Stool microbiome
Stool samples are often used to study the gut microbiome and its effects on health, but also as clinical specimens for a variety of purposes, including the identification of numerous disease-causing bacteria and biomarker detection. Sample collection is simple, painless and sometimes large numbers of samples need to be analyzed.
Scientists have recently demonstrated how microscopic life in our bodies, particularly in our intestines, has a profound impact on our lives. Several diseases are now known to be impacted by the gut microbiome including cancer and autoimmune diseases like multiple sclerosis. The gut microbiome also interacts with and modifies the effect of certain pharmaceuticals.
Nucleic acid purification for stool microbiome profiling
We offer solutions for nucleic acid purification from stool samples in all common formats, from spin columns to magnetic beads, single-spin or high-throughput. The following MACHEREY-NAGEL kits have been optimized for purifying high-quality host, microbial and pathogenic nucleic acids from human and animal stool samples:
Click below for more information about our stool kits
NucleoSpin DNA Stool
- New technology for efficient removal of PCR inhibitors (like polysaccharides or bile salts in stool samples)
- Lysis is supported by mechanical disruption with ceramic beads (MN Bead Tubes Type A)
NucleoSpin DNA Stool procedure
The very efficient, ceramic bead-based lysis procedure achieves unbiased mechanical lysis and makes the NucleoSpin DNA Stool kit ideal for microbiome studies.
740472.50 NucleoSpin DNA Stool Kit
Superior DNA yield and inhibition free amplification of the 16S rRNA gene
NucleoSpin DNA Stool quickly and reliably purifies high-quality microbial, host and pathogenic genomic DNA from various stool samples.
740472.50 NucleoSpin DNA Stool Kit
High genomic DNA yield, and purity from human stool samples
DNA was isolated from human stool samples with the NucleoSpin DNA Stool kit (MN) and with competitor products (MO, Z, Q). The DNA was extracted according to manufacturer’s protocols, and 5 % of the eluate was subjected to gel electrophoresis. DNA yield, and quality of the samples shown in (A) were assessed by means of UV absorption measurement. The genomic DNA isolated with the NucleoSpin DNA Stool kit showed superior yield, and quality.
Efficient removal of PCR inhibitors from various sample sources
DNA was isolated from human, and animal feces samples with the NucleoSpin DNA Stool kit.5 μL of undiluted eluate served as template for the amplification of a 1.5 kb fragment from the bacterial 16S rRNA gene in an endpoint-PCR (35 cycles). The DNA extracted with the NucleoSpin DNA Stool kit works undiluted in a PCR reaction, indicating the successful removal of PCR inhibitors.
Selected citations
Adamczyk et al. Plant roots increase both decomposition, and stable, organic matter formation in boreal forest soil. Nature Communications, volume 10, 3982 (2019).
Goncalves et al. Microbiota stimulation generates LCMV-specific memory CD8+ T cells in SPF mice, and determines their TCR repertoire during LCMV infection. Molecular Immunology, volume 124, pages 125–141 (2020).
NucleoSpin 96 DNA Stool
MACHEREY‑NAGEL has developed a 96-well kit, NucleoSpin 96 DNA Stool, for the reliable, automation-friendly isolation of high quality DNA from human and animal stool samples. The kit combines a robust filtration step, significantly reducing the chance of column clogging, with an efficient DNA extraction procedure based on silica membrane technology.
740473.4 NucleoSpin 96 DNA Stool
Reliable performance and excellent yields
Comparable performance both manually and on epMotion 5075v
Six individual human stool samples were processed manually and on epMotion 5075v in quadruplicates. Yield (blue/grey bars) and purity (A₂₆₀/₂₈₀ nm, orange dots) were measured for all of the preparations. The manual and automated extractions delivered comparable yields with high purity (A₂₆₀/₂₈₀ > 1.7 in all samples)
High quality DNA from rat stool samples
Eight individual rat stool samples were processed on epMotion 5075v. Yield (blue bars), purity (A₂₆₀/₂₈₀ nm, orange dots) and analysis of DNA on the gel indicate the reliably high quality of the extracted DNA.
No downstream inhibition
DNA was purified from a human stool sample on epMotion 5075v using NucleoSpin 96 DNA Stool. A series of 1:4 dilutions, ranging from the undiluted eluate to a 4096fold dilution was analyzed by qPCR using an E.coli specific target and compared against a theoretical standard in a logarithmic plot. The slope of the regression curve (-3.4106) shows an excellent qPCR-performance without PCR inhibition.
Consistently excellent PCR performance
Six individual human stool samples were processed manually and on epMotion 5075v in quadruplicates. From each eluate, 2,5 µL were used in a 25 µL endpoint PCR reaction, amplifying a 1,5 kb fragment of the bacterial 16SrRNA gene. Three µL from each PCR reaction were analyzed on a 1 % agarose/TAE gel. In each case, the samples were successfully amplified, providing a good indication for the robust performance of the DNA in down‑stream applications.
RNA purification from stool samples - NucleoSpin RNA Stool
The gut's diverse microbiome has a huge impact on human health. The use of mRNA sequencing to analyze the transcriptional activity of microorganisms (metatranscriptomics) provides an exciting tool to learn more about their activity.
NucleoSpin RNA procedure
NucleoSpin RNA Stool kit enables efficient isolation of high quality RNA from any kind of stool sample.
740130.50 NucleoSpin RNA Stool
A combination of mechanical homogenization and chemical lysis ensures optimized RNA yield, including small RNA. NucleoSpin Inhibitor Removal Columns efficiently remove PCR inhibitors.
Superior RNA yield and qPCR performance
Highest yield with NucleoSpin RNA Stool
Two human stool samples (250 mg; MN only 200 mg) were processed in triplicates following the standard protocols including the DNase digestion step. The Q protocol was performed including the optional phenol based lysis step. Each eluate was used for UV spectroscopy to determine RNA yield. The NucleoSpin RNA Stool showed the highest RNA yield for the human stool samples.
NucleoSpin RNA Stool shows best performance in qPCR
The NucleoSpin RNA Stool samples as well as the Q samples were eluted with 100 μL, the Z eluate was adjusted to 100 μL to get comparable RNA concentrations in the eluate. 1 μL of eluate was used for qRT-PCR performed on a Roche LightCycler using the SensiFAST™ SYBR No-Rox One Step Kit (amplicon size 466 bp). NucleoSpin RNA Stool showed a better performance in the qRT-PCR compared to the two competitor kits.
NucleoMag DNA Microbiome
The NucleoMag DNA Microbiome kit enables high throughput, automation friendly isolation of microbial DNA from samples such as soil, stool or biofilm. In combination with the MN Bead tubes or the MN 96 bead Plates an efficient and uniform sample disruption is ensured resulting in high DNA yields. The MACHEREY-NAGEL inhibitory removal technology removes PCR inhibitors even from challenging samples.
NucleoMag DNA Microbiome procedure
The NucleoMag DNA Microbiome kit is designed to purify DNA from a variety of samples, including stool for microbiome and metagenomic analysis and employs unique, patented inhibitor removal technology.
744330.4 NucleoMag DNA Microbiome
High quality DNA from human and animal stool
Efficient isolation of DNA from fecal samples
Fecal samples from different animals (rabbit, sheep, chicken, rat) were subjected to a mechanical lysis procedure with MN Bead Tubes Type A. DNA was purified from the homogenates using the NucleoMag DNA Microbiome kit (MN) and a competitor kit (Q) according to the manufacturers instructions. DNA yield and purity were measured photometrically. DNA eluates were used in a qPCR for the bacterial 16s rRNA gene. DNA eluates obtained with NucleoMag DNA Microbiome show a superior purity for all fecal sample types. The yield is comparable (sheep) or better (rabbit, chicken, rat) than with the competitor kit. The qPCR performance is comparable (rabbit, sheep, rat) or better (chicken) than with the competitor kit.
Automated processing of human and animal stool samples
Next-generation sequencing-based analysis and advances in molecular diagnostics require high-quality DNA extracted from stool sample in an automated, high throughput manner that is devoid of PCR inhibitors. MACHEREY-NAGEL offers both, silica-membrane based and magnetic bead based kits.
NucleoSpin HTP solutions
This application note describes the automated processing of human and animal (rat) fecal samples on the epMotion 5075v liquid handling workstation. The novel optimized protocol allows for fully automated processing of samples following the initial disruption step.
NucleoSpin 96 DNA Stool epMotion 5075v
NucleoMag HTP solutions
