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Journal of Microbiological Methods 75 (2008) 432–436

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Journal of Microbiological Methods


j o u r n a l h o m e p a g e : w w w. e l s ev i e r. c o m / l o c a t e / j m i c m e t h

An effective method for isolation of DNA from pig faeces


and comparison of five different methods
Jun-ni Tang, Zhi-guang Zeng, Hong-ning Wang ⁎, Tai Yang, Peng-ju Zhang, Yu-ling Li, An-yun Zhang,
Wen-qiao Fan, Yi Zhang, Xin Yang, Su-jun Zhao, Guo-bao Tian, Li-kou Zou
Bioengineering Research Center for Animal Disease Prevention and Control, School of Life Science, Sichuan University, Chengdu 610064, China

a r t i c l e i n f o a b s t r a c t

Article history: Polymerase chain reaction (PCR) detection of microorganism in faecal specimens is hampered by poor
Received 2 July 2008 recovery of DNA and by the presence of PCR inhibitors. In this paper, we describe a new modified method for
Received in revised form 20 July 2008 extracting PCR-quality microbial community DNA from pig faecal samples, which combines the pretreatment
Accepted 20 July 2008
with polyformaldehyde, and subsequent DNA lysis in the presence of CTAB, salt, PVP, and β-mercaptoethanol,
Available online 23 July 2008
followed by isolation of nucleic acids using chloroform (no phenol) based protocol. The method resulted in a
Keywords:
1.3- to 11-fold increase in DNA yield when compared to four other widely used methods. Genomic DNA
Pig faeces extracted from all five methods was assessed by both agarose gel electrophoresis and polymerase chain
DNA extraction reaction for amplification of 16S rDNA specific fragments. The results showed that the improved method
β-mercaptoethanol represented a reproducible, simple, and rapid technique for routine DNA extraction from faecal specimens
Comparison and was notably better than using the QIAamp® DNA Stool Mini Kit.
PCR © 2008 Elsevier B.V. All rights reserved.

1. Introduction “inhibitors” which can reduce PCR sensitivity by 1000-fold (Ward and
Wang, 2001; Harris and Barletta, 2001). The other problems are often
The intestinal tract of animals harbors a large and complex community encountered in terms of relatively low DNA yields (Yu and Morrison,
of microbes which possess of at least 400–500 different microbial species, 2004). Therefore, extracting DNA from organically complex samples is
constituting a complex ecosystem (Yang et al., 2008). Faecal samples are technically challenging.
increasingly used as sources of DNA for genetic and ecological research, Generally, methods for extracting DNA from faecal samples
which contain intestinal bacteria that may provide useful information previously based on culture enrichment, or extraction of nucleic
concerning gastrointestinal tract health for animals (Zhang et al., 2006). In acids using phenol, ion-exchange chromatography, silica, or combina-
recent years, molecular methods such as PCR-based techniques have also tions (Thornton and Passion, 2004). In the present feasibility study, we
been used to analyze dominant bacterial groups of the animal gut developed a new effective, simple and combined protocol that could
microbiota (Thiel and Blaut, 2005). These studies have generally not relied be used to isolate PCR-quality DNA from pig faeces adaptable to detect
on microbial cultivation, but have been carried out using the specific 16S rDNA fragments and other molecular techniques.
genome DNA of bacterial groups or species of interest from faecal samples.
Such DNA can reveal the complexity of microbial communities living in 2. Materials and methods
these environments through PCR amplification of the 16S ribosomal RNA
(16S rRNA) gene sequence and other molecular phylogenetic techniques 2.1. Collection and preparation of faecal samples
(Barton et al., 2006). To facilitate the study of intestinal microbial com-
munities, several DNA extraction methods have been reported for use Fresh faecal samples were obtained from healthy multiparous
with faecal samples (Ward and Wang, 2001; Subrungruang et al., 2004; sows of Rongchang pig. The samples were collected in sterile bags and
Thornton and Passen, 2004; Nantavisai et al., 2007). Almost all of them are kept on ice, immediately taken to the laboratory and subsequently
difficult and time consuming, dealing with high amount of toxic materials frozen at −20 °C or −70 °C.
like phenol. Their results also vary due to sample collection method and
further purification treatment (Abbaszadegan et al., 2007). Moreover, 2.2. Pretreatment of samples
studies have shown that organic samples, such as faeces, contain
Two different ways of the pretreatment were conducted. The effect
⁎ Corresponding author. Tel./fax: +86 28 8547 1599. of the pretreatment methods was evaluated by using method (M) (see
E-mail address: Whongning@163.com (H. Wang). Section 2.4) with the same subsamples.

0167-7012/$ – see front matter © 2008 Elsevier B.V. All rights reserved.
doi:10.1016/j.mimet.2008.07.014
J. Tang et al. / Journal of Microbiological Methods 75 (2008) 432–436 433

Fig. 1. Average amounts of DNA yield (A) and 1.0% agarose gel image displaying genomic DNA extracted from the pig faecal samples by using various methods run with λ DNA cut with
HindIII (DNA marker) (B). A: Labels are of the form X–Y, where X is the DNA extraction method and Y is the extracted average total DNA yield [μg/g (wet weight)]. DNA was measured
by using a SmartSpec™ plus (Bio-Rad, USA). B: Lanes 1–3: M1; Lanes 4–6: M2; Lanes 7–9: M3 (kit); Lanes 10–12: M4; Lanes 13–15: M (new method).

2.2.1. Treatment A Method (M) was a new method for extracting DNA from pig faecal
The frozen samples (1.6 g) were transferred to a sterile tube (50 ml) samples in this study.
adding 30 ml of ice-cold 0.05 M phosphate-buffered saline (PBS) The detailed extraction protocol was as follows:
(150 mM NaCl, 10 mM Na2HPO4, 20 mM NaH2PO4, pH 7.4), vortexed
1) Transfer each aliquots of 500 μl pretreatment sample into a new
fully. Samples were centrifuged at 500 ×g for 4 min, and the su-
2.0 ml reaction tube;
pernatants were transferred to new 50-ml sterile tube. Pellets were
2) Harvest cells by centrifugation at 16,000 ×g for 10 min;
resuspended in 30 ml PBS buffer, mixed thoroughly and centrifuged at
3) Add 1 ml of hot CTAB extraction buffer (pre-heated at 65 °C water
500 ×g for 4 min. Repeat the procedure two times. All the supernatants
bath) [100 mM Tris–HCl (pH 8.0), 2.0 M NaCl, 20 mM EDTA, 2%
were centrifuged at 9000 ×g for 5 min. The cell pellet was harvested and
CTAB], vortex fully;
resuspended in the mixture of 4 ml of TE buffer (pH 8.0), and stored at
4) Add 1% PVP and vortex fully;
−20 °C for use.
5) Then add 2% β-mercaptoethanol into each tube and vortex fully;
6) Incubate the tubes for 1 h (or 2 h) in a 65 °C water bath with
2.2.2. Treatment B
occasional shaking (~15 min);
The pretreatment method was described by Thiel and Blaut (2005)
7) Centrifuge at 16,000 ×g for 10 min;
previously with some modification. Briefly, the frozen samples (1.6 g)
8) Transfer the supernatant into a new 2.0 ml reaction tube;
were transferred to a sterile tube (50 ml), diluted in 10 ml of ice-cold
9) Add 1 vol of chloroform: isoamyl alcohol (24:1, v/v);
0.05 M PBS buffer (150 mM NaCl, 10 mM Na2HPO4, 20 mM NaH2PO4,
10) Centrifuge at 16,000 ×g for 10 min;
pH 7.4) and homogenized by the addition of ten sterile glass beads
11) Transfer the supernatant into a new 2.0 ml reaction tube;
(3 mm in diameter), vortexed fully for 3 min. Subsequently, the sam-
12) Add 1 vol, equal to the transferred supernatant, of chloroform;
ples were centrifuged at 400 ×g for 2 min to remove glass beads and
13) Centrifuge for 10 min at 16,000 ×g and 4 °C;
larger particles. The larger particles were resuspended in 3 ml of ice-
14) Transfer the supernatant into a new 2.0 ml reaction tube;
cold PBS buffer, mixed thoroughly and centrifuged at 400 ×g for 2 min
15) Add 2 vol of ice-cold absolute ethanol;
again. All the suspension was transferred to a new 50-ml sterile tube
16) Incubate at −20 °C for 30 min;
and mixed with 3 vol of 4% polyformaldehyde, incubated on ice for 1 h.
17) Centrifuge for 10 min at 16,000 ×g;
Following fixation, the cell suspension was centrifuged at 8000 ×g
18) Remove the supernatant completely using a pipette;
for 3 min and the cell pellet was resuspended in 4 ml PBS buffer,
19) Wash DNA pellet with ice-cold 70% ethanol;
mixed with 4 ml absolute ethanol and stored at −20 °C for 20 min.
20) Air dried;
Subsequently, the cell pellet was harvested by centrifugation at
21) Resuspend DNA pellet in 50 μl of sterile ultrafiltered water with
8000 ×g for 3 min and resuspended in 4 ml of TE buffer (pH 8.0) for
RNase (20 μg/ml);
use.
22) Incubate the tube at 37 °C for 30 min;
2.3. Optimization of the buffer components 23) Store DNA at −20 °C before use.

Optimization of β-mercaptoethanol, PVP, and NaCl concentra- Method 1 (M1) was the chemical-enzymatic method of Niemi et al.
tions was carried out in this assay. The optimized concentrations of (2001). Each aliquot of 500 μl pretreatment sample was transferred
β-mercaptoethanol (0%, 1%, 2%, 3%, 4%), and PVP (0.2%, 0.5%, 1%, 2%), into a new 2.0-ml tube. Then cells were disrupted with 25 μl lysozyme
and NaCl (1.4 M, and 2.0 M) in the lysis buffer were tested to extract (20 mg/ml) in 37 °C for 30 min. Subsequently, the tube was added with
DNA by using total DNA yield and gel analysis. 50 μl 10% sodium dodecyl sulfate (SDS), and 15 μl proteinase K (10 mg/
ml) in slightly alkaline TE buffer incubated in a 55 °C water bath for
2.4. DNA isolation methods 2 h. DNA was extracted with phenol:chloroform:isoamyl alcohol
(25:24:1, v/v/v) and precipitated with isopropanol. Finally, the DNA
Genomic DNA was extracted from 0.2 g (wet weight) pig faeces for pellet was suspended in 50 μl of sterile ultrafiltered water.
each tube by using five different methods with all extraction Method 2 (M2) was described by Tang et al. (2006) previously.
techniques being conducted on a subsample of the same homogenized Briefly, the pellet was harvested and suspended in 1 ml of ice-cold 70%
initial sample. M, M1, and M2 were based on the pretreatment of ethanol on ice for 20 min. The cells were collected and resuspended in
samples conducted with treatment B (described in Section 2.2.2). M3 the mixture of 467 μl of Tris–EDTA (TE) (10-mM Tris–Cl, 1-mM EDTA,
(kit), and M4 applied the faecal sample directly. All the extractions pH 8.0), 12 μl of 20-mg/ml lysozyme and 1 μl of 1-mg/ml ribonuclease
were performed in triplicates. (RNase), and incubated on ice for an additional 1 h. The tubes were
434 J. Tang et al. / Journal of Microbiological Methods 75 (2008) 432–436

2.5. Polymerase chain reaction (PCR)

Following the DNA extraction, amplifications by PCR were performed


from each method with 16S rDNA specific primers [forward primer 27F
(5′-AGAGTTTGA TCC TGG CTC AG-3′) and the universal reverse primer
1492R (5′-GGCTTACCTTGTTACGACTT-3′)] (Hayashi et al., 2002). Reac-
tions were carried out in a volume of 20 μl with a 10× PCR buffer, 2 μl;
2.0 mM MgCl2; 200 μM of each nucleotides dATP, dTTP, dGTP and dCTP; 1
1 U of Taq polymerase (TIANGEN), 1 μl of purified sample DNA and with
primers 0.5 μM. The PCR was carried out for 30 cycles at 95 °C for 30 s,
59 °C for 30 s, and 72 °C for 1 min 30 s, with a first cycle of 5 min at 95 °C
and a final cycle of 8 min at 72 °C. Amplifications were performed for a
minimum of three times for each sample, and a negative control (water)
was carried out.

2.6. Statistical analysis

Statistical analyses were performed by using GraphPad PRISM®


software.

3. Results

3.1. Comparison of pretreatment

Two different pretreatment methods were compared. Sample pre-


paration with 4% polyformaldehyde could improve the DNA yields
effectively. The average DNA yield ratio of treatment B and treatment
A was close to 1.6-fold followed by using method (M).
Fig. 2. Average amounts of DNA yield extracted from different concentrations of β-
mercaptoethanol (0%, 1%, 2%, 3%, and 4%) (A) and agarose gel analysis of the extracted
3.2. DNA yield and purity
DNA run with λ DNA cut with HindIII (DNA marker) (B).

Total amounts of DNA yield extracted with five extraction methods


then incubated in a 68 °C water bath, following the addition of 53 μl of varied considerably, with the new method (M) from which the highest
10% sodium dodecyl sulfate (SDS), 87 μl of 5-M NaCl and 69 μl of yields could be obtained being significantly different from others. The
cetyltrimethylammonium bromide (CTAB)/NaCl solution (1% CTAB,
0.73-M NaCl). Subsequently, DNA was extracted with phenol:chlo-
roform:isoamyl alcohol (25:24:1, v/v/v) and precipitated with ethanol.
The DNA pellet was suspended finally in 50 μl of sterile ultrafiltered
water and stored at −20 °C before use.
Method 3 (M3) was conducted by using QIAamp® DNA Stool Mini Kit
(Purchased from QIAGEN) according to the manufacturer's instructions.
Method 4 (M4) was described by Rousselon et al. (2004) previously.
Briefly, faeces (0.2 g/sample) were suspended in 100 μl of 4 M guanidine
thiocyanate −0.1 M Tris (pH 7.5), 30 μl of 10% N-lauroyl sarcosine, and
500 μl 0.1 M phosphate buffer (pH 7.4). Then the tube was incubated at
70 °C for 1 h. 500 μl of 0.1-mm-diameter silica beads (Sigma), previously
sterilized by autoclaving, was added and the tube was shaken for 10 min.
PVP (15 mg) was added to the tube, which was vortexed and centrifuged
for 3 min at 12,000 ×g. After recovery of the supernatant into a 2.0-ml
tube, the pellet was washed with 500 μl of lysis buffer [50 mM Tris (pH
8.0), 20 mM EDTA (pH 8.0), 100 mM NaCl, 1% PVP] then centrifuged for
3 min at 12,000 ×g, and the supernatant was added to the first
supernatant in the same 2.0-ml tube. The washing step was repeated
three times. The pooled supernatant (about 2 ml) was briefly centrifuged
to remove particles and then split into two 2.0-ml tubes. Nucleic acids
were precipitated by the addition of 1 vol of isopropanol for 10 min at
room temperature and centrifuged for 15 min at 20,000 ×g. Pellets were
resuspended and pooled in 100 μl of sterile ultrafiltered water with
RNase (20 μg/ml), and incubated at 37 °C for 10 min.
All extractions were performed in triplicates and eluted in 50 μl of
sterile ultrafiltered water. The purity of DNA was assessed spectrophoto-
metrically by calculating A260/A280 ratios and the yield of DNA was calcu-
lated from the A260 value by using a SmartSpec™ plus (Bio-Rad, USA). The
quality of DNA extracted from each method was evaluated by running 5 μl Fig. 3. Average amounts of DNA yield extracted from different concentrations of PVP
of purified DNA on a 1.0% agarose gel using λ DNA cut with HindIII as DNA (0.2%, 0.5%, 1%, and 2%) (A) and agarose gel analysis of the extracted DNA run with λ
marker (TIANGEN). The presence of PCR inhibitors was analyzed by PCR. DNA cut with HindIII (DNA marker) (B).
J. Tang et al. / Journal of Microbiological Methods 75 (2008) 432–436 435

Fig. 4. PCR amplification of 16S rDNA from extracted DNA of different methods. Gel electrophoresis showing PCR products (1560-bp) following amplification of 1 μl of each DNA
template per reaction tube from different methods. Each method was examined at three separate occasions. Aliquots (8 μl) of PCR products were loaded onto 1% agarose gel, subjected
to electrophoresis for 40 min at 100 V in 1× TAE buffer and visualized with UV illumination. Lanes 1–3: PCR products from M1; Lanes 4–6: PCR from M2; Lanes 7–9: PCR products from
M3 (kit); Lanes 10–12: PCR products from M4; Lanes 13–15: PCR products from M; Lane C: negative control.

average yields for M, M1, M2, M3 and M4 were 163.5±7.34; 124.4±15.33; observed from faecal samples in all five methods (Figs. 1B and 4). In the
82.4±11.03; 14.3±1.13; and 69.9±5.15 μg/g (wet weight) (Fig. 1A). Method study, repetition of testing DNA extract with method (M) provided
(M) accounts for the top 1, resulting in a 1.3- to 11-fold increase in average reproducible results which confirmed the superiority of this method,
DNA yield compared to M1, M2, M3 and M4. The M3 (kit) method with consistently higher levels of DNA yield and PCR product from each
consistently gave lower yields than the other methods. The A260/A280 faecal sample.
ratio, indicating contamination by proteins, is about 2.0 for pure DNA
and should exceed 1.7 for nearly pure nucleic acid extractions from 4. Discussion
environmental samples. In our study, the A260/A280 ratios for M, M1, M2,
M3, and M4 were 1.82±0.014; 1.80±0.030; 1.67±0.010; 1.84±0.010; and The isolation of DNA is one of the most commonly used procedures
1.77±0.017 respectively. With respect to DNA yield and purity in this in genetics, molecular biology and biochemistry. To date, numerous
study, method (M) was the best DNA extraction method for pig faeces. methods have already been devised to isolate genomic DNA from
various biomaterials, depending on the sources used (Ki et al., 2007).
3.3. Evaluation of buffer components and incubation time Faeces are a very complex mixture of biological and non-biological
elements that can significantly inhibit PCR reaction (Iacovacci et al.,
We prepared a series of extraction buffers and concentration to 2003). Very few methods for preparing DNA template from pig faecal
estimate the influence of various reagents in the buffer on successful samples were developed. In this study, we developed a simple, effective,
DNA extraction. Fig. 2 shows examples of the extracted DNA prepared and inexpensive method for DNA extraction from pig faeces by com-
by using different β-mercaptoethanol buffers (0%, 1%, 2%, 3%, 4%). The bining some important factors of existing protocols (Lee et al., 2003;
DNA agarose gel suggested that the presence of β-mercaptoethanol in Rousselon et al., 2004; Rouhibakhsh et al., 2008). Our procedure was
the extraction buffer was essential, and its omission resulted in un- tested by repeating the extraction, which has shown good stability and
successful DNA extraction with our procedure (Fig. 2B). Use of 1%, 2%, repetitiveness. This method allowed us to obtain the high quality mole-
and 3% β-mercaptoethanol led to more effective extraction than did cular weight DNA template from pig faeces samples. Our procedure
use of 4% (Fig. 2A). Fig. 3 shows examples of the extracted DNA pre- contains four major steps: (1) treating the faecal samples by 4% poly-
pared by using different PVP buffers (0.2%, 0.5%, 1%, 2%). Use of different formaldehyde; (2) adding 1% PVP; (3) adding 2% β-mercaptoethanol
PVP buffers all led to effective extraction (Fig. 3B). However, use of 1% in CTAB lysis buffer; and (4) extracting DNA by using chloroform (no
PVP has a higher DNA yield than did use of 0.2%, 0.5%, and 2% (Fig. 3A). phenol). All four steps were proved to be essential for obtaining DNA of
The addition of NaCl was likely to have some advantage in the ex- good quality and relatively large quantity. Our procedure was developed
traction buffer. However, 1.4 M and 2.0 M NaCl have no statistically primarily for isolation of DNA from freshly collected pig faecal sample or
significant difference. Incubation time of 1 h or 2 h in a 65 °C water bath sample stored at −70 °C for up to a few days. Later tests proved that with
after adding CTAB lysis buffer was also found to have no significant this method DNA could also be isolated from the sample stored at −20 °C
difference to the yield of DNA. Therefore, the subsequent extraction of for up to 1 or 2 months. Thus, the new combined method can be po-
DNA applied 1 h incubation in 65 °C water bath to shorten the time. tentially useful for DNA extraction from all faecal samples. This might
have great potential for the study of microbial communities concerning
3.4. Evaluation of DNA extraction methods gastrointestinal tract health for all animals.
Every type of sample, because of its own nature, requires optimiza-
Five different DNA extraction methods were examined to ascertain tion of the extraction methods (Roose-Amsaleg et al., 2001). The faecal
their relative effectiveness, Some of which could extract total DNA sample contains variable concentrations of inhibitory substances such
successfully from pig faeces, as demonstrated by agarose gel detection as biliary salts, proteins, polysaccharide complexes, bilirubins and phe-
and successful 16S rDNA-specific PCR (Figs. 1B and 4). Of the five nolic compounds, depending on diet, intestinal flora and health con-
methods, M was the most effective method for the extraction of ditions of the host (Gonçalves et al., 2008). In designing this protocol, we
DNA prepared from the pretreatment samples. M1, M2, and M4 were investigated several factors influencing the release of nucleic acid from
also effective in extracting DNA from faeces. M3 was a commercial kit the sample. CTAB is included in extraction buffers for DNA as reagents
(QIAamp®) method. The DNA extracted by the kit method could not be for protein denaturation. β-mercaptoethanol is a strong reducing rea-
detected on agarose gel. However, successful PCR outcome could be gent and is included in DNA extraction buffers to prevent oxidation of
436 J. Tang et al. / Journal of Microbiological Methods 75 (2008) 432–436

polyphenols present in the faeces extract. Introduction of PVP that References


assures efficient removal of inhibitors that may coprecipitate with DNA
Abbaszadegan, M.R., Velayati, A., Tavasoli, A., Dadkhah, E., 2007. Rapid DNA extraction
during extraction after treatment with a lysis solution, improved the
protocol from stool, suitable for molecular genetic diagnosis of colon cancer. Iran.
final amplification. In this study, the concentration of the important Biomed. J. 11 (3), 203–208.
factors (β-mercaptoethanol, and PVP) was optimized. The concentration Barton, H.A., Taylor, N.M., Lubbers, B.R., Pemberton, A.C., 2006. DNA extraction from
low-biomass carbonate rock: an improved method with reduced contamination
of β-mercaptoethanol was initially presumed 0–10% and the concentra-
and the low-biomass contaminant database. J. Microbiol. Methods 66 (1), 21–31.
tion of PVP was 0–4% in our preliminary studies. The ultimate range was Foltan, P., Sheppard, S., Konvicka, M., Symondson, W.O.C., 2005. The significance of
reduced gradually according to extraction yields (for β-mercaptoethanol facultative scavenging in generalist predator nutrition: detecting decayed prey in
0–4%; for PVP 0–2%). The adding optimum of β-mercaptoethanol and the guts of predators using PCR. Mol. Ecol. 14 (3), 4147–4158.
Gonçalves, E.M., Araújo, R.S., Orban, M., Matté, G.R., Matté, M.H., Corbett, C.E., 2008.
PVP was further confirmed by total DNA yield and gel analysis. This Protocol for DNA extraction of Cryptosporidium spp. oocysts in fecal samples. Rev
optimized technique would be suitable for other complex matrices, at Inst Med Trop Sao Paulo. ahead of print.
least faeces from other domestic species. The procedure is quite simple Harris, N.B., Barletta, R.G., 2001. Mycobacterium avium subsp. paratuberculosis in
veterinary medicine. Clin. Microbiol. Rev. 14 (3), 489–512.
and rapid, and does not require expensive reagents (proteinase K and Hayashi, H., Sakamoto, M., Benno, Y., 2002. Phylogenetic analysis of the human gut
lysozyme) and hazardous chemical reagents (phenol). Therefore, an easy microbiota using 16S rDNA clone libraries and strictly anaerobic culture-based
and rapid method was optimized for isolating the pig faecal DNA with methods. Microbiol. Immunol. 46 (8), 535–548.
Herrera, A., Cockell, C.S., 2007. Exploring microbial diversity in volcanic environments: a
reduced PCR inhibitors. review of methods in DNA extraction. J. Microbiol. Methods 70 (1), 1–12.
Moreover, DNA yields were found to vary depending on the Iacovacci, G., Serafini, M., Berti, A., Lago, G., 2003. STR typing from human faeces: a
method used. In this study, we compared the efficiency of our method modified DNA extraction method. Int. Congr. Ser. 1239 (19), 917–920.
Ki, J.S., Chang, K.B., Roh, H.J., Lee, B.Y., Yoon, J.Y., Jang, G.Y., 2007. Direct DNA isolation
with other procedures published previously and QIAamp® DNA Stool
from solid biological sources without pretreatments with proteinase-K and/or
Mini Kit. The methods developed to date for extracting microbial DNA homogenization through automated DNA extraction. J. Biosci. Bioeng. 103 (3),
are of two types: cell extraction methods and direct lysis methods 242–246.
Lee, Y.K., Kim, H.W., Liu, C.L., Lee, H.K., 2003. A simple method for DNA extraction from
(Roose-Amsaleg et al., 2001; Herrera et al., 2007). Cell extraction de-
marine bacteria that produce extracellular materials. J. Microbiol. Methods 52,
pends on the isolation of microbial cells from their environmental 245–250.
matrix, prior to lysis to release DNA. These methods use successive Nantavisai, K., Mungthin, M., Tan-ariya, P., Rangsin, R., Naaglor, T., Leelayoova, S., 2007.
cycles of blending and differential centrifugation to recover the intact Evaluation of the sensitivities of DNA extraction and PCR methods for detection of
Giardia duodenalis in stool specimens. J. Clin. Microbiol. 45 (2), 581–583.
microbial cells. Direct lysis method does not require cell isolation, Nechvatal, J.M., Ram, J.L., Basson, M.D., Namprachan, P., Niec, S.R., Badsha, K.Z., Matherly,
including direct cell lysis in the sample after which DNA is extracted. L.H., Majumdar, A.P.N., Kato-Ikuko, 2008. Fecal collection, ambient preservation,
In the study, our improved method (M), M1, and M2 applied the first and DNA extraction for PCR amplification of bacterial and human markers from
human feces. J. Microbiol. Methods 72, 124–132.
approach, M3 (kit) and M4 applied the second approach. The first Niemi, R.M., Heikkilä, M.P., Lahti, K., Kalso, S., Niemelä, S.I., 2001. Comparison of
approach was slightly superior to the direct approach in terms of DNA methods for determining the numbers and species distribution of coliform bacteria
yield and PCR amplification in our research. QIAamp® DNA Stool Mini in well water samples. J. Appl. Microbiol. 90 (6), 850–858.
Roose-Amsaleg, C.L., Garnier-Sillam, E., Harry, M., 2001. Extraction and purification of
Kit was used as a control for extraction and purity of DNA. Though this microbial DNA from soil and sediment samples. Appl. Soil Ecology 18 (1), 47–60.
kit has been proved to be effective at overcoming problems of co- Rousselon, N., Delgenès, J.P., Godon, J.J., 2004. A new real time PCR (TaqMan PCR) system
extracted PCR inhibitors from faeces samples (Foltan, et al., 2005; for detection of the16S rDNA gene associated with fecal bacteria. J. Microbiol.
Methods 59 (1), 15–22.
Nechvatal et al., 2008), and the PCR amplification bands of 16S rDNA
Rouhibakhsh, A., Priya, J., Periasamy, M., Haq, Q.M.I., Malathi, V.G., 2008. An improved
was also successfully obtained in our study, a potential problem with DNA isolation method and PCR protocol for efficient detection of multicomponents
this kit was the low efficiency of DNA yield. of begomovirus in legumes. J. Virol. Methods 147, 37–42.
Subrungruang, I., Mungthin, M., Chavalitshewinkoon-Petmitr, P., Rangsin, R., Naaglor, T.,
In conclusion, the goal of the study was to simplify processing of
Leelayoova, S., 2004. Evaluation of DNA extraction and PCR methods for detection of
faecal specimens and develop a protocol that was amenable to large- Enterocytozoon bienuesi in stool specimens. J. Clin. Microbiol. 42 (8), 3490–3494.
scale manipulation for PCR analyses with efficient extraction of highly Tang, J.N., Shi, X.M., Shi, C.L., Chen, H.C., 2006. Characterization of a duplex PCR assay for
pure DNA. Depending on time, costs, and reproducibility, our method the detection of enterotoxigenic strains of Staphylococcus aureus. J. Rapid Methods
Autom. Microbiol. 14 (3), 201–217.
was demonstrated to be an effective DNA extraction with consistently Thiel, R., Blaut, M., 2005. An improved method for the automated enumeration of
higher levels of DNA yield and relatively inhibitor free from pig faecal fluorescently labelled bacteria in human faeces. J. Microbiol. Methods 61 (3),
specimens. Therefore, our new extraction method could provide a 369–379.
Thornton, C.G., Passen, S., 2004. Inhibition of PCR amplification by phytic acid, and
reference source for other researchers to extract DNA from faecal treatment of bovine fecal specimens with phytase to reduce inhibition. J. Microbiol.
samples in a simple format. Methods 59 (1), 43–52.
Ward, L.A., Wang, Y., 2001. Rapid methods to isolate Cryptosporidium DNA from frozen
feces for PCR. Diagn. Microbiol. Infect. Dis. 41 (1–2), 37–42.
Acknowledgements Yang, J.L., Wang, M.S., Cheng, A.C., Pan, K.C., Li, C.F., Deng, S.X., 2008. A simple and rapid
method for extracting bacterial DNA from intestinal microflora for ERIC-PCR
This research was supported by the National “11th Five-Year Plan” detection. World J. Gastroenterol. 14 (18), 2872–2876.
Yu, Z., Morrison, M., 2004. Improved extraction of PCR-quality community DNA from
Science and Technology Supporting Programs (2007BAD51B05;
digesta and fecal samples. Biotechniques 36 (5), 808–812.
2006BAD14B05-5; 2006BAK02A19) and China Postdoctoral Science Zhang, B.W., Li, M., Ma, L.C., Wei, F.W., 2006. A widely applicable protocol for DNA
Foundation funded project. The authors wish to thank Fu Li-zhi, Zhai isolation from fecal samples. Biochem. Genet. 44 (11–12), 503–512.
Shao-qin, and Fu Wen-gui from Chongqing Academy of Animal Sciences
for their assistance in providing the Rongchang pigs.

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