CN100368566C - Kit for extracting aquatic animal fecal like bacteria DNA and method thereof - Google Patents
Kit for extracting aquatic animal fecal like bacteria DNA and method thereof Download PDFInfo
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- CN100368566C CN100368566C CNB2005101212728A CN200510121272A CN100368566C CN 100368566 C CN100368566 C CN 100368566C CN B2005101212728 A CNB2005101212728 A CN B2005101212728A CN 200510121272 A CN200510121272 A CN 200510121272A CN 100368566 C CN100368566 C CN 100368566C
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Abstract
The present invention relates to a kit for extracting aquatic animal dung sample bacteria DNA and a method thereof. In the method of the present invention, firstly, dung samples can be processed by ethanol and TritonX-100 to increase the sensitivity of dung sample bacteria to cracking liquid; then, cells can be cracked by the cracking liquid with SDS, and the cracking liquid simultaneously comprises PVP which has absorption function to PCR inhibitor; then, the environment with high concentration GuSCN and low pH can be provided, protein in a solution can be further denatured, the water-solubility is enhanced, and DNA can be bonded on a silica gel pole; finally, the DNA can be eluted from the silica gel pole in a buffer solution of low concentration or water. The purpose of obtaining the maximum diversity information and high quality and high output DNA of bacterial community in aquatic animal dung samples can be achieved by the kit and the extraction method thereof. The obtained DNA can be used for the research of molecular ecology, phyletic evolution, etc.
Description
Technical field
The present invention relates to a kind of method of from the aquatic animal fecal sample, extracting the test kit of DNA of bacteria and using this test kit extraction fecal like bacteria DNA.
Background technology
Hydrocoles intestinal bacteria group and its growth, immunity, disease have important relation, come into one's own gradually in recent years.All be based on traditional cultural method for the research that comprises bacterium in the animal intestinal in the environment in the past.This method at first will be cultivated a large amount of bacterial strains from sample separation, does biochemical identification then respectively, therefore wastes time and energy.And owing in physical environment, it is reported that the bacterium that can cultivate only accounts for less than there being 1% of bacterial species, according to cultivating intestinal bacteria group is analyzed, often can not reflect its real composition situation.The development of Protocols in Molecular Biology also makes this gate technique be applied to little ecological Studies apace, and the obvious advantage of this technology does not rely on cultivation exactly, can know most of bacterial species of existence, comprises cultivating.
Adopt molecular biology method to study its intestinal bacteria group for hydrocoles, what at first will carry out is that DNA of bacteria is extracted in the excrement sample.Obtain the different bacterium kind DNA completely that tries one's best, and genomic integrity and output, be from the excrement sample, to extract the primary goal that DNA of bacteria is used for little ecological Studies.Aquatic animal fecal sample ingredient complexity, the inhibition that has the PCR reaction, adopt conventional SDS/ phenol/chloroform extraction, gained DNA purity is very low, and still there is the PCR inhibition, and some bacteriums can not come cracking by the method for routine, cause the DNA of bacteria of gained can not reflect the true composition situation of bacterium in the original excrement sample.Therefore, need a kind of method of from the aquatic animal fecal sample, extracting DNA of bacteria that is applicable to.
Summary of the invention
The object of the invention provide a kind of can be from the aquatic animal fecal sample fast, the test kit of high efficiency extraction bacterial genomes DNA and the extracting method of bacterial genomes DNA thereof, when solving with molecule means research hydrocoles intestinal microflora many, the extraction of traditional method for extracting DNA impurity not entirely, contain defective such as PCR inhibition.
Aquatic animal fecal like bacteria DNA provided by the present invention extracts test kit, includes following reagent:
(a) reagent A: be pretreatment fluid, contain the ethanol of volume fraction 60-80% and the TritonX-100 of volume fraction 0.1-1%;
(b) reagent B: be lysate, contain pH8.0, the CTAB of PVP, the mass concentration 0.5-1% of NaCl, the mass concentration 1-2% of the Tris-Cl of 50-200mM, the EDTA of 50-200mM, 50-100mM and the SDS of mass concentration 2-4%;
(c) reagent C: be RNAase, its concentration is 5-30mg/ml;
(d) reagent D: for DNA connects liquid, contain the GuSCN (guanidinium isothiocyanate) of 4-7.0M and the Tris of 50-100mM, adjust pH to 5-6;
(e) reagent E: for the DNA washings, by pH7.5, the Tris-Cl of 10-20mM and dehydrated alcohol are by 1: the volume ratio of 3-4 mixes;
(f) reagent F: be the DNA elutriant, adopt ddH
2O or pH8.0, the Tris-Cl of 5-20mM.
The prescription of the preferred test kit of the present invention is as follows:
(a) reagent A: contain the ethanol of volume fraction 70% and the Triton X-100 of volume fraction 0.5%;
(b) reagent B: contain pH8.0, the CTAB of the NaCl of the Tris-Cl of 100mM, the EDTA of 100mM, 100mM, the PVP of mass concentration 1%, mass concentration 0.5% and the SDS of mass concentration 2%;
(c) reagent C: concentration is the RNAase of 10mg/ml;
(d) reagent D: contain the GuSCN of 6.5M and the Tris of 50mM, adjust pH to 6;
(e) reagent E: by pH7.5, the Tris-Cl of 10mM and dehydrated alcohol mix by 1: 4 volume ratio;
(f) reagent F:pH is 8.0, the Tris-Cl of 10mM.
In this test kit, destruction bacterial cell membrane and cell walls that reagent A can the part degree, and increase its susceptibility to lysate.Reagent B then provides the pH environment of a lysis, and contains the composition of cracked main component and the special thing of absorption PCR.Reagent C then is used for degradation of rna, prevents that RNA from causing interference to downstream process.Reagent D is that DNA connects liquid, and under the low pH of high density GuSCN, DNA can combine with silica gel.Reagent E is used to rinse out DNA composition in addition, and in the presence of certain density ethanol, in the flushing process, DNA can moltenly not lose.Reagent F provides less salt to stablize the pH environment, is used for eluted dna.
Cardinal principle of the present invention is: the bacterium in the environment usually more is difficult to cracking than the bacterium of simple cultivation, and after the pre-treatment of employing reagent A, cytolemma of bacterium and cell walls are subjected to destruction to a certain degree, and be responsive more for the lysis composition among the reagent B.After reagent B handled, most bacterial cells broke, and DNA overflows.The PCR inhibition adsorption component of reagent B can adsorb the inhibition in the excrement sample.Reagent C then is used for degradation of rna.Reagent D provides that a kind of high DNA can special absorption take place with pellosil under this environment from liquid, low pH environment, simultaneously SCN in the reagent D
-Can strong denatured protein, increase the water-soluble of the nonpolar group of protein, thereby DNA can be kept, and other composition wash-out at first.DNA discharges from pellosil again in the damping fluid of lower concentration or water, separates the separation and purification purpose thereby reach.
Use test kit of the present invention, may further comprise the steps in order to the method for extracting aquatic animal fecal like bacteria DNA:
(1) sample pretreatment: get excrement sample 50-200mg, add 100-400 μ l reagent A, place 10-30min on ice, 10000-12000g, centrifugal 3-6min;
(2) bacterium cracking: abandon supernatant, add reagent B 100-200 μ l in the precipitation, 2-4 μ l reagent C stirs evenly and blows and beats 2-4min with the liquid-transfering gun head.65 ℃ of water-bath 20-30min, during jolting for several times.10000-12000g, centrifugal 5-10min;
(3) DNA connects: get supernatant in the 1.5ml centrifuge tube, add 300-600 μ l reagent D, place 10-30min under the room temperature;
(4) contamination precipitation: 10000-14000g, centrifugal 5-10min gets supernatant;
(5) DNA absorption: the DNA adsorption column is placed in the centrifuge tube, above-mentioned supernatant liquor is all sucked in the DNA adsorption column, leave standstill 1-2min in room temperature.6000-9000g, centrifugal 0.5-1min;
(6) impurity eccysis: abandon filtrate, again the DNA adsorption column is placed in the centrifuge tube, add reagent E 300-600 μ l, 6000-9000g, centrifugal 0.5-1min.Abandon filtrate, again adsorption column is placed in the centrifuge tube;
(7) repeating step (5) is 1-2 time.Adsorption column is placed in the centrifuge tube blank pipe 6000-9000g, centrifugal 0.5-1min;
(8) DNA wash-out: adsorption column is placed in the new centrifuge tube, and adding is preheated to 60 ℃ DNA elutriant 60-120 μ l (deciding on amount of bacteria in the sample) in adsorption column, and water-bath is placed 1-2min for 60 ℃.6000-9000g, centrifugal 0.5-1min joins elutriant in the adsorption column again, places 1-3min, 6000-9000g, centrifugal 0.5-1min.Collect liquid in the centrifuge tube and be fecal like bacteria DNA solution ,-20 ℃ of preservations;
Advantage of the present invention and positively effect:
In the present invention, utilized the characteristics of bacterial membrane and cell wall, and the character of DNA, unique DNA of bacteria method of from the aquatic animal fecal sample, extracting created based on these characteristics and character.Compare with other conventional DNA of bacteria extracting method, the present invention has several tangible advantages and positively effect: 1. extracting method is rapid.This method and test kit can extract the bacterial genomes DNA of better quality from the excrement sample in 3 hours, other method is then more than 5 hours.2. pointed.The present invention has taken into full account the excrement sample and has had the physico-chemical property different with other sample, and at the characteristics of excrement sample, has designed the DNA extraction method that is applicable to this class sample.And other method comes from pure bacterial cultures DNA extraction mostly, is not suitable for this particular surroundings sample of excrement sample.3. leaching process does not use phenol, chloroform, has reduced the healthy injury to the experimenter.4. the DNA that obtains of institute is complete, OD
260/ OD
280More than 1.9, the output height, the bacterial species information that comprises is comprehensive.5. the present invention in some cases, can be used for other animal fecal like bacteria DNA equally and extract except that can be used for the aquatic animal fecal like bacteria DNA extraction.
Embodiment
The following example is further to explanation of the present invention, should not be used as limitation of the present invention.
Embodiment one
Make aquatic animal fecal like bacteria DNA by following prescription and extract test kit:
Reagent A: the Triton X-100 that contains the ethanol and 0.5% (V/V) of 70% (V/V).
Reagent B: the SDS of CTAB and 3% (W/V) that contains the PVP, 1% (W/V) of 50mM Tris-Cl (pH8.0), 50mM EDTA, 50mM NaCl, 2% (W/V).
Reagent C: RNAase concentration is 20mg/ml.
Reagent D: contain 6.5M GuSCN (guanidinium isothiocyanate) and 100mM Tris, adjust pH to 6.
Reagent E: mix by 1: 4 with dehydrated alcohol by 10mM Tris-Cl (pH7.5).
Reagent F:10mM Tris-Cl (pH8.0).
DNA adsorption column: silicagel column
Operate to extract aquatic animal fecal like bacteria DNA by following program:
1. sample pretreatment
Get fish excrement sample 200mg, add 400 μ l reagent A, place 30min on ice, 12000g, centrifugal 5min.
2. bacterium cracking
Abandon supernatant, add reagent B 200 μ l in the precipitation, 4 μ l reagent C stir evenly and blow and beat 2min with the liquid-transfering gun head.65 ℃ of water-bath 25min, during jolting for several times.12000g, centrifugal 10min.
3.DNA connect: get supernatant in the 1.5ml centrifuge tube, add 600 μ l reagent D, place 20min under the room temperature.
4. contamination precipitation: 12000g, centrifugal 10min gets supernatant.
5.DNA absorption: the DNA adsorption column is placed in the centrifuge tube, above-mentioned supernatant liquor is all sucked in the DNA adsorption column, mend room temperature and leave standstill 2min.6000g, centrifugal 0.5min.
6. impurity eccysis: abandon filtrate, again the DNA adsorption column is placed in the centrifuge tube, add reagent E 500 μ l, 8000g, centrifugal 0.5min.Abandon filtrate, again adsorption column is placed in the centrifuge tube.
7. repeating step is (5) 2 times.Adsorption column is placed in the centrifuge tube blank pipe 8000g, centrifugal 1min.
8.DNA wash-out: adsorption column is placed in the new centrifuge tube, and adding is preheated to 60 ℃ DNA elutriant 100 μ l in adsorption column, and water-bath is placed 2min for 60 ℃.8000g, 1min joins elutriant in the adsorption column again, places 2min, 8000g, 1min.Collect liquid in the centrifuge tube and be fecal like bacteria DNA solution ,-20 ℃ of preservations.
Embodiment two
Press following formulated all ingredients:
Reagent A: the Triton X-100 that contains the ethanol and 0.1% (V/V) of 75% (V/V).
Reagent B: contain the PVP of 200mM Tris-Cl (pH 8.0), 100mM EDTA, 100mM NaCl, 1% (W/V), the SDS of the CTAB of 0.5% (W/V) and 2% (W/V).
Reagent C: RNAase concentration is 10mg/ml.
Reagent D: contain 6.5M GuSCN (guanidinium isothiocyanate) and 50mM Tris, adjust pH to 6.
Reagent E: mix at 1: 4 with dehydrated alcohol by 10mM Tris-Cl (pH7.5).
Reagent F:ddH
2O.
DNA adsorption column: silicagel column
Operate to extract aquatic animal fecal like bacteria DNA by following program:
1. sample pretreatment
Get prawn excrement sample 100mg, add 200 μ l reagent A, place 20min on ice, 12000g, centrifugal 5min.
2. bacterium cracking
Abandon supernatant, add reagent B 200 μ l in the precipitation, 4 μ l reagent C stir evenly and blow and beat 2min with the liquid-transfering gun head.65 ℃ of water-bath 20min, during jolting for several times.12000g, centrifugal 5min.
3.DNA connect: get supernatant in the 1.5ml centrifuge tube, add 600 μ l reagent D, place 30min under the room temperature.
4. contamination precipitation: 14000g, centrifugal 10min gets supernatant.
5.DNA absorption: the DNA adsorption column is placed in the centrifuge tube, above-mentioned mixed solution is all sucked in the DNA adsorption column, leave standstill 2min in room temperature.6000g, centrifugal 0.5min.
6. impurity eccysis: abandon filtrate, again the DNA adsorption column is placed in the centrifuge tube, add reagent E 400 μ l, 8000g, centrifugal 0.5min.Abandon filtrate, again adsorption column is placed in the centrifuge tube.
7. repeating step is (5) 1 times.Adsorption column is placed in the centrifuge tube blank pipe 8000g, centrifugal 1min.
8.DNA wash-out: adsorption column is placed in the new centrifuge tube, and adding is preheated to 60 ℃ DNA elutriant 60 μ l in adsorption column, and water-bath is placed 2min for 60 ℃.8000g, centrifugal 1min joins elutriant in the adsorption column again, places 2min, 8000g, centrifugal 1min.Collect liquid in the centrifuge tube and be fecal like bacteria DNA solution ,-20 ℃ of preservations.
Claims (3)
1. extract the DNA of bacteria test kit in an aquatic animal fecal sample, it is characterized in that comprising following reagent:
(a) reagent A: be pretreatment fluid, contain the ethanol of volume fraction 60-80% and the TritonX-100 of volume fraction 0.1-1%;
(b) reagent B: be lysate, contain pH8.0, the CTAB of PVP, the mass concentration 0.5-1% of NaCl, the mass concentration 1-2% of the Tris-Cl of 50-200mM, the EDTA of 50-200mM, 50-100mM and the SDS of mass concentration 2-4%;
(c) reagent C: be RNAase, its concentration is 5-30mg/ml;
(d) reagent D: for DNA connects liquid, contain the guanidinium isothiocyanate of 4-7.0M and the Tris of 50-100mM, adjust pH to 5-6;
(e) reagent E: for the DNA washings, by pH7.5, the Tris-Cl of 10-20mM and dehydrated alcohol are by 1: the volume ratio of 3-4 mixes;
(f) reagent F: be the DNA elutriant, adopt ddH
2O or pH8.0, the Tris-Cl of 5-20mM.
2. according to extracting the DNA of bacteria test kit in the described a kind of aquatic animal fecal sample of claim 1, it is characterized in that each reagent is respectively:
(a) reagent A: contain the ethanol of volume fraction 70% and the Triton X-100 of volume fraction 0.5%;
(b) reagent B: contain pH8.0, the CTAB of the NaCl of the Tris-Cl of 100mM, the EDTA of 100mM, 100mM, the PVP of mass concentration 1%, mass concentration 0.5% and the SDS of mass concentration 2%;
(c) reagent C: concentration is the RNAase of 10mg/ml;
(d) reagent D: contain the GuSCN of 6.5M and the Tris of 50mM, adjust pH to 6;
(e) reagent E: by pH7.5, the Tris-Cl of 10mM and dehydrated alcohol mix by 1: 4 volume ratio;
(f) reagent F:pH is 8.0, the Tris-Cl of 10mM.
3. use the test kit described in the claim 1 or 2 to extract the method for aquatic animal fecal like bacteria DNA, it is characterized in that may further comprise the steps:
(1) sample pretreatment: get excrement sample 50-200mg, add 100-400 μ l reagent A, place 10-30min on ice, 10000-12000g, centrifugal 3-6min;
(2) bacterium cracking: abandon supernatant, add reagent B 100-200 μ l in the precipitation, 2-4 μ l reagent C stirs evenly and blows and beats 2-4min with the liquid-transfering gun head, 65 ℃ of water-bath 20-30min, during jolting for several times, 10000-12000g, centrifugal 5-10min;
(3) DNA connects: get supernatant in the 1.5ml centrifuge tube, add 300-600 μ l reagent D, place 10-30min under the room temperature;
(4) contamination precipitation: 12000-14000g, centrifugal 5-10min gets supernatant;
(e) DNA absorption: the DNA adsorption column is placed in the centrifuge tube, above-mentioned supernatant liquor is all sucked in the DNA adsorption column, leave standstill 1-2min, 6000-9000g, centrifugal 0.5-1min in room temperature;
(5) impurity eccysis: abandon filtrate, again the DNA adsorption column is placed in the centrifuge tube, add reagent E 300-600 μ l, 6000-9000g, centrifugal 0.5-1min abandons filtrate, again adsorption column is placed in the centrifuge tube;
(6) repeating step (5) is 1-2 time, adsorption column is placed in the centrifuge tube blank pipe 6000-9000g, centrifugal 0.5-1min;
(7) DNA wash-out: adsorption column is placed in the new centrifuge tube, in adsorption column, add and be preheated to 60 ℃ DNA elutriant 60-120 μ l, water-bath is placed 1-2min, 6000-9000g, centrifugal 0.5-1min for 60 ℃, again join elutriant in the adsorption column, place 1-3min, 6000-9000g, centrifugal 0.5-1min, collect liquid in the centrifuge tube and be fecal like bacteria DNA solution ,-20 ℃ of preservations.
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