Microorganisms, Microbiomes and Microbiomics

, whether commensal, symbiotic, or pathogenic, are likely to impact almost every facet of human and animal health and their surrounding environments. Depending on whom you ask, microbiomes refer either to the genomes of all of the microorganisms that reside within environmental niches, or the microorganisms themselves. Microbiomics is the study of microbiomes.

Advances in next generation sequencing (NGS) make it easier than ever before to perform multi-laboratory transcriptomic and genomic analysis at high speeds and affordable prices. These advances have contributed to such an explosion in microbiomics in recent years that is it now arguably the fastest growing research field within biological sciences.

The human microbiome is probably the most hotly debated in popular science, and this is not without good reason, since the genes in our microbiome outnumber our own genes by about 100 to 1! This poses billion dollar questions such as: what do all these genes do, and what role does our microbiome play in health and disease? However, the goals of microbiome research extend far beyond the human body, and some of its applications might even surprise you!

What Do Our Customers Use Microbiomics For?

At Nordic BioSite, our clinical, research and industry customers use microbiomics to address diverse goals, including:

› Painting a picture of the microbial composition in the human gut and its influence on certain diseases and conditions e.g., obesity, allergy, and inflammation
› Searching diverse microbial communities for new antibiotics and other therapeutics
› Unravelling the microbial communities on and within plants – how do the microorganisms present influence each other, and what impact if any, does the community composition have on plant disease?
› Building microbial communities to test long-standing hypotheses about the mechanisms of antibiotic resistance gene transfer between organisms
› Profiling microbial communities in aquatic environments with a view to understanding the regulation of processes that influence aquatic health e.g., heavy metal methylation

A typical microbiomics workflow

Accurate Community Representation Is the Holy Grail

Time and time again, and regardless of the researcher’s goal, we hear that all microbiomics investigations share one criterion:

“The need to obtain an accurate representation of the microorganisms that make up the microbial community under investigation”

The Microbiomics Research Community Calls out for Standards

Despite the boom in microbiomics research, funding and publications, proper standards and quality control measures have lagged behind. This makes it difficult to obtain the accuracy that is so critical for reliable community profiling. Poor inter-laboratory reproducibility of microbiomics data and challenges in addressing the many sources of bias and variation in the microbiomics workflow are the subject of a recent Microbiome Quality Control project (MBQC) study, which was initiated to identify the sources and impacts of variation in microbiome studies, and to assess the design and utility of various experimental control strategies (1).

Indeed, the need for standardized methods to improve the reproducibility and quality of microbiomics data is so great that a number of dedicated expert committees have now been set up worldwide, with the ultimate goal to optimize and standardize microbiomics practices.

ZymoBIOMICS - the Future of Microbiomics

While the research community continues to unravel microbial communities from all corners of the Earth, Zymo Research has made it their goal to eliminate bias across the entire microbiomics workflow, paving the way for the much-anticipated standardization in the microbiomics field.

Launched in 2016, their one-of-a-kind ZymoBIOMICS™ range has everything that a researcher could want to perform standardized microbial community profiling from collection to analysis, including the first microbial community standards.

Sample Collection: A Good Start Is More Than Half the Battle

While accurate profiling depends on an entirely optimized workflow, problems stemming from poor sample collection and storage can greatly skew the results before the analysis even begins.

The complex sample types often used for microbial community profiling e.g., soil and feces, are particularly susceptible, not only to nucleic acid degradation, but also to changes in overall community composition, since some microorganisms decay while others continue to grow after collection, unless sample deactivation takes place. Transportation of pathogen-containing biological samples may also be challenging for both safety and financial reasons.

DNA/RNA Shield™ is an all-in-one reagent for sample collection and worry-free DNA and RNA stabilization at ambient, fridge or freezer temperatures. DNA/RNA Shield™ inactivates nucleases, microorganisms and viruses, thus providing an unbiased molecular snapshot of your sample at the time of collection, which is a major step towards accurate microbial community profiling (Figure 1). DNA/RNA Shield™ is available in multiple customizable collection device formats including swabs, fecal scoops, bead-beating lysis tubes, and more! For extra convenience, DNA and RNA can be isolated from your samples without the need for DNA/RNA Shield™ removal.

Figure 1. Microbial composition of stool is unchanged after one month at ambient temperature with DNA/RNA Shield™. Stool samples suspended in DNA/RNA Shield™ and stored at room temperature were compared to stool without preservative for one month. They were sampled at the indicated time points and processed with ZymoBIOMICS™ DNA Mini Kit. The extracted DNA was then subjected to microbial composition profiling via 16S rRNA gene targeted sequencing. Samples stored with DNA/RNA Shield™ had a constant microbial composition while the samples stored without DNA/RNA Shield™ shifted dramatically.

The First Microbial Community 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 contain a well-defined and characterized community of Gram-positive bacteria, Gram-negative bacteria and yeast (Figure 2). The DNA isolated from these standard communities represents a wide GC range (15%-85%) and contains negligible impurities (<0.01%). The features of these standards enable easy exposure of artefacts, errors and bias in microbiomics or metagenomics workflows from extraction right through to analysis, making them excellent controls for inter-laboratory studies.

Figure 2. Benchmarking DNA extraction processes with ZymoBIOMICS™ Microbial Community Standard. DNA was extracted from ZymoBIOMICS™ Microbial Community Standard using the four different DNA extraction methods (ZymoBIOMICS™ DNA Mini Kit, Human Microbiome Project fecal DNA extraction protocol, a DNA extraction kit from Supplier M, and a fecal DNA extraction kit from Supplier Q) and analyzed using 16S rRNA gene sequencing. 16S rRNA genes were amplified with primers targeting v3-4 region and the amplicons were sequenced on Illumina® MiSeq™ (2x250bp). Overlapping paired-end reads were assembled into complete amplicon sequences. The composition profile was determined based on sequence counts after mapping amplicon sequences to the known 16S rRNA genes of the eight different bacterial species contained in the standard. Only ZymoBIOMICS™ DNA Mini Kit provides unbiased profiles in this comparison.

Unbiased Nucleic Acid Isolation from Any Sample Type

Unbiased cell lysis and nucleic acid extraction are imperative to obtaining an accurate representation of the species within the community under investigation. Many of the currently available nucleic acid extraction protocols and kits used for microbiomics suffer bias from incomplete lysis of hard-to-lyse microbes, thus leading to an overrepresentation of easy-to-lyse microbes and an incorrect picture of the microbial community.

The ZymoBIOMICS™ DNA Mini Kits contain Zymo Research's proprietary ultra-high density BashingBeads™, ensuring non-biased genomic DNA isolation from any sample type e.g., feces, soil, water, body fluids, and biofilms (Figure 2). Isolated DNA is ultra-pure, inhibitor-free, and immediately ready for downstream microbiomics applications such as PCR 16S rRNA gene sequencing and shotgun sequencing.

For your convenience, ZymoBIOMICS™ DNA Kits are also available in miniprep, microprep, 96-well and 96-well magnetic bead formats. For researchers interested in metatranscriptomics, the range also includes an RNA miniprep kit as well as a dual DNA/RNA miniprep kit.

PCR and Femto™ Quantification Kits

For robust amplification to detect low copy DNA, ZymoBIOMICS™ PCR PreMix is supplied as a 2X concentrated “master mix", which contains all the reagents needed to perform PCR and other molecular downstream analysis with the addition of probes or fluorescent dyes. Its “hot-start” DNA polymerase has 3’-terminal transferase activity and is validated low-bioburden to ensure non-biased analysis in microbiomics and metagenomic workflows.

The Femto™ DNA Quantification Kits can reliably detect and quantify bacterial, fungal, or human DNA with high sensitivity and specificity, respectively. This is essential for downstream applications that require accurate inputs of DNA including metagenomic monitoring of microbial populations in environmental samples. With the Femto™ DNA Quantification Kits, you can confidently quantify as little as 20 fg of DNA in 1 µl purified from biological liquids, anthropological samples, forensic DNA samples, bacterial/fungal cultures, and more.

Try ZymoBIOMICS™ for Yourself - Get in Touch!

No matter what your research goal, the ZymoBIOMICS™ portfolio will serve you at every step of your microbiomics workflow. If you would like to try any of these products, get in touch with your local Nordic Biosite Representatives, or the head office at info@nordicbiosite.com.

View ZymoBIOMICS™ product listing

1. Sinha RS, Abnet CC, Knight R and Huttenhower C. 2015. The microbiome quality control project: baseline study design and future directions. Genome Biol. (16): 276-281.