution.
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CN113654860A (en) * | 2021-07-28 | 2021-11-16 | 南京百奥菌生物技术有限公司 | Protective liquid suitable for normal-temperature preservation of fecal samples |
CN115486439A (en) * | 2022-09-23 | 2022-12-20 | 深圳微辰生命科技有限公司 | Feces preservation method and application of ethanol in preparation of feces preservation solution and short-chain fatty acid detection reagent or kit |
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