Microbiomics – Optimize your workflow

The advent of Next Generation Sequencing (NGS) has supercharged our ability to explore both human and environmental microbial ecosystems using targeted sequencing approaches such as 16S ribosomal RNA (rRNA) and shotgun sequencing approaches. This has led to an explosion in the field of microbiomics. However, proper standards and quality control measures have lagged behind. The microbiomics community has expressed a need to standardize methods to improve the reproducibility and quality of the data being generated. Nordic BioSite is now pleased to be able to offer a wide selection of tools for the development, evaluation, calibration and validation of complex microbiomics workflows encompassing sample collection, sample preparation and analyses. This also includes Microbial Community Standards to validate every step of the process to ensure that they are accurate. 

1. Sample collection and preservation

Microbial composition shifts and degradation of DNA and RNA in biological samples (post-collection) has posed an obstacle to the accurate study of genetic identification and expression profiling, respectively. During the collection and transportation phase, depending on the quality of the method, microbes can continue to grow and decay. Nucleic acids can also degrade during this phase due to exposure to nucleases, elevated temperatures, pH extremes and other harsh conditions. These factors can lead to overall misrepresentation of the original community profile, causing downstream bias.

DNA/RNA Shield™ is an all-in-one reagent for sample collection and worry-free DNA and RNA stabilization at ambient temperatures.  DNA/RNA Shield™ inactivates nucleases and organisms including pathogens. It provides an unbiased molecular snapshot of your sample at the time of collection, thus ensuring accurate microbial community profiling.  DNA/RNA Shield™ can be purchased in multiple collection device formats including swabs, fecal scoops, bead-beating lysis tubes, and more! DNA and RNA can then be isolated without the need for reagent removal.

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2. Unbiased isolation and microbial standards

Microbial composition profiling techniques powered by NGS are becoming routine in microbiomics and metagenomics studies. However, these analytical techniques can suffer from significant bias and errors caused by DNA isolation, library preparation and bioinformatics methods. The ZymoBIOMICS™ Microbial Community Standards were designed to assess bias and errors in NGS-based microbial composition profiling workflows. The Standards mimic a mixed microbial community of well-defined composition and serve as defined input from the beginning. These standards can be used to guide construction and optimization of entire workflows and act as a control for inter-lab studies.

The Microbial Community Standards contain three easy-to-lyse Gram-negative bacteria, five tough-to-lyse Gram-positive bacteria and two tough-to-lyse yeasts, which includes both prokaryotes and eukaryotes. The microbial standards are accurately characterized, with a wide GC range (15%-85%) and contain negligible impurities (<0.01%). This enables easy exposure of artifacts, errors and bias in microbiomics or metagenomics workflows.

The ZymoBIOMICS™ DNA and RNA Mini Kits are designed for purifying nucleic acids, from a wide array of sample inputs (e.g. feces, soil, water and biofilms), that is immediately ready for microbiome or metagenome analyses. The ZymoBIOMICS™ innovative lysis system eliminates bias associated with unequal lysis efficiencies of different organisms (e.g. Gram-negative and positive bacteria, fungus, protozoans, spores and algae) making it ideal for microbial community profiling. Unbiased mechanical lysis of tough-to-lyse microbes is achieved by bead beating with the innovative ZymoBIOMICS™ ultra-high density BashingBeads™ and validated using the ZymoBIOMICS™ Microbial Community Standards.  In addition, extracted DNA/RNA is inhibitor-free and ultra-pure thanks to the proprietary OneStep™ PCR Inhibitor Removal and Zymo-Spin™ technologies. Purified DNA is ideal for all downstream applications including PCR, arrays, 16S rRNA gene sequencing and shotgun sequencing.

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3. Next Generation Sequencing: Amplicon-Seq

16S rRNA sequencing is an amplicon sequencing technique used to identify and compare species of bacteria present within a given sample. 16S rRNA gene sequencing is used to study phylogeny and taxonomy of samples from complex microbiomes or environments that are difficult to study. 16S rRNA sequencing can be used to specify taxonomic assignments, down to the species level. From Bioo Scientific we provide NEXTflex® 16S Amplicon-Seq Kits (V1-V3, V4 and V5-V6) for this purpose, these are optimized library prep kits developed to simplify 16S rRNA sequencing on the Illumina® MiSeq® sequencing platform, for culture-free identification of bacteria.

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