High-throughput DNA purification from stool

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Nucleic acid purification

Product overview

With the refinement and broader application of next-generation sequencing technologies, researchers in the fields of medical, veterinary, and nutritional sciences have increasingly turned to genomics for meaningful answers regarding the role of gut microbiota in health and disease. While silica-membrane purification technology is well established as the method of choice for isolating high-quality DNA and efficiently removing inhibitors from animal and human fecal samples, this approach can prove challenging in a high-throughput context where columns may be subject to clogging during vacuum processing. An additional challenge involves the ever-present danger of contamination with humic acids, which can be a detriment to downstream analysis.

The NucleoSpin 96 DNA Stool kit has been designed to help researchers overcome these challenges by providing a reliable, automation-friendly method for DNA isolation—combining a robust filtration step to greatly reduce the likelihood of column-clogging with an efficient DNA extraction procedure based on silica-membrane technology. Provided below are application data demonstrating automated processing of stool samples on the epMotion 5075v platform. Processing of 96 samples using this approach takes ~100 minutes to complete.

At-a-glance Manual vs. automated processing DNA quality Removal of inhibitors Downstream performance

At-a-glance

Technology	Silica-membrane technology combined with MN Bead Tubes Type A
Starting material	100–200 mg of human stool* (fresh or frozen)
Format	96-well plate
Handling	Vacuum (manual or automated)
Fragment size	50 bp–approximately 50 kb
Typical yield	3–15 µg (varies by sample and disruption device)
A₂₆₀/A₂₈₀	1.6–1.8
Elution volume	100–200 µl
Preparation time	90 min/96 preps (automated processing)
Binding capacity	50 µg

*For animal stool specimens and challenging samples with high amounts of lipids, polysaccharides, or proteins, it is recommended to first attempt processing of smaller inputs (e.g., 50–100 mg of sample material).

Manual vs. automated processing

Comparable performance with manual or automated processing using NucleoSpin 96 DNA Stool.

DNA quality

High-quality DNA from rat stool samples processed using NucleoSpin 96 DNA Stool.

Removal of inhibitors

Efficient removal of PCR inhibitors with NucleoSpin 96 DNA Stool.

Downstream performance

Consistently excellent PCR performance with NucleoSpin 96 DNA Stool.

Related products

Cat. #	Product	Size	Price
740473.1	NucleoSpin® 96 DNA Stool	1 x 96 Preps	USD $465.00
The NucleoSpin 96 DNA Stool kit provides a comprehensive solution for high-throughput DNA isolation from fresh or frozen stool samples in a 96-well format using silica membrane technology. The kit is designed for processing of 100–200 mg of sample material per prep and employs an optimized lysis chemistry in combination with mechanical disruption (MN Bead Tubes Type A) to enable efficient sample homogenization without enzymatic digestion. Sample processing can be performed manually under vacuum or automated on common liquid handling platforms. The kit enables processing of 96 samples in ~90 minutes using automated processing and typically yields 3–15 µg of DNA per prep. Purified DNA is ready for a variety of downstream applications, including analysis by qPCR or NGS. Cat. # 740473.1 includes sufficient quantities of reagents and materials for processing of 96 samples. Notice to purchaser Our products are to be used for Research Use Only. They may not be used for any other purpose, including, but not limited to, use in humans, therapeutic or diagnostic use, or commercial use of any kind. Our products may not be transferred to third parties, resold, modified for resale, or used to manufacture commercial products or to provide a service to third parties without our prior written approval. Documents Image Data Back 740473.1: NucleoSpin 96 DNA Stool Back High-quality DNA from rat stool samples processed using NucleoSpin 96 DNA Stool High-quality DNA from rat stool samples processed using NucleoSpin 96 DNA Stool. Eight different rat stool samples were processed on an epMotion 5075v using NucleoSpin 96 DNA Stool. Analysis of purity and yield of DNA isolated from each sample indicated the reliably high quality of the extracted DNA. Back Comparable performance with manual or automated processing using NucleoSpin 96 DNA Stool Comparable performance with manual or automated processing using NucleoSpin 96 DNA Stool. Six different stool samples were processed either manually or on an epMotion 5075v using the NucleoSpin 96 DNA Stool kit. Resulting DNA yields (blue and gray bars) and purity (orange dots) were comparable between manual and automated workflows for each sample. Back Efficient removal of PCR inhibitors with NucleoSpin 96 DNA Stool Efficient removal of PCR inhibitors with NucleoSpin 96 DNA Stool. DNA was purified from a human stool sample and sequentially diluted 1:4 up to a 4096-fold dilution. Diluted DNA and a reference standard were analyzed by qPCR using E. coli-specific primers and compared on a logarithmic plot. The slope of the resulting regression curve (-3.4106) indicated excellent qPCR performance without inhibition across the dilution series. Back Consistently excellent PCR performance with NucleoSpin 96 DNA Stool Consistently excellent PCR performance with NucleoSpin 96 DNA Stool. Six different human stool samples were processed either manually or on an epMotion 5075v using the NucleoSpin 96 DNA Stool kit in quadruplicates. 2.5-μl inputs from each eluate were used in a 25-μl endpoint PCR reaction designed to amplify a 1.5-kb portion of the bacterial 16S rRNA gene, and 3-μl outputs from each reaction were analyzed on a 1% agarose gel. Samples were successfully amplified in each case, demonstrating the robust downstream performance of DNA isolated using the kit.
740473.4	NucleoSpin® 96 DNA Stool	4 x 96 Preps	USD $1625.00
The NucleoSpin 96 DNA Stool kit provides a comprehensive solution for high-throughput DNA isolation from fresh or frozen stool samples in a 96-well format using silica membrane technology. The kit is designed for processing of 100–200 mg of sample material per prep and employs an optimized lysis chemistry in combination with mechanical disruption (MN Bead Tubes Type A) to enable efficient sample homogenization without enzymatic digestion. Sample processing can be performed manually under vacuum or automated on common liquid handling platforms. The kit enables processing of 96 samples in ~90 minutes using automated processing and typically yields 3–15 µg of DNA per prep. Purified DNA is ready for a variety of downstream applications, including analysis by qPCR or NGS. Cat. # 740473.4 includes sufficient quantities of reagents and materials for processing of 4 x 96 samples. Notice to purchaser Our products are to be used for Research Use Only. They may not be used for any other purpose, including, but not limited to, use in humans, therapeutic or diagnostic use, or commercial use of any kind. Our products may not be transferred to third parties, resold, modified for resale, or used to manufacture commercial products or to provide a service to third parties without our prior written approval. Documents Image Data Back 740473.4: NucleoSpin 96 DNA Stool Back High-quality DNA from rat stool samples processed using NucleoSpin 96 DNA Stool High-quality DNA from rat stool samples processed using NucleoSpin 96 DNA Stool. Eight different rat stool samples were processed on an epMotion 5075v using NucleoSpin 96 DNA Stool. Analysis of purity and yield of DNA isolated from each sample indicated the reliably high quality of the extracted DNA. Back Comparable performance with manual or automated processing using NucleoSpin 96 DNA Stool Comparable performance with manual or automated processing using NucleoSpin 96 DNA Stool. Six different stool samples were processed either manually or on an epMotion 5075v using the NucleoSpin 96 DNA Stool kit. Resulting DNA yields (blue and gray bars) and purity (orange dots) were comparable between manual and automated workflows for each sample. Back Efficient removal of PCR inhibitors with NucleoSpin 96 DNA Stool Efficient removal of PCR inhibitors with NucleoSpin 96 DNA Stool. DNA was purified from a human stool sample and sequentially diluted 1:4 up to a 4096-fold dilution. Diluted DNA and a reference standard were analyzed by qPCR using E. coli-specific primers and compared on a logarithmic plot. The slope of the resulting regression curve (-3.4106) indicated excellent qPCR performance without inhibition across the dilution series. Back Consistently excellent PCR performance with NucleoSpin 96 DNA Stool Consistently excellent PCR performance with NucleoSpin 96 DNA Stool. Six different human stool samples were processed either manually or on an epMotion 5075v using the NucleoSpin 96 DNA Stool kit in quadruplicates. 2.5-μl inputs from each eluate were used in a 25-μl endpoint PCR reaction designed to amplify a 1.5-kb portion of the bacterial 16S rRNA gene, and 3-μl outputs from each reaction were analyzed on a 1% agarose gel. Samples were successfully amplified in each case, demonstrating the robust downstream performance of DNA isolated using the kit.
740457.4	NucleoSpin® 96 DNA Stool Core Kit	4 x 96 Preps	USD $1400.00
The NucleoSpin 96 DNA Stool kit provides a comprehensive solution for high-throughput DNA isolation from fresh or frozen stool samples in a 96-well format using silica membrane technology. The kit is designed for processing of 100–200 mg of sample material per prep and employs an optimized lysis chemistry in combination with mechanical disruption (MN Bead Tubes Type A) to enable efficient sample homogenization without enzymatic digestion. Sample processing can be performed manually under vacuum or automated on common liquid handling platforms. The kit enables processing of 96 samples in ~90 minutes using automated processing and typically yields 3–15 µg of DNA per prep. Purified DNA is ready for a variety of downstream applications, including analysis by qPCR or NGS. Cat. # 740457.4 includes sufficient quantities of reagents and materials for processing of 4 x 96 samples using automated liquid-handling platforms. Notice to purchaser Our products are to be used for Research Use Only. They may not be used for any other purpose, including, but not limited to, use in humans, therapeutic or diagnostic use, or commercial use of any kind. Our products may not be transferred to third parties, resold, modified for resale, or used to manufacture commercial products or to provide a service to third parties without our prior written approval. Documents Image Data Back 740457.4: NucleoSpin 96 DNA Stool Core Kit Back High-quality DNA from rat stool samples processed using NucleoSpin 96 DNA Stool High-quality DNA from rat stool samples processed using NucleoSpin 96 DNA Stool. Eight different rat stool samples were processed on an epMotion 5075v using NucleoSpin 96 DNA Stool. Analysis of purity and yield of DNA isolated from each sample indicated the reliably high quality of the extracted DNA. Back Comparable performance with manual or automated processing using NucleoSpin 96 DNA Stool Comparable performance with manual or automated processing using NucleoSpin 96 DNA Stool. Six different stool samples were processed either manually or on an epMotion 5075v using the NucleoSpin 96 DNA Stool kit. Resulting DNA yields (blue and gray bars) and purity (orange dots) were comparable between manual and automated workflows for each sample. Back Efficient removal of PCR inhibitors with NucleoSpin 96 DNA Stool Efficient removal of PCR inhibitors with NucleoSpin 96 DNA Stool. DNA was purified from a human stool sample and sequentially diluted 1:4 up to a 4096-fold dilution. Diluted DNA and a reference standard were analyzed by qPCR using E. coli-specific primers and compared on a logarithmic plot. The slope of the resulting regression curve (-3.4106) indicated excellent qPCR performance without inhibition across the dilution series. Back Consistently excellent PCR performance with NucleoSpin 96 DNA Stool Consistently excellent PCR performance with NucleoSpin 96 DNA Stool. Six different human stool samples were processed either manually or on an epMotion 5075v using the NucleoSpin 96 DNA Stool kit in quadruplicates. 2.5-μl inputs from each eluate were used in a 25-μl endpoint PCR reaction designed to amplify a 1.5-kb portion of the bacterial 16S rRNA gene, and 3-μl outputs from each reaction were analyzed on a 1% agarose gel. Samples were successfully amplified in each case, demonstrating the robust downstream performance of DNA isolated using the kit.
740786.50	MN Bead Tubes Type A	50 Preps	USD $135.00
Pack of fifty 2-ml tubes containing ceramic beads for sample homogenization. Use in combination with the MN Bead Tube Holder (Cat. # 740469) and NucleoSpin Soil (e.g., Cat. # 740780.50) or Nucleospin Stool (Cat. # 740472.50), miniprep kits for isolation of total DNA from soil, sediments, or stool samples. Notice to purchaser Our products are to be used for Research Use Only. They may not be used for any other purpose, including, but not limited to, use in humans, therapeutic or diagnostic use, or commercial use of any kind. Our products may not be transferred to third parties, resold, modified for resale, or used to manufacture commercial products or to provide a service to third parties without our prior written approval. Documents You May Also Like Image Data Back 740786.50: NucleoSpin Bead Tubes Type A
740786.B.250	Type A Ceramic Beads, 0.6–0.8 mm (Bulk)	400 g	USD $368.00
Type A Ceramic Beads, 0.6–0.8 mm are recommended for homogenization of soil, sediment, and stool samples to enable more efficient sample lysis in the context of nucleic acid purification workflows. Type A beads are included or recommended for use with the following kits provided by Takara Bio: NucleoSpin Soil, NucleoBond RNA Soil, NucleoSpin DNA Stool, NucleoSpin RNA Stool, and NucleoMag DNA/RNA Water. Type A beads are also provided in single-tube formats as MN Bead Tubes Type A (Cat. # 740786.50) and MN Bead Tubes Type A 5 mL (Cat. # 740799.50). Cat. # 740786.B.250 consists of 400 g of Type A ceramic beads. Notice to purchaser Our products are to be used for Research Use Only. They may not be used for any other purpose, including, but not limited to, use in humans, therapeutic or diagnostic use, or commercial use of any kind. Our products may not be transferred to third parties, resold, modified for resale, or used to manufacture commercial products or to provide a service to third parties without our prior written approval. Image Data Back 740786.B.250: Type A Ceramic Beads, 0.6 - 0.8 mm (Bulk)

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Product overview

At-a-glance

Manual vs. automated processing

DNA quality

Removal of inhibitors

Downstream performance

Related products

Notice to purchaser

740473.1: NucleoSpin 96 DNA Stool

High-quality DNA from rat stool samples processed using NucleoSpin 96 DNA Stool

Comparable performance with manual or automated processing using NucleoSpin 96 DNA Stool

Efficient removal of PCR inhibitors with NucleoSpin 96 DNA Stool

Consistently excellent PCR performance with NucleoSpin 96 DNA Stool

Notice to purchaser

740473.4: NucleoSpin 96 DNA Stool

High-quality DNA from rat stool samples processed using NucleoSpin 96 DNA Stool

Comparable performance with manual or automated processing using NucleoSpin 96 DNA Stool

Efficient removal of PCR inhibitors with NucleoSpin 96 DNA Stool

Consistently excellent PCR performance with NucleoSpin 96 DNA Stool

Notice to purchaser

740457.4: NucleoSpin 96 DNA Stool Core Kit

High-quality DNA from rat stool samples processed using NucleoSpin 96 DNA Stool

Comparable performance with manual or automated processing using NucleoSpin 96 DNA Stool

Efficient removal of PCR inhibitors with NucleoSpin 96 DNA Stool

Consistently excellent PCR performance with NucleoSpin 96 DNA Stool

Notice to purchaser

740786.50: NucleoSpin Bead Tubes Type A

Notice to purchaser

740786.B.250: Type A Ceramic Beads, 0.6 - 0.8 mm (Bulk)